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