CreateAtom
From PyMOLWiki
A script to create an atom C at a point some distance d from a pair of atoms (A, B), along the line of the bond A-B. The main function takes a modelName (usually, the name of the file loaded, like "1pqr" or "peptide"), a distance, and some parameters to identify the atoms A, B.
Use like:createAtomAlongBond("gly", 3, 23, "H", 23, "N", "O").
import cmd from chempy import models, cpv """ Create an atom at a distance 'distance' along the bond between atomA and atomB """ def createAtomAlongBond(modelName, distance, resiA, atomNameA, resiB, atomNameB, atomNameC): model = cmd.get_model(modelName) p1 = getAtomCoords(model, str(resiA), atomNameA) p2 = getAtomCoords(model, str(resiB), atomNameB) if p1 is None: print "atom not found!", modelName, resiA, atomNameA elif p2 is None: print "atom not found!", modelName, resiB, atomNameB else: p3 = calculateNewPoint(p1, p2, distance) # the details of the new atom atomDetails = {} atomDetails['residueName'] = "HOH" atomDetails['residueNumber'] = "1" atomDetails['symbol'] = "O" atomDetails['name'] = atomNameC atomDetails['coords'] = p3 # make an atom with index n+1 and chain "X" newAtom = makeAtom(model.nAtom + 1, atomDetails, "X") model.add_atom(newAtom) model.update_index() cmd.load_model(model, "newpeptide") def getAtomCoords(model, resi, atomName): for a in model.atom: if a.resi == resi and a.name == atomName: return a.coord return None def calculateNewPoint(p1, p2, distance): v1 = cpv.normalize(cpv.sub(p1, p2)) return cpv.add(p1, cpv.scale(v1, distance)) def makeAtom(index, atomDetails, chain): atom = chempy.Atom() atom.index = index atom.name = atomDetails['name'] atom.symbol = atomDetails['symbol'] atom.resn = atomDetails['residueName'] atom.chain = chain atom.resi = atomDetails['residueNumber'] atom.resi_number = int(atomDetails['residueNumber']) atom.coord = atomDetails['coords'] atom.hetatm = False return atom cmd.extend("createAtomAlongBond", createAtomAlongBond)
