Difference between revisions of "BbPlane"

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m (The Source)
(multistate support, simplification of vertex ordering)
Line 32: Line 32:
 
from chempy import cpv
 
from chempy import cpv
  
def bbPlane(objSel='(all)', color='white', transp=0.0):
+
def bbPlane(objSel='(all)', color='white', transp=0.0, state=1, name=None, quiet=1):
 
     """
 
     """
 
DESCRIPTION
 
DESCRIPTION
Line 45: Line 45:
 
   
 
   
 
     transp = float: transparency component (0.0--1.0) {default: 0.0}
 
     transp = float: transparency component (0.0--1.0) {default: 0.0}
 +
 +
    state = integer: object state, 0 for all states {default: 1}
 
   
 
   
 
NOTES
 
NOTES
Line 53: Line 55:
 
     # format input
 
     # format input
 
     transp = float(transp)
 
     transp = float(transp)
 +
    state, quiet = int(state), int(quiet)
 +
    if name is None:
 +
        name = cmd.get_unused_name("backbonePlane")
 +
 +
    if state < 0:
 +
        state = cmd.get_state()
 +
    elif state == 0:
 +
        for state in range(1, cmd.count_states(objSel)+1):
 +
            bbPlane(objSel, color, transp, state, name, quiet)
 +
        return
 +
 
     stored.AAs = []
 
     stored.AAs = []
 
     coords = dict()
 
     coords = dict()
Line 62: Line 75:
 
     for obj in cmd.get_object_list(objSel):
 
     for obj in cmd.get_object_list(objSel):
 
         sel = obj + " and (" + objSel + ")"
 
         sel = obj + " and (" + objSel + ")"
         for a in cmd.get_model(sel + " and n. CA").atom:
+
         for a in cmd.get_model(sel + " and n. CA", state).atom:
 
             key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
 
             key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
 
             stored.AAs.append(key)
 
             stored.AAs.append(key)
 
             coords[key] = [a.coord,None,None]
 
             coords[key] = [a.coord,None,None]
         for a in cmd.get_model(sel + " and n. O").atom:
+
         for a in cmd.get_model(sel + " and n. O", state).atom:
 
             key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
 
             key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
 
             if key in coords:
 
             if key in coords:
 
                 coords[key][1] = a.coord
 
                 coords[key][1] = a.coord
         for a in cmd.get_model("(hydro or n. CD) and nbr. (" + sel + " and n. N)").atom:
+
         for a in cmd.get_model(sel + " and ((n. N extend 1 and e. H) or (r. PRO and n. CD))", state).atom:
 
             key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
 
             key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
 
             if key in coords:
 
             if key in coords:
Line 104: Line 117:
 
         # need to order vertices to generate correct triangles for plane
 
         # need to order vertices to generate correct triangles for plane
 
         #      modified/added by B.Bell 8/18/2011
 
         #      modified/added by B.Bell 8/18/2011
         sumpos = cpv.add(pos[0], cpv.add(pos[1], cpv.add(pos[2], pos[3])))
+
         #      modified by Thomas Holder 2012
        centerpos = [ sumpos[0]/4., sumpos[1]/4., sumpos[2]/4. ]
+
        if cpv.dot_product(cpv.sub(pos[0], pos[1]), cpv.sub(pos[2], pos[3])) < 0:
        angles = [ [ 0., 0 ] ]
+
            vorder = [0,1,2,2,3,0]
        s00 = cpv.sub(pos[0], centerpos)
+
         else:
        for i in range(1,4):
+
             vorder = [0,1,2,3,2,1]
            s = cpv.sub(pos[i], centerpos)
+
 
            ang = cpv.get_angle(s00, s)
 
            angles.append( [ ang, i] )
 
         def sortfirst(a, b):
 
             return cmp(a[0], b[0])
 
        angles.sort(sortfirst)
 
        verts = map(lambda x: x[1], angles)
 
        vorder = [ verts[0], verts[1], verts[2],
 
                  verts[1], verts[3], verts[2] ]
 
 
         # fill in the vertex data for the triangles;  
 
         # fill in the vertex data for the triangles;  
 
         for i in vorder:
 
         for i in vorder:
Line 127: Line 132:
  
 
     # update the UI
 
     # update the UI
    newName =  cmd.get_unused_name("backbonePlane")
+
     cmd.load_cgo(obj, name, state)
     cmd.load_cgo(obj, newName)
+
     cmd.set("cgo_transparency", transp, name)
     cmd.set("cgo_transparency", transp, newName)
 
  
 
cmd.extend("bbPlane", bbPlane)
 
cmd.extend("bbPlane", bbPlane)

Revision as of 09:53, 26 January 2012

This script will draw a CGO plane between the backbone atoms of two neighboring residues. This is to show the planarity of the atoms. The image style this is meant to represent can be found many places, like "Introduction to Protein Structure" by Branden and Tooze (2nd ed. pp. 8).

