Merge branch 'marrink-lab:master' into PTMA-AA-ff

marrink-lab · Aug 21, 2023 · b253dfe · b253dfe
2 parents 6301581 + 1ecd4d5
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diff --git a/.codecov.yml b/.codecov.yml
@@ -10,4 +10,6 @@ coverage:
         patch:
             default:
                 target: 90
+ignore:
+   - polyply/tests
 comment: off
diff --git a/.github/workflows/pypi_deploy.yml b/.github/workflows/pypi_deploy.yml
@@ -13,7 +13,7 @@ jobs:
 
     strategy:
       matrix:
-       py_version: ["3.6", "3.7", "3.8", "3.9"] 
+       py_version: ["3.7", "3.8", "3.9", "3.10", "3.11"] 
 
     steps:
     - uses: actions/checkout@v2
@@ -28,11 +28,15 @@ jobs:
         pip install -r requirements-tests.txt
         
     - name: Run pytest with codecoverage
-      run: |
-        coverage run --source=polyply $(which pytest) -vv polyply
-        coverage report --omit='*/bin/pytest'
-        codecov
-  
+      run:  pytest --cov polyply --cov-report=xml
+    - name: Upload coverage codecov   
+      uses: codecov/codecov-action@v3 
+      with:
+            verbose: true
+            token: ${{ secrets.CODECOV_TOKEN }}
+            files: ./coverage.xml
+            fail_ci_if_error: true
+            verbose: true
 
   deploy:
     needs: test

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
@@ -16,7 +16,7 @@ jobs:
 
     strategy:
       matrix:
-       py_version: ["3.6", "3.7", "3.8", "3.9"] 
+       py_version: ["3.7", "3.8", "3.9", "3.10", "3.11"] 
 
     steps:
     - uses: actions/checkout@v2
@@ -31,11 +31,15 @@ jobs:
         pip install -r requirements-tests.txt
         
     - name: Run pytest with codecoverage
-      run: |
-        coverage run --source=polyply $(which pytest) -vv polyply
-        coverage report --omit='*/bin/pytest'
-        codecov
-        
+      run:  pytest --cov polyply --cov-report=xml
+    - name: Upload coverage codecov   
+      uses: codecov/codecov-action@v3 
+      with:
+            token: ${{ secrets.CODECOV_TOKEN }}
+            files: ./coverage.xml
+            fail_ci_if_error: true
+            verbose: true
+
   lint:
     runs-on: ubuntu-latest
 

