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 readcex(file,*args): # Author: Scott Dixon
import os.path
standardResidues = ("ALA", "ARG", "ASP", "ASN", "ASX", "CYS", "GLY", "GLU",
"GLN", "HIS", "ILE", "LEU", "LYS", "MET", "PHE", "PRO",
"SER", "THR", "TYR", "TRP", "VAL", "HID", "HIE")
def childprop(tag, tree,_self=cmd):
try:
p = CEX.selectChildren(tree,tag)[0].value
if p[0] == '"': p = p[1:-1]
list = map(string.strip,string.split(p,";"))
return list
except IndexError:
return None
f = open(file,"r")
cs = CEX.CEXstream(f)
modelname = os.path.splitext(os.path.basename(file))[0] #get the base filename
if len(args) > 0: modelname = args[0]
while 1:
tree = CEX.readTree(cs)
if not tree: break
if tree.name == "$MOL":
smiles = tree.value
confs = CEX.selectChildren(tree,"XYZ")
try:
name = CEX.selectProperty(tree,"/NAM").value
except AttributeError:
name = ""
anames = childprop("ANAM", tree)
atypes = childprop("ATYPE", tree)
resnos = childprop("RESNO", tree)
resnames = childprop("RESNA", tree)
chains = childprop("CHAIN", tree)
occups = childprop("OCCUP", tree)
bvals = childprop("BVAL", tree)
pcharges = childprop("PCHARGE", tree)
rads = childprop("RAD", tree)
ligsites = childprop("SCORE", tree)
clusters = childprop("CLUSTER", tree)
parser = CEXpyParser()
try:
parser.parse(smiles)
except CEX.CEXsmilesError, data:
print data
break
parser.model.molecule.title = name
for at in parser.model.atom:
i = at.index
if anames: at.name = anames[i]
if resnames:
at.resn = resnames[i]
if at.resn in standardResidues: at.hetatm = 0
if resnos:
at.resi = resnos[i]
at.resi_number = int(resnos[i])
if chains: at.chain = chains[i]
if bvals: at.b = bvals[i]
if occups: at.q = occups[i]
if rads: at.vdw = rads[i]
if atypes: at.text_type = atypes[i]
if pcharges:
chg = pcharges[i]
if chg == "": chg = 0.0
at.partial_charge = float(chg)
if clusters:
at.resi = clusters[i]
at.resi_number = int(clusters[i])
if ligsites: at.b = ligsites[i]
for conf in confs:
if conf.value[0] == '"':
conf.value = conf.value[1:-1]
xyz = map(lambda x:string.split(x,","),string.split(conf.value,";"))
for at in parser.model.atom:
i = at.index
at.coord = [ float(xyz[i][0]), float(xyz[i][1]), float(xyz[i][2]) ]
cmd.load_model(parser.model,modelname,discrete=1,finish=0)
else:
pass
def readcex(file, *args): # Author: Scott Dixon
import os.path
standardResidues = ("ALA", "ARG", "ASP", "ASN", "ASX", "CYS", "GLY", "GLU",
"GLN", "HIS", "ILE", "LEU", "LYS", "MET", "PHE", "PRO",
"SER", "THR", "TYR", "TRP", "VAL", "HID", "HIE")
def childprop(tag, tree, _self=cmd):
try:
p = CEX.selectChildren(tree, tag)[0].value
if p[0] == '"': p = p[1:-1]
list = map(string.strip, string.split(p, ";"))
return list
except IndexError:
return None
f = open(file, "r")
cs = CEX.CEXstream(f)
modelname = os.path.splitext(
os.path.basename(file))[0] #get the base filename
if len(args) > 0: modelname = args[0]
while 1:
tree = CEX.readTree(cs)
if not tree: break
if tree.name == "$MOL":
smiles = tree.value
confs = CEX.selectChildren(tree, "XYZ")
try:
name = CEX.selectProperty(tree, "/NAM").value
except AttributeError:
name = ""
anames = childprop("ANAM", tree)
atypes = childprop("ATYPE", tree)
resnos = childprop("RESNO", tree)
resnames = childprop("RESNA", tree)
chains = childprop("CHAIN", tree)
occups = childprop("OCCUP", tree)
bvals = childprop("BVAL", tree)
pcharges = childprop("PCHARGE", tree)
rads = childprop("RAD", tree)
ligsites = childprop("SCORE", tree)
clusters = childprop("CLUSTER", tree)
parser = CEXpyParser()
try:
parser.parse(smiles)
except CEX.CEXsmilesError, data:
print data
break
parser.model.molecule.title = name
for at in parser.model.atom:
i = at.index
if anames: at.name = anames[i]
if resnames:
at.resn = resnames[i]
if at.resn in standardResidues: at.hetatm = 0
if resnos:
at.resi = resnos[i]
at.resi_number = int(resnos[i])
if chains: at.chain = chains[i]
if bvals: at.b = bvals[i]
if occups: at.q = occups[i]
if rads: at.vdw = rads[i]
if atypes: at.text_type = atypes[i]
if pcharges:
chg = pcharges[i]
if chg == "": chg = 0.0
at.partial_charge = float(chg)
if clusters:
at.resi = clusters[i]
at.resi_number = int(clusters[i])
if ligsites: at.b = ligsites[i]
for conf in confs:
if conf.value[0] == '"':
conf.value = conf.value[1:-1]
xyz = map(lambda x: string.split(x, ","),
string.split(conf.value, ";"))
for at in parser.model.atom:
i = at.index
at.coord = [
float(xyz[i][0]),
float(xyz[i][1]),
float(xyz[i][2])
]
cmd.load_model(parser.model, modelname, discrete=1, finish=0)
else:
pass
