CreateAtom - Revision history

Pyadmin: 5 revisions

2014-03-28T01:21:16Z

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New page

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: <pre>createAtomAlongBond("gly", 3, 23, "H", 23, "N", "O")</pre>.

<source lang="python">
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)
</source>
[[Category:Biochemical_Scripts]]
[[Category:Script_Library]]

Gilleain at 16:05, 23 October 2008

2008-10-23T16:05:03Z

Gilleain at 08:35, 22 October 2008

2008-10-22T08:35:21Z

Gilleain at 08:32, 22 October 2008

2008-10-22T08:32:48Z

Gilleain: New page: 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 load...

2008-10-20T12:31:13Z

New page: 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 load...

New page

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: <pre>createAtomAlongBond("gly", 3, 23, "H", 23, "N", "O")</pre>.

<source lang="python">
import cmd
from chempy import models, protein_residues

"""
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'] = "GLY"
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.sub(p1, p2)
return cpv.add(p2, 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)
</source>

@@ Line 42: / Line 42: @@
 def calculateNewPoint(p1, p2, distance):
-     v1 = cpv.sub(p1, p2)
+     v1 = cpv.normalize(cpv.sub(p1, p2))
-     return cpv.add(p2, cpv.scale(v1, distance))
+     return cpv.add(p1, cpv.scale(v1, distance))
 def makeAtom(index, atomDetails, chain):

@@ Line 5: / Line 5: @@
 <source lang="python">
 import cmd
-from chempy import models, protein_residues, cpv
+from chempy import models, cpv
 """

@@ Line 5: / Line 5: @@
 <source lang="python">
 import cmd
-from chempy import models, protein_residues
+from chempy import models, protein_residues, cpv
 """
@@ Line 23: / Line 23: @@
          # the details of the new atom
          atomDetails = {}
-         atomDetails['residueName'] = "GLY"
+         atomDetails['residueName'] = "HOH"
          atomDetails['residueNumber'] = "1"
          atomDetails['symbol'] = "O"