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Difference between revisions of "CreateAtom"
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<source lang="python"> | <source lang="python"> | ||
import cmd | import cmd | ||
| − | from chempy import models | + | from chempy import models, cpv |
""" | """ | ||
| Line 42: | Line 42: | ||
def calculateNewPoint(p1, p2, distance): | def calculateNewPoint(p1, p2, distance): | ||
| − | v1 = cpv.sub(p1, p2) | + | v1 = cpv.normalize(cpv.sub(p1, p2)) |
| − | return cpv.add( | + | return cpv.add(p1, cpv.scale(v1, distance)) |
def makeAtom(index, atomDetails, chain): | def makeAtom(index, atomDetails, chain): | ||
| Line 60: | Line 60: | ||
cmd.extend("createAtomAlongBond", createAtomAlongBond) | cmd.extend("createAtomAlongBond", createAtomAlongBond) | ||
</source> | </source> | ||
| + | [[Category:Biochemical_Scripts]] | ||
| + | [[Category:Script_Library]] | ||
Latest revision as of 01:21, 28 March 2014
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)