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util.py
# pymol

from chempy import Bond
import copy
import random

# cap gaps in chain as aldehydes and neutral amines...
# (for instance, when

def cap(object):
    from pymol import cmd
    
    model = cmd.get_model(object)
    # guarantee identical ordering
    cmd.delete(object)
    cmd.load_model(model,object)
    n_list = cmd.identify("(n;n &!(n;c a;2.0))")
    c_list = cmd.identify("(n;c &!(n;n a;2.0))")
    print n_list
    print c_list
    for a in n_list:
        newat = copy.deepcopy(model.atom[a])
        newat.coord = [
            newat.coord[0] + random.random(),
            newat.coord[1] + random.random(),
            newat.coord[2] + random.random(),
            ]
        newat.symbol = 'H'
        newat.name = 'HN'
        newat.numeric_type = 43
        bond = Bond()
        bond.order = 1
        bond.stereo = 0
        bond.index = [ a, model.nAtom ]
        print "adding",newat.name,bond.index
        model.add_atom(newat)
        model.add_bond(bond)
    for a in c_list:
        newat = copy.deepcopy(model.atom[a])
        newat.coord = [
            newat.coord[0] + random.random(),
            newat.coord[1] + random.random(),
            newat.coord[2] + random.random(),
            ]
        newat.symbol = 'H'
        newat.name = 'HC'
        newat.numeric_type = 41
        bond = Bond()
        bond.order = 1
        bond.stereo = 0
        bond.index = [ a, model.nAtom ]
        print "adding",newat.name,bond.index
        model.add_atom(newat)
        model.add_bond(bond)
    # reload
    cmd.delete(object)
    cmd.load_model(model,object)
    cmd.sort(object)
    


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