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)
def fromList(self, molList):
model = Indexed()
# read header information
model.molecule.title = string.strip(molList[0])
model.molecule.dim_code = string.strip(molList[1][20:22])
model.molecule.comments = string.strip(molList[2])
try:
model.molecule.chiral = int(molList[3][12:15])
except:
model.molecule.chiral = 0
nAtom = int(molList[3][0:3])
nBond = int(molList[3][3:6])
# read atoms
nameDict = {}
irec = 4
cnt = 0
for a in range(nAtom):
at = Atom()
at.index = cnt
at.coord = [
float(molList[irec][0:10]),
float(molList[irec][10:20]),
float(molList[irec][20:30])
]
at.symbol = string.strip(molList[irec][31:33])
try:
at.stereo = int(molList[irec][39:42])
except:
at.stereo = 0
chg = int(molList[irec][36:39])
if chg > 0: chg = 4 - chg
at.formal_charge = chg
model.atom.append(at)
irec = irec + 1
cnt = cnt + 1
# read bonds
for a in range(nBond):
bnd = Bond()
bnd.index = [
int(molList[irec][0:3]) - 1,
int(molList[irec][3:6]) - 1
]
bnd.order = int(molList[irec][6:9])
try:
bnd.stereo = int(molList[irec][9:12])
except:
bnd.stereo = 0
model.bond.append(bnd)
irec = irec + 1
# obtain formal charges from M CHG record
while molList[irec][0:6] != 'M END':
if molList[irec][0:6] == 'M CHG':
cl = string.split(string.strip(molList[irec][6:]))
cll = int(cl[0]) * 2
a = 1
while a <= cll:
model.atom[int(cl[a]) - 1].formal_charge = int(cl[a + 1])
a = a + 2
irec = irec + 1
if irec >= len(molList): break
return model
def fromList(self,molList):
model = Indexed()
# read header information
model.molecule.title = string.strip(molList[0])
model.molecule.dim_code = string.strip(molList[1][20:22])
model.molecule.comments = string.strip(molList[2])
try:
model.molecule.chiral = int(molList[3][12:15])
except:
model.molecule.chiral = 0
nAtom = int(molList[3][0:3])
nBond = int(molList[3][3:6])
# read atoms
nameDict = {}
irec = 4
cnt = 0
for a in range(nAtom):
at = Atom()
at.index = cnt
at.coord = [float(molList[irec][0:10]),
float(molList[irec][10:20]),float(molList[irec][20:30])]
at.symbol = string.strip(molList[irec][31:33])
try:
at.stereo = int(molList[irec][39:42])
except:
at.stereo = 0
chg=int(molList[irec][36:39])
if chg>0: chg=4-chg
at.formal_charge = chg
model.atom.append(at)
irec = irec + 1
cnt = cnt + 1
# read bonds
for a in range(nBond):
bnd = Bond()
bnd.index = [ int(molList[irec][0:3])-1,int(molList[irec][3:6])-1 ]
bnd.order = int(molList[irec][6:9])
try:
bnd.stereo = int(molList[irec][9:12])
except:
bnd.stereo = 0
model.bond.append(bnd)
irec = irec+1
# obtain formal charges from M CHG record
while molList[irec][0:6]!='M END':
if molList[irec][0:6]=='M CHG':
cl = string.split(string.strip(molList[irec][6:]))
cll = int(cl[0])*2
a=1
while a<=cll:
model.atom[int(cl[a])-1].formal_charge=int(cl[a+1])
a=a+2
irec =irec+1
if irec >= len(molList): break
return model
