diff --git a/poetry.lock b/poetry.lock
index 9321211..5bec7cd 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,10 +1,9 @@
-# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
 version = "0.7.16"
 description = "A light, configurable Sphinx theme"
-category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -12,11 +11,21 @@ files = [
     {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"},
 ]
 
+[[package]]
+name = "annotated-types"
+version = "0.7.0"
+description = "Reusable constraint types to use with typing.Annotated"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"},
+    {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"},
+]
+
 [[package]]
 name = "appnope"
 version = "0.1.4"
 description = "Disable App Nap on macOS >= 10.9"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -24,11 +33,21 @@ files = [
     {file = "appnope-0.1.4.tar.gz", hash = "sha256:1de3860566df9caf38f01f86f65e0e13e379af54f9e4bee1e66b48f2efffd1ee"},
 ]
 
+[[package]]
+name = "apted"
+version = "1.0.3"
+description = "APTED algorithm for the Tree Edit Distance"
+optional = false
+python-versions = "*"
+files = [
+    {file = "apted-1.0.3-py3-none-any.whl", hash = "sha256:74193369d023649d335269e67c4df07f922959e5ac2597de1b79af4e694150e8"},
+    {file = "apted-1.0.3.tar.gz", hash = "sha256:befa5181e2d4457fa88e54995a82604ee048bb2fbc781ea97d8e1856b4715ce9"},
+]
+
 [[package]]
 name = "astroid"
 version = "2.15.8"
 description = "An abstract syntax tree for Python with inference support."
-category = "dev"
 optional = false
 python-versions = ">=3.7.2"
 files = [
@@ -45,7 +64,6 @@ wrapt = {version = ">=1.11,<2", markers = "python_version < \"3.11\""}
 name = "atomicwrites"
 version = "1.4.1"
 description = "Atomic file writes."
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -56,7 +74,6 @@ files = [
 name = "attrs"
 version = "24.2.0"
 description = "Classes Without Boilerplate"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -76,7 +93,6 @@ tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"]
 name = "babel"
 version = "2.16.0"
 description = "Internationalization utilities"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -91,7 +107,6 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
 name = "backcall"
 version = "0.2.0"
 description = "Specifications for callback functions passed in to an API"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -103,7 +118,6 @@ files = [
 name = "black"
 version = "22.12.0"
 description = "The uncompromising code formatter."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -137,18 +151,17 @@ uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "boto3"
-version = "1.34.159"
+version = "1.35.34"
 description = "The AWS SDK for Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "boto3-1.34.159-py3-none-any.whl", hash = "sha256:21120d23cc37c0e80dc4f64434bc5664d2a5645dcd9bf8a8fa97ed5c82164ca0"},
-    {file = "boto3-1.34.159.tar.gz", hash = "sha256:ffe7bbb88ba81b5d54bc8fa0cfb2f3b7fe63a6cffa0f9207df2ef5c22a1c0587"},
+    {file = "boto3-1.35.34-py3-none-any.whl", hash = "sha256:291e7b97a34967ed93297e6171f1bebb8529e64633dd48426760e3fdef1cdea8"},
+    {file = "boto3-1.35.34.tar.gz", hash = "sha256:57e6ee8504e7929bc094bb2afc879943906064179a1e88c23b4812e2c6f61532"},
 ]
 
 [package.dependencies]
-botocore = ">=1.34.159,<1.35.0"
+botocore = ">=1.35.34,<1.36.0"
 jmespath = ">=0.7.1,<2.0.0"
 s3transfer = ">=0.10.0,<0.11.0"
 
@@ -157,14 +170,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "botocore"
-version = "1.34.159"
+version = "1.35.34"
 description = "Low-level, data-driven core of boto 3."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "botocore-1.34.159-py3-none-any.whl", hash = "sha256:7633062491457419a49f5860c014251ae85689f78266a3ce020c2c8688a76b97"},
-    {file = "botocore-1.34.159.tar.gz", hash = "sha256:dc28806eb21e3c8d690c422530dff8b4b242ac033cbe98f160a9d37796c09cb1"},
+    {file = "botocore-1.35.34-py3-none-any.whl", hash = "sha256:ccb0fe397b11b81c9abc0c87029d17298e17bf658d8db5c0c5a551a12a207e7a"},
+    {file = "botocore-1.35.34.tar.gz", hash = "sha256:789b6501a3bb4a9591c1fe10da200cc315c1fa5df5ada19c720d8ef06439b3e3"},
 ]
 
 [package.dependencies]
@@ -176,13 +188,12 @@ urllib3 = [
 ]
 
 [package.extras]
-crt = ["awscrt (==0.21.2)"]
+crt = ["awscrt (==0.22.0)"]
 
 [[package]]
 name = "brotli"
 version = "1.1.0"
 description = "Python bindings for the Brotli compression library"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -275,7 +286,6 @@ files = [
 name = "brotlicffi"
 version = "1.1.0.0"
 description = "Python CFFI bindings to the Brotli library"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -315,7 +325,6 @@ cffi = ">=1.0.0"
 name = "cachedmethods"
 version = "0.1.4"
 description = ""
-category = "main"
 optional = false
 python-versions = ">=3.6.0"
 files = [
@@ -324,91 +333,89 @@ files = [
 
 [[package]]
 name = "certifi"
-version = "2024.7.4"
+version = "2024.8.30"
 description = "Python package for providing Mozilla's CA Bundle."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2024.7.4-py3-none-any.whl", hash = "sha256:c198e21b1289c2ab85ee4e67bb4b4ef3ead0892059901a8d5b622f24a1101e90"},
-    {file = "certifi-2024.7.4.tar.gz", hash = "sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b"},
+    {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"},
+    {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"},
 ]
 
 [[package]]
 name = "cffi"
-version = "1.17.0"
+version = "1.17.1"
 description = "Foreign Function Interface for Python calling C code."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -418,7 +425,6 @@ pycparser = "*"
 name = "cfgv"
 version = "3.4.0"
 description = "Validate configuration and produce human readable error messages."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -430,7 +436,6 @@ files = [
 name = "cgrtools"
 version = "4.1.35"
 description = ""
-category = "main"
 optional = false
 python-versions = ">=3.6.1"
 files = [
@@ -457,7 +462,6 @@ mrv = ["lxml (>=4.1)"]
 name = "charset-normalizer"
 version = "3.3.2"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
-category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
@@ -555,14 +559,13 @@ files = [
 
 [[package]]
 name = "cli-exit-tools"
-version = "1.2.6"
+version = "1.2.7"
 description = "functions to exit an cli application properly"
-category = "main"
 optional = false
 python-versions = ">=3.8.0"
 files = [
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 ]
 
 [package.dependencies]
@@ -576,7 +579,6 @@ test = ["black", "codecov", "coloredlogs", "coverage", "flake8", "mypy", "pytest
 name = "click"
 version = "8.1.7"
 description = "Composable command line interface toolkit"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -591,7 +593,6 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
 name = "cloudpickle"
 version = "3.0.0"
 description = "Pickler class to extend the standard pickle.Pickler functionality"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -603,7 +604,6 @@ files = [
 name = "colorama"
 version = "0.4.6"
 description = "Cross-platform colored terminal text."
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 files = [
@@ -615,7 +615,6 @@ files = [
 name = "coverage"
 version = "7.6.1"
 description = "Code coverage measurement for Python"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -703,7 +702,6 @@ toml = ["tomli"]
 name = "dask"
 version = "2024.2.1"
 description = "Parallel PyData with Task Scheduling"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -735,7 +733,6 @@ test = ["pandas[test]", "pre-commit", "pytest", "pytest-cov", "pytest-rerunfailu
 name = "decorator"
 version = "5.1.1"
 description = "Decorators for Humans"
-category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -747,7 +744,6 @@ files = [
 name = "deprecated"
 version = "1.2.14"
 description = "Python @deprecated decorator to deprecate old python classes, functions or methods."
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -763,14 +759,13 @@ dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"]
 
 [[package]]
 name = "dill"
-version = "0.3.8"
+version = "0.3.9"
 description = "serialize all of Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "dill-0.3.8-py3-none-any.whl", hash = "sha256:c36ca9ffb54365bdd2f8eb3eff7d2a21237f8452b57ace88b1ac615b7e815bd7"},
-    {file = "dill-0.3.8.tar.gz", hash = "sha256:3ebe3c479ad625c4553aca177444d89b486b1d84982eeacded644afc0cf797ca"},
+    {file = "dill-0.3.9-py3-none-any.whl", hash = "sha256:468dff3b89520b474c0397703366b7b95eebe6303f108adf9b19da1f702be87a"},
+    {file = "dill-0.3.9.tar.gz", hash = "sha256:81aa267dddf68cbfe8029c42ca9ec6a4ab3b22371d1c450abc54422577b4512c"},
 ]
 
 [package.extras]
@@ -781,7 +776,6 @@ profile = ["gprof2dot (>=2022.7.29)"]
 name = "distlib"
 version = "0.3.8"
 description = "Distribution utilities"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -793,7 +787,6 @@ files = [
 name = "docutils"
 version = "0.21.2"
 description = "Docutils -- Python Documentation Utilities"
-category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -803,31 +796,29 @@ files = [
 
 [[package]]
 name = "filelock"
-version = "3.15.4"
+version = "3.16.1"
 description = "A platform independent file lock."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "filelock-3.15.4-py3-none-any.whl", hash = "sha256:6ca1fffae96225dab4c6eaf1c4f4f28cd2568d3ec2a44e15a08520504de468e7"},
-    {file = "filelock-3.15.4.tar.gz", hash = "sha256:2207938cbc1844345cb01a5a95524dae30f0ce089eba5b00378295a17e3e90cb"},
+    {file = "filelock-3.16.1-py3-none-any.whl", hash = "sha256:2082e5703d51fbf98ea75855d9d5527e33d8ff23099bec374a134febee6946b0"},
+    {file = "filelock-3.16.1.tar.gz", hash = "sha256:c249fbfcd5db47e5e2d6d62198e565475ee65e4831e2561c8e313fa7eb961435"},
 ]
 
 [package.extras]
-docs = ["furo (>=2023.9.10)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.25.2)"]
-testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8.0.1)", "pytest (>=7.4.3)", "pytest-asyncio (>=0.21)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest-timeout (>=2.2)", "virtualenv (>=20.26.2)"]
-typing = ["typing-extensions (>=4.8)"]
+docs = ["furo (>=2024.8.6)", "sphinx (>=8.0.2)", "sphinx-autodoc-typehints (>=2.4.1)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.6.1)", "diff-cover (>=9.2)", "pytest (>=8.3.3)", "pytest-asyncio (>=0.24)", "pytest-cov (>=5)", "pytest-mock (>=3.14)", "pytest-timeout (>=2.3.1)", "virtualenv (>=20.26.4)"]
+typing = ["typing-extensions (>=4.12.2)"]
 
 [[package]]
 name = "fsspec"
-version = "2024.6.1"
+version = "2024.9.0"
 description = "File-system specification"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "fsspec-2024.6.1-py3-none-any.whl", hash = "sha256:3cb443f8bcd2efb31295a5b9fdb02aee81d8452c80d28f97a6d0959e6cee101e"},
-    {file = "fsspec-2024.6.1.tar.gz", hash = "sha256:fad7d7e209dd4c1208e3bbfda706620e0da5142bebbd9c384afb95b07e798e49"},
+    {file = "fsspec-2024.9.0-py3-none-any.whl", hash = "sha256:a0947d552d8a6efa72cc2c730b12c41d043509156966cca4fb157b0f2a0c574b"},
+    {file = "fsspec-2024.9.0.tar.gz", hash = "sha256:4b0afb90c2f21832df142f292649035d80b421f60a9e1c027802e5a0da2b04e8"},
 ]
 
 [package.extras]
@@ -860,14 +851,13 @@ tqdm = ["tqdm"]
 
 [[package]]
 name = "identify"
-version = "2.6.0"
+version = "2.6.1"
 description = "File identification library for Python"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "identify-2.6.0-py2.py3-none-any.whl", hash = "sha256:e79ae4406387a9d300332b5fd366d8994f1525e8414984e1a59e058b2eda2dd0"},
-    {file = "identify-2.6.0.tar.gz", hash = "sha256:cb171c685bdc31bcc4c1734698736a7d5b6c8bf2e0c15117f4d469c8640ae5cf"},
+    {file = "identify-2.6.1-py2.py3-none-any.whl", hash = "sha256:53863bcac7caf8d2ed85bd20312ea5dcfc22226800f6d6881f232d861db5a8f0"},
+    {file = "identify-2.6.1.tar.gz", hash = "sha256:91478c5fb7c3aac5ff7bf9b4344f803843dc586832d5f110d672b19aa1984c98"},
 ]
 
 [package.extras]
@@ -875,21 +865,22 @@ license = ["ukkonen"]
 
 [[package]]
 name = "idna"
-version = "3.7"
+version = "3.10"
 description = "Internationalized Domain Names in Applications (IDNA)"
-category = "main"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.6"
 files = [
-    {file = "idna-3.7-py3-none-any.whl", hash = "sha256:82fee1fc78add43492d3a1898bfa6d8a904cc97d8427f683ed8e798d07761aa0"},
-    {file = "idna-3.7.tar.gz", hash = "sha256:028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc"},
+    {file = "idna-3.10-py3-none-any.whl", hash = "sha256:946d195a0d259cbba61165e88e65941f16e9b36ea6ddb97f00452bae8b1287d3"},
+    {file = "idna-3.10.tar.gz", hash = "sha256:12f65c9b470abda6dc35cf8e63cc574b1c52b11df2c86030af0ac09b01b13ea9"},
 ]
 
+[package.extras]
+all = ["flake8 (>=7.1.1)", "mypy (>=1.11.2)", "pytest (>=8.3.2)", "ruff (>=0.6.2)"]
+
 [[package]]
 name = "imagesize"
 version = "1.4.1"
 description = "Getting image size from png/jpeg/jpeg2000/gif file"
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -899,29 +890,31 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "8.2.0"
+version = "8.5.0"
 description = "Read metadata from Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "importlib_metadata-8.2.0-py3-none-any.whl", hash = "sha256:11901fa0c2f97919b288679932bb64febaeacf289d18ac84dd68cb2e74213369"},
-    {file = "importlib_metadata-8.2.0.tar.gz", hash = "sha256:72e8d4399996132204f9a16dcc751af254a48f8d1b20b9ff0f98d4a8f901e73d"},
+    {file = "importlib_metadata-8.5.0-py3-none-any.whl", hash = "sha256:45e54197d28b7a7f1559e60b95e7c567032b602131fbd588f1497f47880aa68b"},
+    {file = "importlib_metadata-8.5.0.tar.gz", hash = "sha256:71522656f0abace1d072b9e5481a48f07c138e00f079c38c8f883823f9c26bd7"},
 ]
 
 [package.dependencies]
-zipp = ">=0.5"
+zipp = ">=3.20"
 
 [package.extras]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+enabler = ["pytest-enabler (>=2.2)"]
 perf = ["ipython"]
-test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"]
+test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"]
+type = ["pytest-mypy"]
 
 [[package]]
 name = "iniconfig"
 version = "2.0.0"
 description = "brain-dead simple config-ini parsing"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -933,7 +926,6 @@ files = [
 name = "invoke"
 version = "1.7.3"
 description = "Pythonic task execution"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -945,7 +937,6 @@ files = [
 name = "ipython"
 version = "7.34.0"
 description = "IPython: Productive Interactive Computing"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -982,7 +973,6 @@ test = ["ipykernel", "nbformat", "nose (>=0.10.1)", "numpy (>=1.17)", "pygments"
 name = "isort"
 version = "5.13.2"
 description = "A Python utility / library to sort Python imports."
-category = "dev"
 optional = false
 python-versions = ">=3.8.0"
 files = [
@@ -997,7 +987,6 @@ colors = ["colorama (>=0.4.6)"]
 name = "jedi"
 version = "0.19.1"
 description = "An autocompletion tool for Python that can be used for text editors."
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1017,7 +1006,6 @@ testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
 name = "jinja2"
 version = "3.1.4"
 description = "A very fast and expressive template engine."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1035,7 +1023,6 @@ i18n = ["Babel (>=2.7)"]
 name = "jmespath"
 version = "1.0.1"
 description = "JSON Matching Expressions"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1047,7 +1034,6 @@ files = [
 name = "lazy-object-proxy"
 version = "1.10.0"
 description = "A fast and thorough lazy object proxy."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1094,7 +1080,6 @@ files = [
 name = "lib-detect-testenv"
 version = "2.0.8"
 description = "detects if pytest or doctest or pyrunner on pycharm is running"
-category = "main"
 optional = false
 python-versions = ">=3.8.0"
 files = [
@@ -1109,7 +1094,6 @@ test = ["black", "codecov", "coloredlogs", "coverage", "flake8", "mypy", "pytest
 name = "locket"
 version = "1.0.0"
 description = "File-based locks for Python on Linux and Windows"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -1121,7 +1105,6 @@ files = [
 name = "markupsafe"
 version = "2.1.5"
 description = "Safely add untrusted strings to HTML/XML markup."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1191,7 +1174,6 @@ files = [
 name = "matplotlib-inline"
 version = "0.1.7"
 description = "Inline Matplotlib backend for Jupyter"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1206,7 +1188,6 @@ traitlets = "*"
 name = "mccabe"
 version = "0.7.0"
 description = "McCabe checker, plugin for flake8"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1216,14 +1197,13 @@ files = [
 
 [[package]]
 name = "metaflow"
-version = "2.12.11"
+version = "2.12.24"
 description = "Metaflow: More Data Science, Less Engineering"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
-    {file = "metaflow-2.12.11-py2.py3-none-any.whl", hash = "sha256:fec39343c8794cc9f3aef7998d1a1eb8cfab0b0d628173785a49f6a22c22816f"},
-    {file = "metaflow-2.12.11.tar.gz", hash = "sha256:9b2d3572f992cd08c5c8a893821d9d78c9a5490f17df7837a37ff5ba814fa118"},
+    {file = "metaflow-2.12.24-py2.py3-none-any.whl", hash = "sha256:37c55afc6cfb6a9f842767ff96e198b8ef83d838164188560d64591a3d453e0a"},
+    {file = "metaflow-2.12.24.tar.gz", hash = "sha256:25d4af40361d762c367813a6b3dbd81a51a77b6845b14dea60a2b6ae99f35ba4"},
 ]
 
 [package.dependencies]
@@ -1231,38 +1211,40 @@ boto3 = "*"
 requests = "*"
 
 [package.extras]
-stubs = ["metaflow-stubs (==2.12.11)"]
+stubs = ["metaflow-stubs (==2.12.24)"]
 
 [[package]]
 name = "multiprocess"
-version = "0.70.16"
+version = "0.70.17"
 description = "better multiprocessing and multithreading in Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "multiprocess-0.70.16-pp38-pypy38_pp73-macosx_10_9_x86_64.whl", hash = "sha256:37b55f71c07e2d741374998c043b9520b626a8dddc8b3129222ca4f1a06ef67a"},
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+    {file = "multiprocess-0.70.17-py313-none-any.whl", hash = "sha256:20c28ca19079a6c879258103a6d60b94d4ffe2d9da07dda93fb1c8bc6243f522"},
+    {file = "multiprocess-0.70.17-py38-none-any.whl", hash = "sha256:1d52f068357acd1e5bbc670b273ef8f81d57863235d9fbf9314751886e141968"},
+    {file = "multiprocess-0.70.17-py39-none-any.whl", hash = "sha256:c3feb874ba574fbccfb335980020c1ac631fbf2a3f7bee4e2042ede62558a021"},
+    {file = "multiprocess-0.70.17.tar.gz", hash = "sha256:4ae2f11a3416809ebc9a48abfc8b14ecce0652a0944731a1493a3c1ba44ff57a"},
 ]
 
 [package.dependencies]
-dill = ">=0.3.8"
+dill = ">=0.3.9"
 
 [[package]]
 name = "multivolumefile"
 version = "0.2.3"
 description = "multi volume file wrapper library"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1279,7 +1261,6 @@ type = ["mypy", "mypy-extensions"]
 name = "mypy"
 version = "0.800"
 description = "Optional static typing for Python"
-category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1319,7 +1300,6 @@ dmypy = ["psutil (>=4.0)"]
 name = "mypy-extensions"
 version = "0.4.4"
 description = "Experimental type system extensions for programs checked with the mypy typechecker."
-category = "dev"
 optional = false
 python-versions = ">=2.7"
 files = [
@@ -1330,7 +1310,6 @@ files = [
 name = "nodeenv"
 version = "1.9.1"
 description = "Node.js virtual environment builder"
-category = "dev"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 files = [
@@ -1342,7 +1321,6 @@ files = [
 name = "numpy"
 version = "1.26.4"
 description = "Fundamental package for array computing in Python"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1388,7 +1366,6 @@ files = [
 name = "packaging"
 version = "24.1"
 description = "Core utilities for Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1400,7 +1377,6 @@ files = [
 name = "pandas"
 version = "1.5.3"
 description = "Powerful data structures for data analysis, time series, and statistics"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1448,7 +1424,6 @@ test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"]
 name = "parso"
 version = "0.8.4"
 description = "A Python Parser"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1464,7 +1439,6 @@ testing = ["docopt", "pytest"]
 name = "partd"
 version = "1.4.2"
 description = "Appendable key-value storage"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1483,7 +1457,6 @@ complete = ["blosc", "numpy (>=1.20.0)", "pandas (>=1.3)", "pyzmq"]
 name = "pathspec"
 version = "0.12.1"
 description = "Utility library for gitignore style pattern matching of file paths."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1495,7 +1468,6 @@ files = [
 name = "pexpect"
 version = "4.9.0"
 description = "Pexpect allows easy control of interactive console applications."
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -1510,7 +1482,6 @@ ptyprocess = ">=0.5"
 name = "pickleshare"
 version = "0.7.5"
 description = "Tiny 'shelve'-like database with concurrency support"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -1522,7 +1493,6 @@ files = [
 name = "pillow"
 version = "10.4.0"
 description = "Python Imaging Library (Fork)"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1618,26 +1588,24 @@ xmp = ["defusedxml"]
 
 [[package]]
 name = "platformdirs"
-version = "4.2.2"
+version = "4.3.6"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
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-type = ["mypy (>=1.8)"]
+docs = ["furo (>=2024.8.6)", "proselint (>=0.14)", "sphinx (>=8.0.2)", "sphinx-autodoc-typehints (>=2.4)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=8.3.2)", "pytest-cov (>=5)", "pytest-mock (>=3.14)"]
+type = ["mypy (>=1.11.2)"]
 
 [[package]]
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 version = "1.5.0"
 description = "plugin and hook calling mechanisms for python"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1653,7 +1621,6 @@ testing = ["pytest", "pytest-benchmark"]
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 version = "2.21.0"
 description = "A framework for managing and maintaining multi-language pre-commit hooks."
-category = "dev"
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 python-versions = ">=3.7"
 files = [
@@ -1670,14 +1637,13 @@ virtualenv = ">=20.10.0"
 
 [[package]]
 name = "prompt-toolkit"
-version = "3.0.47"
+version = "3.0.48"
 description = "Library for building powerful interactive command lines in Python"
-category = "dev"
 optional = false
 python-versions = ">=3.7.0"
 files = [
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 ]
 
 [package.dependencies]
@@ -1687,7 +1653,6 @@ wcwidth = "*"
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 description = "Cross-platform lib for process and system monitoring in Python."
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
 files = [
@@ -1717,7 +1682,6 @@ test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"]
 name = "ptyprocess"
 version = "0.7.0"
 description = "Run a subprocess in a pseudo terminal"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -1729,7 +1693,6 @@ files = [
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 description = "library with cross-python path, ini-parsing, io, code, log facilities"
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -1741,7 +1704,6 @@ files = [
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 description = "Pure python 7-zip library"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1772,7 +1734,6 @@ test-compat = ["libarchive-c"]
 name = "pybcj"
 version = "1.0.2"
 description = "bcj filter library"
-category = "main"
 optional = false
 python-versions = ">=3.8"
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@@ -1827,7 +1788,6 @@ test = ["coverage[toml] (>=5.2)", "hypothesis", "pytest (>=6.0)", "pytest-cov"]
 name = "pycparser"
 version = "2.22"
 description = "C parser in Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1837,51 +1797,170 @@ files = [
 
