Updates for 1.4.0 release #17
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Codecov ReportAttention: Patch coverage is
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## main #17 +/- ##
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- Coverage 68.79% 68.73% -0.06%
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Files 21 24 +3
Lines 2416 2911 +495
Branches 427 539 +112
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+ Hits 1662 2001 +339
- Misses 680 828 +148
- Partials 74 82 +8 ☔ View full report in Codecov by Sentry. |
CKannas
reviewed
Mar 12, 2024
CHANGELOG.md
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| ### Features | ||
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| - Adding support reading and processing routes |
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| - Adding support reading and processing routes | |
| - Adding support for reading and processing routes |
CHANGELOG.md
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| ### Trivial changes | ||
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| - Making help for pipeline runner more simple |
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| - Making help for pipeline runner more simple | |
| - Making help for pipeline runner simpler |
docs/routes.rst
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| ------- | ||
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| The simplest route format supported is a text file, where each reaction is written as a reaction SMILES on a line. | ||
| Routes are separated by comma |
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We say that routes are separated by comma but below with separate them with a new line.
docs/routes.rst
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| Reading | ||
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| The simplest route format supported is a text file, where each reaction is written as a reaction SMILES on a line. |
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This should match the information from read_reaction_lists docstring.
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| The simplest route format supported is a text file, where each reaction is written as a reaction SMILES on a line. | |
| The simplest route format supported is a text file, where each reaction is written as a reaction SMILES in a line. |
docs/routes.rst
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| The last line of code also make sure that the second route shares mapping with the first route. | ||
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| Othe readers are available |
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| Othe readers are available | |
| Other readers are available |
rxnutils/routes/base.py
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| class SynthesisRoute: | ||
| """ | ||
| This encapsulates a synthesis route or a reaction tree. | ||
| It provide convinient methods for assigning atom-mapping |
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| It provide convinient methods for assigning atom-mapping | |
| It provides convenient methods for assigning atom-mapping |
rxnutils/routes/base.py
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| It is typically initiallized by one of the readers in the | ||
| `rxnutils.routes.readers` module. | ||
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| The tree depth and the forward step is automatically assigned |
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| The tree depth and the forward step is automatically assigned | |
| The tree depth and the forward step are automatically assigned |
rxnutils/routes/base.py
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| ) -> None: | ||
| """ | ||
| Assign atom-mapping to each reaction in the route and | ||
| ensure that is is consistent from root compound and throughout |
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| ensure that is is consistent from root compound and throughout | |
| ensure that is consistent from root compound and throughout |
rxnutils/routes/base.py
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| """ | ||
| Returns linear sequences or chains extracted from the route. | ||
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| Each chain is a list of a dictionary representing the molecules, only the most |
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| Each chain is a list of a dictionary representing the molecules, only the most | |
| Each chain is a list of dictionaries representing the molecules, only the most |
rxnutils/routes/readers.py
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| def _transform_retrosynthesis_atom_mapping(tree_dict: Dict[str, Any]) -> None: | ||
| """ | ||
| Routes output from AiZynth has atom-mapping from the template-based model, |
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| Routes output from AiZynth has atom-mapping from the template-based model, | |
| Routes output from AiZynth have atom-mapping from the template-based model, |
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@CKannas - fixed your remarks |
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