Lomap

The Lead Optimization Mapper (LOMAP) is an automated algorithm for planning efficient relative free energy calculation networks across a set of ligands, built on freely available tools such as RDKit. With the optional gufe dependency installed, it also integrates with the Open Free Energy ecosystem. The method is described in the original LOMAP publication.

Installation

lomap is available on conda-forge as the lomap2 package. See the installation documentation for install instructions, including the development install and optional dependencies (gufe and pygraphviz).

Quickstart

This example uses LOMAP's optional gufe bindings to load two example ligands bundled with the package and plan a perturbation network between them with the default atom mapper and scorer.

# requires the optional `gufe` dependency (see Installation)
import importlib.resources

import lomap
from gufe import SmallMoleculeComponent

# Two example ligands ship with the package under lomap.tests.data
data = importlib.resources.files("lomap.tests.data")
ligands = [
    SmallMoleculeComponent.from_sdf_file(data / name)
    for name in ["lig_41.sdf", "lig_74.sdf"]
]

# Build a LigandNetwork using LOMAP's scoring and network-construction rules
network = lomap.generate_lomap_network(
    ligands=ligands,
    mappers=lomap.LomapAtomMapper(),
    scorer=lomap.default_lomap_score,
)
print(f"{len(network.nodes)} ligands, {len(network.edges)} edges")

For proposing individual mappings, customising edge scores, and the full set of network options, see the documentation.

Authors

See AUTHORS.md.

History

Open Free Energy took over maintenance of LOMAP in 2022. The original development repository has since been archived, but can be found at https://github.com/MobleyLab/Lomap.