diff --git a/.gitignore b/.gitignore
@@ -3,6 +3,8 @@ est.pdb
 **.pyc
 **.bak
 
+*.idea
+
 **.lprof
 polyply.egg-info
 

diff --git a/LIBRARY.md b/LIBRARY.md
@@ -0,0 +1,28 @@
+
+| Polymer name                  | Abbreviation            | All-atom model(s)                                                     | Coarse-grained model(s)                              |
+|-------------------------------|-------------------------|-----------------------------------------------------------------------|------------------------------------------------------|
+|Polyethylene oxide             |PEO                      |[gromos2016H66](polyply/data/2016H66/polyether_blocks.ff)              |[martini2](polyply/data/martini2/PEO.martini.2.itp)   |
+|                               |                         |[oplsaaLigParGen](polyply/data/oplsaaLigParGen/PEO.oplsaa.LigParGen.ff)|[martini3](polyply/data/martini3/PEO.martini3.ff)     |
+|Polystyrene                    |PS                       |[gromos2016H66](polyply/data/2016H66/polyvinyl_blocks.ff)              |[martini2](polyply/data/martini2/PS.martini.2.itp)    |
+|                               |                         |                                                                       |[martini3](polyply/data/martini3/PS.martini3.ff)      |
+|Polystyrene-b-poly(ethylene oxide)|PS-PEO                |                                                                       |[martini3](polyply/data/martini3/PS_PEO_link.ff)      |
+|Polymethyl acrylate            |PMA                      |[gromos2016H66](polyply/data/2016H66/polyvinyl_blocks.ff)              |[martini3](polyply/data/martini3/PMA.martini3.ff)     |
+|Polymethyl methacrylate        |PMMA                     |[gromos2016H66](polyply/data/2016H66/polyvinyl_blocks.ff)              |[martini3](polyply/data/martini3/PMMA.martini3.ff)    |
+|Polyethylene                   |PE                       |[gromos2016H66](polyply/data/2016H66/polyvinyl_blocks.ff)              |[martini3](polyply/data/martini3/PE.martini3.ff)      |
+|                               |                         |                                                                       |[martini2](polyply/data/martini2/PE.martini.2.itp)    |
+|Polypropylene                  |PP                       |[gromos2016H66](polyply/data/2016H66/polyvinyl_blocks.ff)              |[martini2](polyply/data/martini2/PP.martini.2.itp)    |
+|Poly(3-hexylthiophene)         |P3HT                     |[gromos53A6](polyply/data/gromos53A6/P3HT.gromos.53A6.ff)              |[martini2](polyply/data/martini2/P3HT.martini.2.itp)  |
+|                               |                         |                                                                       |[martini3](polyply/data/martini3/P3HT.martini3.ff)    |
+|Polyvinyl alcohol              |PVA                      |[gromos2016H66](polyply/data/2016H66/polyvinyl_blocks.ff)              |[martini3](polyply/data/martini3/PVA.martini3.ff)     |
+|Poly(2-hydroxyethyl acrylate)  |HEA                      |[gromos2016H66](polyply/data/2016H66/polyvinyl_blocks.ff)              |                                                      |
+|Polyacrylamide                 |PAM                      |[gromos2016H66](polyply/data/2016H66/polyvinyl_blocks.ff)              |                                                      |
+|Poly(methacrylamide)           |PMAM                     |[gromos2016H66](polyply/data/2016H66/polyvinyl_blocks.ff)              |                                                      |
+|Poly(diallyldimethylammonium)  |PDADMA                   |                                                                       |[martini2](polyply/data/martini2/PDADMA.martini.2.itp)|
+|Polystyrene sulfonate          |PSS                      |                                                                       |[martini2](polyply/data/martini2/PSS.martini.2.itp)   |
+|                               |                         |                                                                       |[martini3](polyply/data/martini3/PSS.martini3.ff)     |
+|Poly(para-phenylene ethynylene)|PPE                      |                                                                       |[martini3](polyply/data/martini3/PPE.martini3.ff)     |
+|Poly(TEMPO methacrylate)       |PTMA                     |                                                                       |[martini3](polyply/data/martini3/PTMA.martini3.ff)    |
+|Dextran                        |DEX                      |                                                                       |[martini3](polyply/data/martini3/dextran.martini3.ff) |
+|DNA nucleobases                |Dx, Tx5, Dx3 w/ x=T,G,A,C|[parmbsc1](polyply/data/parmbsc1/dna_final.ff)                         |[martini2](polyply/data/martini2/DNA_M2.ff)           |
+|Aminoacids                     |3 letter code            |                                                                       |[martini3](polyply/data/martini3/aminoacids.ff)       |
+|Polydimethylsiloxane  |PDMS                   |                                                                       |[martini3](polyply/data/martini3/PDMS.martini3.ff)
diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@
 [![Build Status](https://github.com/marrink-lab/polyply_1.0/actions/workflows/python-app.yml/badge.svg)](https://github.com/marrink-lab/polyply_1.0/actions)
 [![PyPI version](https://badge.fury.io/py/polyply.svg)](https://badge.fury.io/py/polyply)
 ![license](https://img.shields.io/github/license/marrink-lab/polyply_1.0)
-![GitHub Workflow Status](https://img.shields.io/github/workflow/status/marrink-lab/polyply_1.0/Upload%20Python%20Package)
+![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/marrink-lab/polyply_1.0/pypi_deploy.yml)
 [![arXiv](https://img.shields.io/badge/arXiv-2105.05890-b31b1b.svg)](https://arxiv.org/abs/2105.05890)
 [![DOI:10.1038/s41467-021-27627-4](https://zenodo.org/badge/DOI/10.1038/s41467-021-27627-4.svg)](https://doi.org/10.1038/s41467-021-27627-4)
 
