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#REDIRECT [[pdb retain ids]]
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[[renumber]] sets new residue numbers (resi) for a polymer based on connectivity.
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== Example ==
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This examples takes a pdb structure with insertion codes and sets a new, linear numbering based on [http://www.uniprot.org/uniprot/Q8N2U3_HUMAN Q8N2U3_HUMAN].
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<syntaxhighlight lang="python">
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fetch 1h4w, async=0
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# move everything which is not polymer to another chain
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alter not polymer, chain="B"
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# renumber polymer, first 27 residues of Q8N2U3_HUMAN missing.
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renumber chain A, 28
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</syntaxhighlight>
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== The Script ==
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<syntaxhighlight lang="python">
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from pymol import cmd, CmdException
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def renumber(selection='all', start=1, startsele=None, quiet=1):
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    '''
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DESCRIPTION
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    Set residue numbering (resi) based on connectivity.
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ARGUMENTS
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    selection = string: atom selection to renumber {default: all}
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    start = integer: counting start {default: 1}
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    startsele = string: residue to start counting from {default: first in
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    selection}
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    '''
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    start, quiet = int(start), int(quiet)
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    model = cmd.get_model(selection)
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    cmd.iterate(selection, 'atom_it.next().model = model',
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            space={'atom_it': iter(model.atom)})
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    if startsele is not None:
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        startidx = cmd.index('first (' + startsele + ')')[0]
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        for atom in model.atom:
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            if (atom.model, atom.index) == startidx:
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                startatom = atom
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                break
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        else:
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            print ' Error: startsele not in selection'
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            raise CmdException
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    else:
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        startatom = model.atom[0]
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    for atom in model.atom:
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        atom.adjacent = []
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        atom.visited = False
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    for bond in model.bond:
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        atoms = [model.atom[i] for i in bond.index]
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        atoms[0].adjacent.append(atoms[1])
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        atoms[1].adjacent.append(atoms[0])
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    def traverse(atom, resi):
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        atom.resi = resi
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        atom.visited = True
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        for other in atom.adjacent:
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            if other.visited:
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                continue
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            if (atom.name, other.name) in [('C','N'), ("O3'", 'P')]:
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                traverse(other, resi+1)
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            elif (atom.name, other.name) in [('N','C'), ('P', "O3'")]:
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                traverse(other, resi-1)
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            elif (atom.name, other.name) not in [('SG', 'SG')]:
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                traverse(other, resi)
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    traverse(startatom, start)
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    cmd.alter(selection, 'resi = atom_it.next().resi',
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            space={'atom_it': iter(model.atom)})
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cmd.extend('renumber', renumber)
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# vi:expandtab:smarttab
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</syntaxhighlight>
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== See Also ==
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* [[alter]]
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* [[rename]]
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* [[pdb_retain_ids]]
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[[Category:Script_Library]]

Revision as of 10:31, 31 January 2012

renumber sets new residue numbers (resi) for a polymer based on connectivity.

Example

This examples takes a pdb structure with insertion codes and sets a new, linear numbering based on Q8N2U3_HUMAN.

fetch 1h4w, async=0

# move everything which is not polymer to another chain
alter not polymer, chain="B"

# renumber polymer, first 27 residues of Q8N2U3_HUMAN missing.
renumber chain A, 28

The Script

from pymol import cmd, CmdException

def renumber(selection='all', start=1, startsele=None, quiet=1):
    '''
DESCRIPTION

    Set residue numbering (resi) based on connectivity.

ARGUMENTS

    selection = string: atom selection to renumber {default: all}

    start = integer: counting start {default: 1}

    startsele = string: residue to start counting from {default: first in
    selection}
    '''
    start, quiet = int(start), int(quiet)
    model = cmd.get_model(selection)
    cmd.iterate(selection, 'atom_it.next().model = model',
            space={'atom_it': iter(model.atom)})
    if startsele is not None:
        startidx = cmd.index('first (' + startsele + ')')[0]
        for atom in model.atom:
            if (atom.model, atom.index) == startidx:
                startatom = atom
                break
        else:
            print ' Error: startsele not in selection'
            raise CmdException
    else:
        startatom = model.atom[0]
    for atom in model.atom:
        atom.adjacent = []
        atom.visited = False
    for bond in model.bond:
        atoms = [model.atom[i] for i in bond.index]
        atoms[0].adjacent.append(atoms[1])
        atoms[1].adjacent.append(atoms[0])
    def traverse(atom, resi):
        atom.resi = resi
        atom.visited = True
        for other in atom.adjacent:
            if other.visited:
                continue
            if (atom.name, other.name) in [('C','N'), ("O3'", 'P')]:
                traverse(other, resi+1)
            elif (atom.name, other.name) in [('N','C'), ('P', "O3'")]:
                traverse(other, resi-1)
            elif (atom.name, other.name) not in [('SG', 'SG')]:
                traverse(other, resi)
    traverse(startatom, start)
    cmd.alter(selection, 'resi = atom_it.next().resi',
            space={'atom_it': iter(model.atom)})

cmd.extend('renumber', renumber)

# vi:expandtab:smarttab

See Also