""" This module provides methods for the conversion of cns atomnames in pseudoatomes and vice versa. The nomenclature of the pseudoatoms is in the same spirit as in: Markley et al. JMB 280, 933-952 (1998) Methods: Pseudo2Atom(atom) e.g. 'QA' -> 'ha#' 'QR' -> 'hd# or name he# or name hz' Pseudo2Tuple(atom) e.g. 'QA' -> ('ha#',) 'QR' -> ('hd#', 'he#', 'hz#') Atom2Pseudo(atomname, aminoacid) e.g. 'HB1', 'TYR' -> ('QB', ) 'HG11', 'VAL' -> ('QG1', 'QQG') Pseudo2IupacTuple(threelettercode, atomname) """ __author__ = "$Author: habeck $" __revision__ = "$Revision: 1.1 $" __date__ = "$Date: 2003/02/26 19:08:28 $" import re, string ############################################################################### def Pseudo2Atom(atom): """ converts pseudoatoms into a CNS readable format input: atom name (can be a pseudoatom) output: CNS readable atom name """ replacedic = {'QA': 'ha#', 'QB': 'hb#', 'QG': 'hg#', 'QG1': 'hg1#', 'QG2': 'hg2#', 'QQG': 'hg#', 'QD': 'hd#', 'QD1': 'hd1#', 'QD2': 'hd2#', 'QQD': 'hd#', 'QE': 'he#', 'QE2': 'he2#', 'QR': 'hd# or name he# or name hz', 'QZ': 'hz#', 'QH1': 'hh1#', 'QH2': 'hh2#'} atom = string.upper(atom) atom = string.strip(atom) if replacedic.has_key(atom): atom = replacedic[atom] return atom def Pseudo2IupacTuple(threelettercode, atomname): """ converting pseudoatoms into tuples of atomnames in IUPAC nomenclature input: atomname (in IUPAC nomenclature, but may contain pseudoatoms as specified in Markley et al. JMB 280, 933-952 (1998), may contain wildcards #?%*, may be without the final number in the atomname, e.g 'HB' instead of 'HB%') atomnamemust be a string! No tuples or lists! threelettercode must be a string, e.g. 'TRP' output: tuple of IUPAC atomnames, without wildcards the output is a tuple of strings! example: Pseudo2IupacTuple('ALA', 'HB%') returns the tuple of strings: ('HB1', 'HB2', 'HB3') Note: the strings threelettercode and atomname may be upper or lower case The returned atomname is ALWAYS upper case! """ #convert wildcards "#", "?", "*" to "%": atomname = re.sub('\#', '%', atomname) atomname = re.sub('\?', '%', atomname) atomname = re.sub('\*', '%', atomname) atomname = string.upper(atomname) atomname = string.strip(atomname) threelettercode = string.upper(threelettercode) threelettercode = string.strip(threelettercode) #define the dictionaries for the conversion: # some notes: # HZ in TYR is not included