yypdb
Command line PDB query and access
Features
Search the PDB for molecular, methodological, genomic, chemical, strucutral, ontological, and taxonomical information using site-side REST search services and XML query. See usage for instructions (--help).
Usage
YYPDB
FETCH SERVICES:
usage: yypdb [flags] [str]
--vb verbose mode
--molid [PDBID] get molecule info
--head [PDBID] get header info
--seq [PDBID.A.B.C ...] --clr --hi get amino acid sequence for each chain;
use colors based on amino acid type;
highlight (nonpolar,polar,positive,negative,aromatic)
--lig [PDBID] get ligand info
--go [PDBID] get gene associated ontology info
--grab [PDBID] save pbd file to local directory
SEARCH SERVICES:
usage: yypdb [optional verbose] --search [search type] [params]
--vb verbose mode
title [str] search PDBIDs by title
author [str] search PDBIDs by citation author
organism [str] search PDBIDs by associated organism
seqMotif --motif [str] search PDBIDs by sequence filter
revisionDate --min [y-m-d] --max [y-m-d]
search PDBIDs by revision dates
releaseDate --min [y-m-d] --max [y-m-d]
search PDBIDs by release dates
macromolecu:wle --protein [y/n] --DNA [y/n] --RNA [y/n]
--hybrid [y/n] serach PDBIDs by macromolecule type
chainNum --assembly [asymmetric/biological]
--min [min] --max [max] search PDBIDs by number of chains
entNum --min [min] --max [max] search PDBIDs by entity number
binding --min [min] --max[max] search PDBIDS by ki binding affinity
chemName --name [str] --target [str] --polymerType [str]
search PDBIDs by chemical subcomponent
Aside (Please Read)
Why Perl? I like Perl. And first/foremost this is meant to a commandline tool. Whether it is used to simply retrieve information from the PDB without leaving the terminal, log information to file, or it plays a role in a chain of UNIX tools or scripts, I hope that it finds some use.
The PDB and and some of the third party resources it may use are for public use. Please avoid spamming XML requests or making unduly large requests. Continued behaviors such as this will prompt your requests to moved to a slower access lane or outright blocked for a temporary time. Please respect the use of these generous libraries. Enjoy!
Dependencies
- Perl 5
- wget
- LibXML