ccp4_contact.py

'''
See more here: http://www.pymolwiki.org/index.php/ccp4_contact

    ccp4_contact -- parses CCP4/CONTACT log file and selects residues and atoms.
    http://www.ccp4.ac.uk/html/contact.html
 
    PARAMS
        contactsfile
            filename of the CCP4/CONTACT log file
 
        selName1
            the name prefix for the _res and _atom selections returned for the
            source set of chain
 
        selName2
            the name prefix for the _res and _atom selections returned for the 
            target set of chain
 
    RETURNS
        4 selections of interface residues and atoms are created and named
        depending on what you passed into selName1 and selName2
 
    REPOSITORY
        https://github.com/GerhardR/pymol-scripts
 
    AUTHOR
        Gerhard Reitmayr and Dalia Daujotyte, 2011.
'''
from pymol import cmd
import re
 
def parseCONTACTContacts( f ):
    # Lys    24A  ca  Asp   263D  CG   ...  4.94    [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
    conParser = re.compile("(\S*)\s*(\d+)([A-Z])\s*(\w+)")
    s1 = []
    s2 = []
    for line in f:
        if line.startswith('#'):
            continue
        matches = conParser.findall(line)
        if len(matches) == 2:
            s1.append(matches[0])
            s2.append(matches[1])
        elif len(matches) == 1:
            s2.append(matches[0])
 
    return (s1, s2)
 
def ccp4_contact( contactsfile, selName1 = "source", selName2 = "target" ):
    # read and parse contacts file into two lists of contact atoms and contact pair list
    s1, s2 = parseCONTACTContacts(open(contactsfile))
 
    # create a selection for the first contact list
 
    # create the PYMOL selection macros for the residues 
    resNames = [chain+"/"+residue+"/" for (type, residue, chain, atom) in s1]
    # put them in a set to remove duplicates and then join with 'or'
    resSel = " or ".join(frozenset(resNames))
    # finally select them under the new name
    cmd.select(selName1 + "_res", resSel)
 
    atomNames = [chain+"/"+residue+"/"+atom for (type, residue, chain, atom) in s1]
    atomSel = " or ".join(frozenset(atomNames))
    cmd.select(selName1 + "_atom", atomSel)
 
    # create a selection for the second contact list
 
    resNames = [chain+"/"+residue+"/" for (type, residue, chain, atom) in s2]
    resSel = " or ".join(frozenset(resNames))
    cmd.select(selName2 + "_res", resSel)
 
    atomNames = [chain+"/"+residue+"/"+atom for (type, residue, chain, atom) in s2]
    atomSel = " or ".join(frozenset(atomNames))
    cmd.select(selName2 + "_atom", atomSel)
 
cmd.extend("ccp4_contact", ccp4_contact)