@@ -29,14 +29,16 @@ force-field, molecule parameters and this program.
 ## Quick references
 [Installation Guide](https://github.com/marrink-lab/polyply_1.0/wiki/Installation)\
 [FAQs](https://github.com/marrink-lab/polyply_1.0/wiki/FAQs)\
+[Current Polyply Polymer Library](./LIBRARY.md)\
 [Submissions to Martini Polymer Library](https://github.com/marrink-lab/polyply_1.0/wiki/Submit-polymer-parameters)\
 [Tutorial: Martini Polymers](https://github.com/marrink-lab/polyply_1.0/wiki/Tutorial:-martini-polymer-melts)\
 [Tutorial: GROMOS Polymers](https://github.com/marrink-lab/polyply_1.0/wiki/Tutorial:-GROMOS-polymer-melts)\
-[Tutorial: PEGylated lipid bilayers](https://github.com/marrink-lab/polyply_1.0/wiki/Tutorial:-PEGylated-lipid-bilayers)
-
+[Tutorial: PEGylated lipid bilayers](https://github.com/marrink-lab/polyply_1.0/wiki/Tutorial:-PEGylated-lipid-bilayers)\
+[Tutorial: Single-stranded DNA](https://github.com/marrink-lab/polyply_1.0/wiki/Tutorial:-Single-stranded-circular-DNA)
 ## News 
-- (Feb 8) **Featured Research Article in Nature Communcations.** Our article on the polyply software suite is now featured on the [Editors' Highlights](https://www.nature.com/collections/hhfigaahch) for Structural biology, biochemistry and biophysics in Nature Communications. The Editors’ Highlights pages aims to showcase the 50 best papers recently published in an area. The development team is beyond happy to receive this honor.   
-- (May 23) **Fighting Cancer with polyply.** Dane et al. used polyply to setup simulations of vesicles and lipid nanodiscs (LNDs) containing PEGylated lipids, which are used as nanocarriers for cancer therapeutics. They find that LNDs are more effective in delivery likely due to their higher flexibility.  Check it out in [Nature Materials](https://www.nature.com/articles/s41563-022-01251-z). 
+- (Feb 8, 22') **Featured Research Article in Nature Communcations.** Our article on the polyply software suite is now featured on the [Editors' Highlights](https://www.nature.com/collections/hhfigaahch) for Structural biology, biochemistry and biophysics in Nature Communications. The Editors’ Highlights pages aims to showcase the 50 best papers recently published in an area. The development team is beyond happy to receive this honor.   
+- (May 23, 22') **Fighting Cancer with polyply.** Dane et al. used polyply to setup simulations of vesicles and lipid nanodiscs (LNDs) containing PEGylated lipids, which are used as nanocarriers for cancer therapeutics. They find that LNDs are more effective in delivery likely due to their higher flexibility.  Check it out in [Nature Materials](https://www.nature.com/articles/s41563-022-01251-z). 
+- (Jan 18, 23') **Towards whole cell simulations with polyply.** In [a perspective on whole-cell simulations](https://www.frontiersin.org/articles/10.3389/fchem.2023.1106495/full) using the Martini force field, Stevens *et al.* utilize polyply to construct the full 0.5 Mio bp chromosome of the Syn3A minimal cell. This impressive task is a good example of the power of the upcoming DNA implementation into polyply and the role of polyply in the Martini Ecosystem.
 
 ## Contributions & Support
 We are happy to accept submissions of polymer parameters to the polyply library. To submit parameters simply 

diff --git a/bin/polyply b/bin/polyply
@@ -24,7 +24,7 @@ from pathlib import Path
 import numpy as np
 import polyply
 from polyply import (gen_itp, gen_coords, gen_seq, DATA_PATH)
-from polyply.src.load_library import load_library
+from polyply.src.load_library import load_ff_library
 from polyply.src.logging import LOGGER, LOGLEVELS
 
 VERSION = 'polyply version {}'.format(polyply.__version__) # pylint: disable=consider-using-f-string
@@ -56,19 +56,19 @@ def main(): # pylint: disable=too-many-locals,too-many-statements
     # Input Arguments for the itp generation tool
     # =============================================================================
 