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-version = "3.20.0"
+version = "3.21.0"
 description = "Cryptographic library for Python"
-category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
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+    {file = "pydantic_core-2.23.4-pp39-pypy39_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:88ad334a15b32a791ea935af224b9de1bf99bcd62fabf745d5f3442199d86d59"},
+    {file = "pydantic_core-2.23.4-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:233710f069d251feb12a56da21e14cca67994eab08362207785cf8c598e74577"},
+    {file = "pydantic_core-2.23.4-pp39-pypy39_pp73-manylinux_2_5_i686.manylinux1_i686.whl", hash = "sha256:19442362866a753485ba5e4be408964644dd6a09123d9416c54cd49171f50744"},
+    {file = "pydantic_core-2.23.4-pp39-pypy39_pp73-musllinux_1_1_aarch64.whl", hash = "sha256:624e278a7d29b6445e4e813af92af37820fafb6dcc55c012c834f9e26f9aaaef"},
+    {file = "pydantic_core-2.23.4-pp39-pypy39_pp73-musllinux_1_1_x86_64.whl", hash = "sha256:f5ef8f42bec47f21d07668a043f077d507e5bf4e668d5c6dfe6aaba89de1a5b8"},
+    {file = "pydantic_core-2.23.4-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:aea443fffa9fbe3af1a9ba721a87f926fe548d32cab71d188a6ede77d0ff244e"},
+    {file = "pydantic_core-2.23.4.tar.gz", hash = "sha256:2584f7cf844ac4d970fba483a717dbe10c1c1c96a969bf65d61ffe94df1b2863"},
+]
+
+[package.dependencies]
+typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0"
+
 [[package]]
 name = "pygments"
 version = "2.18.0"
 description = "Pygments is a syntax highlighting package written in Python."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1896,7 +1975,6 @@ windows-terminal = ["colorama (>=0.4.6)"]
 name = "pylint"
 version = "2.17.7"
 description = "python code static checker"
-category = "dev"
 optional = false
 python-versions = ">=3.7.2"
 files = [
@@ -1923,7 +2001,6 @@ testutils = ["gitpython (>3)"]
 name = "pyppmd"
 version = "0.18.3"
 description = "PPMd compression/decompression library"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2015,7 +2092,6 @@ test = ["coverage[toml] (>=5.2)", "hypothesis", "pytest (>=6.0)", "pytest-benchm
 name = "pytest"
 version = "6.2.5"
 description = "pytest: simple powerful testing with Python"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2040,7 +2116,6 @@ testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xm
 name = "pytest-black"
 version = "0.3.12"
 description = "A pytest plugin to enable format checking with black"
-category = "dev"
 optional = false
 python-versions = ">=2.7"
 files = [
@@ -2056,7 +2131,6 @@ toml = "*"
 name = "pytest-cov"
 version = "3.0.0"
 description = "Pytest plugin for measuring coverage."
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2075,7 +2149,6 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtuale
 name = "pytest-datadir"
 version = "1.5.0"
 description = "pytest plugin for test data directories and files"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2090,7 +2163,6 @@ pytest = ">=5.0"
 name = "pytest-mccabe"
 version = "2.0"
 description = "pytest plugin to run the mccabe code complexity checker."
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -2106,7 +2178,6 @@ pytest = ">=5.4.0"
 name = "pytest-mock"
 version = "3.14.0"
 description = "Thin-wrapper around the mock package for easier use with pytest"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2124,7 +2195,6 @@ dev = ["pre-commit", "pytest-asyncio", "tox"]
 name = "python-dateutil"
 version = "2.9.0.post0"
 description = "Extensions to the standard Python datetime module"
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
@@ -2137,21 +2207,19 @@ six = ">=1.5"
 
 [[package]]
 name = "pytz"
-version = "2024.1"
+version = "2024.2"
 description = "World timezone definitions, modern and historical"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
-    {file = "pytz-2024.1-py2.py3-none-any.whl", hash = "sha256:328171f4e3623139da4983451950b28e95ac706e13f3f2630a879749e7a8b319"},
-    {file = "pytz-2024.1.tar.gz", hash = "sha256:2a29735ea9c18baf14b448846bde5a48030ed267578472d8955cd0e7443a9812"},
+    {file = "pytz-2024.2-py2.py3-none-any.whl", hash = "sha256:31c7c1817eb7fae7ca4b8c7ee50c72f93aa2dd863de768e1ef4245d426aa0725"},
+    {file = "pytz-2024.2.tar.gz", hash = "sha256:2aa355083c50a0f93fa581709deac0c9ad65cca8a9e9beac660adcbd493c798a"},
 ]
 
 [[package]]
 name = "pyyaml"
 version = "6.0.2"
 description = "YAML parser and emitter for Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2214,7 +2282,6 @@ files = [
 name = "pyzstd"
 version = "0.16.1"
 description = "Python bindings to Zstandard (zstd) compression library."
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -2313,7 +2380,6 @@ files = [
 name = "rdchiral"
 version = "1.1.0"
 description = "Wrapper for RDKit's RunReactants to improve stereochemistry handling"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -2325,7 +2391,6 @@ files = [
 name = "rdkit"
 version = "2023.9.6"
 description = "A collection of chemoinformatics and machine-learning software written in C++ and Python"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2364,7 +2429,6 @@ Pillow = "*"
 name = "requests"
 version = "2.32.3"
 description = "Python HTTP for Humans."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2386,7 +2450,6 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 name = "s3transfer"
 version = "0.10.2"
 description = "An Amazon S3 Transfer Manager"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2404,7 +2467,6 @@ crt = ["botocore[crt] (>=1.33.2,<2.0a.0)"]
 name = "scipy"
 version = "1.13.1"
 description = "Fundamental algorithms for scientific computing in Python"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -2445,26 +2507,28 @@ test = ["array-api-strict", "asv", "gmpy2", "hypothesis (>=6.30)", "mpmath", "po
 
 [[package]]
 name = "setuptools"
-version = "72.1.0"
+version = "75.1.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "setuptools-72.1.0-py3-none-any.whl", hash = "sha256:5a03e1860cf56bb6ef48ce186b0e557fdba433237481a9a625176c2831be15d1"},
-    {file = "setuptools-72.1.0.tar.gz", hash = "sha256:8d243eff56d095e5817f796ede6ae32941278f542e0f941867cc05ae52b162ec"},
+    {file = "setuptools-75.1.0-py3-none-any.whl", hash = "sha256:35ab7fd3bcd95e6b7fd704e4a1539513edad446c097797f2985e0e4b960772f2"},
+    {file = "setuptools-75.1.0.tar.gz", hash = "sha256:d59a21b17a275fb872a9c3dae73963160ae079f1049ed956880cd7c09b120538"},
 ]
 
 [package.extras]
-core = ["importlib-metadata (>=6)", "importlib-resources (>=5.10.2)", "jaraco.text (>=3.7)", "more-itertools (>=8.8)", "ordered-set (>=3.1.1)", "packaging (>=24)", "platformdirs (>=2.6.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"]
-doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "mypy (>=1.11.0,<1.12.0)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (<0.4)", "pytest-ruff (>=0.2.1)", "pytest-ruff (>=0.3.2)", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)", "ruff (>=0.5.2)"]
+core = ["importlib-metadata (>=6)", "importlib-resources (>=5.10.2)", "jaraco.collections", "jaraco.functools", "jaraco.text (>=3.7)", "more-itertools", "more-itertools (>=8.8)", "packaging", "packaging (>=24)", "platformdirs (>=2.6.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"]
+cover = ["pytest-cov"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
+enabler = ["pytest-enabler (>=2.2)"]
+test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-home (>=0.5)", "pytest-perf", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel (>=0.44.0)"]
+type = ["importlib-metadata (>=7.0.2)", "jaraco.develop (>=7.21)", "mypy (==1.11.*)", "pytest-mypy"]
 
 [[package]]
 name = "six"
 version = "1.16.0"
 description = "Python 2 and 3 compatibility utilities"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 files = [
@@ -2476,7 +2540,6 @@ files = [
 name = "snowballstemmer"
 version = "2.2.0"
 description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -2488,7 +2551,6 @@ files = [
 name = "sphinx"
 version = "7.4.7"
 description = "Python documentation generator"
-category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -2525,7 +2587,6 @@ test = ["cython (>=3.0)", "defusedxml (>=0.7.1)", "pytest (>=8.0)", "setuptools
 name = "sphinxcontrib-applehelp"
 version = "2.0.0"
 description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
-category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -2542,7 +2603,6 @@ test = ["pytest"]
 name = "sphinxcontrib-devhelp"
 version = "2.0.0"
 description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
-category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -2559,7 +2619,6 @@ test = ["pytest"]
 name = "sphinxcontrib-htmlhelp"
 version = "2.1.0"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
-category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -2576,7 +2635,6 @@ test = ["html5lib", "pytest"]
 name = "sphinxcontrib-jsmath"
 version = "1.0.1"
 description = "A sphinx extension which renders display math in HTML via JavaScript"
-category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -2591,7 +2649,6 @@ test = ["flake8", "mypy", "pytest"]
 name = "sphinxcontrib-qthelp"
 version = "2.0.0"
 description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents"
-category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -2608,7 +2665,6 @@ test = ["defusedxml (>=0.7.1)", "pytest"]
 name = "sphinxcontrib-serializinghtml"
 version = "2.0.0"
 description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)"
-category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -2625,7 +2681,6 @@ test = ["pytest"]
 name = "swifter"
 version = "1.4.0"
 description = "A package which efficiently applies any function to a pandas dataframe or series in the fastest available manner"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2646,7 +2701,6 @@ notebook = ["ipywidgets (>=7.0.0)"]
 name = "texttable"
 version = "1.7.0"
 description = "module to create simple ASCII tables"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2658,7 +2712,6 @@ files = [
 name = "toml"
 version = "0.10.2"
 description = "Python Library for Tom's Obvious, Minimal Language"
-category = "dev"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 files = [
@@ -2668,45 +2721,41 @@ files = [
 
 [[package]]
 name = "tomli"
-version = "2.0.1"
+version = "2.0.2"
 description = "A lil' TOML parser"
-category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
-    {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
+    {file = "tomli-2.0.2-py3-none-any.whl", hash = "sha256:2ebe24485c53d303f690b0ec092806a085f07af5a5aa1464f3931eec36caaa38"},
+    {file = "tomli-2.0.2.tar.gz", hash = "sha256:d46d457a85337051c36524bc5349dd91b1877838e2979ac5ced3e710ed8a60ed"},
 ]
 
 [[package]]
 name = "tomlkit"
-version = "0.13.0"
+version = "0.13.2"
 description = "Style preserving TOML library"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "tomlkit-0.13.0-py3-none-any.whl", hash = "sha256:7075d3042d03b80f603482d69bf0c8f345c2b30e41699fd8883227f89972b264"},
-    {file = "tomlkit-0.13.0.tar.gz", hash = "sha256:08ad192699734149f5b97b45f1f18dad7eb1b6d16bc72ad0c2335772650d7b72"},
+    {file = "tomlkit-0.13.2-py3-none-any.whl", hash = "sha256:7a974427f6e119197f670fbbbeae7bef749a6c14e793db934baefc1b5f03efde"},
+    {file = "tomlkit-0.13.2.tar.gz", hash = "sha256:fff5fe59a87295b278abd31bec92c15d9bc4a06885ab12bcea52c71119392e79"},
 ]
 
 [[package]]
 name = "toolz"
-version = "0.12.1"
+version = "1.0.0"
 description = "List processing tools and functional utilities"
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "toolz-0.12.1-py3-none-any.whl", hash = "sha256:d22731364c07d72eea0a0ad45bafb2c2937ab6fd38a3507bf55eae8744aa7d85"},
-    {file = "toolz-0.12.1.tar.gz", hash = "sha256:ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d"},
+    {file = "toolz-1.0.0-py3-none-any.whl", hash = "sha256:292c8f1c4e7516bf9086f8850935c799a874039c8bcf959d47b600e4c44a6236"},
+    {file = "toolz-1.0.0.tar.gz", hash = "sha256:2c86e3d9a04798ac556793bced838816296a2f085017664e4995cb40a1047a02"},
 ]
 
 [[package]]
 name = "tqdm"
 version = "4.66.5"
 description = "Fast, Extensible Progress Meter"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2727,7 +2776,6 @@ telegram = ["requests"]
 name = "traitlets"
 version = "5.14.3"
 description = "Traitlets Python configuration system"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2743,7 +2791,6 @@ test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,
 name = "typed-ast"
 version = "1.4.3"
 description = "a fork of Python 2 and 3 ast modules with type comment support"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -2783,7 +2830,6 @@ files = [
 name = "typing-extensions"
 version = "4.12.2"
 description = "Backported and Experimental Type Hints for Python 3.8+"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2793,14 +2839,13 @@ files = [
 
 [[package]]
 name = "urllib3"
-version = "1.26.19"
+version = "1.26.20"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
 files = [
-    {file = "urllib3-1.26.19-py2.py3-none-any.whl", hash = "sha256:37a0344459b199fce0e80b0d3569837ec6b6937435c5244e7fd73fa6006830f3"},
-    {file = "urllib3-1.26.19.tar.gz", hash = "sha256:3e3d753a8618b86d7de333b4223005f68720bcd6a7d2bcb9fbd2229ec7c1e429"},
+    {file = "urllib3-1.26.20-py2.py3-none-any.whl", hash = "sha256:0ed14ccfbf1c30a9072c7ca157e4319b70d65f623e91e7b32fadb2853431016e"},
+    {file = "urllib3-1.26.20.tar.gz", hash = "sha256:40c2dc0c681e47eb8f90e7e27bf6ff7df2e677421fd46756da1161c39ca70d32"},
 ]
 
 [package.extras]
@@ -2810,14 +2855,13 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
 [[package]]
 name = "virtualenv"
-version = "20.26.3"
+version = "20.26.6"
 description = "Virtual Python Environment builder"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "virtualenv-20.26.3-py3-none-any.whl", hash = "sha256:8cc4a31139e796e9a7de2cd5cf2489de1217193116a8fd42328f1bd65f434589"},
-    {file = "virtualenv-20.26.3.tar.gz", hash = "sha256:4c43a2a236279d9ea36a0d76f98d84bd6ca94ac4e0f4a3b9d46d05e10fea542a"},
+    {file = "virtualenv-20.26.6-py3-none-any.whl", hash = "sha256:7345cc5b25405607a624d8418154577459c3e0277f5466dd79c49d5e492995f2"},
+    {file = "virtualenv-20.26.6.tar.gz", hash = "sha256:280aede09a2a5c317e409a00102e7077c6432c5a38f0ef938e643805a7ad2c48"},
 ]
 
 [package.dependencies]
@@ -2833,7 +2877,6 @@ test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess
 name = "wcwidth"
 version = "0.2.13"
 description = "Measures the displayed width of unicode strings in a terminal"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -2845,7 +2888,6 @@ files = [
 name = "wrapt"
 version = "1.16.0"
 description = "Module for decorators, wrappers and monkey patching."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2925,7 +2967,6 @@ files = [
 name = "wrapt-timeout-decorator"
 version = "1.5.1"
 description = "The better timout decorator"
-category = "main"
 optional = false
 python-versions = ">=3.8.0"
 files = [
@@ -2951,7 +2992,6 @@ test = ["black", "codecov", "coloredlogs", "coverage", "flake8", "mypy", "pytest
 name = "xxhash"
 version = "2.0.2"
 description = "Python binding for xxHash"
-category = "main"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 files = [
@@ -3025,7 +3065,6 @@ files = [
 name = "zipfile-deflate64"
 version = "0.2.0"
 description = "Extract Deflate64 ZIP archives with Python's zipfile API."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -3049,21 +3088,24 @@ files = [
 
 [[package]]
 name = "zipp"
-version = "3.20.0"
+version = "3.20.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.20.0-py3-none-any.whl", hash = "sha256:58da6168be89f0be59beb194da1250516fdaa062ccebd30127ac65d30045e10d"},
-    {file = "zipp-3.20.0.tar.gz", hash = "sha256:0145e43d89664cfe1a2e533adc75adafed82fe2da404b4bbb6b026c0157bdb31"},
+    {file = "zipp-3.20.2-py3-none-any.whl", hash = "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350"},
+    {file = "zipp-3.20.2.tar.gz", hash = "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29"},
 ]
 
 [package.extras]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+enabler = ["pytest-enabler (>=2.2)"]
+test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
+type = ["pytest-mypy"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.11"
-content-hash = "c7cd5352d183e1641123a6c066615245e2bd5160854dae25d00c519189e16a88"
+content-hash = "eeac29b154c59b17959559d2e86dae8378598062ed2eba88f4c8d3accd87d773"
diff --git a/pyproject.toml b/pyproject.toml
index 94db71f..d531b78 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "reaction_utils"
-version = "1.6.0"
+version = "1.7.0"
 description = "Utilities for working with reactions, reaction templates and template extraction"
 authors = ["Genheden, Samuel <samuel.genheden@astrazeneca.com>", "Kannas, Christos <christos.kannas@astrazeneca.com>"]
 license = "Apache-2.0"
@@ -28,6 +28,8 @@ numpy = "^1.0.0"
 rdkit = "^2023.9.1"
 cgrtools = "^4.1.35"
 scipy = "^1.11.4"
+pydantic = "^2.8.2"
+apted = "^1.0.3"
 
 [tool.poetry.dev-dependencies]
 pytest = "^6.2.2"
diff --git a/rxnutils/chem/augmentation.py b/rxnutils/chem/augmentation.py
new file mode 100644
index 0000000..7e9fd83
--- /dev/null
+++ b/rxnutils/chem/augmentation.py
@@ -0,0 +1,22 @@
+""" Routines for augmenting chemical reactions
+"""
+
+_SINGLE_REACTANT_REAGENTS = {"10.1.1": "Br", "10.1.2": "Cl"}
+
+
+def single_reactant_augmentation(smiles: str, classification: str) -> str:
+    """
+    Augment single-reactant reaction with additional reagent if possible
+    based on the classification of the reaction
+    :param smiles: the reaction SMILES to augment
+    :param classification: the classification of the reaction or an empty string
+    :return: the processed SMILES
+    """
+    reactants = smiles.split(">")[0]
+    if "." in reactants:
+        return smiles
+    classification = classification.split(" ")[0]
+    new_reactant = _SINGLE_REACTANT_REAGENTS.get(classification)
+    if new_reactant:
+        return new_reactant + "." + smiles
+    return smiles
diff --git a/rxnutils/chem/cgr.py b/rxnutils/chem/cgr.py
index bff91b4..13eac3a 100644
--- a/rxnutils/chem/cgr.py
+++ b/rxnutils/chem/cgr.py
@@ -4,9 +4,9 @@
 import warnings
 from typing import List
 
-from CGRtools.files.SDFrw import SDFRead
-from CGRtools.containers.reaction import ReactionContainer
 from CGRtools.containers.molecule import MoleculeContainer
+from CGRtools.containers.reaction import ReactionContainer
+from CGRtools.files.SDFrw import SDFRead
 from rdkit import Chem
 
 from rxnutils.chem.reaction import ChemicalReaction
diff --git a/rxnutils/chem/disconnection_sites/atom_map_tagging.py b/rxnutils/chem/disconnection_sites/atom_map_tagging.py
index 83f7c2b..e705d26 100644
--- a/rxnutils/chem/disconnection_sites/atom_map_tagging.py
+++ b/rxnutils/chem/disconnection_sites/atom_map_tagging.py
@@ -95,6 +95,30 @@ def get_atom_list(reactants_smiles: str, product_smiles: str) -> List[int]:
     return atom_list
 
 
+def atom_map_tag_reactants(mapped_rxn: str) -> str:
+    """
+    Given atom-mapped reaction, returns disconnection site-tagged reactants where atoms
+    with changed atom environment are represented by [<atom>:1].
+
+    :param mapped_rxn: Atom-mapped reaction SMILES
+    :return: SMILES of the reactants containing tags corresponding to atoms changed in the
+        reaction.
+    """
+    reactants_smiles, _, product_smiles = mapped_rxn.split(">")
+
+    reactants_mol = Chem.MolFromSmiles(reactants_smiles)
+    atom_list = get_atom_list(reactants_smiles, product_smiles)
+
+    # Set atoms in product with a different environment in reactants to 1
+    for atom in reactants_mol.GetAtoms():
+        if atom.GetAtomMapNum() in atom_list:
+            atom.SetAtomMapNum(1)
+        else:
+            atom.SetAtomMapNum(0)
+
+    return Chem.MolToSmiles(reactants_mol)
+
+
 def atom_map_tag_products(mapped_rxn: str) -> str:
     """
     Given atom-mapped reaction, returns disconnection site-tagged product where atoms
diff --git a/rxnutils/chem/disconnection_sites/tag_converting.py b/rxnutils/chem/disconnection_sites/tag_converting.py
index 152e789..154a675 100644
--- a/rxnutils/chem/disconnection_sites/tag_converting.py
+++ b/rxnutils/chem/disconnection_sites/tag_converting.py
@@ -15,10 +15,16 @@ def smiles_tokens(smiles: str) -> List[str]:
     :param smiles: SMILES to tokenize
     :return: List of tokens identified in SMILES.
     """
-    pattern = r"(\[[^\]]+]|Br?|Cl?|N|O|S|P|F|I|b|c|n|o|s|p|\(|\)|\.|=|#|-|\+|\\\\|\/|:|~|@|\?|>|\*|\!|\$|\%[0-9]{2}|[0-9])"
+    pattern = r"(\[[^\]]+]|Br?|Cl?|N|O|S|P|F|I|b|c|n|o|s|p|\(|\)|\.|=|#|-|\+|\\\\|\\|\/|:|~|@|\?|>|\*|\!|\$|\%[0-9]{2}|[0-9])"
     regex = re.compile(pattern)
     tokens = [token for token in regex.findall(smiles)]
-    assert smiles == "".join(tokens)
+
+    tokenized_smiles = "".join(tokens)
+    if smiles != tokenized_smiles:
+        raise AssertionError(
+            f"tokenized SMILES not the same as input SMILES: {tokenized_smiles}, "
+            "{smiles}, tokens: {tokens}"
+        )
     return tokens
 
 
@@ -68,8 +74,6 @@ def tagged_smiles_from_tokens(
         reaction using "<atom>!", and SMILES of the (reconstructed) untagged product
     """
 
-    print(product_tagged_tokens)
-
     product_converted = ""
     product_untagged = ""
 
diff --git a/rxnutils/chem/reaction.py b/rxnutils/chem/reaction.py
index 6d9e22b..3aea3a5 100644
--- a/rxnutils/chem/reaction.py
+++ b/rxnutils/chem/reaction.py
@@ -1,19 +1,16 @@
 """Module containing a class to handle chemical reactions"""
 import hashlib
-from typing import List, Tuple, Optional, Dict, Any
+from typing import Any, Dict, List, Optional, Tuple
 
 import wrapt_timeout_decorator
+from rdchiral import template_extractor as extractor
 from rdkit import Chem
 from rdkit.Chem import AllChem
-from rdchiral import template_extractor as extractor
 
-from rxnutils.chem.rinchi import rinchi_api
 from rxnutils.chem import utils
+from rxnutils.chem.rinchi import rinchi_api
 from rxnutils.chem.template import ReactionTemplate
-from rxnutils.chem.utils import (
-    reassign_rsmi_atom_mapping,
-    split_smiles_from_reaction,
-)
+from rxnutils.chem.utils import reassign_rsmi_atom_mapping, split_smiles_from_reaction
 
 
 class ReactionException(Exception):
diff --git a/rxnutils/chem/rinchi/download_rinchi.py b/rxnutils/chem/rinchi/download_rinchi.py
index bd2c993..6ef9f1a 100644
--- a/rxnutils/chem/rinchi/download_rinchi.py
+++ b/rxnutils/chem/rinchi/download_rinchi.py
@@ -1,9 +1,9 @@
 """Module for downloading InChI Trust Reaction InChI."""
+import logging
 import os
-import sys
 import stat
+import sys
 from zipfile import ZipFile
-import logging
 
 import requests
 
diff --git a/rxnutils/chem/rinchi/rinchi_api.py b/rxnutils/chem/rinchi/rinchi_api.py
index 57d6ac3..d34e17f 100644
--- a/rxnutils/chem/rinchi/rinchi_api.py
+++ b/rxnutils/chem/rinchi/rinchi_api.py
@@ -1,16 +1,15 @@
 """Module containing an API to the Reaction InChI program"""
 import logging
 import os
-import sys
 import subprocess
+import sys
 import tempfile
 from collections import namedtuple
 
 from rdkit.Chem import AllChem
 
 from rxnutils.chem.rinchi import download_rinchi
-from rxnutils.chem.rinchi.download_rinchi import RInChIError, PLATFORM2FOLDER
-
+from rxnutils.chem.rinchi.download_rinchi import PLATFORM2FOLDER, RInChIError
 
