bbPlane.py

'''
http://pymolwiki.org/index.php/bbPlane

Draws a CGO plane across the backbone atoms of neighboring amino acids

Author: Jason Vertrees, 06/2010
  Modified by Thomas Holder, 2010-2012
  Modified by Blaine Bell, 08/2011

(c) 2010 Schrodinger

License: MIT
'''

from pymol import cmd


def bbPlane(selection='(all)', color='gray', transp=0.3, state=-1, name=None, quiet=1):
    """
DESCRIPTION

    Draws a plane across the backbone for a selection

ARGUMENTS

    selection = 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)
    """
    from pymol.cgo import BEGIN, TRIANGLES, COLOR, VERTEX, END
    from pymol import cgo
    from chempy import cpv

    # 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(selection) + 1):
            bbPlane(selection, color, transp, state, name, quiet)
        return

    AAs = []
    coords = dict()

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

    # get the list of residue ids
    for obj in cmd.get_object_list(selection):
        sel = obj + " and (" + selection + ")"
        for a in cmd.get_model(sel + " and n. CA", state).atom:
            key = '/%s/%s/%s/%s' % (obj, a.segi, a.chain, a.resi)
            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(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,
    ]

    for res in range(0, len(AAs) - 1):
        curIdx, nextIdx = str(AAs[res]), str(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:
            if not quiet:
                print(' bbPlane: peptide bond %s -> %s incomplete' % (curIdx, nextIdx))
            continue

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

        normal = cpv.normalize(cpv.cross_product(
            cpv.sub(pos[1], pos[0]),
            cpv.sub(pos[2], pos[0])))

        obj.append(cgo.NORMAL)
        obj.extend(normal)

        # need to order vertices to generate correct triangles for plane
        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, zoom=0)
    cmd.set("cgo_transparency", transp, name)
    cmd.color(color, name)

cmd.extend("bbPlane", bbPlane)

# tab-completion of arguments
cmd.auto_arg[0]['bbPlane'] = cmd.auto_arg[1]['color']
cmd.auto_arg[1]['bbPlane'] = cmd.auto_arg[0]['color']

# vi:expandtab