in pseudoatom QR # QD and QD2 are used in ASN # QE and QE2 are used in GLN # QD and QD1 are used in ILE replacedic = {'ALA': {'QB': ('HB1', 'HB2', 'HB3'),\ 'HB%': ('HB1', 'HB2', 'HB3'),\ 'HB': ('HB1', 'HB2', 'HB3')},\ 'ARG': {'QB': ('HB2', 'HB3'),\ 'HB%': ('HB2', 'HB3'),\ 'HB': ('HB2', 'HB3'),\ 'QG': ('HG2', 'HG3'),\ 'HG%': ('HG2', 'HG3'),\ 'HG': ('HG2', 'HG3'),\ 'QD': ('HD2', 'HD3'),\ 'HD%': ('HD2', 'HD3'),\ 'HD': ('HD2', 'HD3'),\ 'QH1': ('HH11', 'HH12'),\ 'HH1%':('HH11', 'HH12'),\ 'HH1': ('HH11', 'HH12'),\ 'QH2': ('HH21', 'HH22'),\ 'HH2%':('HH21', 'HH22'),\ 'HH2': ('HH21', 'HH22')},\ 'ASN': {'QB': ('HB2', 'HB3'),\ 'HB%': ('HB2', 'HB3'),\ 'HB': ('HB2', 'HB3'),\ 'QD2': ('HD21', 'HD22'),\ 'HD2%':('HD21', 'HD22'),\ 'HD2': ('HD21', 'HD22'),\ 'QD': ('HD21', 'HD22'),\ 'HD%': ('HD21', 'HD22'),\ 'HD': ('HD21', 'HD22')},\ 'ASP': {'QB': ('HB2', 'HB3'),\ 'HB%': ('HB2', 'HB3'),\ 'HB': ('HB2', 'HB3')},\ 'CYS': {'QB': ('HB2', 'HB3'),\ 'HB%': ('HB2', 'HB3'),\ 'HB': ('HB2', 'HB3')},\ 'CYC': {'QB': ('HB2', 'HB3'),\ 'HB%': ('HB2', 'HB3'),\ 'HB': ('HB2', 'HB3'),\ 'QG': ('HG2', 'HG3'),\ 'HG%': ('HG2', 'HG3'),\ 'HG': ('HG2', 'HG3')},\ 'GLN': {'QB': ('HB2', 'HB3'),\ 'HB%': ('HB2', 'HB3'),\ 'HB': ('HB2', 'HB3'),\ 'QG': ('HG2', 'HG3'),\ 'HG%': ('HG2', 'HG3'),\ 'HG': ('HG2', 'HG3'),\ 'QE2': ('HE21', 'HE22'),\ 'HE2%':('HE21', 'HE22'),\ 'HE2': ('HE21', 'HE22'),\ 'QE': ('HE21', 'HE22'),\ 'HE%': ('HE21', 'HE22'),\ 'HE': ('HE21', 'HE22'), },\ 'GLX': {'QB': ('HB2', 'HB3'),\ 'HB%': ('HB2', 'HB3'),\ 'HB': ('HB2', 'HB3'),\ 'QG': ('HG2', 'HG3'),\ 'HG%': ('HG2', 'HG3'),\ 'HG': ('HG2', 'HG3'),\ 'QE2': ('HE21', 'HE22'),\ 'HE2%':('HE21', 'HE22'),\ 'HE2': ('HE21', 'HE22'),\ 'QE': ('HE21', 'HE22'),\ 'HE%': ('HE21', 'HE22'),\ 'HE': ('HE21', 'HE22'), },\ 'GLU': {'QB': ('HB2', 'HB3'),\ 'HB%': ('HB2', 'HB3'),\ 'HB': ('HB2', 'HB3'),\ 'QG': ('HG2', 'HG3'),\ 'HG%': ('HG2', 'HG3'),\ 'HG': ('HG2', 'HG3')},\ 'GLY': {'QA': ('HA2', 'HA3'),\ 'HA%': ('HA2', 'HA3'),\ 'HA': ('HA2', 'HA3')},\ 'GLI': {'QA': ('HA2', 'HA3'),\ 'HA%': ('HA2', 'HA3'),\ 'HA': ('HA2', 'HA3')},\ 'HIS': {'QB': ('HB2', 'HB3'),\ 'HB%': ('HB2', 'HB3'),\ 'HB': ('HB2', 'HB3')}, 'ILE': {'QG1': ('HG12', 'HG13'),\ 'HG1%':('HG12', 'HG13'),\ 'HG1': ('HG12', 'HG13'),\ 'QG2': ('HG21', 'HG22', 'HG23'),\ 'HG2%':('HG21', 'HG22', 'HG23'),\ 'HG2': ('HG21', 'HG22', 'HG23'),\ 'QQG': ('HG12', 'HG13', 'HG21', 'HG22', 'HG23'),\ 'HG%': ('HG12', 'HG13', 