Difference between revisions of "Renumber"

Type	Python Module
Download	renumber.py
Author(s)	Thomas Holder
License	BSD-2-Clause
	This code has been put under version control in the project Pymol-script-repo

Revision as of 05:44, 1 February 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

@@ Line 1: / Line 1: @@
+{{Infobox script-repo
+|type      = module
+|filename  = renumber.py
+|author    = [[User:Speleo3|Thomas Holder]]
+|license   = BSD-2-Clause
+}}
 [[renumber]] sets new residue numbers (resi) for a polymer based on connectivity.
@@ Line 13: / Line 20: @@
 # renumber polymer, first 27 residues of Q8N2U3_HUMAN missing.
 renumber chain A, 28
-</syntaxhighlight>
-== The Script ==
-<syntaxhighlight lang="python">
-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
 </syntaxhighlight>

Difference between revisions of "Renumber"

Revision as of 05:44, 1 February 2012

Example

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