synkit 0.0.2__tar.gz → 0.0.4__tar.gz

{synkit-0.0.2 → synkit-0.0.4}/.github/workflows/test-and-lint.yml

@@ -34,7 +34,7 @@ jobs:
       run: |
         conda create --name synkit-env python=3.11 -y
         conda activate synkit-env
-        conda install -c jakobandersen -c conda-forge mod
+        conda install -c jakobandersen -c conda-forge mod>=0.17
         pip install flake8 pytest
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
       shell: bash -l {0}

{synkit-0.0.2 → synkit-0.0.4}/.gitignore

@@ -8,4 +8,11 @@ test_mod.py
 test_format.py
 *dev_zone
 *.pkl.gz
-dev_scripts/*
+dev_scripts/*
+*.pdf
+out
+summary
+Data/Benchmark/its.json.gz
+Data/Benchmark/rc.json.gz
+*.log
+.coverage

synkit-0.0.4/CHANGELOG.md

@@ -0,0 +1,89 @@
+
+# Changelog v0.0.4
+
+## Highlights
+
+### New Features & Enhancements
+
+#### Refactor Source Code Structure
+- **Merged** the ITS and Graph subpackages for improved modularity.
+- **Separated** `its_decompose` and `get_rc` into a dedicated Python file: `its_decompose.py`.
+- **Created** a new `Utils` subpackage for future utility functions and support tools.
+
+#### Performance Improvements
+- **Optimized** the `BatchCluster` process for faster clustering of reaction centers.
+
+#### Bug Fixes
+- **Fixed** issues with *Subgraph* searching: `networkx` now handles both *monomorphism* and *induced subgraph*, whereas `GML` was limited to *monomorphism* only.
+
+#### New Features
+- **Implemented** `CRN` (Chemical Reaction Networks) in the `Reactor` module.
+- **Implemented** `PathFinder` to find pathways from a starting compound to the target compound in `CRN`.
+- **Introduced** `RetroReactor` in the `Rule` module, enabling the use of A* algorithm to search from target to starting compound without requiring a full system like `CRN`.
+
+## Known Limitations
+
+### Rule Composition
+- **Bug** in the valence constraint of rule composition.
+- **Partial matching** in rule composition may result in invalid compounds.
+
+### Retro
+- **Directed CRN** can only find one solution, though it is 500 times faster than expanding CRN and using `PathFinder`.
+- **Retro framework** using rule composition may result in invalid compounds.
+
+### Reactor
+- `ReactorEngine` currently only supports **balanced reactions**.
+- **Performance issue**: `ReactorEngine` is slow in certain cases.
+- **Memory leak** in `CoreEngine` when scaled up.
+
+
+
+
+# Changelog v0.0.3
+
+## Highlights
+
+### New Features & Enhancements
+
+#### Reduce Dependency and Update Version
+- Removed dependency on `drfp` and `rxnmapper`.
+- Updated versions of `numpy` and `torch` to 2.2.0.
+
+#### Enhance `Reactor`
+- `CoreEngine` and `ReactorEngine` have consistent function `_inference`.
+- `CoreEngine` is refractored to handle reagents.
+
+#### Add Visualization
+- Added visualization for Double Pushout rules.
+
+#### Graph Isomorphism and Subgraph Isomorphism
+- Separated graph and rule morphism.
+- Implemented subgraph isomorphism in `networkx` and `gml`.
+- Added WL hash function to filter graphs before doing isomorphism check; does not work for subgraph isomorphism.
+
+#### Chemical Conversion
+- Added function to add implicit and explicit hydrogen.
+- Enhanced conversion capabilities, now can handle both implicit and explicit hydrogen effectively.
+- Added new functions for conversion between ITS and GML.
+
+#### Atom-Atom Map
+- Added `FixAAM` to handle AAM generated by MOD.
+- `ReactorEngine` now works well to generate complete AAM from partial AAM, but only in good AAM cases.
+- Fixed `Normalize` class issue of removing hydrogen without adding the implicit hydrogen to the graph. Now it is compatible with RDKit.
+
+#### Rule
+- Fixed issue of memory leakage when doing rule composition by adding argument `add=False` to `ruleGMLString`.
+
+## Known Limitations
+
+### BatchCluster
+- The processing speed of `BatchCluster` is slower compared to `GraphCluster`. There may be an internal issue affecting performance.
+
+### Reactor
+- `ReactorEngine` currently only works with balanced reactions.
+- `ReactorEngine` performs slowly in a few cases.
+- `CoreEngine` exhibited memory leak when scaled up.
+
+### Subgraph Isomorphism
+- For `networkx` version, it performs very fast with filter, ~0.7s for searching 1 subgraph along with 33,000 graphs, however, the result is not correct ~330 subgraphs are incorrect.
+- For `GML` version, it performs perfectly, but slow ~8s for searching 1 subgraph along with 33,000 graphs.