 RInChIStructure = namedtuple(
     "RInChI", "rinchi rauxinfo long_rinchikey short_rinchikey web_rinchikey"
diff --git a/rxnutils/chem/template.py b/rxnutils/chem/template.py
index daa9522..5b306c8 100644
--- a/rxnutils/chem/template.py
+++ b/rxnutils/chem/template.py
@@ -1,18 +1,17 @@
 """Module containing useful representations of templates
 """
-import re
 import hashlib
 import logging
+import re
 from collections import defaultdict
 from itertools import permutations
-from typing import List, Dict, Set, Iterator, Tuple, Any
+from typing import Any, Dict, Iterator, List, Set, Tuple
 
 import numpy as np
 import rdchiral.main as rdc
-from xxhash import xxh32
 from rdkit import Chem, DataStructs
 from rdkit.Chem import AllChem, SanitizeFlags  # pylint: disable=all
-
+from xxhash import xxh32
 
 DELIM_REGEX_STR = r"[&:\]]"
 AROMATIC_REGEX_STR = r"&a" + DELIM_REGEX_STR
diff --git a/rxnutils/chem/utils.py b/rxnutils/chem/utils.py
index bc3982d..93dcd48 100644
--- a/rxnutils/chem/utils.py
+++ b/rxnutils/chem/utils.py
@@ -1,12 +1,9 @@
 """Module containing various chemical utility routines"""
-
-import logging
 import functools
+import logging
 from typing import List, Tuple
 
-
 import rdchiral.template_extractor
-
 from rdkit import Chem
 from rdkit.Chem import AllChem
 from rdkit.Chem.MolStandardize import rdMolStandardize
@@ -292,7 +289,7 @@ def get_special_groups(mol) -> List[Tuple[Tuple[int, ...], Tuple[int, ...]]]:
 
     # Build list
     groups = []
-    for add_if_match, template in group_templates:
+    for (add_if_match, template) in group_templates:
         matches = mol.GetSubstructMatches(
             Chem.MolFromSmarts(template), useChirality=True
         )
diff --git a/rxnutils/data/base_pipeline.py b/rxnutils/data/base_pipeline.py
index 91df7ae..63364aa 100644
--- a/rxnutils/data/base_pipeline.py
+++ b/rxnutils/data/base_pipeline.py
@@ -1,15 +1,14 @@
 """Module containing base class for data pipelines
 """
-import os
 import math
+import os
 from pathlib import Path
+from typing import List, Tuple
 
 import pandas as pd
 from metaflow import FlowSpec, Parameter
 
-from typing import List, Tuple
-
-from rxnutils.data.batch_utils import create_csv_batches, combine_csv_batches
+from rxnutils.data.batch_utils import combine_csv_batches, create_csv_batches
 
 # This is hack to only import the validation_runner if rxnmapper is not installed
 try:
diff --git a/rxnutils/data/mapping_pipeline.py b/rxnutils/data/mapping_pipeline.py
index 56c1383..53af1dc 100644
--- a/rxnutils/data/mapping_pipeline.py
+++ b/rxnutils/data/mapping_pipeline.py
@@ -4,7 +4,7 @@
 """
 from pathlib import Path
 
-from metaflow import step, Parameter
+from metaflow import Parameter, step
 
 from rxnutils.data.base_pipeline import DataBaseFlow
 from rxnutils.data.mapping import main as map_data
diff --git a/rxnutils/data/ord/import_ord_dataset.py b/rxnutils/data/ord/import_ord_dataset.py
index 5ec93cb..9808e53 100644
--- a/rxnutils/data/ord/import_ord_dataset.py
+++ b/rxnutils/data/ord/import_ord_dataset.py
@@ -1,9 +1,9 @@
 """
 Module containing script to import ORD dataset to a CSV file
 """
-import re
 import argparse
 import os
+import re
 from collections import defaultdict
 from typing import Optional, Sequence
 
diff --git a/rxnutils/data/ord/preparation_pipeline.py b/rxnutils/data/ord/preparation_pipeline.py
index 358d450..f76e119 100644
--- a/rxnutils/data/ord/preparation_pipeline.py
+++ b/rxnutils/data/ord/preparation_pipeline.py
@@ -6,7 +6,7 @@
 import os
 from pathlib import Path
 
-from metaflow import step, Parameter
+from metaflow import Parameter, step
 
 from rxnutils.data.base_pipeline import DataPreparationBaseFlow
 from rxnutils.data.ord.import_ord_dataset import main as import_data
diff --git a/rxnutils/data/uspto/combine.py b/rxnutils/data/uspto/combine.py
index c162d89..350f975 100644
--- a/rxnutils/data/uspto/combine.py
+++ b/rxnutils/data/uspto/combine.py
@@ -5,12 +5,15 @@
     * preserve the ReactionSmiles and Year columns
     * create an ID from PatentNumber and ParagraphNum and row index in the original file
 """
+
 import argparse
 from pathlib import Path
 from typing import Optional, Sequence
 
 import pandas as pd
 
+from rxnutils.data.uspto.uspto_yield import UsptoYieldCuration
+
 DEFAULT_FILENAMES = [
     "1976_Sep2016_USPTOgrants_smiles.rsmi",
     "2001_Sep2016_USPTOapplications_smiles.rsmi",
@@ -29,6 +32,12 @@ def main(args: Optional[Sequence[str]] = None) -> None:
         "--output", default="uspto_data.csv", help="the output filename"
     )
     parser.add_argument("--folder", default=".", help="folder with downloaded files")
+    parser.add_argument(
+        "--with_yields",
+        action="store_true",
+        default=False,
+        help="if to add yield columns",
+    )
     args = parser.parse_args(args)
 
     filenames = [Path(args.folder) / filename for filename in args.filenames]
@@ -42,11 +51,18 @@ def main(args: Optional[Sequence[str]] = None) -> None:
     para_num = data["ParagraphNum"].fillna("")
     row_num = data.index.astype(str)
     data["ID"] = data["PatentNumber"] + ";" + para_num + ";" + row_num
-    data2 = data[["ID", "Year", "ReactionSmiles"]]
+    columns = ["ID", "Year", "ReactionSmiles"]
+    if args.with_yields:
+        columns += ["TextMinedYield", "CalculatedYield"]
+    data2 = data[columns]
 
     print(f"Total number of unique IDs: {len(set(data2['ID']))}")
     print(f"Total number of records: {len(data2)}")
 
+    if args.with_yields:
+        print("Curating yields...")
+        data2 = UsptoYieldCuration()(data2)
+
     data2.to_csv(Path(args.folder) / args.output, sep="\t", index=False)
 
 
diff --git a/rxnutils/data/uspto/download.py b/rxnutils/data/uspto/download.py
index 8719772..edf4165 100644
--- a/rxnutils/data/uspto/download.py
+++ b/rxnutils/data/uspto/download.py
@@ -1,14 +1,13 @@
 """Module containing a script to download USPTO files Figshare
 """
-import os
 import argparse
+import os
 from pathlib import Path
 from typing import Optional, Sequence
 
-import tqdm
-import requests
 import py7zr
-
+import requests
+import tqdm
 
 FILES_TO_DOWNLOAD = [
     {
diff --git a/rxnutils/data/uspto/preparation_pipeline.py b/rxnutils/data/uspto/preparation_pipeline.py
index a28df43..348acf0 100644
--- a/rxnutils/data/uspto/preparation_pipeline.py
+++ b/rxnutils/data/uspto/preparation_pipeline.py
@@ -2,13 +2,14 @@
 Module containing pipeline for downloading, transforming and cleaning USPTO data
 This needs to be run in an environment with rxnutils installed
 """
+
 from pathlib import Path
 
 from metaflow import step
 
 from rxnutils.data.base_pipeline import DataPreparationBaseFlow
-from rxnutils.data.uspto.download import main as download_uspto
 from rxnutils.data.uspto.combine import main as combine_uspto
+from rxnutils.data.uspto.download import main as download_uspto
 
 
 class UsptoDataPreparationFlow(DataPreparationBaseFlow):
diff --git a/rxnutils/data/uspto/uspto_yield.py b/rxnutils/data/uspto/uspto_yield.py
new file mode 100644
index 0000000..c5c2a79
--- /dev/null
+++ b/rxnutils/data/uspto/uspto_yield.py
@@ -0,0 +1,51 @@
+"""
+Code for curating USPTO yields.
+
+Inspiration from this code: https://github.com/DocMinus/Yield_curation_USPTO
+
+This could potentially be an action, but since it only make sens to use it
+with USPTO data, it resides here for now.
+"""
+
+from dataclasses import dataclass
+
+import numpy as np
+import pandas as pd
+
+
+@dataclass
+class UsptoYieldCuration:
+    """
+    Action for curating USPTO yield columns
+    """
+
+    text_yield_column: str = "TextMinedYield"
+    calc_yield_column: str = "CalculatedYield"
+    out_column: str = "CuratedYield"
+
+    def __call__(self, data: pd.DataFrame) -> pd.DataFrame:
+        calc_yield = data[self.calc_yield_column].str.rstrip("%")
+        calc_yield = pd.to_numeric(calc_yield, errors="coerce")
+        calc_yield[(calc_yield < 0) | (calc_yield > 100)] = np.nan
+
+        text_yield = data[self.text_yield_column].str.lstrip("~")
+        text_yield = text_yield.str.rstrip("%")
+        text_yield = text_yield.str.replace(">=", "", regex=False)
+        text_yield = text_yield.str.replace(">", "", regex=False)
+        text_yield = text_yield.str.replace("<", "", regex=False)
+        text_yield = text_yield.str.replace(r"\d{1,2}\sto\s", "", regex=True)
+        text_yield = pd.to_numeric(text_yield, errors="coerce")
+        text_yield[(text_yield < 0) | (text_yield > 100)] = np.nan
+
+        curated_yield = text_yield.copy()
+
+        sel = (~calc_yield.isna()) & (~text_yield.isna())
+        curated_yield[sel] = np.maximum(calc_yield[sel], text_yield[sel])
+
+        sel = (~calc_yield.isna()) & (text_yield.isna())
+        curated_yield[sel] = calc_yield[sel]
+
+        return data.assign(**{self.out_column: curated_yield})
+
+    def __str__(self) -> str:
+        return f"{self.pretty_name} (create one column with curated yield values)"
diff --git a/rxnutils/pipeline/actions/reaction_mod.py b/rxnutils/pipeline/actions/reaction_mod.py
index 5fe65c6..8d16211 100644
--- a/rxnutils/pipeline/actions/reaction_mod.py
+++ b/rxnutils/pipeline/actions/reaction_mod.py
@@ -18,9 +18,9 @@
 from rxnutils.chem.disconnection_sites.tag_converting import convert_atom_map_tag
 from rxnutils.chem.utils import (
     atom_mapping_numbers,
+    desalt_molecules,
     neutralize_molecules,
     remove_atom_mapping,
-    desalt_molecules,
 )
 from rxnutils.pipeline.base import ReactionActionMixIn, action, global_apply
 
diff --git a/rxnutils/pipeline/actions/reaction_props.py b/rxnutils/pipeline/actions/reaction_props.py
index aeb6ce8..67f3400 100644
--- a/rxnutils/pipeline/actions/reaction_props.py
+++ b/rxnutils/pipeline/actions/reaction_props.py
@@ -5,7 +5,7 @@
 import os
 from collections import defaultdict
 from dataclasses import dataclass
-from typing import ClassVar, List, Set, Tuple, Optional
+from typing import ClassVar, List, Optional, Set, Tuple
 
 import pandas as pd
 from rdkit import Chem, RDLogger
@@ -14,11 +14,8 @@
 from rdkit.Chem.rdMolDescriptors import CalcNumRings
 from rdkit.Chem.rdmolops import FindPotentialStereo
 
-from rxnutils.pipeline.base import (
-    action,
-    global_apply,
-    ReactionActionMixIn,
-)
+from rxnutils.chem.cgr import CondensedGraphReaction
+from rxnutils.chem.reaction import ChemicalReaction
 from rxnutils.chem.utils import (
     atom_mapping_numbers,
     has_atom_mapping,
@@ -26,8 +23,7 @@
     reaction_centres,
     split_smiles_from_reaction,
 )
-from rxnutils.chem.reaction import ChemicalReaction
-from rxnutils.chem.cgr import CondensedGraphReaction
+from rxnutils.pipeline.base import ReactionActionMixIn, action, global_apply
 
 rd_logger = RDLogger.logger()
 rd_logger.setLevel(RDLogger.CRITICAL)
diff --git a/rxnutils/pipeline/actions/templates.py b/rxnutils/pipeline/actions/templates.py
index 3261cb4..c0f4cc5 100644
--- a/rxnutils/pipeline/actions/templates.py
+++ b/rxnutils/pipeline/actions/templates.py
@@ -1,16 +1,16 @@
 """Module containing template validation actions"""
 from __future__ import annotations
+
 from dataclasses import dataclass
-from typing import ClassVar, Set, Sequence
+from typing import ClassVar, Sequence, Set
 
 import pandas as pd
-from rdkit import RDLogger
-from rdkit import Chem
+from rdkit import Chem, RDLogger
 from rdkit.Chem import AllChem
 
-from rxnutils.pipeline.base import action, global_apply
 from rxnutils.chem.template import ReactionTemplate
 from rxnutils.chem.utils import split_smiles_from_reaction
+from rxnutils.pipeline.base import action, global_apply
 
 rd_logger = RDLogger.logger()
 rd_logger.setLevel(RDLogger.CRITICAL)
diff --git a/rxnutils/pipeline/base.py b/rxnutils/pipeline/base.py
index 35a9684..57d5316 100644
--- a/rxnutils/pipeline/base.py
+++ b/rxnutils/pipeline/base.py
@@ -1,16 +1,15 @@
 """Module containing routines for the validation framework"""
 from __future__ import annotations
-from typing import Any
-from typing import Callable
-from typing import Dict, Optional, Tuple, List
+
 from collections import defaultdict
 from dataclasses import fields
+from typing import Any, Callable, Dict, List, Optional, Tuple
 
 import pandas as pd
 import swifter  # noqa #pylint: disable=unused-import
 from tqdm import tqdm
 
-from rxnutils.chem.utils import split_smiles_from_reaction, join_smiles_from_reaction
+from rxnutils.chem.utils import join_smiles_from_reaction, split_smiles_from_reaction
 
 ActionType = Callable[[pd.DataFrame], pd.DataFrame]
 
diff --git a/rxnutils/pipeline/runner.py b/rxnutils/pipeline/runner.py
index 846e996..2e48949 100644
--- a/rxnutils/pipeline/runner.py
+++ b/rxnutils/pipeline/runner.py
@@ -1,18 +1,19 @@
 """Module containg routines and interface to run pipelines"""
 import argparse
-from typing import Dict, Any, Optional, Sequence
+from typing import Any, Dict, Optional, Sequence
 
-import yaml
 import pandas as pd
+import yaml
+
+import rxnutils.pipeline.actions.dataframe_mod  # noqa
 
 # imports needed to register all the actions
 # pylint: disable=unused-import
 import rxnutils.pipeline.actions.reaction_mod  # noqa
 import rxnutils.pipeline.actions.reaction_props  # noqa
 import rxnutils.pipeline.actions.templates  # noqa
-import rxnutils.pipeline.actions.dataframe_mod  # noqa
-from rxnutils.pipeline.base import create_action, global_apply, list_actions
 from rxnutils.data.batch_utils import read_csv_batch
+from rxnutils.pipeline.base import create_action, global_apply, list_actions
 
 
 def run_pipeline(
diff --git a/rxnutils/routes/base.py b/rxnutils/routes/base.py
index 6f0425f..35ffd87 100644
--- a/rxnutils/routes/base.py
+++ b/rxnutils/routes/base.py
@@ -4,43 +4,50 @@
 and drawing the route
 """
 
-from typing import Dict, Any, List, Callable, Union
+import warnings
 from copy import deepcopy
 from operator import itemgetter
+from typing import Any, Callable, Dict, List, Set, Tuple, Union
 
 import pandas as pd
 from PIL.Image import Image as PilImage
 from rdkit import Chem
 
-from rxnutils.pipeline.actions.reaction_mod import NameRxn, RxnMapper
-from rxnutils.routes.image import RouteImageFactory
+from rxnutils.chem.augmentation import single_reactant_augmentation
 from rxnutils.chem.utils import (
     atom_mapping_numbers,
-    split_smiles_from_reaction,
     join_smiles_from_reaction,
+    split_smiles_from_reaction,
 )
+from rxnutils.pipeline.actions.reaction_mod import NameRxn, RxnMapper
+from rxnutils.routes.image import RouteImageFactory
+from rxnutils.routes.utils.validation import validate_dict
 
 
 class SynthesisRoute:
     """
     This encapsulates a synthesis route or a reaction tree.
-    It provide convenient methods for assigning atom-mapping
+    It provide convinient methods for assigning atom-mapping
     to the reactions, and for providing reaction-level data
     of the route
 
     It is typically initiallized by one of the readers in the
     `rxnutils.routes.readers` module.
 
-    The tree depth and the forward step are automatically assigned
+    The tree depth and the forward step is automatically assigned
     to each reaction node.
 
+    The `max_depth` attribute holds the longest-linear-sequence (LLS)
+
     :param reaction_tree: the tree structure representing the route
     """
 
     def __init__(self, reaction_tree: Dict[str, Any]) -> None:
+        validate_dict(reaction_tree)
         self.reaction_tree = reaction_tree
         self.max_depth = _assign_tree_depth(reaction_tree)
         _assign_forward_step(reaction_tree, self.max_depth)
+        self._nsteps = -1
 
     @property
     def mapped_root_smiles(self) -> str:
@@ -61,6 +68,13 @@ def mapped_root_smiles(self) -> str:
 
         return first_reaction["metadata"]["mapped_reaction_smiles"].split(">")[-1]
 
+    @property
+    def nsteps(self) -> int:
+        """Return the number of reactions in the route"""
+        if self._nsteps == -1:
+            self._nsteps = len(self.reaction_smiles())
+        return self._nsteps
+
     def atom_mapped_reaction_smiles(self) -> List[str]:
         """Returns a list of the atom-mapped reaction SMILES in the route"""
         smiles = []
@@ -68,9 +82,7 @@ def atom_mapped_reaction_smiles(self) -> List[str]:
         return smiles
 
     def assign_atom_mapping(
-        self,
-        overwrite: bool = False,
-        only_rxnmapper: bool = False,
+        self, overwrite: bool = False, only_rxnmapper: bool = False
     ) -> None:
         """
         Assign atom-mapping to each reaction in the route and
@@ -138,18 +150,49 @@ def chains(
                     mol["chain"] = "sub1"
         return chains
 
-    def image(self, show_atom_mapping=False) -> PilImage:
+    def image(
+        self, show_atom_mapping: bool = False, factory_kwargs: Dict[str, Any] = None
+    ) -> PilImage:
         """
         Depict the route.
 
         :param show_atom_mapping: if True, will show the atom-mapping
+        :param factory_kwargs: additional keyword arguments sent to the `RouteImageFactory`
         :returns: the image of the route
         """
+        factory_kwargs = factory_kwargs or {}
         if show_atom_mapping:
             dict_ = self._create_atom_mapping_tree()
         else:
             dict_ = self.reaction_tree
-        return RouteImageFactory(dict_).image
+        return RouteImageFactory(dict_, **factory_kwargs).image
+
+    def is_solved(self) -> bool:
+        """
+        Find if this route is solved, i.e. if all starting material
+        is in stock.
+
+        To be accurate, each molecule node need to have an extra
+        boolean property called `in_stock`.
+        """
+        try:
+            _find_leaves_not_in_stock(self.reaction_tree)
+        except ValueError:
+            return False
+        return True
+
+    def leaves(
+        self,
+    ) -> Set[str]:
+        """
+        Extract a set with the SMILES of all the leaf nodes, i.e.
+        starting material
+
+        :return: a set of SMILES strings
+        """
+        leaves = set()
+        _collect_leaves(self.reaction_tree, leaves)
+        return leaves
 
     def reaction_data(self) -> List[Dict[str, Any]]:
         """
@@ -161,13 +204,41 @@ def reaction_data(self) -> List[Dict[str, Any]]:
         _collect_reaction_data(self.reaction_tree, data)
         return data
 
-    def reaction_smiles(self) -> List[str]:
-        """Returns a list of the un-mapped reaction SMILES"""
-        smiles = []
-        _collect_reaction_smiles(self.reaction_tree, smiles)
-        return smiles
+    def reaction_ngrams(self, nitems: int, metadata_key: str) -> List[Tuple[Any, ...]]:
+        """
+        Extract an n-gram representation of the route by building up n-grams
+        of the reaction metadata.
 
-    def remap(self, other: "SynthesisRoute") -> None:
+        :param nitems: the length of the gram
+        :param metadata_key: the metadata to extract
+        :return: the collected n-grams
+        """
+        if self.max_depth < nitems:
+            return []
+        first_reaction = self.reaction_tree["children"][0]
+        ngrams = []
+        _collect_ngrams(first_reaction, nitems, metadata_key, ngrams)
+        return ngrams
+
+    def reaction_smiles(self, augment: bool = False) -> List[str]:
+        """
+        Returns a list of the un-mapped reaction SMILES
+        :param augment: if True will add reagents to single-reactant
+                          reagents whenever possible
+        """
+        if not augment:
+            smiles_list = []
+            _collect_reaction_smiles(self.reaction_tree, smiles_list)
+            return smiles_list
+
+        smiles_list = []
+        for data in self.reaction_data():
+            smiles = data["reaction_smiles"]
+            classification = data.get("classification", "")
+            smiles_list.append(single_reactant_augmentation(smiles, classification))
+        return smiles_list
+
+    def remap(self, other: Union["SynthesisRoute", str, Dict[int, int]]) -> None:
         """
         Remap the reaction so that it follows the mapping of a
         1) root compound in a reference route, 2) a ref compound given
@@ -206,7 +277,18 @@ def _assign_mapping(
         df = pd.DataFrame({"smiles": list(set(self.reaction_smiles()))})
         nextmove_action = NameRxn(in_column="smiles", nm_rxn_column="mapped_smiles")
         rxnmapper_action = RxnMapper(in_column="smiles")
-        df = rxnmapper_action(nextmove_action(df))
+        if not only_rxnmapper:
+            try:
+                df = nextmove_action(df)
+            # Raised by nextmove_action if namerxn not in path
+            except FileNotFoundError:
+                df = df.assign(NMC=["0.0"] * len(df), mapped_smiles=[""] * len(df))
+                warnings.warn(
+                    "namerxn does not appear to be in $PATH. Run failed and proceeding with rxnmapper only"
+                )
+        else:
+            df = df.assign(NMC=["0.0"] * len(df), mapped_smiles=[""] * len(df))
+        df = rxnmapper_action(df)
         if only_rxnmapper:
             df["mapped_smiles"] = df["RxnmapperRxnSmiles"]
         else:
@@ -349,7 +431,7 @@ def smiles2inchikey(smiles: str, ignore_stereo: bool = False) -> str:
 
 
 def _assign_atom_mapped_smiles(
-    tree_dict: Dict[str, Any], reaction_smiles: str = ""
+    tree_dict: Dict[str, Any], reactants_smiles: List[str] = None
 ) -> None:
     """
     Used to copy the atom-mapped SMILES from the reaction metadata
@@ -360,23 +442,26 @@ def _assign_atom_mapped_smiles(
     based on partial InChI key without stereoinformation
 
     :param tree_dict: the current molecule node
-    :param reaction_smiles: the reaction SMILES of the parent reaction
+    :param reactants_smiles: the list of reactants SMILES of the parent reaction
     """
     tree_dict["unmapped_smiles"] = tree_dict["smiles"]
     # For leaf nodes
     if not tree_dict.get("children", []):
-        inchi2mapped = {
-            smiles2inchikey(smiles, ignore_stereo=True): smiles
-            for smiles in split_smiles_from_reaction(reaction_smiles.split(">")[0])
-        }
         inchi = smiles2inchikey(tree_dict["smiles"], ignore_stereo=True)
-        tree_dict["smiles"] = inchi2mapped.get(inchi, tree_dict["smiles"])
+        found = -1
+        for idx, smi in enumerate(reactants_smiles):
+            if inchi == smiles2inchikey(smi, ignore_stereo=True):
+                found = idx
+                break
+        if found > -1:
+            tree_dict["smiles"] = reactants_smiles.pop(found)
     else:
         reaction_dict = tree_dict["children"][0]
         reaction_smiles = reaction_dict["metadata"]["mapped_reaction_smiles"]
         tree_dict["smiles"] = reaction_smiles.split(">")[-1]
+        reactants_smiles = split_smiles_from_reaction(reaction_smiles.split(">")[0])
         for grandchild in reaction_dict["children"]:
-            _assign_atom_mapped_smiles(grandchild, reaction_smiles)
+            _assign_atom_mapped_smiles(grandchild, reactants_smiles)
 
 
 def _assign_forward_step(
@@ -435,6 +520,58 @@ def _collect_atom_mapped_smiles(tree_dict: Dict[str, Any], smiles: List[str]) ->
         _collect_atom_mapped_smiles(grandchild, smiles)
 
