kartograf 0.5.2

Kartograf is a package for mapping geometrically atoms of two molecules. (like you need it with hybrid topology)

Kartograf: A 3D Atom Graph Mapper

Kartograf offers a geometric atom mapper approach, that allows to map a given set of ligand coordinates. (can be used for hybrid topology RBFE calculations) This package can be used standalone, or from the OpenFE environment.

More will be here soon!

Usage

from rdkit import Chem
from kartograf.atom_align import align_mol_shape
from kartograf import KartografAtomMapper, SmallMoleculeComponent

#Preprocessing from Smiles - Here you can add your Input!
# Generate Data: START
smiles = ["c1ccccc1", "c1ccccc1(CO)"]
rdmols = [Chem.MolFromSmiles(s) for s in smiles]
rdmols = [Chem.AddHs(m, addCoords=True) for m in rdmols]
[Chem.rdDistGeom.EmbedMolecule(m, useRandomCoords=False, randomSeed = 0) for m in rdmols]
# Generate Data: END

# Build Small Molecule Components
molA, molB = [SmallMoleculeComponent.from_rdkit(m) for m in rdmols]

# Align the mols first - this might not needed, depends on input.
a_molB = align_mol_shape(molB, ref_mol=molA)


# Build Kartograf Atom Mapper
mapper = KartografAtomMapper(atom_map_hydrogens=True)

# Get Mapping
kartograf_mapping = next(mapper.suggest_mappings(molA, a_molB))

kartograf_mapping

Installation

you can install Kartograf via the package manager of your choice:

pip install kartograf

conda install -c conda-forge kartograf

Or use Kartograf from the OpenFE Environment (soon).

For Developing Kartograf, you might want to use this approach:

git clone https://github.com/OpenFreeEnergy/kartograf.git

cd kartograf
conda env create -f environment.yml

conda activate kartograf
pip install .

References