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

__init__(f_in=None)[source]
Parameters:f_in (str) – 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’)
atomLines(s)[source]
Parameters:s – str, atom block
parseResidue(s)[source]
Parameters:s – str, residue record
createResidue(res, atoms)[source]
residueDict()[source]
Returns:dict, residue types indexed by 3-letter residue code, example: {‘ala’:[AmberResidueType ALA], ‘cys’:[…}