 
+def _collect_leaves(tree_dict: Dict[str, Any], leaves: Set[str]) -> None:
+    """
+    Traverse the tree and collect SMILES of molecule nodes that has no children
+
+    :param tree_dict: the current molecule node
+    :param leaves: the list of collected leaves
+    """
+    children = tree_dict.get("children", [])
+    if children:
+        for child in children:
+            _collect_leaves(child, leaves)
+    else:
+        leaves.add(tree_dict["smiles"])
+
+
+def _collect_ngrams(
+    tree_dict: Dict[str, Any],
+    nitems: int,
+    metadata_key: str,
+    result: List[Tuple[Any, ...]],
+    accumulation: List[str] = None,
+):
+    """
+    Collect ngrams from reaction metadata
+
+    :param tree_dict: the current reaction node in the recursion
+    :param nitems: the length of the gram
+    :param metadata_key: the metadata to extract
+    :param result: the collected ngrams
+    :param accumulation: the accumulate items in the recursion
+    :raise ValueError: if this routine is initialized from a molecule node
+    """
+    accumulation = accumulation or []
+    if tree_dict["type"] == "mol":
+        raise ValueError(
+            "Found _collect_ngrams at molecule node. This should not happen."
+        )
+
+    data = tree_dict.get("metadata", {}).get(metadata_key)
+    accumulation.append(data)
+
+    if len(accumulation) == nitems:
+        result.append(tuple(accumulation))
+        accumulation.pop(0)
+
+    for mol_child in tree_dict["children"]:
+        for rxn_grandchild in mol_child.get("children", []):
+            _collect_ngrams(
+                rxn_grandchild, nitems, metadata_key, result, list(accumulation)
+            )
+
+
 def _collect_reaction_data(
     tree_dict: Dict[str, Any], data: List[Dict[str, Any]]
 ) -> None:
@@ -553,6 +690,20 @@ def _extract_chain_molecules(
     chain_molecules.append(mol_dict)
 
 
+def _find_leaves_not_in_stock(tree_dict: Dict[str, Any]) -> None:
+    """
+    Traverse the tree and check the `in_stock` value of molecule
+    nodes without children (leaves). If one is found that is not
+    in stock this raises an exception, which stops the traversal.
+    """
+    children = tree_dict.get("children", [])
+    if not children and not tree_dict.get("in_stock", True):
+        raise ValueError(f"child not in stock {tree_dict}")
+    elif children:
+        for child in children:
+            _find_leaves_not_in_stock(child)
+
+
 def _inherit_atom_mapping(
     tree_dict: Dict[str, Any], new_atomnum: int, parent_smiles: str = ""
 ) -> None:
diff --git a/rxnutils/routes/comparison.py b/rxnutils/routes/comparison.py
new file mode 100644
index 0000000..4e0bd70
--- /dev/null
+++ b/rxnutils/routes/comparison.py
@@ -0,0 +1,222 @@
+""" Contains routines for computing route similarities
+"""
+import functools
+from typing import Any, Callable, Dict, List, Sequence, Set, Tuple
+
+import numpy as np
+
+from rxnutils.chem.reaction import ChemicalReaction
+from rxnutils.chem.utils import atom_mapping_numbers
+from rxnutils.routes.base import SynthesisRoute
+from rxnutils.routes.ted.distances_calculator import ted_distances_calculator
+
+RouteDistancesCalculator = Callable[[Sequence[SynthesisRoute]], np.ndarray]
+
+
+def simple_route_similarity(routes: Sequence[SynthesisRoute]) -> np.ndarray:
+    """
+    Returns the geometric mean of the simple bond forming similarity, and
+    the atom matching bonanza similarity
+
+    :param routes: the sequence of routes to compare
+    :return: the pairwise similarity
+    """
+    bond_score = simple_bond_forming_similarity(routes)
+    atom_score = atom_matching_bonanza_similarity(routes)
+    return np.sqrt(bond_score * atom_score)
+
+
+def atom_matching_bonanza_similarity(routes: Sequence[SynthesisRoute]) -> np.ndarray:
+    """
+    Calculates the pairwise similarity of a sequence of routes
+    based on the overlap of the atom-mapping numbers of the compounds
+    in the routes.
+
+    :param routes: the sequence of routes to compare
+    :return: the pairwise similarity
+    """
+    sims = np.zeros((len(routes), len(routes)))
+    for idx1, route1 in enumerate(routes):
+        mols1 = _extract_atom_mapping_numbers(route1)
+        n1 = len(mols1) - 1
+        mols1 = [mol for mol in mols1 if mol]
+        for idx2, route2 in enumerate(routes):
+            if idx1 == idx2:
+                sims[idx1, idx2] = 1.0
+                continue
+            # If both of the routes have not reactions, we assume
+            # they are identical and it is assignes a score of 1.0
+            if route1.max_depth == 0 and route2.max_depth == 0:
+                sims[idx1, idx2] = 1.0
+                continue
+            # If just one the route has no reactions, we assume
+            # they are maximal dissimilar and assigns a score 0.0 (see how `sims` is initialized)
+            if route1.max_depth == 0 or route2.max_depth == 0:
+                continue
+
+            mols2 = _extract_atom_mapping_numbers(route2)
+            n2 = len(mols2) - 1
+            mols2 = [mol for mol in mols2 if mol]
+
+            o = _calc_overlap_matrix(mols1[1:], mols2[1:])
+            sims[idx1, idx2] = (o.max(axis=1).sum() + o.max(axis=0).sum()) / (n1 + n2)
+    return sims
+
+
+def simple_bond_forming_similarity(routes: Sequence[SynthesisRoute]) -> np.ndarray:
+    """
+    Calculates the pairwise similarity of a sequence of routes
+    based on the overlap of formed bonds in the reactions.
+
+    :param routes: the sequence of routes to compare
+    :return: the pairwise similarity
+    """
+    sims = np.ones((len(routes), len(routes)))
+    for idx1, route1 in enumerate(routes):
+        bonds1 = _extract_formed_bonds(route1)
+        for idx2, route2 in enumerate(routes):
+            if idx2 <= idx1:
+                continue
+            # If both of the routes have not reactions, we assume
+            # they are identical and it is assignes a score of 1.0 (see how `sims` is initialized)
+            if route1.max_depth == 0 and route2.max_depth == 0:
+                continue
+            # If just one the route has no reactions, we assume
+            # they are maximal dissimilar and assigns a score 0.0
+            if route1.max_depth == 0 or route2.max_depth == 0:
+                sims[idx1, idx2] = sims[idx2, idx1] = 0.0
+                continue
+
+            bonds2 = _extract_formed_bonds(route2)
+            sims[idx1, idx2] = _bond_formed_overlap_score(bonds1, bonds2)
+            sims[idx2, idx1] = sims[idx1, idx2]  # Score is symmetric
+    return sims
+
+
+def route_distances_calculator(model: str, **kwargs: Any) -> RouteDistancesCalculator:
+    """
+    Return a callable that given a list routes as dictionaries
+    calculate the squared distance matrix
+
+    :param model: the route distance model name
+    :param kwargs: additional keyword arguments for the model
+    :return: the appropriate route distances calculator
+    """
+    if model not in ["ted", "lstm"]:
+        raise ValueError("Model must be either 'ted' or 'lstm'")
+
+    if model == "ted":
+        model_kwargs = _copy_kwargs(["content", "timeout"], **kwargs)
+        return functools.partial(ted_distances_calculator, **model_kwargs)
+
+    # Placeholder for LSTM distances calculation
+    # model_kwargs = _copy_kwargs(["model_path"], **kwargs)
+    # return lstm_distances_calculator(**model_kwargs)
+    raise NotImplementedError("LSTM route distances calculator not implemented yet.")
+
+
+def _copy_kwargs(keys_to_copy: List[str], **kwargs: Any) -> Dict[str, Any]:
+    """Copy selected keyword arguments."""
+    new_kwargs = {}
+    for key in keys_to_copy:
+        if key in kwargs:
+            new_kwargs[key] = kwargs[key]
+    return new_kwargs
+
+
+def _calc_overlap_matrix(mols1: List[List[int]], mols2: List[List[int]]) -> np.ndarray:
+    """
+    Calculate the pairwise overlap matrix between
+    the molecules in the two input vectors
+
+    :param mols1: the atom-mapping numbers of the first molecule
+    :param mols2: the atom-mapping numbers of the second molecule
+    :return: the computed matrix
+    """
+
+    def mol_overlap(mol1, mol2):
+        if not mol1 and not mol2:
+            return 0
+        return len(set(mol1).intersection(mol2)) / max(len(mol1), len(mol2))
+
+    overlaps = np.zeros((len(mols1), len(mols2)))
+    for idx1, mol1 in enumerate(mols1):
+        for idx2, mol2 in enumerate(mols2):
+            overlaps[idx1, idx2] = mol_overlap(mol1, mol2)
+    return overlaps
+
+
+def _extract_atom_mapping_numbers(route: SynthesisRoute) -> List[List[int]]:
+    """
+    Extract all the compounds in a synthesis routes as a set of
+    atom-mapping numbers of the atoms in the compounds.
+
+    Only account for atom-mapping numbers that exists in the root compound
+    """
+    if route.max_depth == 0:
+        return []
+
+    root_atom_numbers = sorted(atom_mapping_numbers(route.mapped_root_smiles))
+    mapping_list = [root_atom_numbers]
+    for reaction_smiles in route.atom_mapped_reaction_smiles():
+        reactants_smiles = reaction_smiles.split(">")[0]
+        for smi in reactants_smiles.split("."):
+            atom_numbers = sorted(
+                [num for num in atom_mapping_numbers(smi) if num in root_atom_numbers]
+            )
+            mapping_list.append(atom_numbers)
+    return mapping_list
+
+
+def _extract_formed_bonds(route: SynthesisRoute) -> List[Tuple[int, int]]:
+    """
+    Extract a set of bonds formed in the synthesis routes.
+    Only bonds contributing to the root compound is accounted for.
+    """
+    if route.max_depth == 0:
+        return []
+
+    formed_bonds = []
+    root_atom_numbers = set(atom_mapping_numbers(route.mapped_root_smiles))
+    for reaction_smiles in route.atom_mapped_reaction_smiles():
+        rxn_obj = ChemicalReaction(reaction_smiles, clean_smiles=False)
+        product_bonds = set()
+        product_bonds = _extract_molecule_bond_tuple(rxn_obj.products)
+        reactants_bonds = _extract_molecule_bond_tuple(rxn_obj.reactants)
+        for idx1, idx2 in product_bonds - reactants_bonds:
+            if idx1 in root_atom_numbers and idx2 in root_atom_numbers:
+                formed_bonds.append(tuple(sorted([idx1, idx2])))
+    return formed_bonds
+
+
+def _extract_molecule_bond_tuple(molecules: List) -> Set[int]:
+    """
+    Returns the sorted set of atom-mapping number pairs for each
+    bonds in a list of rdkit molecules
+    """
+    bonds = set()
+    for bond in [bond for mol in molecules for bond in mol.GetBonds()]:
+        bonds.add(
+            tuple(
+                sorted(
+                    [
+                        bond.GetBeginAtom().GetAtomMapNum(),
+                        bond.GetEndAtom().GetAtomMapNum(),
+                    ]
+                )
+            )
+        )
+    return bonds
+
+
+def _bond_formed_overlap_score(
+    bonds1: List[Tuple[int]], bonds2: List[Tuple[int]]
+) -> float:
+    """
+    Computes a similarity score of two routes by comparing the overlap
+    of bonds formed in the synthesis routes.
+    """
+    overlap = len(set(bonds1).intersection(bonds2))
+    if not bonds1 and not bonds2:
+        return 0
+    return overlap / max(len(bonds1), len(bonds2))
diff --git a/rxnutils/routes/image.py b/rxnutils/routes/image.py
index 03f3035..53eb048 100644
--- a/rxnutils/routes/image.py
+++ b/rxnutils/routes/image.py
@@ -11,15 +11,7 @@
 
 if TYPE_CHECKING:
     # pylint: disable=ungrouped-imports
-    from typing import (
-        Any,
-        Optional,
-        Dict,
-        List,
-        Sequence,
-        Tuple,
-        Union,
-    )
+    from typing import Any, Callable, Dict, List, Optional, Sequence, Tuple, Union
 
     PilColor = Union[str, Tuple[int, int, int]]
     FrameColors = Optional[Dict[bool, PilColor]]
@@ -47,6 +39,7 @@ def molecules_to_images(
     mols: Sequence[Chem.rdchem.Mol],
     frame_colors: Sequence[PilColor],
     size: int = 300,
+    draw_kwargs: Dict[str, Any] = None,
 ) -> List[PilImage]:
     """
     Create pretty images of molecules with a colored frame around each one of them.
@@ -56,12 +49,12 @@ def molecules_to_images(
     :param smiles_list: the molecules
     :param frame_colors: the color of the frame for each molecule
     :param size: the sub-image size
+    :param draw_kwargs: additional keyword-arguments sent to `MolsToGridImage`
     :return: the produced images
     """
+    draw_kwargs = draw_kwargs or {}
     all_mols = Draw.MolsToGridImage(
-        mols,
-        molsPerRow=len(mols),
-        subImgSize=(size, size),
+        mols, molsPerRow=len(mols), subImgSize=(size, size), **draw_kwargs
     )
     if not hasattr(all_mols, "crop"):  # Is not a PIL image
         fileobj = io.BytesIO(all_mols.data)
@@ -153,6 +146,9 @@ class RouteImageFactory:
     :param in_stock_colors: the colors around molecules, defaults to {True: "green", False: "orange"}
     :param show_all: if True, also show nodes that are marked as hidden
     :param margin: the margin between images
+    :param mol_size: the size of the molecule
+    :param mol_draw_kwargs: additional arguments sent to the drawing routine
+    :param replace_mol_func: an optional function to replace molecule images
     """
 
     def __init__(
@@ -161,6 +157,9 @@ def __init__(
         in_stock_colors: FrameColors = None,
         show_all: bool = True,
         margin: int = 100,
+        mol_size: int = 300,
+        mol_draw_kwargs: Dict[str, Any] = None,
+        replace_mol_func: Callable[[Dict[str, Any]], None] = None,
     ) -> None:
         in_stock_colors = in_stock_colors or {
             True: "green",
@@ -172,9 +171,13 @@ def __init__(
         self._stock_lookup: Dict[str, Any] = {}
         self._mol_lookup: Dict[str, Any] = {}
         self._extract_molecules(route)
+        if replace_mol_func is not None:
+            replace_mol_func(self._mol_lookup)
         images = molecules_to_images(
             list(self._mol_lookup.values()),
             [in_stock_colors[val] for val in self._stock_lookup.values()],
+            size=mol_size,
+            draw_kwargs=mol_draw_kwargs or {},
         )
         self._image_lookup = dict(zip(self._mol_lookup.keys(), images))
 
diff --git a/rxnutils/routes/readers.py b/rxnutils/routes/readers.py
index 033d265..308adfb 100644
--- a/rxnutils/routes/readers.py
+++ b/rxnutils/routes/readers.py
@@ -1,13 +1,14 @@
 """Routines for reading routes from various formats"""
+
 import copy
-from typing import Sequence, List, Dict, Any
+from typing import Any, Dict, List, Sequence
 
 import pandas as pd
 from rdkit import Chem
+from rdkit.Chem import AllChem
 
-from rxnutils.routes.base import SynthesisRoute
-from rxnutils.routes.base import smiles2inchikey
-from rxnutils.chem.utils import split_smiles_from_reaction, join_smiles_from_reaction
+from rxnutils.chem.utils import join_smiles_from_reaction, split_smiles_from_reaction
+from rxnutils.routes.base import SynthesisRoute, smiles2inchikey
 
 
 def read_reaction_lists(filename: str) -> List[SynthesisRoute]:
@@ -169,9 +170,44 @@ def make_dict(product_smiles):
     return SynthesisRoute(make_dict(inchi_map[target_inchi]))
 
