def categorizeVariables(variable_names):
categories = DictWithDefault([])
for name in variable_names:
words = (name.split('_'))
try:
c = _category[words[-1]]
except KeyError:
c = ''
if c:
categories[c].append(name)
for list in categories.values():
list.sort()
if categories.has_key('energy'):
list = categories['energy']
for variable in ['kinetic_energy', 'potential_energy']:
if variable in list:
list.remove(variable)
list = [variable] + list
categories['energy'] = list
return categories
def categorizeVariables(variable_names):
categories = DictWithDefault([])
for name in variable_names:
words = string.split(name, '_')
try:
c = _category[words[-1]]
except KeyError:
c = ''
if c:
categories[c].append(name)
for list in categories.values():
list.sort()
if categories.has_key('energy'):
list = categories['energy']
for variable in ['kinetic_energy', 'potential_energy']:
if variable in list:
list.remove(variable)
list = [variable] + list
categories['energy'] = list
return categories
def findHydrogenPositions(self):
"""Find reasonable positions for hydrogen atoms that have no
position assigned.
This method uses a heuristic approach based on standard geometry
data. It was developed for proteins and DNA and may not give
good results for other molecules. It raises an exception
if presented with a topology it cannot handle."""
self.setBondAttributes()
try:
unknown = DictWithDefault([])
for a in self.atoms:
if a.position() is None:
if a.symbol != 'H':
raise ValueError, 'position of ' + a.fullName() + \
' is undefined'
bonded = a.bondedTo()[0]
unknown[bonded].append(a)
for a, list in unknown.items():
bonded = a.bondedTo()
n = len(bonded)
known = []
for b in bonded:
if b.position() is not None:
known.append(b)
nb = len(list)
if a.symbol == 'C':
if n == 4:
if nb == 1:
self._C4oneH(a, known, list)
elif nb == 2:
self._C4twoH(a, known, list)
elif nb == 3:
self._C4threeH(a, known, list)
elif n == 3:
if nb == 1:
self._C3oneH(a, known, list)
else:
self._C3twoH(a, known, list)
else:
print a
raise ValueError, "Can't handle C with "+`n`+" bonds"
elif a.symbol == 'N':
if n == 4:
if nb == 3:
self._N4threeH(a, known, list)
elif nb == 2:
self._N4twoH(a, known, list)
elif n == 3:
if nb == 1:
self._N3oneH(a, known, list)
elif nb == 2:
self._N3twoH(a, known, list)
else:
print a
raise ValueError, "Can't handle N with "+`n`+" bonds"
elif a.symbol == 'O' and n == 2:
self._O2(a, known, list)
elif a.symbol == 'S' and n == 2:
self._S2(a, known, list)
else:
print a
raise ValueError, "Can't handle this yet: " + \
a.symbol + ' with ' + `n` + ' bonds (' + \
a.fullName() + ').'
finally:
self.clearBondAttributes()
def findHydrogenPositions(self):
"""Find reasonable positions for hydrogen atoms that have no
position assigned.
This method uses a heuristic approach based on standard geometry
data. It was developed for proteins and DNA and may not give
good results for other molecules. It raises an exception
if presented with a topology it cannot handle."""
self.setBondAttributes()
try:
unknown = DictWithDefault([])
for a in self.atoms:
if a.position() is None:
if a.symbol != 'H':
raise ValueError('position of ' + a.fullName() + \
' is undefined')
bonded = a.bondedTo()[0]
unknown[bonded].append(a)
for a, list in unknown.items():
bonded = a.bondedTo()
n = len(bonded)
known = []
for b in bonded:
if b.position() is not None:
known.append(b)
nb = len(list)
if a.symbol == 'C':
if n == 4:
if nb == 1:
self._C4oneH(a, known, list)
elif nb == 2:
self._C4twoH(a, known, list)
elif nb == 3:
self._C4threeH(a, known, list)
elif n == 3:
if nb == 1:
self._C3oneH(a, known, list)
else:
self._C3twoH(a, known, list)
elif n == 2:
self._C2oneH(a, known, list)
else:
print a
raise ValueError("Can't handle C with " + ` n ` +
" bonds")
elif a.symbol == 'N':
if n == 4:
if nb == 3:
self._N4threeH(a, known, list)
elif nb == 2:
self._N4twoH(a, known, list)
elif nb == 1:
self._N4oneH(a, known, list)
elif n == 3:
if nb == 1:
self._N3oneH(a, known, list)
elif nb == 2:
self._N3twoH(a, known, list)
elif n == 2:
self._N2oneH(a, known, list)
else:
print a
raise ValueError("Can't handle N with " + ` n ` +
" bonds")
elif a.symbol == 'O' and n == 2:
self._O2(a, known, list)
elif a.symbol == 'S' and n == 2:
self._S2(a, known, list)
else:
print a
raise ValueError("Can't handle this yet: " + a.symbol +
' with ' + ` n ` + ' bonds (' +
a.fullName() + ').')
finally:
self.clearBondAttributes()
def __init__(self, file, modifications=[]):
if isinstance(file, str):
file = TextFile(file)
title = file.readline()[:-1]
self.atom_types = DictWithDefault(None)
self._readAtomTypes(file)
format = FortranFormat('20(A2,2X)')
done = 0
while not done:
l = FortranLine(file.readline()[:-1], format)
for entry in l:
name = _normalizeName(entry)
if len(name) == 0:
done = 1
break
try: # ignore errors for now
self.atom_types[name].hydrophylic = 1
except:
pass
self.bonds = {}
self._readBondParameters(file)
self.bond_angles = {}
self._readAngleParameters(file)
self.dihedrals = {}
self.dihedrals_2 = {}
self._readDihedralParameters(file)
self.impropers = {}
self.impropers_1 = {}
self.impropers_2 = {}
self._readImproperParameters(file)
self.hbonds = {}
self._readHbondParameters(file)
self.lj_equivalent = {}
format = FortranFormat('20(A2,2X)')
while 1:
l = FortranLine(file.readline()[:-1], format)
if l.isBlank(): break
name1 = _normalizeName(l[0])
for s in l[1:]:
name2 = _normalizeName(s)
self.lj_equivalent[name2] = name1
self.ljpar_sets = {}
while 1:
l = FortranLine(file.readline()[:-1], 'A4,6X,A2')
if l[0] == 'END ': break
set_name = _normalizeName(l[0])
ljpar_set = AmberLJParameterSet(set_name, l[1])
self.ljpar_sets[set_name] = ljpar_set
self._readLJParameters(file, ljpar_set)
file.close()
for mod, ljname in modifications:
if isinstance(mod, str):
file = TextFile(mod)
else:
file = mod
title = file.readline()[:-1]
blank = file.readline()[:-1]
while 1:
keyword = file.readline()
if not keyword: break
keyword = string.strip(keyword)[:4]
if keyword == 'MASS':
self._readAtomTypes(file)
elif keyword == 'BOND':
self._readBondParameters(file)
elif keyword == 'ANGL':
self._readAngleParameters(file)
elif keyword == 'DIHE':
self._readDihedralParameters(file)
elif keyword == 'IMPR':
self._readImproperParameters(file)
elif keyword == 'HBON':
self._readHbondParameters(file)
elif keyword == 'NONB':
self._readLJParameters(file, self.ljpar_sets[ljname])