'HG21', 'HG22', 'HG23'),\ 'HG': ('HG12', 'HG13', 'HG21', 'HG22', 'HG23'),\ 'QD1': ('HD11', 'HD12', 'HD13'),\ 'HD1%':('HD11', 'HD12', 'HD13'),\ 'HD1': ('HD11', 'HD12', 'HD13'),\ 'QD': ('HD11', 'HD12', 'HD13'),\ 'HD%': ('HD11', 'HD12', 'HD13'),\ 'HD': ('HD11', 'HD12', 'HD13')},\ 'LEU': {'QB': ('HB2', 'HB3'),\ 'HB%': ('HB2', 'HB3'),\ 'HB': ('HB2', 'HB3'),\ 'QD1': ('HD11', 'HD12', 'HD13'),\ 'HD1%':('HD11', 'HD12', 'HD13'),\ 'HD1': ('HD11', 'HD12', 'HD13'),\ 'QD2': ('HD21', 'HD22', 'HD23'),\ 'HD2%':('HD21', 'HD22', 'HD23'),\ 'HD2': ('HD21', 'HD22', 'HD23'),\ 'QQD': ('HD11', 'HD12', 'HD13', 'HD21', 'HD22', 'HD23'),\ 'HD%': ('HD11', 'HD12', 'HD13', 'HD21', 'HD22', 'HD23'),\ 'HD': ('HD11', 'HD12', 'HD13', 'HD21', 'HD22', 'HD23')},\ 'LYS': {'QB': ('HB2', 'HB3'),\ 'HB%': ('HB2', 'HB3'),\ 'HB': ('HB2', 'HB3'),\ 'QG': ('HG2', 'HG3'),\ 'HG%': ('HG2', 'HG3'),\ 'HG': ('HG2', 'HG3'),\ 'QD': ('HD2', 'HD3'),\ 'HD%': ('HD2', 'HD3'),\ 'HD': ('HD2', 'HD3'),\ 'QE': ('HE2', 'HE3'),\ 'HE%': ('HE2', 'HE3'),\ 'HE': ('HE2', 'HE3'),\ 'QZ': ('HZ1', 'HZ2', 'HZ3'),\ 'HZ%': ('HZ1', 'HZ2', 'HZ3'),\ 'HZ': ('HZ1', 'HZ2', 'HZ3')},\ 'NLE': {'QB': ('HB2', 'HB3'),\ 'HB%': ('HB2', 'HB3'),\ 'HB': ('HB2', 'HB3'),\ 'QG': ('HG2', 'HG3'),\ 'HG%': ('HG2', 'HG3'),\ 'HG': ('HG2', 'HG3'),\ 'QD': ('HD2', 'HD3'),\ 'HD%': ('HD2', 'HD3'),\ 'HD': ('HD2', 'HD3'),\ 'QE': ('HE1', 'HE2', 'HE3'),\ 'HE%': ('HE1', 'HE2', 'HE3'),\ 'HE': ('HE1', 'HE2', 'HE3')},\ 'MET': {'QB': ('HB2', 'HB3'),\ 'HB%': ('HB2', 'HB3'),\ 'HB': ('HB2', 'HB3'),\ 'QG': ('HG2', 'HG3'),\ 'HG%': ('HG2', 'HG3'),\ 'HG': ('HG2', 'HG3'),\ 'QE': ('HE1', 'HE2', 'HE3'),\ 'HE%': ('HE1', 'HE2', 'HE3'),\ 'HE': ('HE1', 'HE2', 'HE3')},\ 'PHE': {'QB': ('HB2', 'HB3'),\ 'HB%': ('HB2', 'HB3'),\ 'HB': ('HB2', 'HB3'),\ 'QD': ('HD1', 'HD2'),\ 'HD%': ('HD1', 'HD2'),\ 'HD': ('HD1', 'HD2'),\ 'QE': ('HE1', 'HE2'),\ 'HE%': ('HE1', 'HE2'),\ 'HE': ('HE1', 'HE2'),\ 'QR': ('HD1', 'HD2', 'HE1', 'HE2', 'HZ'),\ 'HR%': ('HD1', 'HD2', 'HE1', 'HE2', 'HZ'),\ 'HR': ('HD1', 'HD2', 'HE1', 'HE2', 'HZ')},\ 'PRO': {'QB': ('HB2', 'HB3'),\ 'HB%': ('HB2', 'HB3'),\ 'HB': ('HB2', 'HB3'),\ 'QG': ('HG2', 'HG3'),\ 'HG%': ('HG2', 'HG3'),\ 'HG': ('HG2', 'HG3'),\ 'QD': ('HD2', 'HD3'),\ 'HD%': ('HD2', 'HD3'),\ 'HD': ('HD2', 'HD3')},\ 'SER': {'QB': ('HB2', 'HB3'),\ 'HB%': ('HB2', 'HB3'),\ 'HB': ('HB2', 'HB3')},\ 'THR': {'QB': ('HB', ),\ 'HB%': ('HB', ),\ 'HB': ('HB', ),\ 'QG2': ('HG21', 'HG22', 'HG23'),\ 'HG2%':('HG21', 'HG22', 'HG23'),\ 'HG2': ('HG21', 'HG22', 'HG23')},\ 'TRP': {'QB': ('HB2', 'HB3'),\ 'HB%': ('HB2', 'HB3'),\ 'HB': ('HB2', 'HB3'),\ 'QG2': ('HG21', 'HG22', 'HG23'),\ 'HG2%':('HG21', 'HG22', 'HG23'),\ 'HG2': ('HG21', 'HG22', 'HG23')}, 'TYR': {'QB': ('HB2', 'HB3'),\ 'HB%': ('HB2', 'HB3'),\ 'HB': ('HB2', 'HB3'),\ 'QD': ('HD1', 'HD2'),\ 'HD%': ('HD1', 'HD2'),\ 'HD': ('HD1', 'HD2'),\ 'QE': ('HE1', 'HE2'),\ 'HE%': ('HE1', 'HE2'),\ 'HE': ('HE1', 'HE2'),\ 'QR': ('HD1', 'HD2', 'HE1', 'HE2'),\ 'HR%': ('HD1', 'HD2', 'HE1', 'HE2'),\ 'HR': ('HD1', 'HD2', 'HE1', 'HE2')},\ 'VAL': {'QG1': ('HG11', 'HG12', 'HG13'),\ 'HG1%':('HG11', 'HG12', 'HG13'),\ 'HG1': ('HG11', 'HG12', 'HG13'),\ 'QG2': ('HG21', 'HG22', 'HG23'),\ 'HG2%':('HG21', 'HG22', 'HG23'),\ 'HG2': ('HG21', 'HG22', 'HG23'),\ 'QQG': ('HG11', 'HG12', 'HG13', 'HG21', 'HG22', 'HG23'),\ 'HG%': ('HG11', 'HG12', 'HG13', 'HG21', 'HG22', 'HG23'),\ 'HG': ('HG11', 'HG12', 'HG13', 'HG21', 'HG22', 'HG23')}} if replacedic.has_key(threelettercode): if replacedic[threelettercode].has_key(atomname): atomname = replacedic[threelettercode][atomname] else: atomname = (atomname, ) else: atomname = (atomname, ) return atomname ############################################################################### def Pseudo2Tuple(atom): """ converts pseudoatoms into a tuple of atomnames in a CNS readable format input: atom name (can be a pseudoatom) output: tuple of CNS readable atoms """ replacedic = {'QA': ('ha#', ), 'QB': ('hb#', ), 'QG': ('hg#', ), 'QG1': ('hg1#', ), 'QG2': ('hg2#', ), 'QQG': ('hg#', ), 'QD': ('hd#', ), 'QD1': ('hd1#', ), 'QD2': ('hd2#', ), 'QQD': ('hd#', ), 'QE': ('he#', ), 'QE2': ('he2#', ), 'QR': ('hd#', 'he#', 'hz'), 'QZ': ('hz#', ), 'QH1': ('hh1#', ), 'QH2': ('hh2#', )} atom = string.upper(atom) atom = string.strip(atom) if replacedic.has_key(atom): atom = replacedic[atom] else: atom = (atom, ) return atom ############################################################################### def Atom2Pseudo(atomname, aminoacid): """ INPUT: cns atomname and aminoacid type in 3-letter code OUTPUT: returns a tuple of possible pseudoatoms, best hit comes first within the tuple if it is not possible to find a pseudoatom, an empty tuple will be returned The nomenclature of the pseudoatoms is in the same spirit as in: Markley et al. JMB 280, 933-952 (1998) easy: ALA, ASP, ASN, CYS, GLN, GLU, GLY, HIS, LYS, MET, PRO, SER, THR, TRP ambiguous: ARG: QH1, QH2 or QH ILE: QG1, QG2 or QQG LEU: QD1, QD2 or QQD PHE: QR TYR: QR VAL: QG1, QG2 or QQG """ pseudoatom = () aminoacid = string.upper(aminoacid) aminoacid = string.strip(aminoacid) atomname = string.upper(atomname) atomname = string.strip(atomname) if aminoacid == 'ALA': if atomname in ['HB1', 'HB2', 'HB3', 'HB%', 'HB#']: pseudoatom = ('QB', ) elif aminoacid == 'ARG': if atomname in ['HB1', 'HB2', 'HB3', 'HB%', 'HB#']: pseudoatom = ('QB', ) elif atomname in ['HG1', 'HG2', 'HG3', 'HG%', 'HG#']: pseudoatom = ('QG', ) elif atomname in ['HD1', 'HD2', 'HD3', 'HD%', 'HD#']: pseudoatom = ('QD', ) elif atomname in ['HH11', 'HH12', 'HH13', 'HH1%', 'HH1#']: pseudoatom = ('QH1', ) elif atomname in ['HH21', 'HH22', 'HH23', 'HH2%', 'HH2#']: pseudoatom = ('QH2', ) elif aminoacid == 'ASN': if atomname in ['HB1', 'HB2', 'HB3', 'HB%', 'HB#']: pseudoatom = ('QB', ) elif atomname in ['HD21', 'HD22', 'HD23', 'HD%', 'HD#']: pseudoatom = ('QD2', ) elif aminoacid == 'ASP': if atomname in ['HB1', 'HB2', 'HB3', 'HB%', 'HB#']: pseudoatom = ('QB', ) elif aminoacid == 'CYS': if atomname in ['HB1', 'HB2', 'HB3', 'HB%', 'HB#']: pseudoatom = ('QB', ) elif aminoacid == 'GLU': if atomname in ['HB1', 'HB2', 'HB3', 'HB%', 'HB#']: pseudoatom = ('QB', ) elif atomname in ['HG1', 'HG2', 'HG3', 'HG%', 'HG#']: pseudoatom = ('QG', ) elif aminoacid == 'GLN': if atomname in ['HB1', 'HB2', 'HB3', 'HB%', 'HB#']: pseudoatom = ('QB', ) elif atomname in ['HG1', 'HG2', 'HG3', 'HG%', 'HG#']: pseudoatom = ('QG', ) elif atomname in ['HE21', 'HE22', 'HE2%', 'HE2#']: pseudoatom = ('QE2', ) elif aminoacid == 'GLY': if atomname in ['HA1', 'HA2', 'HA3', 'HA%', 'HA#']: pseudoatom = ('QA', ) elif aminoacid == 'HIS': if atomname in ['HB1', 'HB2', 'HB3', 'HB%', 'HB#']: pseudoatom = ('QB', ) elif aminoacid == 'ILE': if atomname in ['HD11', 'HD12', 'HD13', 'HD1%', 'HD1#']: pseudoatom = ('QD1', ) elif atomname in ['HG11', 'HG12', 'HG13', 'HG1%', 'HG1#']: pseudoatom = ('QG1', 'QQG') elif atomname in ['HG21', 'HG22', 'HG23', 'HG2%', 'HG2#']: pseudoatom = ('QG2', 'QQG') elif atomname[:2] == 'HG': pseudoatom == ('QQG', 'QG1', 'QG2') elif aminoacid == 'LEU': if atomname in ['HB1', 'HB2', 'HB3', 'HB%', 'HB#']: pseudoatom = ('QB', ) elif atomname in ['HD11', 'HD12', 'HD13', 'HD1%', 'HD1#']: pseudoatom = ('QD1', 'QQD') elif atomname in ['HD21', 'HD22', 'HD23', 'HD2%', 'HD2#']: pseudoatom = ('QD2', 'QQD') elif atomname[:2] == 'HD': pseudoatom = ('QQD', 'QD1', 'QD2') elif aminoacid == 'LYS': if atomname in ['HB1', 'HB2', 'HB3', 'HB%', 'HB#']: pseudoatom = ('QB', ) elif atomname in ['HG1', 'HG2', 'HG3', 'HG%', 'HG#']: pseudoatom = ('QG', ) elif atomname in ['HD1', 'HD2', 'HD3', 'HD%', 'HD#']: pseudoatom = ('QD', ) elif atomname in ['HE1', 'HE2', 'HE3', 'HE%', 'HE#']: pseudoatom = ('QE', ) elif atomname in ['HZ1', 'HZ2', 'HZ3', 'HZ%', 'HZ#']: pseudoatom = ('QZ', ) elif aminoacid == 'MET': if atomname in ['HB1', 'HB2', 'HB3', 'HB%', 'HB#']: pseudoatom = ('QB', ) elif atomname in ['HG1', 'HG2', 'HG3', 'HG%', 'HG#']: pseudoatom = ('QG', ) elif atomname in ['HE1', 'HE2', 'HE3', 'HE%', 'HE#']: pseudoatom = ('QE', ) elif aminoacid == 'PHE': if atomname in ['HB1', 'HB2', 'HB3', 'HB%', 'HB#']: pseudoatom = ('QB', ) elif atomname in ['HD1', 'HD2', 'HD3', 'HD%', 'HD#']: pseudoatom = ('QD', 'QR') elif atomname in ['HE1', 'HE2', 'HE3', 'HE%', 'HE#']: pseudoatom = ('QE', 'QR') elif aminoacid == 'PRO': if atomname in ['HB1', 'HB2', 'HB3', 'HB%', 'HB#']: pseudoatom = ('QB', ) elif atomname in ['HG1', 'HG2', 'HG3', 'HG%', 'HG#']: pseudoatom = ('QG', ) elif atomname in ['HD1', 'HD2', 'HD3', 'HD%', 'HD#']: pseudoatom = ('QD', ) elif aminoacid == 'SER': if atomname in ['HB1', 'HB2', 'HB3', 'HB%', 'HB#']: pseudoatom = ('QB', ) elif aminoacid == 'THR': if atomname in ['HG21', 'HG22', 'HG23', 'HG2%', 'HG2#']: pseudoatom = ('QG2', ) elif aminoacid == 'TRP': if atomname in ['HB1', 'HB2', 'HB3', 'HB%', 'HB#']: pseudoatom = ('QB', ) elif aminoacid == 'TYR': if atomname in ['HB1', 'HB2', 'HB3', 'HB%', 'HB#']: pseudoatom = ('QB', ) elif atomname in ['HD1', 'HD2', 'HD3', 'HD%', 'HD#']: pseudoatom = ('QD', 'QR') elif atomname in ['HE1', 'HE2', 'HE3', 'HE%', 'HE#']: pseudoatom = ('QE', 'QR') elif aminoacid == 'VAL': if atomname in ['HG11', 'HG12', 'HG13', 'HG1%', 'HG1#']: pseudoatom = ('QG1', 'QQG') elif atomname in ['HG21', 'HG22', 'HG23', 'HG2%', 'HG2#']: pseudoatom = ('QG2', 'QQG') elif pseudoatom[:2] == 'HG': pseudoatom = ('QQG', 'QG1', 'QG2') return pseudoatom ############################################################################### #test code: if __name__ == "__main__": print 'testing module:\n' print " converting ('TYR', 'QR,) to:", Pseudo2IupacTuple('tyr', 'QR') print " should be IUPAC nomenclature..." print '\nciao.'