-    parser_gen_itp.add_argument('-name', required=True, type=str, dest="name",
-                                help="name of the final molecule")
+    parser_gen_itp.add_argument('-name', required=False, type=str, dest="name",
+                                help="name of the final molecule", default='polymer')
     parser_gen_itp.add_argument('-v', dest='verbosity', action='count',
                                 help='Enable debug logging output. Can be given '
                                 'multiple times.', default=0)
 
     file_group = parser_gen_itp.add_argument_group('Input and output options')
-    file_group.add_argument('-lib', dest='lib', required=False, type=str,
+    file_group.add_argument('-lib', dest='lib', required=False, type=Path, default=[],
                             help='force-fields to include from library', nargs='*')
-    file_group.add_argument('-f', dest='inpath', required=False, type=Path,
-                            help='Input file (ITP|FF)', nargs="*")
+    file_group.add_argument('-f', dest='inpath', type=Path, required=False, default=[],
+                            help='Input file (ITP|FF)', nargs='*')
     file_group.add_argument('-o', dest='outpath', type=Path,
-                            help='Output ITP (ITP)')
+                            help='Output ITP (ITP)', default=Path('polymer.itp'))
     seq_group = file_group.add_mutually_exclusive_group(required=True)
     seq_group.add_argument('-seq', dest='seq', type=str, nargs='+',
                            help='A linear sequence of residue names.')
@@ -81,7 +81,7 @@ def main(): # pylint: disable=too-many-locals,too-many-statements
     #           Input Arguments for the coordinate generation tool
     # ============================================================================
 
-    parser_gen_coords.add_argument('-name', required=True, type=str, dest="name",
+    parser_gen_coords.add_argument('-name', required=False, type=str, dest="name", default='molname',
                                    help="name of the final molecule")
 
     parser_gen_coords.add_argument('-v', dest='verbosity', action='count',
@@ -91,14 +91,16 @@ def main(): # pylint: disable=too-many-locals,too-many-statements
     file_group = parser_gen_coords.add_argument_group('Input and output files')
     file_group.add_argument('-p', dest='toppath', required=False, type=Path,
                             help='topology file (.top)')
-    file_group.add_argument('-o', dest='outpath', type=Path,
+    file_group.add_argument('-o', dest='outpath', type=Path, default='coords.gro',
                             help='output GRO (.gro)')
     file_group.add_argument('-c', dest='coordpath', type=Path,
                             help='input file molecules (.gro)', default=None)
     file_group.add_argument('-mc', dest='coordpath_meta', type=Path,
                             help='input file meta-molecule (.gro)', default=None)
-    file_group.add_argument('-b', dest='build', type=Path, default=None,
+    file_group.add_argument('-b', dest='build', type=Path, required=False, default=[], nargs='*',
                             help=('input file; specify molecule specific building options'))
+    file_group.add_argument('-lib', dest='lib', required=False, type=Path, default=None,
+                            help='molecule templates can be loaded from force field library')
 
     topology_group = parser_gen_coords.add_argument_group('Change or modify topology')
     topology_group.add_argument('-res', dest='build_res', type=str,
@@ -195,7 +197,7 @@ def main(): # pylint: disable=too-many-locals,too-many-statements
                                   "is <tag:molecule name>.")
 
     seq_group = parser_gen_seq.add_argument_group('Definition of sequence')
-    seq_group.add_argument('-seq', dest='seq', nargs='+', type=str,
+    seq_group.add_argument('-seq', dest='seq', nargs='+', type=str, required=True,
                            help="Define the sequence order in which to combine macros."
                                 "The format is <macro_tag, macro_tag, ...>. For example, "
                                 "to combine three blocks called A, B, which are defined by the "
@@ -238,7 +240,7 @@ def main(): # pylint: disable=too-many-locals,too-many-statements
         parser.exit()
 
     if args.list_blocks:
-        force_field = load_library("libs", args.list_blocks, [])
+        force_field = load_ff_library("libs", args.list_blocks, [])
         msg = 'The following Blocks are present in the following libraries: {}:'
         print(msg.format(args.list_blocks))
         for block in force_field.blocks:

diff --git a/polyply/data/gromos53A6/links.ff b/polyply/data/gromos53A6/links.ff
@@ -58,3 +58,13 @@ CT2 {"replace": {"charge": -0.394}}
  CT3  CT2 +H1      2     126.0      575.0   {"comment":"H-CT2-link", "group": "termini"}
 [ dihedrals ]
 +H1   ST1  CT3  CT2  2     0.0   167.42309  {"comment":"H-CT2-link", "group": "termini"}
+
+
+[ link ]
+[ atoms ]
+CT2 {"resname": "P3HT"}
+[ warning ]
+You should patch P3HT with a H-terminal residues. Use -seq Hter:1 P3HT:4 Hter:1
+[ non-edges ]
+CT2 +H1
+CT2 +CT5
diff --git a/polyply/data/martini3/PDMS.martini3.ff b/polyply/data/martini3/PDMS.martini3.ff
@@ -0,0 +1,87 @@
+[ citations ]
+Martini3
+polyply
+M3_PDMS
+;
+[ moleculetype ]
+; molname        nrexcl
+PDMS             1
+;
+[ atoms ]
+;  id  type  resnr  residue    atom  cgnr    charge     mass
+    1    DMS      1     PDMS    PDMS   1      0.00000     72.00
+;
+[ link ]
+resname "PDMS"
+[ bonds ]
+;   i     j   funct   length   force.c.
+  PDMS   +PDMS     1    0.448  11500           ; 2
+;
+[ link ]
+resname "PDMS"
+[ angles ]
+;   i     j     k   funct     angle   force.c.
+  PDMS   +PDMS   ++PDMS       1     86     45.89           ; 2
+;
+[ link ]
+resname "PDMS"
+[ dihedrals ]
+;   i     j     k     l   funct     dihedral   force.c.   mult.
+  PDMS   +PDMS   ++PDMS   +++PDMS       1         1.18    1.4       1     ; 2
+;
+[ moleculetype ]
+PDMSter  1
+[ atoms ]
+  1    DMS      1     PDMSter     END   1      0.00000     72.00
+[ info ]
+Parameters for this model are custom and available for download at: https://github.com/marrink-lab/martini-forcefields/blob/main/martini_forcefields/regular/v3.0.0/gmx_files_contributed/DMS_martini3_v1.itp
+
+[ link ]
+resname "PDMSter|PDMS"
+[ bonds ]
+  END    +PDMS       1    0.446  11000     {"group": "END-PDMS"}
+
+[ link ]
+resname "PDMS|PDMSter"
+[ bonds ]
+  PDMS    +END       1    0.446  11000     {"group": "PDMS-END"}  
+
+
+[ link ]
+resname "PDMSter|PDMS"
+[ angles ]
+END   +PDMS   ++PDMS   1     87     78  {"group": "END-PDMS"} 
+
+[ link ]
+resname "PDMS|PDMSter"
+[ angles ]
+PDMS   +PDMS   ++END   1     87     78  {"group": "PDMS-END"} 
+
+
+[ link ]
+resname "PDMSter|PDMS"
+[ dihedrals ]
+END  +PDMS  ++PDMS  +++PDMS  1    1.85    1.2    1 {"group": "END-PDMS"}
+
+[ link ]
+resname "PDMS|PDMSter"
+[ dihedrals ]
+PDMS  +PDMS  ++PDMS  +++END  1    1.85    1.2    1 {"group": "PDMS-END"}
+
+[ link ]
+[ atoms ]
+PDMS {"resname": "PDMS"}
+[ warning ]
+You should patch PDMS with a terminal residue. Use -seq PDMSter:1 PDMS:4 PDMSter:1
+[ non-edges ]
+PDMS +PDMS
+PDMS +END
+
+[ link ]
+[ atoms ]
+PDMS {"resname": "PDMS"}
+[ warning ]
+You should patch PDMS with a terminal residue. Use -seq PDMSter:1 PDMS:4 PDMSter:1
+[ non-edges ]
+PDMS -PDMS
+PDMS -END