Examples

# download the source and save as bbPlane.py
run bbPlane.py
fetch 1cll
# make planes for residues 4-9
bbPlane i. 4-10

The Source

#
# -- bbPlane.py - draws a CGO plane across the backbone atoms of
#                 neighboring amino acids
# 
# Author: Jason Vertrees, 06/2010
#   Modified by Thomas Holder, 06/2010
#   Modified by Blaine Bell, 08/2011
# Copyright (C) Schrodinger
# Open Source License: MIT
#
from pymol.cgo import *    # get constants
from pymol import cmd, stored
from chempy import cpv

def bbPlane(objSel='(all)', color='white', transp=0.0, state=1, name=None, quiet=1):
    """
DESCRIPTION
 
    Draws a plane across the backbone for a selection
 
ARGUMENTS
 
    objSel = string: protein object or selection {default: (all)}
 
    color = string: color name or number {default: white}
 
    transp = float: transparency component (0.0--1.0) {default: 0.0}

    state = integer: object state, 0 for all states {default: 1}
 
NOTES
 
    You need to pass in an object or selection with at least two
    amino acids.  The plane spans CA_i, O_i, N-H_(i+1), and CA_(i+1)
    """
    # format input
    transp = float(transp)
    state, quiet = int(state), int(quiet)
    if name is None:
        name = cmd.get_unused_name("backbonePlane")

    if state < 0:
        state = cmd.get_state()
    elif state == 0:
        for state in range(1, cmd.count_states(objSel)+1):
            bbPlane(objSel, color, transp, state, name, quiet)
        return

    stored.AAs = []
    coords = dict()

    # need hydrogens on peptide nitrogen
    cmd.h_add('(%s) and n. N' % objSel)

    # get the list of residue ids
    for obj in cmd.get_object_list(objSel):
        sel = obj + " and (" + objSel + ")"
        for a in cmd.get_model(sel + " and n. CA", state).atom:
            key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
            stored.AAs.append(key)
            coords[key] = [a.coord,None,None]
        for a in cmd.get_model(sel + " and n. O", state).atom:
            key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
            if key in coords:
                coords[key][1] = a.coord
        for a in cmd.get_model(sel + " and ((n. N extend 1 and e. H) or (r. PRO and n. CD))", state).atom:
            key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
            if key in coords:
                coords[key][2] = a.coord

    # need at least two amino acids
    if len(stored.AAs) <= 1:
        print "ERROR: Please provide at least two amino acids, the alpha-carbon on the 2nd is needed."
        return

    # prepare the cgo
    obj = [
        BEGIN, TRIANGLES,
        COLOR,
        ]
    obj.extend(cmd.get_color_tuple(color))

    for res in range(0, len(stored.AAs)-1):
        curIdx, nextIdx = str(stored.AAs[res]), str(stored.AAs[res+1])

        # populate the position array
        pos = [coords[curIdx][0], coords[curIdx][1], coords[nextIdx][2], coords[nextIdx][0]]

        # if the data are incomplete for any residues, ignore
        if None in pos:
            print 'peptide bond %s -> %s incomplete' % (curIdx, nextIdx)
            continue

        if cpv.distance(pos[0], pos[3]) > 4.0:
            print '%s and %s not adjacent' % (curIdx, nextIdx)
            continue

        # need to order vertices to generate correct triangles for plane
        #      modified/added by B.Bell 8/18/2011
        #      modified by Thomas Holder 2012
        if cpv.dot_product(cpv.sub(pos[0], pos[1]), cpv.sub(pos[2], pos[3])) < 0:
            vorder = [0,1,2,2,3,0]
        else:
            vorder = [0,1,2,3,2,1]

        # fill in the vertex data for the triangles; 
        for i in vorder:
            obj.append(VERTEX)
            obj.extend(pos[i])
           
    # finish the CGO
    obj.append(END)

    # update the UI
    cmd.load_cgo(obj, name, state)
    cmd.set("cgo_transparency", transp, name)

cmd.extend("bbPlane", bbPlane)