PairMap

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PairMap: An Intermediate Insertion Approach for Improving the Accuracy of Relative Free Energy Perturbation Calculations for Distant Compound Transformations

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# PairMap

PairMap is a comprehensive tool for the calculation of relative binding free energies in complex compound transformations. It involves the exhaustive generation of intermediates and the construction of intermediate-induced perturbation maps.

## Installation

```bash
conda install -c conda-forge lomap2
pip install .
```

## Dependencies

PairMap requires the following dependencies:

- lomap2
- networkx
- numpy
- rdkit>=2021.03.1
- tqdm

These dependencies will be automatically installed when you install PairMap using pip.

## Usage

### Intermediate Generation
```python
from pairmap import IntermediateGenerator
source_ligand = Chem.MolFromMolFile("/path/to/source_ligand.mol")
target_ligand = Chem.MolFromMolFile("/path/to/target_ligand.mol")

# Generate intermediates
searchIntm = SearchIntermediates(source_ligand, target_ligand)
intermediates = searchIntm.search()

# ligand preparation with openbabel and extract same formal charge
obabel_path = "/path/to/obabel"
intermediates_avail = execute_ligand_preparation(intermediates, obabel_path = obabel_path, extract_same_formal_charge=True)

# Generate map
mapGen = MapGenerator(intermediates_avail, maxPathLength=4, cycleLength=3, maxOptimalPathLength=3, jobs=-1)
mapGen.build_map()
```

### Intermediate Graph Generation

You can run the sample as follows:

```
python tests/test.py tests/intermediate_graph/TYK2/config.yaml
```

## Reference
Furui K, Shimizu T, Akiyama Y, Kimura SR, Terada Y, Ohue M. PairMap: An Intermediate Insertion Approach for Improving the Accuracy of Relative Free Energy Perturbation Calculations for Distant Compound Transformations. _Journal of Chemical Information and Modeling_, 65(2): 705-721, 2025. https://doi.org/10.1021/acs.jcim.4c01634

PairMap

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