 
+def read_rdf_file(filename: str) -> SynthesisRoute:
+    def finish_reaction():
+        if not rxnblock:
+            return
+        rxn = AllChem.ReactionFromRxnBlock(
+            "\n".join(rxnblock), sanitize=False, strictParsing=False
+        )
+        reactions.append(AllChem.ReactionToSmiles(rxn))
+
+    with open(filename, "r") as fileobj:
+        lines = fileobj.read().splitlines()
+
+    reactions = []
+    rxnblock = []
+    read_rxn = skip_entry = False
+    for line in lines:
+        if line.startswith("$RFMT"):
+            read_rxn = skip_entry = False
+            finish_reaction()
+            rxnblock = []
+        elif line.startswith(("$MFMT", "$DATUM")):
+            # Ignore MFMT and DATUM entries for now
+            skip_entry = True
+        elif skip_entry:
+            continue
+        elif line.startswith("$RXN"):
+            rxnblock = [line]
+            read_rxn = True
+        elif read_rxn:
+            rxnblock.append(line)
+    finish_reaction()
+
+    return reactions2route(reactions)
+
+
 def _transform_retrosynthesis_atom_mapping(tree_dict: Dict[str, Any]) -> None:
     """
-    Routes output from AiZynth have atom-mapping from the template-based model,
+    Routes output from AiZynth has atom-mapping from the template-based model,
     but it needs to be processed
     1. Remove atom-mapping from reactants not in product
     2. Reverse reaction SMILES
diff --git a/rxnutils/routes/retro_bleu/__init__.py b/rxnutils/routes/retro_bleu/__init__.py
new file mode 100644
index 0000000..5946c1d
--- /dev/null
+++ b/rxnutils/routes/retro_bleu/__init__.py
@@ -0,0 +1,4 @@
+from rxnutils.routes.retro_bleu.scoring import (
+    ngram_overlap_score,  # noqa
+    retro_bleu_score,
+)
diff --git a/rxnutils/routes/retro_bleu/ngram_collection.py b/rxnutils/routes/retro_bleu/ngram_collection.py
new file mode 100644
index 0000000..bb0d3a1
--- /dev/null
+++ b/rxnutils/routes/retro_bleu/ngram_collection.py
@@ -0,0 +1,111 @@
+"""
+Contains routines for creating, reading, and writing n-gram collections
+
+Can be run as a module to create a collection from a set of routes:
+
+    python -m rxnutils.routes.retro_bleu.ngram_collection --filename routes.json --output ngrams.json --nitems 2 --metadata template_hash
+
+"""
+
+from __future__ import annotations
+
+import json
+from dataclasses import dataclass
+from typing import Any, Set, Tuple
+
+from tqdm import tqdm
+
+from rxnutils.routes.base import SynthesisRoute
+
+
+@dataclass
+class NgramCollection:
+    """
+    Class to create, read, and write a collection of n-grams
+
+    :param nitems: the length of each n-gram
+    :param metadata_key: the key used to extract the n-grams from the reactions
+    :param ngrams: the extracted n-grams
+    """
+
+    nitems: int
+    metadata_key: str
+    ngrams: Set[Tuple[str, ...]]
+
+    @classmethod
+    def from_file(cls, filename: str) -> "NgramCollection":
+        """
+        Read an n-gram collection from a JSON-file
+
+        :param filename: the path to the file
+        :return: the n-gram collection
+        """
+        with open(filename, "r") as fileobj:
+            dict_ = json.load(fileobj)
+        ngrams = {tuple(item.split("\t")) for item in dict_["ngrams"]}
+        return NgramCollection(dict_["nitems"], dict_["metadata_key"], ngrams)
+
+    @classmethod
+    def from_tree_collection(
+        cls, filename: str, nitems: int, metadata_key: str
+    ) -> "NgramCollection":
+        """
+        Make a n-gram collection by extracting them from a collection of
+        synthesis routes.
+
+        :param filename: the path to a file with a list of synthesis routes
+        :param nitems: the length of the gram
+        :param metadata_key: the metadata to extract
+        :return: the n-gram collection
+        """
+        with open(filename, "r") as fileobj:
+            tree_list = json.load(fileobj)
+
+        ngrams = set()
+        for tree_dict in tqdm(tree_list, leave=False):
+            route = SynthesisRoute(tree_dict)
+            ngrams = ngrams.union(route.reaction_ngrams(nitems, metadata_key))
+        return NgramCollection(nitems, metadata_key, ngrams)
+
+    def save_to_file(self, filename: str) -> None:
+        """
+        Save an n-gram collection to a JSON-file
+
+        :param filename: the path to the file
+        """
+        dict_ = {
+            "nitems": self.nitems,
+            "metadata_key": self.metadata_key,
+            "ngrams": ["\t".join(ngram) for ngram in self.ngrams],
+        }
+        with open(filename, "w") as fileobj:
+            json.dump(dict_, fileobj)
+
+
+if __name__ == "__main__":
+    import argparse
+
+    parser = argparse.ArgumentParser(
+        "Tool for making n-gram collections from a set of synthesis routes"
+    )
+    parser.add_argument(
+        "--filename", nargs="+", help="the path to the synthesis routes"
+    )
+    parser.add_argument("--output", help="the path to the n-gram collection")
+    parser.add_argument("--nitems", type=int, help="the length of the gram")
+    parser.add_argument(
+        "--metadata", help="the reaction metadata to extract for making the n-grams"
+    )
+    args = parser.parse_args()
+
+    collection = None
+    for filename in args.filename:
+        temp = NgramCollection.from_tree_collection(
+            filename, args.nitems, args.metadata
+        )
+        if collection is None:
+            collection = temp
+        else:
+            collection.ngrams = collection.ngrams.union(temp.ngrams)
+    print(f"Collected unique {len(collection.ngrams)} {args.nitems}-grams")
+    collection.save_to_file(args.output)
diff --git a/rxnutils/routes/retro_bleu/scoring.py b/rxnutils/routes/retro_bleu/scoring.py
new file mode 100644
index 0000000..72f6921
--- /dev/null
+++ b/rxnutils/routes/retro_bleu/scoring.py
@@ -0,0 +1,48 @@
+""" Contains routine to score routes according to Retro-BLEU paper
+"""
+
+import numpy as np
+
+from rxnutils.routes.base import SynthesisRoute
+from rxnutils.routes.retro_bleu.ngram_collection import NgramCollection
+
+
+def ngram_overlap_score(
+    route: SynthesisRoute,
+    ref: NgramCollection,
+) -> float:
+    """
+    Calculate the fractional n-gram overlap of the n-grams in the given
+    route and the reference n-gram collection
+
+    :param route: the route to score
+    :param ref: the reference n-gram collection
+    :return: the calculated score
+    """
+    route_ngrams = set(route.reaction_ngrams(ref.nitems, ref.metadata_key))
+    if not route_ngrams:
+        return np.nan
+    return len(route_ngrams.intersection(ref.ngrams)) / len(route_ngrams)
+
+
+def retro_bleu_score(
+    route: SynthesisRoute, ref: NgramCollection, ideal_steps: int = 3
+) -> float:
+    """
+    Calculate the Retro-BLEU score according to the paper:
+
+    Li, Junren, Lei Fang, och Jian-Guang Lou.
+    ”Retro-BLEU: quantifying chemical plausibility of retrosynthesis routes through reaction template sequence analysis”.
+    Digital Discovery 3, nr 3 (2024): 482–90. https://doi.org/10.1039/D3DD00219E.
+
+    :param route: the route to score
+    :param ref: the reference n-gram collection
+    :param ideal_steps: a length-penalization hyperparameter (see Eq 2 in ref)
+    :return: the calculated score
+    """
+    overlap = ngram_overlap_score(route, ref)
+
+    nreactions = len(route.reaction_smiles())
+    heuristic_score = ideal_steps / max(nreactions, ideal_steps)
+
+    return np.exp(overlap) + np.exp(heuristic_score)
diff --git a/rxnutils/routes/scoring.py b/rxnutils/routes/scoring.py
new file mode 100644
index 0000000..1c16bb4
--- /dev/null
+++ b/rxnutils/routes/scoring.py
@@ -0,0 +1,86 @@
+""" Routines for scoring synthesis routes
+"""
+
+from typing import Any, Callable, Dict, List, Tuple
+
+import numpy as np
+
+from rxnutils.routes.base import SynthesisRoute
+from rxnutils.routes.retro_bleu.scoring import (
+    ngram_overlap_score,  # noqa
+    retro_bleu_score,
+)
+
+
+def route_sorter(
+    routes: List[SynthesisRoute], scorer: Callable[..., float], **kwargs: Any
+) -> Tuple[List[SynthesisRoute], List[float]]:
+    """
+    Scores and sort a list of routes.
+    Returns a tuple of the sorted routes and their scores.
+
+    :param routes: the routes to score
+    :param scorer: the scorer function
+    :param kwargs: additional argument given to the scorer
+    :return: the sorted routes and their scores
+    """
+    scores = np.asarray([scorer(route, **kwargs) for route in routes])
+    sorted_idx = np.argsort(scores)
+    routes = [routes[idx] for idx in sorted_idx]
+    return routes, scores[sorted_idx].tolist()
+
+
+def route_ranks(scores: List[float]) -> List[int]:
+    """
+    Compute the rank of route scores. Rank starts at 1
+
+    :param scores: the route scores
+    :return: a list of ranks for each route
+    """
+    ranks = [1]
+    for idx in range(1, len(scores)):
+        if abs(scores[idx] - scores[idx - 1]) < 1e-8:
+            ranks.append(ranks[idx - 1])
+        else:
+            ranks.append(ranks[idx - 1] + 1)
+    return ranks
+
+
+def badowski_route_score(
+    route: SynthesisRoute,
+    mol_costs: Dict[bool, float] = None,
+    average_yield: float = 0.8,
+    reaction_cost: float = 1.0,
+) -> float:
+    """
+    Calculate the score of route using the method from
+    (Badowski et al. Chem Sci. 2019, 10, 4640).
+
+    The reaction cost is constant and the yield is an average yield.
+    The starting materials are assigned a cost based on whether they are in
+    stock or not. By default starting material in stock is assigned a
+    cost of 1 and starting material not in stock is assigned a cost of 10.
+
+    To be accurate, each molecule node need to have an extra
+    boolean property called `in_stock`.
+
+    :param route: the route to analyze
+    :param mol_costs: the starting material cost
+    :param average_yield: the average yield, defaults to 0.8
+    :param reaction_cost: the reaction cost, defaults to 1.0
+    :return: the computed cost
+    """
+
+    def traverse(tree_dict):
+        mol_cost = mol_costs or {True: 1, False: 10}
+
+        reactions = tree_dict.get("children", [])
+        if not reactions:
+            return mol_cost[tree_dict.get("in_stock", True)]
+
+        child_sum = sum(
+            1 / average_yield * traverse(child) for child in reactions[0]["children"]
+        )
+        return reaction_cost + child_sum
+
+    return traverse(route.reaction_tree)
diff --git a/rxnutils/routes/ted/__init__.py b/rxnutils/routes/ted/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/rxnutils/routes/ted/distances_calculator.py b/rxnutils/routes/ted/distances_calculator.py
new file mode 100644
index 0000000..338a699
--- /dev/null
+++ b/rxnutils/routes/ted/distances_calculator.py
@@ -0,0 +1,35 @@
+""" Module contain method to compute distance matrix using TED """
+import time
+from typing import Sequence
+
+import numpy as np
+
+from rxnutils.routes.base import SynthesisRoute
+from rxnutils.routes.ted.reactiontree import ReactionTreeWrapper
+
+
+def ted_distances_calculator(
+    routes: Sequence[SynthesisRoute], content: str = "both", timeout: int = None
+) -> np.ndarray:
+    """
+    Compute the TED distances between each pair of routes
+
+    :param routes: the routes to calculate pairwise distance on
+    :param content: determine what part of the synthesis trees to include in the calculation,
+            options 'molecules', 'reactions' and 'both', default 'both'
+    :param timeout: if given, raises an exception if timeout is taking longer time
+    :return: the square distance matrix
+    """
+    distances = np.zeros([len(routes), len(routes)])
+    distance_wrappers = [ReactionTreeWrapper(route, content) for route in routes]
+    time0 = time.perf_counter()
+    for i, iwrapper in enumerate(distance_wrappers):
+        # fmt: off
+        for j, jwrapper in enumerate(distance_wrappers[i + 1:], i + 1):
+            distances[i, j] = iwrapper.distance_to(jwrapper)
+            distances[j, i] = distances[i, j]
+        # fmt: on
+        time_past = time.perf_counter() - time0
+        if timeout is not None and time_past > timeout:
+            raise ValueError(f"Unable to compute distance matrix in {timeout} s")
+    return distances
diff --git a/rxnutils/routes/ted/reactiontree.py b/rxnutils/routes/ted/reactiontree.py
new file mode 100644
index 0000000..91ab3aa
--- /dev/null
+++ b/rxnutils/routes/ted/reactiontree.py
@@ -0,0 +1,301 @@
+"""
+Module containing helper classes to compute the distance between to reaction trees using the APTED method
+Since APTED is based on ordered trees and the reaction trees are unordered, plenty of
+heuristics are implemented to deal with this.
+"""
+from __future__ import annotations
+
+import itertools
+import math
+from copy import deepcopy
+from logging import getLogger
+from typing import Any, Callable, Dict, Iterable, List, Optional, Tuple, Union
+
+import numpy as np
+from apted import APTED as Apted
+
+from rxnutils.routes.base import SynthesisRoute
+from rxnutils.routes.ted.utils import (
+    AptedConfig,
+    StandardFingerprintFactory,
+    TreeContent,
+)
+
+StrDict = Dict[str, Any]
+_FloatIterator = Iterable[float]
+
+
+class ReactionTreeWrapper:
+    """
+    Wrapper for a reaction tree that can calculate distances between
+    trees.
+
+    :param route: the synthesis route to wrap
+    :param content: the content of the route to consider in the distance calculation, default 'molecules'
+    :param exhaustive_limit: if the number of possible ordered trees are below this limit create them all, default 20
+    :param fp_factory: the factory of the fingerprint, Morgan fingerprint for molecules and reactions by default
+    :param dist_func: the distance function to use when renaming nodes
+    """
+
+    _index_permutations = {
+        n: list(itertools.permutations(range(n), n)) for n in range(1, 8)
+    }
+
+    def __init__(
+        self,
+        route: SynthesisRoute,
+        content: Union[str, TreeContent] = TreeContent.MOLECULES,
+        exhaustive_limit: int = 20,
+        fp_factory: Callable[[StrDict, Optional[StrDict]], None] = None,
+        dist_func: Callable[[np.ndarray, np.ndarray], float] = None,
+    ) -> None:
+        single_node_tree = not bool(route.reaction_smiles())
+        if single_node_tree and content == TreeContent.REACTIONS:
+            raise ValueError(
+                "Cannot create wrapping with content = reactions for a tree without reactions"
+            )
+
+        self._logger = getLogger()
+        # Will convert string input automatically
+        self._content = TreeContent(content)
+        self._base_tree = deepcopy(route.reaction_tree)
+
+        self._fp_factory = fp_factory or StandardFingerprintFactory()
+        self._add_fingerprints(self._base_tree)
+
+        if self._content != TreeContent.MOLECULES and not single_node_tree:
+            self._add_fingerprints(self._base_tree["children"][0], self._base_tree)
+
+        if self._content == TreeContent.MOLECULES:
+            self._base_tree = self._remove_children_nodes(self._base_tree)
+        elif not single_node_tree and self._content == TreeContent.REACTIONS:
+            self._base_tree = self._remove_children_nodes(
+                self._base_tree["children"][0]
+            )
+
+        self._trees = []
+        self._tree_count, self._node_index_list = self._inspect_tree()
+        self._enumeration = self._tree_count <= exhaustive_limit
+
+        if self._enumeration:
+            self._create_all_trees()
+        else:
+            self._trees.append(self._base_tree)
+
+        self._dist_func = dist_func
+
+    @property
+    def info(self) -> StrDict:
+        """Return a dictionary with internal information about the wrapper"""
+        return {
+            "content": self._content,
+            "tree count": self._tree_count,
+            "enumeration": self._enumeration,
+        }
+
+    @property
+    def first_tree(self) -> StrDict:
+        """Return the first created ordered tree"""
+        return self._trees[0]
+
+    @property
+    def trees(self) -> List[StrDict]:
+        """Return a list of all created ordered trees"""
+        return self._trees
+
+    def distance_iter(
+        self, other: "ReactionTreeWrapper", exhaustive_limit: int = 20
+    ) -> _FloatIterator:
+        """
+        Iterate over all distances computed between this and another tree
+
+        There are three possible enumeration of distances possible dependent
+        on the number of possible ordered trees for the two routes that are compared
+
+        * If the product of the number of possible ordered trees for both routes are
+          below `exhaustive_limit` compute the distance between all pair of trees
+        * If both self and other has been fully enumerated (i.e. all ordered trees has been created)
+          compute the distances between all trees of the route with the most ordered trees and
+          the first tree of the other route
+        * Compute `exhaustive_limit` number of distances by shuffling the child order for
+          each of the routes.
+
+        The rules are applied top-to-bottom.
+
+        :param other: another tree to calculate distance to
+        :param exhaustive_limit: used to determine what type of enumeration to do
+        :yield: the next computed distance between self and other
+        """
+        if self._tree_count * other.info["tree count"] < exhaustive_limit:
+            yield from self._distance_iter_exhaustive(other)
+        elif self._enumeration or other.info["enumeration"]:
+            yield from self._distance_iter_semi_exhaustive(other)
+        else:
+            yield from self._distance_iter_random(other, exhaustive_limit)
+
+    def distance_to(
+        self, other: "ReactionTreeWrapper", exhaustive_limit: int = 20
+    ) -> float:
+        """
+        Calculate the minimum distance from this route to another route
+
+        Enumerate the distances using `distance_iter`.
+
+        :param other: another tree to calculate distance to
+        :param exhaustive_limit: used to determine what type of enumeration to do
+        :return: the minimum distance
+        """
+        min_dist = 1e6
+        min_iter = -1
+        for iteration, distance in enumerate(
+            self.distance_iter(other, exhaustive_limit)
+        ):
+            if distance < min_dist:
+                min_iter = iteration
+                min_dist = distance
+        self._logger.debug(f"Found minimum after {min_iter} iterations")
+        return min_dist
+
+    def distance_to_with_sorting(self, other: "ReactionTreeWrapper") -> float:
+        """
+        Compute the distance to another tree, by simpling sorting the children
+        of both trees. This is not guaranteed to return the minimum distance.
+
+        :param other: another tree to calculate distance to
+        :return: the distance
+        """
+        config = AptedConfig(sort_children=True, dist_func=self._dist_func)
+        return Apted(self.first_tree, other.first_tree, config).compute_edit_distance()
+
+    def _add_fingerprints(self, tree: StrDict, parent: StrDict = None) -> None:
+        if "fingerprint" not in tree:
+            try:
+                self._fp_factory(tree, parent)
+            except ValueError:
+                pass
+        if "fingerprint" not in tree:
+            tree["fingerprint"] = []
+        tree["sort_key"] = "".join(f"{digit}" for digit in tree["fingerprint"])
+        if "children" not in tree:
+            tree["children"] = []
+
+        for child in tree["children"]:
+            for grandchild in child["children"]:
+                self._add_fingerprints(grandchild, child)
+
+    def _create_all_trees(self) -> None:
+        self._trees = []
+        # Iterate over all possible combinations of child order
+        for order_list in itertools.product(*self._node_index_list):
+            self._trees.append(
+                self._create_tree_recursively(self._base_tree, list(order_list))
+            )
+
+    def _create_tree_recursively(
+        self,
+        node: StrDict,
+        order_list: List[List[int]],
+    ) -> StrDict:
+        new_tree = self._make_base_copy(node)
+        children = node.get("children", [])
+        if children:
+            child_order = order_list.pop(0)
+            assert len(child_order) == len(children)
+            new_children = [
+                self._create_tree_recursively(child, order_list) for child in children
+            ]
+            new_tree["children"] = [new_children[idx] for idx in child_order]
+        return new_tree
+
+    def _distance_iter_exhaustive(self, other: "ReactionTreeWrapper") -> _FloatIterator:
+        self._logger.debug(
+            f"APTED: Exhaustive search. {len(self.trees)} {len(other.trees)}"
+        )
+        config = AptedConfig(randomize=False, dist_func=self._dist_func)
+        for tree1, tree2 in itertools.product(self.trees, other.trees):
+            yield Apted(tree1, tree2, config).compute_edit_distance()
+
+    def _distance_iter_random(
+        self, other: "ReactionTreeWrapper", ntimes: int
+    ) -> _FloatIterator:
+        self._logger.debug(
+            f"APTED: Heuristic search. {len(self.trees)} {len(other.trees)}"
+        )
+        config = AptedConfig(randomize=False, dist_func=self._dist_func)
+        yield Apted(self.first_tree, other.first_tree, config).compute_edit_distance()
+
+        config = AptedConfig(randomize=True, dist_func=self._dist_func)
+        for _ in range(ntimes):
+            yield Apted(
+                self.first_tree, other.first_tree, config
+            ).compute_edit_distance()
+
+    def _distance_iter_semi_exhaustive(
+        self, other: "ReactionTreeWrapper"
+    ) -> _FloatIterator:
+        self._logger.debug(
+            f"APTED: Semi-exhaustive search. {len(self.trees)} {len(other.trees)}"
+        )
+        if len(self.trees) < len(other.trees):
+            first_wrapper = self
+            second_wrapper = other
+        else:
+            first_wrapper = other
+            second_wrapper = self
+
+        config = AptedConfig(randomize=False, dist_func=self._dist_func)
+        for tree1 in first_wrapper.trees:
+            yield Apted(
+                tree1, second_wrapper.first_tree, config
+            ).compute_edit_distance()
+
+    def _inspect_tree(self) -> Tuple[int, List[List[int]]]:
+        """
+        Find the number of children for each node in the tree, which
+        will be used to compute the number of possible combinations of child orders
+
+        Also accumulate the possible child orders for the nodes.
+        """
+
+        def _recurse_tree(node):
+            children = node.get("children", [])
+            nchildren = len(children)
+            permutations.append(math.factorial(nchildren))
+
+            if nchildren > 0:
+                node_index_list.append(list(self._index_permutations[nchildren]))
+            for child in children:
+                _recurse_tree(child)
+
+        permutations: List[int] = []
+        node_index_list: List[List[int]] = []
+        _recurse_tree(self._base_tree)
+        if not permutations:
+            return 0, []
+        return int(np.prod(permutations)), node_index_list
+
+    @staticmethod
+    def _make_base_copy(node: StrDict) -> StrDict:
+        return {
+            "type": node["type"],
+            "smiles": node.get("smiles", ""),
+            "metadata": node.get("metadata"),
+            "fingerprint": node["fingerprint"],
+            "sort_key": node["sort_key"],
+            "children": [],
+        }
+
+    @staticmethod
+    def _remove_children_nodes(tree: StrDict) -> StrDict:
+        new_tree = ReactionTreeWrapper._make_base_copy(tree)
+
+        if tree.get("children"):
+            new_tree["children"] = []
+            for child in tree["children"]:
+                new_tree["children"].extend(
+                    [
+                        ReactionTreeWrapper._remove_children_nodes(grandchild)
+                        for grandchild in child.get("children", [])
+                    ]
+                )
+        return new_tree
diff --git a/rxnutils/routes/ted/utils.py b/rxnutils/routes/ted/utils.py
new file mode 100644
index 0000000..81c3fc6
--- /dev/null
+++ b/rxnutils/routes/ted/utils.py
@@ -0,0 +1,110 @@
+""" Module containing utilities for TED calculations """
+from __future__ import annotations
+
+import random
+from enum import Enum
+from operator import itemgetter
+from typing import Any, Callable, Dict, List
+
+import numpy as np
+from apted import Config as BaseAptedConfig
+from rdkit import Chem, DataStructs
+from rdkit.Chem import AllChem
+from scipy.spatial.distance import jaccard as jaccard_dist
+
+StrDict = Dict[str, Any]
+
+
+class TreeContent(str, Enum):
+    """Possibilities for distance calculations on reaction trees"""
+
+    MOLECULES = "molecules"
+    REACTIONS = "reactions"
+    BOTH = "both"
+
+
+class AptedConfig(BaseAptedConfig):
+    """
+    This is a helper class for the tree edit distance
+    calculation. It defines how the substitution
+    cost is calculated and how to obtain children nodes.
+
+    :param randomize: if True, the children will be shuffled
+    :param sort_children: if True, the children will be sorted
+    :param dist_func: the distance function used for renaming nodes, Jaccard by default
+    """
+
+    def __init__(
+        self,
+        randomize: bool = False,
+        sort_children: bool = False,
+        dist_func: Callable[[np.ndarray, np.ndarray], float] = None,
+    ) -> None:
+        super().__init__()
+        self._randomize = randomize
+        self._sort_children = sort_children
+        self._dist_func = dist_func or jaccard_dist
+
+    def rename(self, node1: StrDict, node2: StrDict) -> float:
+        if node1["type"] != node2["type"]:
+            return 1
+
+        fp1 = node1["fingerprint"]
+        fp2 = node2["fingerprint"]
+        return self._dist_func(fp1, fp2)
+
+    def children(self, node: StrDict) -> List[StrDict]:
+        if self._sort_children:
+            return sorted(node["children"], key=itemgetter("sort_key"))
+        if not self._randomize:
+            return node["children"]
+        children = list(node["children"])
+        random.shuffle(children)
+        return children
+
+
+class StandardFingerprintFactory:
+    """
+    Calculate Morgan fingerprint for molecules, and difference fingerprints for reactions
+
+    :param radius: the radius of the fingerprint
+    :param nbits: the fingerprint lengths
+    """
+
+    def __init__(self, radius: int = 2, nbits: int = 2048) -> None:
+        self._fp_params = (radius, nbits)
+
+    def __call__(self, tree: StrDict, parent: StrDict = None) -> None:
+        if tree["type"] == "reaction":
+            if parent is None:
+                raise ValueError(
+                    "Must specify parent when making Morgan fingerprints for reaction nodes"
+                )
+            self._add_rxn_fingerprint(tree, parent)
+        else:
+            self._add_mol_fingerprints(tree)
+
+    def _add_mol_fingerprints(self, tree: StrDict) -> None:
+        if "fingerprint" not in tree:
+            mol = Chem.MolFromSmiles(tree["smiles"])
+            rd_fp = AllChem.GetMorganFingerprintAsBitVect(mol, *self._fp_params)
+            tree["fingerprint"] = np.zeros((1,), dtype=np.int8)
+            DataStructs.ConvertToNumpyArray(rd_fp, tree["fingerprint"])
+        tree["sort_key"] = "".join(f"{digit}" for digit in tree["fingerprint"])
+        if "children" not in tree:
+            tree["children"] = []
+
+        for child in tree["children"]:
+            for grandchild in child["children"]:
+                self._add_mol_fingerprints(grandchild)
+
+    def _add_rxn_fingerprint(self, node: StrDict, parent: StrDict) -> None:
+        if "fingerprint" not in node:
+            node["fingerprint"] = parent["fingerprint"].copy()
+            for reactant in node["children"]:
+                node["fingerprint"] -= reactant["fingerprint"]
+        node["sort_key"] = "".join(f"{digit}" for digit in node["fingerprint"])
+
+        for child in node["children"]:
+            for grandchild in child.get("children", []):
+                self._add_rxn_fingerprint(grandchild, child)
diff --git a/rxnutils/routes/utils/__init__.py b/rxnutils/routes/utils/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/rxnutils/routes/utils/validation.py b/rxnutils/routes/utils/validation.py
new file mode 100644
index 0000000..9f2905b
--- /dev/null
+++ b/rxnutils/routes/utils/validation.py
@@ -0,0 +1,39 @@
+""" Module containing routes to validate AiZynthFinder-like input dictionaries """
+from __future__ import annotations
+
+from typing import Any, Dict, List, Optional
+
+from pydantic import BaseModel, StringConstraints, ValidationError, conlist
+from typing_extensions import Annotated
+
+StrDict = Dict[str, Any]
+
+
+class ReactionNode(BaseModel):
+    """Node representing a reaction"""
+
+    type: Annotated[str, StringConstraints(pattern=r"^reaction$")]
+    children: List[MoleculeNode]
+
+
+class MoleculeNode(BaseModel):
+    """Node representing a molecule"""
+
+    smiles: str
+    type: Annotated[str, StringConstraints(pattern=r"^mol$")]
+    children: Optional[conlist(ReactionNode, min_length=1, max_length=1)] = None
+
+
+MoleculeNode.update_forward_refs()
+
+
+def validate_dict(dict_: StrDict) -> None:
+    """
+    Check that the route dictionary is a valid structure
+
+    :param dict_: the route as dictionary
+    """
+    try:
+        MoleculeNode(**dict_, extra="ignore")
+    except ValidationError as err:
+        raise ValueError(f"Invalid input: {err.json()}")
diff --git a/tests/conftest.py b/tests/conftest.py
index 8ae4692..9bb0e3e 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,9 +1,11 @@
 import copy
+import json
 
 import pandas as pd
 import pytest
 
 from rxnutils.routes.base import SynthesisRoute
+from rxnutils.routes.readers import reactions2route
 
 
 @pytest.fixture
@@ -66,6 +68,17 @@ def branched_synthesis_route():
     return SynthesisRoute(dict_)
 
