Index

A

add() (openpharmacophore.Pharmacophore method) add_chem_feats() (openpharmacophore.Viewer method) add_components() (openpharmacophore.Viewer method) add_conformers() (openpharmacophore.Ligand method)

add_hydrogens() (openpharmacophore.Ligand method) (openpharmacophore.Protein method) add_pharmacophore() (openpharmacophore.Viewer method) add_pharmacophores() (openpharmacophore.VirtualScreening static method) atoms_at_distance() (openpharmacophore.Protein method)

C

ComplexBindingSite (class in openpharmacophore)

concatenate() (openpharmacophore.Protein method)

D

draw() (openpharmacophore.Ligand method)

draw_ligands() (in module openpharmacophore) draw_ligands_chem_feats() (in module openpharmacophore)

E

extract() (openpharmacophore.LigandBasedPharmacophore method) (openpharmacophore.LigandReceptorPharmacophore method)

extract_chain() (openpharmacophore.Protein method)

F

fix_bond_order() (openpharmacophore.Ligand method) from_file() (openpharmacophore.screening.mol_db.MolDB method) from_file_list() (openpharmacophore.screening.mol_db.MolDB method)

from_rdkit() (openpharmacophore.screening.mol_db.InMemoryMolDB method) from_smiles() (openpharmacophore.screening.mol_db.InMemoryMolDB method) from_string() (openpharmacophore.Ligand class method)

G

generate_conformers() (openpharmacophore.Ligand method) get_atoms() (openpharmacophore.ComplexBindingSite method) get_chem_feats() (openpharmacophore.ComplexBindingSite method) (openpharmacophore.Ligand method)

get_chem_feats_with_directionality() (openpharmacophore.Ligand method) get_conformer() (openpharmacophore.Ligand method) get_ligand() (openpharmacophore.Protein method) get_residues() (openpharmacophore.ComplexBindingSite method) get_valid_features() (openpharmacophore.PharmacophoricPoint static method)

H

has_aromatic_bonds() (openpharmacophore.Ligand method) has_chem_feats (openpharmacophore.Viewer property) has_double_bonds() (openpharmacophore.Ligand method)

has_hydrogens (openpharmacophore.Ligand property) has_ligand (openpharmacophore.Viewer property) has_pharmacophore (openpharmacophore.Viewer property) has_protein (openpharmacophore.Viewer property)

I

InMemoryMolDB (class in openpharmacophore.screening.mol_db)

L

lig_id (openpharmacophore.Ligand property) Ligand (class in openpharmacophore) LigandBasedPharmacophore (class in openpharmacophore)

LigandReceptorPharmacophore (class in openpharmacophore) load() (in module openpharmacophore) load_component() (openpharmacophore.Viewer method) load_ligands() (in module openpharmacophore)

M

mol2_supplier() (in module openpharmacophore.io.mol_files)

MolDB (class in openpharmacophore.screening.mol_db)

P

Pharmacophore (class in openpharmacophore)

PharmacophoricPoint (class in openpharmacophore) Protein (class in openpharmacophore)

R

read_json() (in module openpharmacophore.io.pharmacophore_reader) read_ligandscout() (in module openpharmacophore.io.pharmacophore_reader) read_mol2() (in module openpharmacophore.io.mol_files) (in module openpharmacophore.io.pharmacophore_reader) read_ph4() (in module openpharmacophore.io.pharmacophore_reader)

read_sdf() (in module openpharmacophore.io.mol_files) remove() (openpharmacophore.Pharmacophore method) remove_all_ligands() (openpharmacophore.Protein method) remove_ligand() (openpharmacophore.Protein method) remove_solvent_and_ions() (openpharmacophore.Protein method)

S

save_json() (in module openpharmacophore.io.pharmacophore_writer) save_mol2() (in module openpharmacophore.io.pharmacophore_writer) save_ph4() (in module openpharmacophore.io.pharmacophore_writer) save_pml() (in module openpharmacophore.io.pharmacophore_writer)

screen() (openpharmacophore.VirtualScreening method) set_protein_style() (openpharmacophore.Viewer method) show() (openpharmacophore.Viewer method) slice() (openpharmacophore.Protein method) smiles_from_pdb_id() (in module openpharmacophore)

T

to_matrix() (openpharmacophore.Pharmacophore method) to_nglview() (openpharmacophore.Viewer method)

to_rdkit() (openpharmacophore.ComplexBindingSite method) (openpharmacophore.Ligand method)

V

Viewer (class in openpharmacophore)

VirtualScreening (class in openpharmacophore)