This module defines classes and functions to fetch, parse, and write structural data files, execute structural analysis programs, and to access and search structural databases, e.g. ProteinDataBank.
You can use following functions to manage PDB file resources:
Following functions can be used to handle local PDB files:
Blast search PDB¶
The following are for blast searching PDB content.
PDB clusters biopolymer chains using blast weekly. These clusters can be retrieved using the following functions. Using cluster data is as good as blast searching PDB most of the time and incredibly faster always.
Parse/write PDB files¶
Following ProDy functions are for parsing and writing
.pqr format is similar to
.pdb format, following
functions come as bonus features:
Following functions allow editing structures using structural data from PDB header records:
PDB header data¶
Use the following to parse and access header data in PDB files:
Following function can be used to fetch meta data on PDB ligands:
fetchPDBLigand()- retrieve ligand from Ligand-Expo
Following functions can be used to match, align, and map polypeptide chains:
Following functions can be used to adjust alignment parameters:
Following functions can be used to execute DSSP structural analysis program and/or parse results:
Following functions can be used to execute STRIDE structural analysis program and/or parse results: