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#
# $Id: pKa_utility_functions.py 361 2007-05-06 11:44:10Z nielsen $
#
# pKa utility functions
#
# Copyright (C) Jens Erik Nielsen, EMBL 2000, UCSD/HHMI 2002-2003
# University College Dublin 2003 -
# All rights reserved
#
#
# Routines for getting WHAT IF residue identifiers
#
def getWI_resid(line):
#
# Take a WHAT IF line of the form:
# Residue: 1 LYS ( 1 ) (Prp= 1.00)
#
# and return a unique resid
#
import string
split=string.split(line)
residuename=split[2]
last=string.split(line,'(')[1]
number=string.split(last,')')[0]
if len(string.strip(string.split(last,')')[1]))>0:
chainID=string.split(string.split(last,')')[1])[0]
else:
chainID=''
number=string.strip(number)
resid='%s:%4s:%3s' %(chainID,string.zfill(number,4),residuename)
return resid
def getWI_resid2(line,format=None):
"""
Convert a WHAT IF line of the form:
43 ASP ( 43 ) xxxxxx
or
182 SER ( 182 ) A
and return a unique resid
If format is pdb2pka, then just return the line"""
import string
if format=='pdb2pka':
return string.strip(line.split(' ')[0])
#
# WHAT IF format
#
split=string.split(line)[:-1]
line=string.join(split)
#
# Line reformatted
#
residuename=split[1]
last=string.split(line,'(')[1]
number=string.split(last,')')[0]
last_part=string.strip(string.split(last,')')[1])
last_split=string.split(last_part)
if len(last_split)==1:
chainID=last_split[0]
else:
chainID=''
number=string.strip(number)
resid='%s:%4s:%3s' %(chainID,string.zfill(number,4),residuename)
return resid
def getWI_resid3(line):
#
# Take a WHAT IF line of the form:
# Residue: 1 THR 1 A Prp= 0.00
# and return a unique resid
#
import string
split=string.split(line)
residuename=split[2]
number=split[3]
cid=split[4]
chainID=''
if len(cid)==1:
chainID=cid
else:
chainID=''
number=string.strip(number)
resid='%s:%4s:%3s' %(chainID,string.zfill(number,4),residuename)
return resid
def getWI_resid4(line):
#
# Take a WHAT IF line of the form:
# 1 THR ( 1 ) N xxxxxxx
# and return a unique resid
#
import string
#
# First trim the string
#
line=string.join(string.split(line.strip())[:-1])
#
# Now the line looks like: 1 THR ( 1 ) N
#
split=string.split(line)
atomname=split[-1]
residuename=split[1]
last=string.split(line,'(')[1]
number=string.strip(string.split(last,')')[0])
# Chain ID
laststrip=string.strip(last)
lastsplit=string.split(last,')')[1]
split_lastsplit=string.split(lastsplit)
if len(split_lastsplit)>1:
chainID=split_lastsplit[0]
else:
chainID=''
resid='%s:%4s:%3s:%s' %(chainID,string.zfill(number,4),residuename,atomname)
return resid
#
# -----
#
def get_resid(uniqueid):
import string
return string.join(string.split(uniqueid,':')[:2],':')
def get_resnum(uniqueid):
import string
# Given a uniqueid this function returns the residue number
return string.split(uniqueid,':')[1]
def get_resname(uniqueid):
import string
return string.split(uniqueid,':')[2]
def get_chainid(self,uniqueid):
import string
return string.split(uniqueid,':')[0]
def is_terminal(uniqueid):
#
# Is this residue a terminal titratable group?
#
if string.split(uniqueid,':')[-1]=='TERM':
return 1
return None
acidbase={'ARG':1,'HIS':1,'LYS':1,'TYR':-1,'ASP':-1,'GLU':-1,'CYS':-1,'CTERM':-1,'NTERM':1,'SER':-1,'THR':-1}
charged=['ARG','LYS','HIS','ASP','GLU']
def is_normally_titratable(uniqueid):
"""Does this group have a pKa value in the range 2-12"""
type=uniqueid.split(':')[-1]
if istitratable(uniqueid) and type!='SER' and type!='THR':
return 1
return None
def is_titratable(uniqueid):
return istitratable(uniqueid)
def istitratable(uniqueid):
import string
type=string.split(uniqueid,':')[-1]
if type in acidbase:
return 1
else:
return None
def is_charged(uniqueid):
import string
type=string.split(uniqueid,':')[-1]
if type in charged:
return 1
return None
def isacid(uniqueid):
#
# Is the residue a base or an acid?
#
import string
type=string.split(uniqueid,':')[-1]
val=acidbase[type]
if val==-1:
return 1
return None
def acibas(uniqueid):
#
# Return -1 (acid) or 1 (base)
#
if isacid(uniqueid):
return -1
return 1
def reformat_name(oldname,Nterm=None,format='WHAT IF'):
#
# Reformat the residue names
#
if format=='WHAT IF':
import copy
residue=copy.copy(oldname)
newname=''
Tflag=None
if residue[0]=='T':
Tflag=1
residue=residue[1:]
number=residue[:4]
name=residue[4:7]
chainID=''
if len(residue)==8:
chainID=residue[7]
newname='%s:%4s:%3s' %(chainID,number,name)
if Tflag:
#
# Nterm is 1 for an Nterm and 0 for a Cterm
#
if Nterm==1:
newname=newname+':NTERM'
else:
newname=newname+':CTERM'
else:
import string
return string.strip(oldname)
return newname
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