Ccp4 pisa: Difference between revisions

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{{Infobox script-repo
|type      = script
|filename  = ccp4_pisa.py
|author    = [[User:Dalyte|Gerhard Reitmayr and Dalia Daujotyte]]
|license  = GPL
}}
== Overview ==
== Overview ==


The script selects atoms from the list of the contacts found by PISA.
The script selects atoms from the list of the contacts found by PISA.
First, we run PISA on our pdb file to find the interfaces. Then by using the selectPISAContacts script in PyMOL we separately select atoms for all interface types and individual interfaces. This generates many selections, two for each interface, allowing quick manipulation of (sometimes) extensive lists in PISA log file.
First, we run PISA on our pdb file to find the interfaces. Then by using the ccp4_pisa script in PyMOL we separately select atoms for all interface types and individual interfaces. This generates many selections, two for each interface, allowing quick manipulation of (sometimes) extensive lists in PISA log file.
      
      
== Usage ==
== Usage ==


selectPISAContacts( pisafile )
ccp4_pisa( pisafile )




== Examples ==
== Example 1 ==


The script parses the XML output files from the PISA service or command line tool. A short description of how to download the XML output files is available here http://www.ebi.ac.uk/msd-srv/prot_int/pi_download.html.  
The script parses the XML output files from the PISA service or command line tool. A short description of how to download the XML output files is available here http://www.ebi.ac.uk/msd-srv/prot_int/pi_download.html.  
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(For example, the following URL downloads the interfaces in 2c7r.pdb http://www.ebi.ac.uk/pdbe/pisa/cgi-bin/interfaces.pisa?2c7r)
(For example, the following URL downloads the interfaces in 2c7r.pdb http://www.ebi.ac.uk/pdbe/pisa/cgi-bin/interfaces.pisa?2c7r)


Make sure you've run the selectPISAContacts script first.
Make sure you import the ccp4_pisa script first.
   
   
fetch 2c7r
{{Template:PymolScriptRepoDownload|examples/ccp4_pisa_1.pml}}
selectPISAContacts interfaces_2c7r.pisa
<include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/ccp4_pisa_1.pml" highlight="python" />
 
== The Code ==
<source lang="python">
from xml.etree import ElementTree
 
def parseElement( element ):
    """ creates a dict for the sub elements of the element"""
    result = { }
    for l in range(len(element)):
        if element[l].text != None:
            result[element[l].tag.strip()] = element[l].text.strip()
    return result;
 
def parseBond( elementDir ):
    """ puts bond information into tuples"""
    return ((elementDir['chain-1'], elementDir['seqnum-1'], elementDir['atname-1']), (elementDir['chain-2'], elementDir['seqnum-2'], elementDir['atname-2']))
 
def parseInterface( interface, bondname ):
    """ parses a single interface into the interface id, the two chain names connected
        and two lists of atoms for each chain"""
    bonds = interface.findall(bondname)
    id = interface.find('id').text.strip()
    if len(bonds) == 0:
        return None
    left = []
    right = []
    for b in bonds:
        l, r = parseBond(parseElement(b))
        left.append(l)
        right.append(r)
    left_chain = left[0][0]
    right_chain = right[0][0]
    if left_chain > right_chain:
        return id, (right_chain, left_chain), right, left
    return id, (left_chain, right_chain), left, right
 
def createSelectionList( atomlist ):
    """creates a PYMOL selection string for a list of atoms"""
    atomnames = [chain+'/'+res+'/'+atom for chain, res, atom in atomlist]
    return " or ".join(atomnames)
 
def createInterfaceSelection( interface, prefix ):
    """creates two selections for an interfaces"""
    id, e, l, r = interface
    leftname = prefix+'_' + str(id) + '_' + e[0] + e[1]
    rightname = prefix+'_' + str(id) + '_' + e[1] + e[0]
    if e[0] == e[1]:
        leftname = leftname + '1'
        rightname = rightname + '2'
    leftlist = createSelectionList(l)
    rightlist = createSelectionList(r)
    try:
        cmd.select(leftname, leftlist)
        cmd.select(rightname, rightlist)
    except:
        print leftname, '\t', leftlist
        print rightname, '\t', rightlist
    return leftname, rightname
 
def parsePISAContacts( filename ):
    """ parse a PISA contact file and create atoms selections for all interfaces
       
        For each interface, two selections are created containing the atoms of
        the interface on each chain. The selection names follow the convention
        bondtype_#Id_Chain1Chain2. If Chain1 equals Chain2 then the two selections are
        numbered.
       
        bondtype corresponds to h-bonds, salt-bridges, ss-bonds and cov-bonds and
        are marked with the prefixes hb, sb, ss and cov.
       
        For example, all h-bonds in interface 3 between chain A and D create the selections
        hb_3_AD and hb_3_DA.
       
        Salt-bridges in interface 4 between chain A and a symmetry copy of A creates the selections
        sb_4_AA1 and sb_4_AA2.
   
    PARAMS
        filename
            filename of the PISA contacts file
   
    RETURNS
        a set of selections in PYMOL.
 
    REPOSITORY
        https://github.com/GerhardR/pymol-scripts
 
    AUTHOR
        Gerhard Reitmayr and Dalia Daujotyte, 2011.
    """
   
    bond_types = [
        ('h-bonds', 'h-bonds/bond', 'hb'),
        ('salt-bridges', 'salt-bridges/bond', 'sb'),
        ('ss-bonds', 'ss-bonds/bond', 'ss'),
        ('cov-bonds', 'cov-bonds/bond', 'cv')
    ]
   
    tree = ElementTree.parse(open(filename))
    interfaces = tree.findall('//interface')
   
    result = []
    for name, path, prefix in bond_types:
        allcontacts = [edge for edge in [parseInterface(i, path) for i in interfaces] if edge != None]
       
        allselections = []
        for c in allcontacts:
            allselections.extend( createInterfaceSelection(c, prefix) )
       
        result.append(len(allselections)/2)
        if len(allselections) > 0:
            try:
                cmd.select(name, " or ".join(allselections))
            except:
                print name, '\t', " or ".join(allselections)
   
    print 'selectPISAContacts found interfaces with',
    for number, type in zip(result, bond_types):
        print number, type[0], ",",
 
try:
    cmd.extend("selectPISAContacts", parsePISAContacts)
except:
    # for debugging
    parsePISAContacts('../pisa/interfaces_2c7r.pisa')
</source>


== Code repository ==


The latest version of this script and related scripts is available at https://github.com/GerhardR/pymol-scripts.


[[Category:Script_Library]] [[Category:ThirdParty Scripts]] [[Category:Structural Biology Scripts]]
[[Category:Script_Library]]
[[Category:ThirdParty Scripts]]
[[Category:Structural Biology Scripts]]
[[Category:Pymol-script-repo]]

Latest revision as of 17:17, 13 February 2012

Type Python Script
Download ccp4_pisa.py
Author(s) Gerhard Reitmayr and Dalia Daujotyte
License GPL
This code has been put under version control in the project Pymol-script-repo

Overview

The script selects atoms from the list of the contacts found by PISA. First, we run PISA on our pdb file to find the interfaces. Then by using the ccp4_pisa script in PyMOL we separately select atoms for all interface types and individual interfaces. This generates many selections, two for each interface, allowing quick manipulation of (sometimes) extensive lists in PISA log file.

Usage

ccp4_pisa( pisafile )


Example 1

The script parses the XML output files from the PISA service or command line tool. A short description of how to download the XML output files is available here http://www.ebi.ac.uk/msd-srv/prot_int/pi_download.html.

(For example, the following URL downloads the interfaces in 2c7r.pdb http://www.ebi.ac.uk/pdbe/pisa/cgi-bin/interfaces.pisa?2c7r)

Make sure you import the ccp4_pisa script first.

Download: examples/ccp4_pisa_1.pml
This code has been put under version control in the project Pymol-script-repo

<include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/ccp4_pisa_1.pml" highlight="python" />

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