 
+@pytest.fixture
+def augmentable_sythesis_route():
+    smiles0 = ["c1ccccc1>>Clc1ccccc1", "Cc1ccccc1>>c1ccccc1", "c1ccccc1O.C>>c1ccccc1C"]
+    metadata = [
+        {"classification": "10.1.2 chlorination", "hash": "xyz"},
+        {"hash": "xyy"},
+        {"hash": "xxz"},
+    ]
+    return reactions2route(smiles0, metadata)
+
+
 @pytest.fixture
 def setup_mapper(mocker, shared_datadir):
     df = pd.read_csv(shared_datadir / "mapped_tests_reactions.csv", sep="\t")
@@ -73,3 +86,43 @@ def setup_mapper(mocker, shared_datadir):
     namerxn_mock.return_value.return_value = df
     namerxn_mock = mocker.patch("rxnutils.routes.base.RxnMapper")
     namerxn_mock.return_value.return_value = df
+
+
+@pytest.fixture
+def setup_mapper_no_namerxn(mocker, shared_datadir):
+    df = pd.read_csv(shared_datadir / "mapped_tests_reactions.csv", sep="\t")
+    namerxn_mock = mocker.patch("rxnutils.routes.base.NameRxn")
+    namerxn_mock.return_value.side_effect = FileNotFoundError("No namerxn")
+    namerxn_mock = mocker.patch("rxnutils.routes.base.RxnMapper")
+    df["NMC"] = "0.0"
+    namerxn_mock.return_value.return_value = df
+
+
+@pytest.fixture
+def load_reaction_tree(shared_datadir):
+    def wrapper(filename, index=0):
+        filename = str(shared_datadir / filename)
+        with open(filename, "r") as fileobj:
+            trees = json.load(fileobj)
+        if isinstance(trees, dict):
+            return trees
+        elif index == -1:
+            return trees
+        else:
+            return trees[index]
+
+    return wrapper
+
+
+@pytest.fixture
+def setup_stock():
+    def traverse(tree_dict, stock):
+        if tree_dict["type"] == "mol":
+            tree_dict["in_stock"] = tree_dict["smiles"] in stock
+        for child in tree_dict.get("children", []):
+            traverse(child, stock)
+
+    def wrapper(route, stock):
+        traverse(route.reaction_tree, stock)
+
+    return wrapper
diff --git a/tests/data/atorvastatin_routes.json b/tests/data/atorvastatin_routes.json
new file mode 100644
index 0000000..967dc44
--- /dev/null
+++ b/tests/data/atorvastatin_routes.json
@@ -0,0 +1,404 @@
+[
+    {
+        "type": "mol",
+        "smiles": "CC(C)c1c(C(=O)Nc2ccccc2)c(-c2ccccc2)c(-c2ccc(F)cc2)n1CC[C@@H](O)C[C@@H](O)CC(=O)O",
+        "children": [
+            {
+                "type": "reaction",
+                "metadata": {
+                    "reaction_smiles": "CC(C)c1c(C(=O)Nc2ccccc2)c(-c2ccccc2)c(-c2ccc(F)cc2)n1CC[C@@H](O)C[C@@H](O)CC(=O)N(c1ccccc1)c1ccccc1.O>>CC(C)c1c(C(=O)Nc2ccccc2)c(-c2ccccc2)c(-c2ccc(F)cc2)n1CC[C@@H](O)C[C@@H](O)CC(=O)O",
+                    "tree_depth": 1,
+                    "forward_step": 7,
+                    "classification": "9.7.351",
+                    "mapped_reaction_smiles": "[OH2:41].c1ccc(N(c2ccccc2)[C:39]([CH2:38][C@@H:36]([CH2:35][C@@H:33]([CH2:32][CH2:31][n:30]2[c:4]([CH:2]([CH3:1])[CH3:3])[c:5]([C:6](=[O:7])[NH:8][c:9]3[cH:10][cH:11][cH:12][cH:13][cH:14]3)[c:15](-[c:16]3[cH:17][cH:18][cH:19][cH:20][cH:21]3)[c:22]2-[c:23]2[cH:24][cH:25][c:26]([F:27])[cH:28][cH:29]2)[OH:34])[OH:37])=[O:40])cc1>>[CH3:1][CH:2]([CH3:3])[c:4]1[c:5]([C:6](=[O:7])[NH:8][c:9]2[cH:10][cH:11][cH:12][cH:13][cH:14]2)[c:15](-[c:16]2[cH:17][cH:18][cH:19][cH:20][cH:21]2)[c:22](-[c:23]2[cH:24][cH:25][c:26]([F:27])[cH:28][cH:29]2)[n:30]1[CH2:31][CH2:32][C@@H:33]([OH:34])[CH2:35][C@@H:36]([OH:37])[CH2:38][C:39](=[O:40])[OH:41]"
+                },
+                "children": [
+                    {
+                        "type": "mol",
+                        "smiles": "CC(C)c1c(C(=O)Nc2ccccc2)c(-c2ccccc2)c(-c2ccc(F)cc2)n1CC[C@@H](O)C[C@@H](O)CC(=O)N(c1ccccc1)c1ccccc1",
+                        "children": [
+                            {
+                                "type": "reaction",
+                                "metadata": {
+                                    "reaction_smiles": "CC(C)c1c(C(=O)Nc2ccccc2)c(-c2ccccc2)c(-c2ccc(F)cc2)n1CC[C@@H]1C[C@H](CC(=O)N(c2ccccc2)c2ccccc2)OC(C)(C)O1>>CC(C)c1c(C(=O)Nc2ccccc2)c(-c2ccccc2)c(-c2ccc(F)cc2)n1CC[C@@H](O)C[C@@H](O)CC(=O)N(c1ccccc1)c1ccccc1",
+                                    "tree_depth": 2,
+                                    "forward_step": 6,
+                                    "classification": "6.3.16",
+                                    "mapped_reaction_smiles": "CC1(C)[O:34][C@H:33]([CH2:32][CH2:31][n:30]2[c:4]([CH:2]([CH3:1])[CH3:3])[c:5]([C:6](=[O:7])[NH:8][c:9]3[cH:10][cH:11][cH:12][cH:13][cH:14]3)[c:15](-[c:16]3[cH:17][cH:18][cH:19][cH:20][cH:21]3)[c:22]2-[c:23]2[cH:24][cH:25][c:26]([F:27])[cH:28][cH:29]2)[CH2:35][C@H:36]([CH2:38][C:39](=[O:40])[N:142]([c:143]2[cH:144][cH:145][cH:146][cH:147][cH:148]2)[c:149]2[cH:150][cH:151][cH:152][cH:153][cH:154]2)[O:37]1>>[CH3:1][CH:2]([CH3:3])[c:4]1[c:5]([C:6](=[O:7])[NH:8][c:9]2[cH:10][cH:11][cH:12][cH:13][cH:14]2)[c:15](-[c:16]2[cH:17][cH:18][cH:19][cH:20][cH:21]2)[c:22](-[c:23]2[cH:24][cH:25][c:26]([F:27])[cH:28][cH:29]2)[n:30]1[CH2:31][CH2:32][C@@H:33]([OH:34])[CH2:35][C@@H:36]([OH:37])[CH2:38][C:39](=[O:40])[N:142]([c:143]1[cH:144][cH:145][cH:146][cH:147][cH:148]1)[c:149]1[cH:150][cH:151][cH:152][cH:153][cH:154]1"
+                                },
+                                "children": [
+                                    {
+                                        "type": "mol",
+                                        "smiles": "CC(C)c1c(C(=O)Nc2ccccc2)c(-c2ccccc2)c(-c2ccc(F)cc2)n1CC[C@@H]1C[C@H](CC(=O)N(c2ccccc2)c2ccccc2)OC(C)(C)O1",
+                                        "children": [
+                                            {
+                                                "type": "reaction",
+                                                "metadata": {
+                                                    "reaction_smiles": "CC(C)C(=O)C(C(=O)Nc1ccccc1)C(C(=O)c1ccc(F)cc1)c1ccccc1.CC1(C)O[C@H](CCN)C[C@H](CC(=O)N(c2ccccc2)c2ccccc2)O1>>CC(C)c1c(C(=O)Nc2ccccc2)c(-c2ccccc2)c(-c2ccc(F)cc2)n1CC[C@@H]1C[C@H](CC(=O)N(c2ccccc2)c2ccccc2)OC(C)(C)O1",
+                                                    "tree_depth": 3,
+                                                    "forward_step": 5,
+                                                    "classification": "4.1.14",
+                                                    "mapped_reaction_smiles": "O=[C:4]([CH:2]([CH3:1])[CH3:3])[CH:5]([C:6](=[O:7])[NH:8][c:9]1[cH:10][cH:11][cH:12][cH:13][cH:14]1)[CH:15]([c:16]1[cH:17][cH:18][cH:19][cH:20][cH:21]1)[C:22](=O)[c:23]1[cH:24][cH:25][c:26]([F:27])[cH:28][cH:29]1.[NH2:30][CH2:31][CH2:32][C@H:33]1[O:34][C:155]([CH3:156])([CH3:157])[O:37][C@@H:36]([CH2:38][C:39](=[O:40])[N:142]([c:143]2[cH:144][cH:145][cH:146][cH:147][cH:148]2)[c:149]2[cH:150][cH:151][cH:152][cH:153][cH:154]2)[CH2:35]1>>[CH3:1][CH:2]([CH3:3])[c:4]1[c:5]([C:6](=[O:7])[NH:8][c:9]2[cH:10][cH:11][cH:12][cH:13][cH:14]2)[c:15](-[c:16]2[cH:17][cH:18][cH:19][cH:20][cH:21]2)[c:22](-[c:23]2[cH:24][cH:25][c:26]([F:27])[cH:28][cH:29]2)[n:30]1[CH2:31][CH2:32][C@H:33]1[O:34][C:155]([CH3:156])([CH3:157])[O:37][C@@H:36]([CH2:38][C:39](=[O:40])[N:142]([c:143]2[cH:144][cH:145][cH:146][cH:147][cH:148]2)[c:149]2[cH:150][cH:151][cH:152][cH:153][cH:154]2)[CH2:35]1"
+                                                },
+                                                "children": [
+                                                    {
+                                                        "type": "mol",
+                                                        "smiles": "CC(C)C(=O)C(C(=O)Nc1ccccc1)C(C(=O)c1ccc(F)cc1)c1ccccc1",
+                                                        "children": [
+                                                            {
+                                                                "type": "reaction",
+                                                                "metadata": {
+                                                                    "reaction_smiles": "CC(C)C(=O)/C(=C/c1ccccc1)C(=O)Nc1ccccc1.O=Cc1ccc(F)cc1>>CC(C)C(=O)C(C(=O)Nc1ccccc1)C(C(=O)c1ccc(F)cc1)c1ccccc1",
+                                                                    "tree_depth": 4,
+                                                                    "forward_step": 4,
+                                                                    "classification": "0.0",
+                                                                    "mapped_reaction_smiles": "[CH3:1][CH:2]([CH3:3])[C:4](/[C:5]([C:6](=[O:7])[NH:8][c:9]1[cH:10][cH:11][cH:12][cH:13][cH:14]1)=[CH:15]/[c:16]1[cH:17][cH:18][cH:19][cH:20][cH:21]1)=[O:158].[CH:22]([c:23]1[cH:24][cH:25][c:26]([F:27])[cH:28][cH:29]1)=[O:159]>>[CH3:1][CH:2]([CH3:3])[C:4]([CH:5]([C:6](=[O:7])[NH:8][c:9]1[cH:10][cH:11][cH:12][cH:13][cH:14]1)[CH:15]([c:16]1[cH:17][cH:18][cH:19][cH:20][cH:21]1)[C:22]([c:23]1[cH:24][cH:25][c:26]([F:27])[cH:28][cH:29]1)=[O:159])=[O:158]"
+                                                                },
+                                                                "children": [
+                                                                    {
+                                                                        "type": "mol",
+                                                                        "smiles": "CC(C)C(=O)/C(=C/c1ccccc1)C(=O)Nc1ccccc1",
+                                                                        "children": [
+                                                                            {
+                                                                                "type": "reaction",
+                                                                                "metadata": {
+                                                                                    "reaction_smiles": "CC(C)C(=O)CC(=O)Nc1ccccc1.O=Cc1ccccc1>>CC(C)C(=O)/C(=C/c1ccccc1)C(=O)Nc1ccccc1",
+                                                                                    "tree_depth": 5,
+                                                                                    "forward_step": 3,
+                                                                                    "classification": "3.11.146",
+                                                                                    "mapped_reaction_smiles": "O=[CH:15][c:16]1[cH:17][cH:18][cH:19][cH:20][cH:21]1.[CH3:1][CH:2]([CH3:3])[C:4]([CH2:5][C:6](=[O:7])[NH:8][c:9]1[cH:10][cH:11][cH:12][cH:13][cH:14]1)=[O:158]>>[CH3:1][CH:2]([CH3:3])[C:4](/[C:5]([C:6](=[O:7])[NH:8][c:9]1[cH:10][cH:11][cH:12][cH:13][cH:14]1)=[CH:15]/[c:16]1[cH:17][cH:18][cH:19][cH:20][cH:21]1)=[O:158]"
+                                                                                },
+                                                                                "children": [
+                                                                                    {
+                                                                                        "type": "mol",
+                                                                                        "smiles": "CC(C)C(=O)CC(=O)Nc1ccccc1"
+                                                                                    },
+                                                                                    {
+                                                                                        "type": "mol",
+                                                                                        "smiles": "O=Cc1ccccc1"
+                                                                                    }
+                                                                                ]
+                                                                            }
+                                                                        ]
+                                                                    },
+                                                                    {
+                                                                        "type": "mol",
+                                                                        "smiles": "O=Cc1ccc(F)cc1"
+                                                                    }
+                                                                ]
+                                                            }
+                                                        ]
+                                                    },
+                                                    {
+                                                        "type": "mol",
+                                                        "smiles": "CC1(C)O[C@H](CCN)C[C@H](CC(=O)N(c2ccccc2)c2ccccc2)O1",
+                                                        "children": [
+                                                            {
+                                                                "type": "reaction",
+                                                                "metadata": {
+                                                                    "reaction_smiles": "CC1(C)O[C@H](CC#N)C[C@H](CC(=O)N(c2ccccc2)c2ccccc2)O1>>CC1(C)O[C@H](CCN)C[C@H](CC(=O)N(c2ccccc2)c2ccccc2)O1",
+                                                                    "tree_depth": 4,
+                                                                    "forward_step": 4,
+                                                                    "classification": "7.3.1",
+                                                                    "mapped_reaction_smiles": "[N:30]#[C:31][CH2:32][C@H:33]1[O:34][C:155]([CH3:156])([CH3:157])[O:37][C@@H:36]([CH2:38][C:39](=[O:40])[N:142]([c:143]2[cH:144][cH:145][cH:146][cH:147][cH:148]2)[c:149]2[cH:150][cH:151][cH:152][cH:153][cH:154]2)[CH2:35]1>>[NH2:30][CH2:31][CH2:32][C@H:33]1[O:34][C:155]([CH3:156])([CH3:157])[O:37][C@@H:36]([CH2:38][C:39](=[O:40])[N:142]([c:143]2[cH:144][cH:145][cH:146][cH:147][cH:148]2)[c:149]2[cH:150][cH:151][cH:152][cH:153][cH:154]2)[CH2:35]1"
+                                                                },
+                                                                "children": [
+                                                                    {
+                                                                        "type": "mol",
+                                                                        "smiles": "CC1(C)O[C@H](CC#N)C[C@H](CC(=O)N(c2ccccc2)c2ccccc2)O1",
+                                                                        "children": [
+                                                                            {
+                                                                                "type": "reaction",
+                                                                                "metadata": {
+                                                                                    "reaction_smiles": "COC(C)(C)OC.N#CC[C@@H](O)C[C@@H](O)CC(=O)N(c1ccccc1)c1ccccc1>>CC1(C)O[C@H](CC#N)C[C@H](CC(=O)N(c2ccccc2)c2ccccc2)O1",
+                                                                                    "tree_depth": 5,
+                                                                                    "forward_step": 3,
+                                                                                    "classification": "4.2.39",
+                                                                                    "mapped_reaction_smiles": "CO[C:155](OC)([CH3:156])[CH3:157].[N:30]#[C:31][CH2:32][C@@H:33]([OH:34])[CH2:35][C@@H:36]([OH:37])[CH2:38][C:39](=[O:40])[N:142]([c:143]1[cH:144][cH:145][cH:146][cH:147][cH:148]1)[c:149]1[cH:150][cH:151][cH:152][cH:153][cH:154]1>>[N:30]#[C:31][CH2:32][C@H:33]1[O:34][C:155]([CH3:156])([CH3:157])[O:37][C@@H:36]([CH2:38][C:39](=[O:40])[N:142]([c:143]2[cH:144][cH:145][cH:146][cH:147][cH:148]2)[c:149]2[cH:150][cH:151][cH:152][cH:153][cH:154]2)[CH2:35]1"
+                                                                                },
+                                                                                "children": [
+                                                                                    {
+                                                                                        "type": "mol",
+                                                                                        "smiles": "COC(C)(C)OC"
+                                                                                    },
+                                                                                    {
+                                                                                        "type": "mol",
+                                                                                        "smiles": "N#CC[C@@H](O)C[C@@H](O)CC(=O)N(c1ccccc1)c1ccccc1",
+                                                                                        "children": [
+                                                                                            {
+                                                                                                "type": "reaction",
+                                                                                                "metadata": {
+                                                                                                    "reaction_smiles": "N#CC[C@@H](O)CC(=O)CC(=O)N(c1ccccc1)c1ccccc1>>N#CC[C@@H](O)C[C@@H](O)CC(=O)N(c1ccccc1)c1ccccc1",
+                                                                                                    "tree_depth": 6,
+                                                                                                    "forward_step": 2,
+                                                                                                    "classification": "7.5.1",
+                                                                                                    "mapped_reaction_smiles": "[N:30]#[C:31][CH2:32][C@@H:33]([OH:34])[CH2:35][C:36](=[O:37])[CH2:38][C:39](=[O:40])[N:142]([c:143]1[cH:144][cH:145][cH:146][cH:147][cH:148]1)[c:149]1[cH:150][cH:151][cH:152][cH:153][cH:154]1>>[N:30]#[C:31][CH2:32][C@@H:33]([OH:34])[CH2:35][C@@H:36]([OH:37])[CH2:38][C:39](=[O:40])[N:142]([c:143]1[cH:144][cH:145][cH:146][cH:147][cH:148]1)[c:149]1[cH:150][cH:151][cH:152][cH:153][cH:154]1"
+                                                                                                },
+                                                                                                "children": [
+                                                                                                    {
+                                                                                                        "type": "mol",
+                                                                                                        "smiles": "N#CC[C@@H](O)CC(=O)CC(=O)N(c1ccccc1)c1ccccc1",
+                                                                                                        "children": [
+                                                                                                            {
+                                                                                                                "type": "reaction",
+                                                                                                                "metadata": {
+                                                                                                                    "reaction_smiles": "CC(=O)N(c1ccccc1)c1ccccc1.CCOC(=O)C[C@H](O)CC#N>>N#CC[C@@H](O)CC(=O)CC(=O)N(c1ccccc1)c1ccccc1",
+                                                                                                                    "tree_depth": 7,
+                                                                                                                    "forward_step": 1,
+                                                                                                                    "classification": "3.11.93",
+                                                                                                                    "mapped_reaction_smiles": "CCO[C:36]([CH2:35][C@@H:33]([CH2:32][C:31]#[N:30])[OH:34])=[O:37].[CH3:38][C:39](=[O:40])[N:142]([c:143]1[cH:144][cH:145][cH:146][cH:147][cH:148]1)[c:149]1[cH:150][cH:151][cH:152][cH:153][cH:154]1>>[N:30]#[C:31][CH2:32][C@@H:33]([OH:34])[CH2:35][C:36](=[O:37])[CH2:38][C:39](=[O:40])[N:142]([c:143]1[cH:144][cH:145][cH:146][cH:147][cH:148]1)[c:149]1[cH:150][cH:151][cH:152][cH:153][cH:154]1"
+                                                                                                                },
+                                                                                                                "children": [
+                                                                                                                    {
+                                                                                                                        "type": "mol",
+                                                                                                                        "smiles": "CC(=O)N(c1ccccc1)c1ccccc1"
+                                                                                                                    },
+                                                                                                                    {
+                                                                                                                        "type": "mol",
+                                                                                                                        "smiles": "CCOC(=O)C[C@H](O)CC#N"
+                                                                                                                    }
+                                                                                                                ]
+                                                                                                            }
+                                                                                                        ]
+                                                                                                    }
+                                                                                                ]
+                                                                                            }
+                                                                                        ]
+                                                                                    }
+                                                                                ]
+                                                                            }
+                                                                        ]
+                                                                    }
+                                                                ]
+                                                            }
+                                                        ]
+                                                    }
+                                                ]
+                                            }
+                                        ]
+                                    }
+                                ]
+                            }
+                        ]
+                    },
+                    {
+                        "type": "mol",
+                        "smiles": "O"
+                    }
+                ]
+            }
+        ]
+    },
+    {
+        "type": "mol",
+        "smiles": "CC(C)c1c(C(=O)Nc2ccccc2)c(-c2ccccc2)c(-c2ccc(F)cc2)n1CC[C@@H](O)C[C@@H](O)CC(=O)O",
+        "children": [
+            {
+                "type": "reaction",
+                "metadata": {
+                    "reaction_smiles": "CC(C)c1c(C(=O)Nc2ccccc2)c(-c2ccccc2)c(-c2ccc(F)cc2)n1CC[C@@H]1C[C@@H](O)CC(=O)O1.O>>CC(C)c1c(C(=O)Nc2ccccc2)c(-c2ccccc2)c(-c2ccc(F)cc2)n1CC[C@@H](O)C[C@@H](O)CC(=O)O",
+                    "tree_depth": 1,
+                    "forward_step": 9,
+                    "classification": "9.7.61",
+                    "mapped_reaction_smiles": "[CH3:1][CH:2]([CH3:3])[c:4]1[c:5]([C:6](=[O:7])[NH:8][c:9]2[cH:10][cH:11][cH:12][cH:13][cH:14]2)[c:15](-[c:16]2[cH:17][cH:18][cH:19][cH:20][cH:21]2)[c:22](-[c:23]2[cH:24][cH:25][c:26]([F:27])[cH:28][cH:29]2)[n:30]1[CH2:31][CH2:32][C@H:33]1[O:34][C:39](=[O:40])[CH2:38][C@H:36]([OH:37])[CH2:35]1.[OH2:41]>>[CH3:1][CH:2]([CH3:3])[c:4]1[c:5]([C:6](=[O:7])[NH:8][c:9]2[cH:10][cH:11][cH:12][cH:13][cH:14]2)[c:15](-[c:16]2[cH:17][cH:18][cH:19][cH:20][cH:21]2)[c:22](-[c:23]2[cH:24][cH:25][c:26]([F:27])[cH:28][cH:29]2)[n:30]1[CH2:31][CH2:32][C@@H:33]([OH:34])[CH2:35][C@@H:36]([OH:37])[CH2:38][C:39](=[O:40])[OH:41]"
+                },
+                "children": [
+                    {
+                        "type": "mol",
+                        "smiles": "CC(C)c1c(C(=O)Nc2ccccc2)c(-c2ccccc2)c(-c2ccc(F)cc2)n1CC[C@@H]1C[C@@H](O)CC(=O)O1",
+                        "children": [
+                            {
+                                "type": "reaction",
+                                "metadata": {
+                                    "reaction_smiles": "COC(=O)CC(=O)C[C@H](O)CCn1c(-c2ccc(F)cc2)c(-c2ccccc2)c(C(=O)Nc2ccccc2)c1C(C)C>>CC(C)c1c(C(=O)Nc2ccccc2)c(-c2ccccc2)c(-c2ccc(F)cc2)n1CC[C@@H]1C[C@@H](O)CC(=O)O1",
+                                    "tree_depth": 2,
+                                    "forward_step": 8,
+                                    "classification": "0.0",
+                                    "mapped_reaction_smiles": "CO[C:39]([CH2:38][C:36]([CH2:35][C@@H:33]([CH2:32][CH2:31][n:30]1[c:4]([CH:2]([CH3:1])[CH3:3])[c:5]([C:6](=[O:7])[NH:8][c:9]2[cH:10][cH:11][cH:12][cH:13][cH:14]2)[c:15](-[c:16]2[cH:17][cH:18][cH:19][cH:20][cH:21]2)[c:22]1-[c:23]1[cH:24][cH:25][c:26]([F:27])[cH:28][cH:29]1)[OH:34])=[O:37])=[O:40]>>[CH3:1][CH:2]([CH3:3])[c:4]1[c:5]([C:6](=[O:7])[NH:8][c:9]2[cH:10][cH:11][cH:12][cH:13][cH:14]2)[c:15](-[c:16]2[cH:17][cH:18][cH:19][cH:20][cH:21]2)[c:22](-[c:23]2[cH:24][cH:25][c:26]([F:27])[cH:28][cH:29]2)[n:30]1[CH2:31][CH2:32][C@H:33]1[O:34][C:39](=[O:40])[CH2:38][C@H:36]([OH:37])[CH2:35]1"
+                                },
+                                "children": [
+                                    {
+                                        "type": "mol",
+                                        "smiles": "COC(=O)CC(=O)C[C@H](O)CCn1c(-c2ccc(F)cc2)c(-c2ccccc2)c(C(=O)Nc2ccccc2)c1C(C)C",
+                                        "children": [
+                                            {
+                                                "type": "reaction",
+                                                "metadata": {
+                                                    "reaction_smiles": "CC(C)c1c(C(=O)Nc2ccccc2)c(-c2ccccc2)c(-c2ccc(F)cc2)n1CCC=O.COC(=O)CC(C)=O>>COC(=O)CC(=O)C[C@H](O)CCn1c(-c2ccc(F)cc2)c(-c2ccccc2)c(C(=O)Nc2ccccc2)c1C(C)C",
+                                                    "tree_depth": 3,
+                                                    "forward_step": 7,
+                                                    "classification": "3.11.1",
+                                                    "mapped_reaction_smiles": "[CH3:35][C:36](=[O:37])[CH2:38][C:39](=[O:40])[O:143][CH3:142].[CH3:1][CH:2]([CH3:3])[c:4]1[c:5]([C:6](=[O:7])[NH:8][c:9]2[cH:10][cH:11][cH:12][cH:13][cH:14]2)[c:15](-[c:16]2[cH:17][cH:18][cH:19][cH:20][cH:21]2)[c:22](-[c:23]2[cH:24][cH:25][c:26]([F:27])[cH:28][cH:29]2)[n:30]1[CH2:31][CH2:32][CH:33]=[O:34]>>[CH3:1][CH:2]([CH3:3])[c:4]1[c:5]([C:6](=[O:7])[NH:8][c:9]2[cH:10][cH:11][cH:12][cH:13][cH:14]2)[c:15](-[c:16]2[cH:17][cH:18][cH:19][cH:20][cH:21]2)[c:22](-[c:23]2[cH:24][cH:25][c:26]([F:27])[cH:28][cH:29]2)[n:30]1[CH2:31][CH2:32][C@@H:33]([OH:34])[CH2:35][C:36](=[O:37])[CH2:38][C:39](=[O:40])[O:143][CH3:142]"
+                                                },
+                                                "children": [
+                                                    {
+                                                        "type": "mol",
+                                                        "smiles": "CC(C)c1c(C(=O)Nc2ccccc2)c(-c2ccccc2)c(-c2ccc(F)cc2)n1CCC=O",
+                                                        "children": [
+                                                            {
+                                                                "type": "reaction",
+                                                                "metadata": {
+                                                                    "reaction_smiles": "CC(C)c1c(C(=O)Nc2ccccc2)c(-c2ccccc2)c(-c2ccc(F)cc2)n1CCC1OCCO1>>CC(C)c1c(C(=O)Nc2ccccc2)c(-c2ccccc2)c(-c2ccc(F)cc2)n1CCC=O",
+                                                                    "tree_depth": 4,
+                                                                    "forward_step": 6,
+                                                                    "classification": "6.5.2",
+                                                                    "mapped_reaction_smiles": "C1C[O:34][CH:33]([CH2:32][CH2:31][n:30]2[c:4]([CH:2]([CH3:1])[CH3:3])[c:5]([C:6](=[O:7])[NH:8][c:9]3[cH:10][cH:11][cH:12][cH:13][cH:14]3)[c:15](-[c:16]3[cH:17][cH:18][cH:19][cH:20][cH:21]3)[c:22]2-[c:23]2[cH:24][cH:25][c:26]([F:27])[cH:28][cH:29]2)O1>>[CH3:1][CH:2]([CH3:3])[c:4]1[c:5]([C:6](=[O:7])[NH:8][c:9]2[cH:10][cH:11][cH:12][cH:13][cH:14]2)[c:15](-[c:16]2[cH:17][cH:18][cH:19][cH:20][cH:21]2)[c:22](-[c:23]2[cH:24][cH:25][c:26]([F:27])[cH:28][cH:29]2)[n:30]1[CH2:31][CH2:32][CH:33]=[O:34]"
+                                                                },
+                                                                "children": [
+                                                                    {
+                                                                        "type": "mol",
+                                                                        "smiles": "CC(C)c1c(C(=O)Nc2ccccc2)c(-c2ccccc2)c(-c2ccc(F)cc2)n1CCC1OCCO1",
+                                                                        "children": [
+                                                                            {
+                                                                                "type": "reaction",
+                                                                                "metadata": {
+                                                                                    "reaction_smiles": "CC(C)C(=O)N(CCC1OCCO1)C(C(=O)O)c1ccc(F)cc1.O=C(C#Cc1ccccc1)Nc1ccccc1>>CC(C)c1c(C(=O)Nc2ccccc2)c(-c2ccccc2)c(-c2ccc(F)cc2)n1CCC1OCCO1",
+                                                                                    "tree_depth": 5,
+                                                                                    "forward_step": 5,
+                                                                                    "classification": "0.0",
+                                                                                    "mapped_reaction_smiles": "O=C(O)[CH:22]([c:23]1[cH:24][cH:25][c:26]([F:27])[cH:28][cH:29]1)[N:30]([C:4](=O)[CH:2]([CH3:1])[CH3:3])[CH2:31][CH2:32][CH:33]1[O:34][CH2:144][CH2:145][O:146]1.[C:5]([C:6](=[O:7])[NH:8][c:9]1[cH:10][cH:11][cH:12][cH:13][cH:14]1)#[C:15][c:16]1[cH:17][cH:18][cH:19][cH:20][cH:21]1>>[CH3:1][CH:2]([CH3:3])[c:4]1[c:5]([C:6](=[O:7])[NH:8][c:9]2[cH:10][cH:11][cH:12][cH:13][cH:14]2)[c:15](-[c:16]2[cH:17][cH:18][cH:19][cH:20][cH:21]2)[c:22](-[c:23]2[cH:24][cH:25][c:26]([F:27])[cH:28][cH:29]2)[n:30]1[CH2:31][CH2:32][CH:33]1[O:34][CH2:144][CH2:145][O:146]1"
+                                                                                },
+                                                                                "children": [
+                                                                                    {
+                                                                                        "type": "mol",
+                                                                                        "smiles": "CC(C)C(=O)N(CCC1OCCO1)C(C(=O)O)c1ccc(F)cc1",
+                                                                                        "children": [
+                                                                                            {
+                                                                                                "type": "reaction",
+                                                                                                "metadata": {
+                                                                                                    "reaction_smiles": "CCOC(=O)C(c1ccc(F)cc1)N(CCC1OCCO1)C(=O)C(C)C>>CC(C)C(=O)N(CCC1OCCO1)C(C(=O)O)c1ccc(F)cc1",
+                                                                                                    "tree_depth": 6,
+                                                                                                    "forward_step": 4,
+                                                                                                    "classification": "6.2.1",
+                                                                                                    "mapped_reaction_smiles": "CC[O:150][C:148]([CH:22]([c:23]1[cH:24][cH:25][c:26]([F:27])[cH:28][cH:29]1)[N:30]([C:4]([CH:2]([CH3:1])[CH3:3])=[O:147])[CH2:31][CH2:32][CH:33]1[O:34][CH2:144][CH2:145][O:146]1)=[O:149]>>[CH3:1][CH:2]([CH3:3])[C:4]([N:30]([CH:22]([c:23]1[cH:24][cH:25][c:26]([F:27])[cH:28][cH:29]1)[C:148](=[O:149])[OH:150])[CH2:31][CH2:32][CH:33]1[O:34][CH2:144][CH2:145][O:146]1)=[O:147]"
+                                                                                                },
+                                                                                                "children": [
+                                                                                                    {
+                                                                                                        "type": "mol",
+                                                                                                        "smiles": "CCOC(=O)C(c1ccc(F)cc1)N(CCC1OCCO1)C(=O)C(C)C",
+                                                                                                        "children": [
+                                                                                                            {
+                                                                                                                "type": "reaction",
+                                                                                                                "metadata": {
+                                                                                                                    "reaction_smiles": "CC(C)C(=O)Cl.CCOC(=O)C(NCCC1OCCO1)c1ccc(F)cc1>>CCOC(=O)C(c1ccc(F)cc1)N(CCC1OCCO1)C(=O)C(C)C",
+                                                                                                                    "tree_depth": 7,
+                                                                                                                    "forward_step": 3,
+                                                                                                                    "classification": "2.1.1",
+                                                                                                                    "mapped_reaction_smiles": "Cl[C:4]([CH:2]([CH3:1])[CH3:3])=[O:147].[CH:22]([c:23]1[cH:24][cH:25][c:26]([F:27])[cH:28][cH:29]1)([NH:30][CH2:31][CH2:32][CH:33]1[O:34][CH2:144][CH2:145][O:146]1)[C:148](=[O:149])[O:150][CH2:152][CH3:151]>>[CH3:1][CH:2]([CH3:3])[C:4]([N:30]([CH:22]([c:23]1[cH:24][cH:25][c:26]([F:27])[cH:28][cH:29]1)[C:148](=[O:149])[O:150][CH2:152][CH3:151])[CH2:31][CH2:32][CH:33]1[O:34][CH2:144][CH2:145][O:146]1)=[O:147]"
+                                                                                                                },
+                                                                                                                "children": [
+                                                                                                                    {
+                                                                                                                        "type": "mol",
+                                                                                                                        "smiles": "CC(C)C(=O)Cl"
+                                                                                                                    },
+                                                                                                                    {
+                                                                                                                        "type": "mol",
+                                                                                                                        "smiles": "CCOC(=O)C(NCCC1OCCO1)c1ccc(F)cc1",
+                                                                                                                        "children": [
+                                                                                                                            {
+                                                                                                                                "type": "reaction",
+                                                                                                                                "metadata": {
+                                                                                                                                    "reaction_smiles": "CCOC(=O)C(Br)c1ccc(F)cc1.NCCC1OCCO1>>CCOC(=O)C(NCCC1OCCO1)c1ccc(F)cc1",
+                                                                                                                                    "tree_depth": 8,
+                                                                                                                                    "forward_step": 2,
+                                                                                                                                    "classification": "1.6.2",
+                                                                                                                                    "mapped_reaction_smiles": "Br[CH:22]([c:23]1[cH:24][cH:25][c:26]([F:27])[cH:28][cH:29]1)[C:148](=[O:149])[O:150][CH2:152][CH3:151].[NH2:30][CH2:31][CH2:32][CH:33]1[O:34][CH2:144][CH2:145][O:146]1>>[CH:22]([c:23]1[cH:24][cH:25][c:26]([F:27])[cH:28][cH:29]1)([NH:30][CH2:31][CH2:32][CH:33]1[O:34][CH2:144][CH2:145][O:146]1)[C:148](=[O:149])[O:150][CH2:152][CH3:151]"
+                                                                                                                                },
+                                                                                                                                "children": [
+                                                                                                                                    {
+                                                                                                                                        "type": "mol",
+                                                                                                                                        "smiles": "CCOC(=O)C(Br)c1ccc(F)cc1",
+                                                                                                                                        "children": [
+                                                                                                                                            {
+                                                                                                                                                "type": "reaction",
+                                                                                                                                                "metadata": {
+                                                                                                                                                    "reaction_smiles": "CCOC(=O)Cc1ccc(F)cc1.O=C1CCC(=O)N1Br>>CCOC(=O)C(Br)c1ccc(F)cc1",
+                                                                                                                                                    "tree_depth": 9,
+                                                                                                                                                    "forward_step": 1,
+                                                                                                                                                    "classification": "10.1.5",
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+                                                                                                                                                },
+                                                                                                                                                "children": [
+                                                                                                                                                    {
+                                                                                                                                                        "type": "mol",
+                                                                                                                                                        "smiles": "CCOC(=O)Cc1ccc(F)cc1"
+                                                                                                                                                    },
+                                                                                                                                                    {
+                                                                                                                                                        "type": "mol",
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+                                                                                                                                                    }
+                                                                                                                                                ]
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+                                                                                                                                        ]
+                                                                                                                                    },
+                                                                                                                                    {
+                                                                                                                                        "type": "mol",
+                                                                                                                                        "smiles": "NCCC1OCCO1"
+                                                                                                                                    }
+                                                                                                                                ]
+                                                                                                                            }
+                                                                                                                        ]
+                                                                                                                    }
+                                                                                                                ]
+                                                                                                            }
+                                                                                                        ]
+                                                                                                    }
+                                                                                                ]
+                                                                                            }
+                                                                                        ]
+                                                                                    },
+                                                                                    {
+                                                                                        "type": "mol",
+                                                                                        "smiles": "O=C(C#Cc1ccccc1)Nc1ccccc1",
+                                                                                        "children": [
+                                                                                            {
+                                                                                                "type": "reaction",
+                                                                                                "metadata": {
+                                                                                                    "reaction_smiles": "Nc1ccccc1.O=C(O)C#Cc1ccccc1>>O=C(C#Cc1ccccc1)Nc1ccccc1",
+                                                                                                    "tree_depth": 6,
+                                                                                                    "forward_step": 4,
+                                                                                                    "classification": "2.1.2",
+                                                                                                    "mapped_reaction_smiles": "O[C:6]([C:5]#[C:15][c:16]1[cH:17][cH:18][cH:19][cH:20][cH:21]1)=[O:7].[NH2:8][c:9]1[cH:10][cH:11][cH:12][cH:13][cH:14]1>>[C:5]([C:6](=[O:7])[NH:8][c:9]1[cH:10][cH:11][cH:12][cH:13][cH:14]1)#[C:15][c:16]1[cH:17][cH:18][cH:19][cH:20][cH:21]1"
+                                                                                                },
+                                                                                                "children": [
+                                                                                                    {
+                                                                                                        "type": "mol",
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+                                                                                                    },
+                                                                                                    {
+                                                                                                        "type": "mol",
+                                                                                                        "smiles": "O=C(O)C#Cc1ccccc1"
+                                                                                                    }
+                                                                                                ]
+                                                                                            }
+                                                                                        ]
+                                                                                    }
+                                                                                ]
+                                                                            }
+                                                                        ]
+                                                                    }
+                                                                ]
+                                                            }
+                                                        ]
+                                                    },
+                                                    {
+                                                        "type": "mol",
+                                                        "smiles": "COC(=O)CC(C)=O"
+                                                    }
+                                                ]
+                                            }
+                                        ]
+                                    }
+                                ]
+                            }
+                        ]
+                    },
+                    {
+                        "type": "mol",
+                        "smiles": "O"
+                    }
+                ]
+            }
+        ]
+    }
+]
\ No newline at end of file
diff --git a/tests/data/example_reactions_ids.csv b/tests/data/example_reactions_ids.csv
new file mode 100644
index 0000000..6ce24ea
--- /dev/null
+++ b/tests/data/example_reactions_ids.csv
@@ -0,0 +1 @@
+EN12797-88
diff --git a/tests/data/example_route.rdf b/tests/data/example_route.rdf
new file mode 100644
index 0000000..ee7888c
--- /dev/null
+++ b/tests/data/example_route.rdf
@@ -0,0 +1,68 @@
+$RDFILE 1
+$DATM 05.22.2024 09:48:44
+$RFMT $RIREG 1
+$RXN
+
+      RDKit
+
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+undefined
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+  3  5  1  0
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+$RFMT $RIREG 2
+$RXN
+
+      RDKit
+
+  1  1
+$MOL
+undefined
+     RDKit          2D
+
+  4  3  0  0  0  0  0  0  0  0999 V2000
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+  1  2  1  0
+  2  3  1  0
+  3  4  1  0
+M  END
+$MOL
+undefined
+     RDKit          2D
+
+  4  3  0  0  0  0  0  0  0  0999 V2000
+    0.0007    0.0004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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+  1  2  1  0
+  2  3  1  0
+  3  4  2  0
+M  END
\ No newline at end of file
diff --git a/tests/data/example_routes.json b/tests/data/example_routes.json
new file mode 100644
index 0000000..4de5b7b
--- /dev/null
+++ b/tests/data/example_routes.json
@@ -0,0 +1,148 @@
+[
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diff --git a/tests/data/longer_routes.json b/tests/data/longer_routes.json
new file mode 100644
index 0000000..8fcc8c8
--- /dev/null
+++ b/tests/data/longer_routes.json
@@ -0,0 +1,327 @@
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+                              }
+                            ],
+                            "hide": false,
+                            "in_stock": false,
+                            "is_chemical": true,
+                            "smiles": "CC(C)(C)OC(=O)NC(N)=NCCN=c1[nH]c(=O)[nH]c(=O)[nH]1",
+                            "type": "mol"
+                          }
+                        ],
+                        "hide": false,
+                        "is_reaction": true,
+                        "metadata": {},
+                        "smiles": "[N:1][CH3:2]>>CC(C)(C)OC(=O)[N:1][CH3:2]",
+                        "type": "reaction"
+                      }
+                    ],
+                    "hide": false,
+                    "in_stock": false,
+                    "is_chemical": true,
+                    "smiles": "NC(N)=NCCN=c1[nH]c(=O)[nH]c(=O)[nH]1",
+                    "type": "mol"
+                  },
+                  {
+                    "hide": false,
+                    "in_stock": true,
+                    "is_chemical": true,
+                    "smiles": "O=[N+]([O-])c1ccc(CBr)cc1",
+                    "type": "mol"
+                  }
+                ],
+                "hide": false,
+                "is_reaction": true,
+                "metadata": {},
+                "smiles": "[C:1]([cH3:2])[n:4]([cH2:3])[cH2:5]>>Br[C:1][cH3:2].[cH2:3][n:4][cH2:5]",
+                "type": "reaction"
+              }
+            ],
+            "hide": false,
+            "in_stock": false,
+            "is_chemical": true,
+            "smiles": "NC(N)=NCCN=c1[nH]c(=O)n(Cc2ccc([N+](=O)[O-])cc2)c(=O)[nH]1",
+            "type": "mol"
+          }
+        ],
+        "hide": false,
+        "is_reaction": true,
+        "metadata": {},
+        "smiles": "[C:1]([cH3:2])[n:5]([cH:4]:[NH:3])[cH2:6]>>Cl[C:1][cH3:2].[NH:3]:[cH:4][n:5][cH2:6]",
+        "type": "reaction"
+      }
+    ],
+    "hide": false,
+    "in_stock": false,
+    "is_chemical": true,
+    "smiles": "COc1ccc(Cn2c(=NCCN=C(N)N)[nH]c(=O)n(Cc3ccc([N+](=O)[O-])cc3)c2=O)cc1",
+    "type": "mol"
+  }
+]
diff --git a/tests/test_chem_utils.py b/tests/test_chem_utils.py
index ce3a7c0..22e9e41 100644
--- a/tests/test_chem_utils.py
+++ b/tests/test_chem_utils.py
@@ -14,6 +14,7 @@
     get_special_groups,
     reaction_centres,
 )
+from rxnutils.chem.augmentation import single_reactant_augmentation
 
