mmtfPyspark.webservices.piscesDownloader module¶

piscesDownloader.py

This class downloads representative protein chains from the PISCES CulledPDB sets. A CulledPDB set is selected by specifying sequenceIdentity and resolution cutoff values from the following list:

sequenceIdentity = [20, 25, 30, 40, 50, 60, 70, 80, 90]
resolution = [1.6, 1.8, 2.0, 2.2, 2.5, 3.0]

References¶

PISCES: http://dunbrack.fccc.edu/PISCES.php
1. Wang and R. L. Dunbrack, Jr. PISCES: a protein sequence culling server. Bioinformatics, 19:1589-1591, 2003.

class PiscesDownloader(sequenceIdentity=0, resolution=0.0)[source]¶

Bases: object

Downloads representative protein chains from the PISCES CulledPDB sets. A CulledPDB set is selected by specifying sequenceIdentity and resolution cutoff values from the following lists: - sequenceIdentity = 20, 25, 30, 40, 50, 60, 70, 80, 90 - resolution = 1.6, 1.8, 2.0, 2.2, 2.5, 3.0

Attributes

sequenceIdentity	(int) sequence identity [0]
resoltion	(int) resoltion for pisces filter [0.0]

Methods

get_structure_chain_ids()

RESOLUTION_LIST = [1.6, 1.8, 2.0, 2.2, 2.5, 3.0]¶

SEQ_ID_LIST = [20, 25, 30, 40, 50, 60, 70, 80, 90]¶

URL = 'http://dunbrack.fccc.edu/Guoli/culledpdb_hh'¶

get_structure_chain_ids()[source]¶