Compounds Analysis

This module defines classes and functions to fetch, parse, and write structural data files associated with compounds and to access and search structural databases, e.g. ProteinDataBank.

Ligand data

The following function can be used to fetch metadata on PDB ligands:

fetchPDBLigand() - retrieve ligand from Ligand-Expo

BIRD data

The following functions can be used to fetch metadata from the Biologically Interesting Reference Dictionary (BIRD) for peptide-like ligands:

fetchBIRDviaFTP() - retrieve BIRD data from PDB

parseBIRD() - parse BIRD data for a particular compound or family

CCD data

The following function can be used to fetch metadata from the Chemical Component Dictionary (CCD) for residues within ligands:

parseCCD() - parse CCD data for a particular component

Functions

The following functions can be used to calculate 2D similarity using Morgan Fingerprints:

calc2DSimilarity() - calculate 2D similarity for a pair of SMILES

calc2DSimilarityMatrix() - calculate 2D similarity matrix for a collection of SMILES