 
 @pytest.mark.parametrize(
@@ -140,3 +141,37 @@ def test_reaction_centers(smiles, expected):
     rxn.Initialize()
 
     assert reaction_centres(rxn) == expected
+
+
+@pytest.mark.parametrize(
+    ("smiles", "classification", "expected"),
+    [
+        (
+            "A.B>>C",
+            "",
+            "A.B>>C",
+        ),
+        (
+            "A.B>>C",
+            "0.0",
+            "A.B>>C",
+        ),
+        (
+            "A>>C",
+            "0.0",
+            "A>>C",
+        ),
+        (
+            "A>>C",
+            "10.1.1",
+            "Br.A>>C",
+        ),
+        (
+            "A>>C",
+            "10.1.2 Chlorination",
+            "Cl.A>>C",
+        ),
+    ],
+)
+def test_single_reactant_agumentation(smiles, classification, expected):
+    assert single_reactant_augmentation(smiles, classification) == expected
diff --git a/tests/test_product_tagging.py b/tests/test_product_tagging.py
index 71577f9..14c2339 100644
--- a/tests/test_product_tagging.py
+++ b/tests/test_product_tagging.py
@@ -1,6 +1,7 @@
 import pytest
 from rxnutils.chem.disconnection_sites.atom_map_tagging import (
     atom_map_tag_products,
+    atom_map_tag_reactants,
     get_atom_list,
 )
 from rxnutils.chem.disconnection_sites.tag_converting import (
@@ -49,6 +50,26 @@ def test_atom_map_tag_products(reactants_smiles, product_smiles, expected):
     assert tagged_product == expected
 
 
+@pytest.mark.parametrize(
+    ("reactants_smiles", "product_smiles", "expected"),
+    [
+        (
+            "[Cl:2].[CH:1]1=[CH:7][CH:6]=[CH:5][CH:4]=[CH:3]1",
+            "[Cl:2][C:1]1=[CH:7][CH:6]=[CH:5][CH:4]=[CH:3]1",
+            "[Cl:1].c1cc[cH:1]cc1",
+        ),
+        (
+            "Cl.[CH:1]1=[CH:7][CH:6]=[CH:5][CH:4]=[CH:3]1",
+            "Cl[C:1]1=[CH:7][CH:6]=[CH:5][CH:4]=[CH:3]1",
+            "Cl.c1cc[cH:1]cc1",
+        ),
+    ],
+)
+def test_atom_map_tag_reactants(reactants_smiles, product_smiles, expected):
+    tagged_reactants = atom_map_tag_reactants(f"{reactants_smiles}>>{product_smiles}")
+    assert tagged_reactants == expected
+
+
 @pytest.mark.parametrize(
     ("product_smiles", "expected"),
     [
diff --git a/tests/test_routes_base.py b/tests/test_routes_base.py
index 960a631..a9b02d2 100644
--- a/tests/test_routes_base.py
+++ b/tests/test_routes_base.py
@@ -9,10 +9,22 @@
 
 def test_collect_reaction_smiles(synthesis_route):
     smiles = synthesis_route.reaction_smiles()
+    assert synthesis_route.nsteps == 2
     assert len(smiles) == 2
     assert smiles[0] == "CO.Clc1ccccc1>>COc1ccccc1"
 
 
+def test_collect_reaction_smiles_augmented(augmentable_sythesis_route):
+    smiles = augmentable_sythesis_route.reaction_smiles(augment=True)
+
+    assert len(smiles) == 3
+    assert smiles == [
+        "Cl.c1ccccc1>>Clc1ccccc1",
+        "Cc1ccccc1>>c1ccccc1",
+        "Oc1ccccc1.C>>Cc1ccccc1",
+    ]
+
+
 def test_atom_mapping(synthesis_route, setup_mapper):
 
     synthesis_route.assign_atom_mapping()
@@ -33,6 +45,39 @@ def test_atom_mapping(synthesis_route, setup_mapper):
     )
 
 
+def test_atom_mapping_no_namerxn(synthesis_route, setup_mapper_no_namerxn, recwarn):
+    synthesis_route.assign_atom_mapping()
+
+    assert len(recwarn) == 1
+    assert "namerxn" in str(recwarn[0])
+
+    data = pd.DataFrame(synthesis_route.reaction_data())
+
+    assert len(data) == 2
+    assert data["classification"].to_list() == ["0.0", "0.0"]
+    assert (
+        data["mapped_reaction_smiles"][0]
+        == "Cl[c:3]1[cH:4][cH:5][cH:6][cH:7][cH:8]1.[CH3:1][OH:2]>>[CH3:1][O:2][c:3]1[cH:4][cH:5][cH:6][cH:7][cH:8]1"
+    )
+
+
+def test_atom_mapping_no_namerxn_choose_rxnmapper(
+    synthesis_route, setup_mapper_no_namerxn, recwarn
+):
+    synthesis_route.assign_atom_mapping(only_rxnmapper=True)
+
+    assert len(recwarn) == 0
+
+    data = pd.DataFrame(synthesis_route.reaction_data())
+
+    assert len(data) == 2
+    assert data["classification"].to_list() == ["0.0", "0.0"]
+    assert (
+        data["mapped_reaction_smiles"][0]
+        == "Cl[c:3]1[cH:4][cH:5][cH:6][cH:7][cH:8]1.[CH3:1][OH:2]>>[CH3:1][O:2][c:3]1[cH:4][cH:5][cH:6][cH:7][cH:8]1"
+    )
+
+
 def test_root_smiles(synthesis_route, setup_mapper):
     with pytest.raises(ValueError):
         SynthesisRoute({"smiles": "C"}).mapped_root_smiles
@@ -160,3 +205,58 @@ def test_extract_branched_chains(branched_synthesis_route):
     assert chains[1][2]["step"] == 2
     assert chains[1][2]["chain"] == "sub1"
     assert chains[1][2]["type"] == "branch"
+
+
+def test_route_leaves(synthesis_route):
+    leaves = synthesis_route.leaves()
+
+    assert leaves == {"c1ccccc1", "Cl", "CO"}
+
+
+def test_route_is_solved(synthesis_route, setup_stock):
+    assert synthesis_route.is_solved()
+
+    setup_stock(synthesis_route, {"c1ccccc1", "Cl", "CO"})
+    assert synthesis_route.is_solved()
+
+    setup_stock(synthesis_route, {"Cl", "CO"})
+    assert not synthesis_route.is_solved()
+
+
+def test_extract_monograms(synthesis_route):
+    monograms = synthesis_route.reaction_ngrams(1, "reaction_smiles")
+
+    assert len(monograms) == 2
+    assert monograms[0] == ("CO.Clc1ccccc1>>COc1ccccc1",)
+    assert monograms[1] == ("Cl.c1ccccc1>>Clc1ccccc1",)
+
+
+def test_extract_bigrams(synthesis_route):
+    bigrams = synthesis_route.reaction_ngrams(2, "reaction_smiles")
+
+    assert len(bigrams) == 1
+    assert bigrams[0] == ("CO.Clc1ccccc1>>COc1ccccc1", "Cl.c1ccccc1>>Clc1ccccc1")
+
+
+def test_extract_bigrams_branched(branched_synthesis_route):
+    bigrams = branched_synthesis_route.reaction_ngrams(2, "reaction_smiles")
+
+    assert len(bigrams) == 2
+    assert bigrams[0] == ("CO.Clc1ccccc1>>COc1ccccc1", "C.O>>CO")
+    assert bigrams[1] == ("CO.Clc1ccccc1>>COc1ccccc1", "Cl.c1ccccc1>>Clc1ccccc1")
+
+
+def test_extract_trigrams_too_short(synthesis_route):
+    trigrams = synthesis_route.reaction_ngrams(3, "reaction_smiles")
+
+    assert len(trigrams) == 0
+
+
+def test_extract_grams_augmentable(augmentable_sythesis_route):
+    route = augmentable_sythesis_route
+    bigrams = route.reaction_ngrams(2, "hash")
+
+    assert bigrams == [("xyz", "xyy"), ("xyy", "xxz")]
+
+    trigrams = route.reaction_ngrams(3, "hash")
+    assert trigrams == [("xyz", "xyy", "xxz")]
diff --git a/tests/test_routes_comparison.py b/tests/test_routes_comparison.py
new file mode 100644
index 0000000..7c9097e
--- /dev/null
+++ b/tests/test_routes_comparison.py
@@ -0,0 +1,85 @@
+import json
+from socket import timeout
+
+import pytest
+
+from rxnutils.routes.base import SynthesisRoute
+from rxnutils.routes.comparison import (
+    simple_route_similarity,
+    simple_bond_forming_similarity,
+    atom_matching_bonanza_similarity,
+    route_distances_calculator,
+)
+
+
+@pytest.fixture
+def example_routes(shared_datadir):
+    with open(shared_datadir / "atorvastatin_routes.json", "r") as fileobj:
+        dicts = json.load(fileobj)
+    return [SynthesisRoute(dicts[0]), SynthesisRoute(dicts[1])]
+
+
+def test_bond_similarity(example_routes):
+    similarity = simple_bond_forming_similarity(example_routes)
+
+    assert similarity.tolist() == [[1, 0.5], [0.5, 1.0]]
+
+
+def test_atom_similarity(example_routes):
+    similarity = atom_matching_bonanza_similarity(example_routes)
+
+    assert pytest.approx(similarity.tolist()[0], rel=1e-4) == [1, 0.6871]
+    assert pytest.approx(similarity.tolist()[1], rel=1e-4) == [0.6871, 1]
+
+
+def test_simple_route_similarity(example_routes):
+    similarity = simple_route_similarity(example_routes)
+
+    assert pytest.approx(similarity.tolist()[0], rel=1e-4) == [1, 0.5861]
+    assert pytest.approx(similarity.tolist()[1], rel=1e-4) == [0.5861, 1]
+
+
+def test_simple_route_similarity_one_no_rxns(example_routes):
+    example_routes[0].max_depth = 0.0
+    example_routes[0].reaction_tree["children"] = []
+
+    similarity = simple_route_similarity(example_routes)
+
+    assert pytest.approx(similarity.tolist()[0], rel=1e-4) == [1, 0.0]
+    assert pytest.approx(similarity.tolist()[1], rel=1e-4) == [0.0, 1]
+
+
+def test_simple_route_similarity_two_no_rxns(example_routes):
+    for route in example_routes:
+        route.max_depth = 0.0
+        route.reaction_tree["children"] = []
+
+    similarity = simple_route_similarity(example_routes)
+
+    assert pytest.approx(similarity.tolist()[0], rel=1e-4) == [1, 1.0]
+    assert pytest.approx(similarity.tolist()[1], rel=1e-4) == [1.0, 1]
+
+
+def test_ted_distance_calculator(example_routes):
+    ted_distance_calc = route_distances_calculator(model="ted")
+
+    route_distances = ted_distance_calc(example_routes)
+
+    assert route_distances.shape == (2, 2)
+    assert route_distances[0, 1] == route_distances[1, 0]
+    assert route_distances[0, 0] == route_distances[1, 1] == 0
+
+
+def test_ted_distance_calculator_with_kwargs(example_routes):
+    ted_distance_calc = route_distances_calculator(model="ted", timeout=10)
+
+    route_distances = ted_distance_calc(example_routes)
+
+    assert route_distances.shape == (2, 2)
+    assert route_distances[0, 1] == route_distances[1, 0]
+    assert route_distances[0, 0] == route_distances[1, 1] == 0
+
+
+def test_lstm_distance_calulator_not_implemented(example_routes):
+    with pytest.raises(NotImplementedError):
+        _ = route_distances_calculator(model="lstm")
diff --git a/tests/test_routes_readers.py b/tests/test_routes_readers.py
index b6cb5fa..8d1755d 100644
--- a/tests/test_routes_readers.py
+++ b/tests/test_routes_readers.py
@@ -6,6 +6,7 @@
 from rxnutils.routes.readers import (
     read_reactions_dataframe,
     read_aizynthcli_dataframe,
+    read_rdf_file,
 )
 
