AmberPrepParser¶
-
class
biskit.
AmberPrepParser
(f_in=None)[source]¶ Bases:
object
Parse Amber Residue libraries (off or prep files) which are usually found in amber/dat/leap/prep.
Usage:
p = AmberOffParser( 'all_amino03.in' ) residues = [ r for r in p.residueTypes() ]
Returns AmberResidue instances that can be handled like a PDBModel although the xyz array contains relative Z-coordinates not real cartesian ones. Atom profiles of the AmberResidue instance include:
- charge … atomic partial charge (float)
- name … atom name (str)
- amber_type … Amber atom type (str)
Methods Overview
__init__
param f_in: amber “off” or “prep” file with residue definitions if not existing, we will look for a file with this name in the Biskit data folder (data/amber/residues) (default: ‘all_amino03.in’) :type f_in: str atomLines
param s: str, atom block createResidue
parseCharges
parseResidue
param s: str, residue record residueBlocks
residueDict
return: dict, residue types indexed by 3-letter residue code, example: {‘ala’:[AmberResidueType ALA], ‘cys’:[…} residueTypes
Attributes Overview
F_DEFAULT
AmberPrepParser Method & Attribute Details