Package schrodinger :: Package protein :: Module getpdb_utility

Module getpdb_utility


Copy a PDB file out of the PDB directory, or, if not found, download it from the
rcsb repository: http://www.rcsb.org/pdb/files/.

Note: the location of the PDB directory can be specified via environment
variables; the order of precedence is:
 * SCHRODINGER_PDB
 * SCHRODINGER_THIRDPARTY
 * SCHRODINGER/thirdparty (the default)

Copyright Schrodinger, LLC. All rights reserved.

Classes

[hide private]

WholePDB
Class to take care of the file work for entire PDB files.

Chain
Class to handle splitting a chain out of a PDB file.

Code
Class to handle all the various files for each PDB code.

Functions

[hide private]

parse_arguments(args)

ez_print(message)
Prints a list of strings all on one line

invalid_code(acode)
Print a warning that a given code is invalid

download_format(pdb_code, file_format, chain=None)
Attemps to download the file of requested format for the given given PDB ID and (optinally) chain.

from_maestro(*args)

main(args)

Variables

[hide private]

__doc__ = ...

QtWidgets = None
hash(x)

ProxyPasswordManagerQt = None
hash(x)

current_dir = 'data/structures/divided/pdb/'

obsolete_dir = 'data/structures/obsolete/pdb/'

auto_write_lines = ['MODEL', 'ENDMDL', 'TITLE', 'REMARK']

error_code = 0
hash(x)

__package__ = 'schrodinger.protein'

Function Details

[hide private]

download_format(pdb_code, file_format, chain=None)

Attemps to download the file of requested format for the given given PDB ID and (optinally) chain.

Parameters:

pdb_code (str) - PDB ID of the file to download
file_format (str) - Format extention. One of: pdb, cif, xml, sf, fasta.
chain (str or None) - The chain name to download. If None, the file will contain all chains

Variables Details

[hide private]

doc

Value:

"""
Copy a PDB file out of the PDB directory, or, if not found, download i
t from the
rcsb repository: http://www.rcsb.org/pdb/files/.

Note: the location of the PDB directory can be specified via environme
nt
variables; the order of precedence is:
...