 
@@ -68,3 +69,14 @@ def test_create_route_from_aizynth_cli(shared_datadir):
         routes[0][0].reaction_smiles()[-1]
         == "NC1CCCCC1.C1=CCC=C1>>NC1CCCC(C2C=CC=C2)C1"
     )
+
+
+def test_create_route_from_rdf(shared_datadir):
+    filename = str(shared_datadir / "example_route.rdf")
+
+    route = read_rdf_file(filename)
+
+    reactions = route.reaction_smiles()
+    assert len(reactions) == 2
+    assert reactions[0] == "CCC=O>>CCC(=O)O"
+    assert reactions[1] == "CCCN>>CCC=O"
diff --git a/tests/test_routes_scoring.py b/tests/test_routes_scoring.py
new file mode 100644
index 0000000..511e71a
--- /dev/null
+++ b/tests/test_routes_scoring.py
@@ -0,0 +1,99 @@
+import copy
+import json
+import os
+
+import pandas as pd
+import pytest
+import requests
+
+from rxnutils.routes.scoring import (
+    route_sorter,
+    route_ranks,
+    badowski_route_score,
+    retro_bleu_score,
+    ngram_overlap_score,
+)
+from rxnutils.routes.retro_bleu.ngram_collection import NgramCollection
+
+
+def test_route_sorter(synthesis_route, setup_stock):
+    route1 = copy.deepcopy(synthesis_route)
+    setup_stock(route1, {"Cl", "CO"})
+    route2 = copy.deepcopy(synthesis_route)
+    setup_stock(route2, {"Cl", "CO", "c1ccccc1"})
+    routes = [route1, route2]
+
+    sorted_routes, route_scores = route_sorter(routes, badowski_route_score)
+
+    assert route_scores == pytest.approx([6.625, 20.6875], abs=1e-4)
+    assert sorted_routes[0] is route2
+    assert sorted_routes[1] is route1
+
+
+def test_route_rank():
+
+    assert route_ranks([4.0, 5.0, 5.0]) == [1, 2, 2]
+    assert route_ranks([4.0, 4.0, 5.0]) == [1, 1, 2]
+    assert route_ranks([4.0, 5.0, 6.0]) == [1, 2, 3]
+    assert route_ranks([4.0, 5.0, 5.0, 6.0]) == [1, 2, 2, 3]
+
+
+def test_badowski_score(synthesis_route, setup_stock):
+    setup_stock(synthesis_route, {"Cl", "CO"})
+
+    assert badowski_route_score(synthesis_route) == pytest.approx(20.6875, abs=1e-4)
+
+    setup_stock(synthesis_route, {"Cl", "CO", "c1ccccc1"})
+
+    assert badowski_route_score(synthesis_route) == pytest.approx(6.625, abs=1e-4)
+
+
+def test_read_and_write_ngram_collection(tmpdir):
+    collection = NgramCollection(2, "dummy", {("a", "b"), ("a", "c")})
+
+    filename = str(tmpdir / "ngrams.json")
+    collection.save_to_file(filename)
+
+    assert os.path.exists(filename)
+
+    collection2 = NgramCollection.from_file(filename)
+
+    assert collection2.nitems == collection.nitems
+    assert collection2.metadata_key == collection.metadata_key
+    assert collection2.ngrams == collection.ngrams
+
+
+def test_create_ngram_collection(augmentable_sythesis_route, tmpdir):
+    filename = str(tmpdir / "routes.json")
+    with open(filename, "w") as fileobj:
+        json.dump([augmentable_sythesis_route.reaction_tree], fileobj)
+
+    collection = NgramCollection.from_tree_collection(filename, 2, "hash")
+
+    assert collection.nitems == 2
+    assert collection.metadata_key == "hash"
+    assert collection.ngrams == {("xyz", "xyy"), ("xyy", "xxz")}
+
+
+def test_ngram_overlap_score(augmentable_sythesis_route):
+    ref = NgramCollection(2, "hash", {("xyz", "xyy"), ("xxyy", "xxz")})
+
+    score = ngram_overlap_score(augmentable_sythesis_route, ref)
+
+    assert score == 0.5
+
+
+def test_retro_bleu_score(augmentable_sythesis_route):
+    ref = NgramCollection(2, "hash", {("xyz", "xyy"), ("xxyy", "xxz")})
+
+    score = retro_bleu_score(augmentable_sythesis_route, ref)
+
+    assert pytest.approx(score, abs=1e-4) == 4.3670
+
+
+def test_retro_bleu_score_short_nsteps(augmentable_sythesis_route):
+    ref = NgramCollection(2, "hash", {("xyz", "xyy"), ("xxyy", "xxz")})
+
+    score = retro_bleu_score(augmentable_sythesis_route, ref, 1)
+
+    assert pytest.approx(score, abs=1e-4) == 3.0443
diff --git a/tests/test_ted.py b/tests/test_ted.py
new file mode 100644
index 0000000..207b2a4
--- /dev/null
+++ b/tests/test_ted.py
@@ -0,0 +1,367 @@
+import json
+
+import pytest
+
+from rxnutils.routes.base import SynthesisRoute
+from rxnutils.routes.ted.utils import (
+    AptedConfig,
+    TreeContent,
+    StandardFingerprintFactory,
+)
+from rxnutils.routes.ted.reactiontree import ReactionTreeWrapper
+from rxnutils.routes.ted.distances_calculator import ted_distances_calculator
+
+
+def collect_smiles(tree, query_type, smiles_list):
+    if tree["type"] == query_type:
+        smiles_list.append(tree["smiles"])
+    for child in tree.get("children", []):
+        collect_smiles(child, query_type, smiles_list)
+
+
+node1 = {"type": "mol", "fingerprint": [0, 1, 0], "children": ["A", "B", "C"]}
+
+node2 = {"type": "mol", "fingerprint": [1, 1, 0]}
+
+example_tree = {
+    "type": "mol",
+    "smiles": "Cc1ccc2nc3ccccc3c(Nc3ccc(NC(=S)Nc4ccccc4)cc3)c2c1",
+    "children": [
+        {
+            "type": "reaction",
+            "metadata": {},
+            "children": [
+                {
+                    "type": "mol",
+                    "smiles": "Cc1ccc2nc3ccccc3c(Cl)c2c1",
+                },
+                {
+                    "type": "mol",
+                    "smiles": "Nc1ccc(NC(=S)Nc2ccccc2)cc1",
+                },
+            ],
+        }
+    ],
+}
+
+
+def test_rename_cost_different_types():
+    config = AptedConfig()
+
+    cost = config.rename({"type": "type1"}, {"type": "type2"})
+
+    assert cost == 1
+
+
+def test_rename_cost_same_types():
+    config = AptedConfig()
+
+    cost = config.rename(node1, node2)
+
+    assert cost == 0.5
+
+
+def test_get_children_fixed():
+    config = AptedConfig()
+
+    assert config.children(node1) == ["A", "B", "C"]
+
+
+def test_get_children_random():
+    config = AptedConfig(randomize=True)
+
+    children = config.children(node1)
+
+    assert len(children) == 3
+    for expected_child in ["A", "B", "C"]:
+        assert expected_child in children
+
+
+@pytest.mark.parametrize(
+    "route_index",
+    [1, 2],
+)
+def test_create_wrapper(load_reaction_tree, route_index):
+    tree = load_reaction_tree("example_routes.json", route_index)
+    route = SynthesisRoute(tree)
+    wrapper = ReactionTreeWrapper(route)
+
+    assert wrapper.info["content"] == TreeContent.MOLECULES
+    assert wrapper.info["tree count"] == 4
+    assert wrapper.first_tree["type"] == "mol"
+    assert len(wrapper.trees) == 4
+
+    wrapper = ReactionTreeWrapper(route, TreeContent.REACTIONS)
+
+    assert wrapper.info["content"] == TreeContent.REACTIONS
+    assert wrapper.info["tree count"] == 1
+    assert wrapper.first_tree["type"] == "reaction"
+    assert len(wrapper.trees) == 1
+
+    wrapper = ReactionTreeWrapper(route, TreeContent.BOTH)
+
+    assert wrapper.info["content"] == TreeContent.BOTH
+    assert wrapper.info["tree count"] == 4
+    assert len(wrapper.trees) == 4
+
+
+def test_create_wrapper_no_reaction():
+    tree = {"smiles": "CCC", "type": "mol"}
+    route = SynthesisRoute(tree)
+
+    wrapper = ReactionTreeWrapper(route)
+    assert wrapper.info["tree count"] == 1
+    assert len(wrapper.trees) == 1
+
+    with pytest.raises(ValueError):
+        ReactionTreeWrapper(route, TreeContent.REACTIONS)
+
+    wrapper = ReactionTreeWrapper(route, TreeContent.BOTH)
+    assert wrapper.info["tree count"] == 1
+    assert wrapper.first_tree["type"] == "mol"
+    assert len(wrapper.trees) == 1
+
+
+def test_create_one_tree_of_molecules(load_reaction_tree):
+    tree = load_reaction_tree("example_routes.json", 0)
+    route = SynthesisRoute(tree)
+
+    wrapper = ReactionTreeWrapper(route, exhaustive_limit=1)
+
+    assert wrapper.info["tree count"] == 2
+    assert len(wrapper.trees) == 1
+
+    assert wrapper.first_tree["smiles"] == tree["smiles"]
+    assert len(wrapper.first_tree["children"]) == 2
+
+    child_smiles = [child["smiles"] for child in wrapper.first_tree["children"]]
+    expected_smiles = [node["smiles"] for node in tree["children"][0]["children"]]
+    assert child_smiles == expected_smiles
+
+
+def test_create_one_tree_of_reactions(load_reaction_tree):
+    tree = load_reaction_tree("example_routes.json", 0)
+    route = SynthesisRoute(tree)
+
+    wrapper = ReactionTreeWrapper(
+        route, content=TreeContent.REACTIONS, exhaustive_limit=1
+    )
+
+    assert wrapper.info["tree count"] == 1
+    assert len(wrapper.trees) == 1
+
+    rxn_nodes = []
+    collect_smiles(tree, "reaction", rxn_nodes)
+    assert wrapper.first_tree["smiles"] == rxn_nodes[0]
+    assert len(wrapper.first_tree["children"]) == 0
+
+
+def test_create_one_tree_of_everything(load_reaction_tree):
+    tree = load_reaction_tree("example_routes.json", 0)
+    route = SynthesisRoute(tree)
+
+    wrapper = ReactionTreeWrapper(route, content=TreeContent.BOTH, exhaustive_limit=1)
+
+    assert wrapper.info["tree count"] == 2
+    assert len(wrapper.trees) == 1
+
+    mol_nodes = []
+    collect_smiles(tree, "mol", mol_nodes)
+    rxn_nodes = []
+    collect_smiles(tree, "reaction", rxn_nodes)
+    assert wrapper.first_tree["smiles"] == tree["smiles"]
+    assert len(wrapper.first_tree["children"]) == 1
+
+    child1 = wrapper.first_tree["children"][0]
+    assert child1["smiles"] == rxn_nodes[0]
+    assert len(child1["children"]) == 2
+
+    child_smiles = [child["smiles"] for child in child1["children"]]
+    assert child_smiles == mol_nodes[1:]
+
+
+def test_create_all_trees_of_molecules(load_reaction_tree):
+    tree = load_reaction_tree("example_routes.json", 0)
+    route = SynthesisRoute(tree)
+
+    wrapper = ReactionTreeWrapper(route)
+
+    assert wrapper.info["tree count"] == 2
+    assert len(wrapper.trees) == 2
+
+    mol_nodes = []
+    collect_smiles(tree, "mol", mol_nodes)
+    # Assert first tree
+    assert wrapper.first_tree["smiles"] == mol_nodes[0]
+    assert len(wrapper.first_tree["children"]) == 2
+
+    child_smiles = [child["smiles"] for child in wrapper.first_tree["children"]]
+    assert child_smiles == mol_nodes[1:]
+
+    # Assert second tree
+    assert wrapper.trees[1]["smiles"] == mol_nodes[0]
+    assert len(wrapper.trees[1]["children"]) == 2
+
+    child_smiles = [child["smiles"] for child in wrapper.trees[1]["children"]]
+    assert child_smiles == mol_nodes[1:][::-1]
+
+
+def test_create_two_trees_of_everything(load_reaction_tree):
+    tree = load_reaction_tree("example_routes.json", 0)
+    route = SynthesisRoute(tree)
+
+    wrapper = ReactionTreeWrapper(route, content=TreeContent.BOTH)
+
+    assert wrapper.info["tree count"] == 2
+    assert len(wrapper.trees) == 2
+
+    mol_nodes = []
+    collect_smiles(tree, "mol", mol_nodes)
+    rxn_nodes = []
+    collect_smiles(tree, "reaction", rxn_nodes)
+    # Assert first tree
+    assert wrapper.first_tree["smiles"] == mol_nodes[0]
+    assert len(wrapper.first_tree["children"]) == 1
+
+    child1 = wrapper.first_tree["children"][0]
+    assert child1["smiles"] == rxn_nodes[0]
+    assert len(child1["children"]) == 2
+
+    child_smiles = [child["smiles"] for child in child1["children"]]
+    assert child_smiles == mol_nodes[1:]
+
+    # Assert second tree
+    assert wrapper.trees[1]["smiles"] == mol_nodes[0]
+    assert len(wrapper.trees[1]["children"]) == 1
+
+    child1 = wrapper.trees[1]["children"][0]
+    assert child1["smiles"] == rxn_nodes[0]
+    assert len(child1["children"]) == 2
+
+    child_smiles = [child["smiles"] for child in child1["children"]]
+    assert child_smiles == mol_nodes[1:][::-1]
+
+
+def test_route_self_distance(load_reaction_tree):
+    tree = load_reaction_tree("example_routes.json", 0)
+    route = SynthesisRoute(tree)
+
+    wrapper = ReactionTreeWrapper(route, exhaustive_limit=1)
+
+    assert wrapper.distance_to(wrapper) == 0.0
+
+
+def test_route_distances_random(load_reaction_tree):
+    tree1 = load_reaction_tree("example_routes.json", 0)
+    route1 = SynthesisRoute(tree1)
+    wrapper1 = ReactionTreeWrapper(route1, exhaustive_limit=1)
+
+    tree2 = load_reaction_tree("example_routes.json", 1)
+    route2 = SynthesisRoute(tree2)
+    wrapper2 = ReactionTreeWrapper(route2, exhaustive_limit=1)
+
+    distances = list(wrapper1.distance_iter(wrapper2, exhaustive_limit=1))
+
+    assert len(distances) == 2
+    assert pytest.approx(distances[0], abs=1e-2) == 2.6522
+
+
+def test_route_distances_exhaustive(load_reaction_tree):
+    tree1 = load_reaction_tree("example_routes.json", 0)
+    route1 = SynthesisRoute(tree1)
+    wrapper1 = ReactionTreeWrapper(route1, exhaustive_limit=2)
+
+    tree2 = load_reaction_tree("example_routes.json", 1)
+    route2 = SynthesisRoute(tree2)
+    wrapper2 = ReactionTreeWrapper(route2, exhaustive_limit=2)
+
+    distances = list(wrapper1.distance_iter(wrapper2, exhaustive_limit=40))
+
+    assert len(distances) == 2
+    assert pytest.approx(distances[0], abs=1e-2) == 2.6522
+    assert pytest.approx(min(distances), abs=1e-2) == 2.6522
+
+
+def test_route_distances_semi_exhaustive(load_reaction_tree):
+    tree1 = load_reaction_tree("example_routes.json", 0)
+    route1 = SynthesisRoute(tree1)
+    wrapper1 = ReactionTreeWrapper(route1, exhaustive_limit=1)
+
+    tree2 = load_reaction_tree("example_routes.json", 1)
+    route2 = SynthesisRoute(tree2)
+    wrapper2 = ReactionTreeWrapper(route2, exhaustive_limit=2)
+
+    distances = list(wrapper1.distance_iter(wrapper2, exhaustive_limit=1))
+
+    assert len(distances) == 2
+    assert pytest.approx(distances[0], abs=1e-2) == 2.6522
+    assert pytest.approx(min(distances), abs=1e-2) == 2.6522
+
+
+def test_route_distances_longer_routes(load_reaction_tree):
+    tree1 = load_reaction_tree("longer_routes.json", 0)
+    route1 = SynthesisRoute(tree1)
+    wrapper1 = ReactionTreeWrapper(route1, content="both")
+
+    tree2 = load_reaction_tree("longer_routes.json", 1)
+    route2 = SynthesisRoute(tree2)
+    wrapper2 = ReactionTreeWrapper(route2, content="both")
+
+    distances = list(wrapper1.distance_iter(wrapper2))
+
+    assert len(distances) == 21
+    assert pytest.approx(distances[0], abs=1e-2) == 4.14
+
+
+def test_distance_matrix(load_reaction_tree):
+    routes = [
+        SynthesisRoute(load_reaction_tree("example_routes.json", idx))
+        for idx in range(3)
+    ]
+
+    dist_mat = ted_distances_calculator(routes, content="molecules")
+
+    assert len(dist_mat) == 3
+    assert pytest.approx(dist_mat[0, 1], abs=1e-2) == 2.6522
+    assert pytest.approx(dist_mat[0, 2], abs=1e-2) == 3.0779
+    assert pytest.approx(dist_mat[2, 1], abs=1e-2) == 0.7483
+
+
+def test_distance_matrix_timeout(load_reaction_tree):
+    routes = [
+        SynthesisRoute(load_reaction_tree("example_routes.json", idx))
+        for idx in range(3)
+    ]
+
+    with pytest.raises(ValueError):
+        ted_distances_calculator(routes, content="molecules", timeout=0)
+
+
+def test_fingerprint_calculations():
+    example_route = SynthesisRoute(example_tree)
+    wrapper = ReactionTreeWrapper(
+        example_route, content="both", fp_factory=StandardFingerprintFactory(nbits=128)
+    )
+
+    fp = wrapper.first_tree["sort_key"]
+    mol1 = "1000010000000000000010001000100101000101100000010000010000100001"
+    mol2 = "1100000001110110011000100010000001001000000100100000110000100100"
+    assert fp == mol1 + mol2
+
+    fp = wrapper.first_tree["children"][0]["sort_key"]
+    rxn1 = "00000-1000000-1000-100-2000000000000000000000000000-10-20000000000000-1"
+    rxn2 = "-10000000001000100-10000-100-10000000000-10-1000000000000-11000-10000100"
+    assert fp == rxn1 + rxn2
+
+
+def test_custom_fingerprint_calculations():
+    def factory(tree, parent):
+        if tree["type"] != "reaction":
+            return
+        tree["fingerprint"] = [1, 2, 3, 4]
+
+    example_route = SynthesisRoute(example_tree)
+    wrapper = ReactionTreeWrapper(example_route, content="both", fp_factory=factory)
+
+    assert wrapper.first_tree["sort_key"] == ""
+    assert wrapper.first_tree["children"][0]["sort_key"] == "1234"
diff --git a/tests/test_uspto.py b/tests/test_uspto.py
index 49d9c2e..623783f 100644
--- a/tests/test_uspto.py
+++ b/tests/test_uspto.py
@@ -1,9 +1,10 @@
 import pandas as pd
 
 from rxnutils.data.uspto.combine import main as combine_uspto
+from rxnutils.data.uspto.uspto_yield import UsptoYieldCuration
 
 
-def test_combine_uspto(shared_datadir, tmpdir):
+def test_combine_uspto(shared_datadir):
     combine_uspto(
         ["--filenames", "uspto_example_reactions.rsmi", "--folder", str(shared_datadir)]
     )
@@ -13,3 +14,45 @@ def test_combine_uspto(shared_datadir, tmpdir):
     assert len(data) == 9
     assert data.columns.to_list() == ["ID", "Year", "ReactionSmiles"]
     assert data["ID"].to_list()[:2] == ["US03930836;;0", "US03930836;;1"]
+
+
+def test_uspto_yield_curation():
+
+    data = pd.DataFrame(
+        {
+            "TextMinedYield": [
+                "~10",
+                "50%",
+                ">40",
+                ">=50",
+                "<30",
+                "20 to 50",
+                "-50",
+                "100",
+                "50",
+                "",
+                "",
+            ],
+            "CalculatedYield": [
+                "12%",
+                "110",
+                "40",
+                "51",
+                "",
+                "40",
+                "-40",
+                "120",
+                "40",
+                "70",
+                "",
+            ],
+        }
+    )
+    action = UsptoYieldCuration()
+
+    data2 = action(data)
+
+    expected = [False] * 6 + [True] + [False] * 3 + [True]
+    assert data2["CuratedYield"].isna().tolist() == expected
+    assert data2["CuratedYield"].tolist()[:6] == [12, 50, 40, 51, 30, 50]
+    assert data2["CuratedYield"].tolist()[7:-1] == [100, 50, 70]
diff --git a/tests/test_validation.py b/tests/test_validation.py
new file mode 100644
index 0000000..882522f
--- /dev/null
+++ b/tests/test_validation.py
@@ -0,0 +1,21 @@
+import pytest
+
+from rxnutils.routes.utils.validation import validate_dict
+
+
+@pytest.mark.parametrize(
+    "route_index",
+    [0, 1, 2],
+)
+def test_validate_example_trees(load_reaction_tree, route_index):
+    validate_dict(load_reaction_tree("example_routes.json", route_index))
+
+
+def test_validate_only_mols():
+    dict_ = {
+        "smiles": "CCC",
+        "type": "mol",
+        "children": [{"smiles": "CCC", "type": "mol"}],
+    }
+    with pytest.raises(ValueError, match="String should match pattern"):
+        validate_dict(dict_)