API Documentation

Molecular Systems

openpharmacophore.Protein(topology, coords)

Represents a protein and optionally its different structures if it comes from a MD trajectory.

openpharmacophore.Ligand(mol)

Represents a ligand.

openpharmacophore.ComplexBindingSite(...)

Class to extract and find chemical features in the binding site of a protein-ligand complex.

Pharmacophores

openpharmacophore.PharmacophoricPoint(...[, ...])

Class to store pharmacophoric points of any feature type.

openpharmacophore.Pharmacophore([points, ...])

A PharmacophoricPoint container.

openpharmacophore.LigandBasedPharmacophore(ligands)

Class to store and extract pharmacophores from a set of ligands.

openpharmacophore.LigandReceptorPharmacophore(...)

Class to store, and extract pharmacophores from protein-ligand complexes.

Visualization

openpharmacophore.Viewer()

Class to visualize molecular systems and pharmacophores.

openpharmacophore.draw_ligands(ligands, ...)

Draw multiple ligands

openpharmacophore.draw_ligands_chem_feats(...)

Draw the ligands with their chemical features highlighted.

File IO

openpharmacophore.io.pharmacophore_reader.read_mol2(...)

Loads pharmacophores from a mol2 file.

openpharmacophore.io.pharmacophore_reader.read_ph4(...)

Loads a pharmacophore from a MOE ph4 file.

openpharmacophore.io.pharmacophore_reader.read_json(...)

Loads a pharmacophore from a json file

openpharmacophore.io.pharmacophore_reader.read_ligandscout(...)

Reads a ligandscout pharmacophore (pml) file.

openpharmacophore.io.pharmacophore_writer.save_mol2(...)

Save several pharmacophores to a mol2 file.

openpharmacophore.io.pharmacophore_writer.save_ph4(...)

Save a pharmacophore to a ph4 (MOE) file.

openpharmacophore.io.pharmacophore_writer.save_json(...)

Save a pharmacophore to a JSON file.

openpharmacophore.io.pharmacophore_writer.save_pml(...)

Save a pharmacophore to a pml (Ligand Scout) file.

openpharmacophore.io.mol_files.read_mol2(...)

Load molecules from a mol2 file.

openpharmacophore.io.mol_files.mol2_supplier(...)

A molecule generator for mol2 files.

openpharmacophore.io.mol_files.read_sdf(...)

Load an sdf file with molecules that may contain multiple conformers.

Virtual Screening

openpharmacophore.VirtualScreening(...)

Class to perform virtual screening with pharmacophores.

openpharmacophore.screening.mol_db.InMemoryMolDB()

A repository of molecules that are stored in memory.

openpharmacophore.screening.mol_db.MolDB()

A repository of molecules that are stored in files or file like objects.

Others

openpharmacophore.load(file_name[, ...])

Load ligands, protein, protein-ligand complexes, or MD trajectories from a file.

openpharmacophore.load_ligands(ligands, form)

Load ligands from a list of SMILES, SMARTS, Inchi, Mol2 block or PDB block.

openpharmacophore.smiles_from_pdb_id(pdb_id)

Obtain a smiles from a ligand pdb id.