def _readImproperParameters(self, file):
format = FortranFormat('A2,1X,A2,1X,A2,1X,A2,I4,3F15.2')
while True:
l = FortranLine(file.readline()[:-1], format)
if l.isBlank(): break
name1 = _normalizeName(l[0])
name2 = _normalizeName(l[1])
name3 = _normalizeName(l[2])
name4 = _normalizeName(l[3])
if name1 == 'X':
if name2 == 'X':
name1 = name3
name2 = name4
name3 = 'X'
name4 = 'X'
else:
name1 = name3
name2, name3 = _sort(name2, name4)
name4 = 'X'
else:
name1, name2, name3, name4 = \
(name3, ) + _sort3(name1, name2, name4)
p = AmberImproperParameters(self.atom_types[name1],
self.atom_types[name2],
self.atom_types[name3],
self.atom_types[name4],
l[4], l[5], l[6], l[7])
if name4 == 'X':
if name3 == 'X':
self.impropers_2[(name1, name2)] = p
else:
self.impropers_1[(name1, name2, name3)] = p
else:
self.impropers[(name1, name2, name3, name4)] = p
def _readLJParameters(self, file, ljpar_set):
format = FortranFormat('2X,A2,6X,3F10.6')
while True:
l = FortranLine(file.readline()[:-1], format)
if l.isBlank(): break
name = _normalizeName(l[0])
ljpar_set.addEntry(name, l[1], l[2], l[3])
def _readAtomTypes(self, file):
format = FortranFormat('A2,1X,F10.2')
while True:
l = FortranLine(file.readline()[:-1], format)
if l.isBlank(): break
name = _normalizeName(l[0])
self.atom_types[name] = AmberAtomType(name, l[1])
def _readLJParameters(self, file, ljpar_set):
format = FortranFormat('2X,A2,6X,3F10.6')
while 1:
l = FortranLine(file.readline()[:-1], format)
if l.isBlank(): break
name = _normalizeName(l[0])
ljpar_set.addEntry(name, l[1], l[2], l[3])
def _readImproperParameters(self, file):
format = FortranFormat('A2,1X,A2,1X,A2,1X,A2,I4,3F15.2')
while 1:
l = FortranLine(file.readline()[:-1], format)
if l.isBlank(): break
name1 = _normalizeName(l[0])
name2 = _normalizeName(l[1])
name3 = _normalizeName(l[2])
name4 = _normalizeName(l[3])
if name1 == 'X':
if name2 == 'X':
name1 = name3
name2 = name4
name3 = 'X'
name4 = 'X'
else:
name1 = name3
name2, name3 = _sort(name2, name4)
name4 = 'X'
else:
name1, name2, name3, name4 = \
(name3, ) + _sort3(name1, name2, name4)
p = AmberImproperParameters(self.atom_types[name1],
self.atom_types[name2],
self.atom_types[name3],
self.atom_types[name4], l[4], l[5],
l[6], l[7])
if name4 == 'X':
if name3 == 'X':
self.impropers_2[(name1, name2)] = p
else:
self.impropers_1[(name1, name2, name3)] = p
else:
self.impropers[(name1, name2, name3, name4)] = p
def _readDihedralParameters(self, file):
format = FortranFormat('A2,1X,A2,1X,A2,1X,A2,I4,3F15.2')
append = None
while 1:
l = FortranLine(file.readline()[:-1], format)
if l.isBlank(): break
name1 = _normalizeName(l[0])
name2 = _normalizeName(l[1])
name3 = _normalizeName(l[2])
name4 = _normalizeName(l[3])
name1, name2, name3, name4 = _sort4(name1, name2, name3, name4)
if append is not None:
append.addTerm(l[4], l[5], l[6], l[7])
if l[7] >= 0: append = None
else:
p = AmberDihedralParameters(self.atom_types[name1],
self.atom_types[name2],
self.atom_types[name3],
self.atom_types[name4], l[4], l[5],
l[6], l[7])
if name1 == 'X' and name4 == 'X':
self.dihedrals_2[(name2, name3)] = p
else:
self.dihedrals[(name1, name2, name3, name4)] = p
if l[7] < 0: append = p
def _readAtomTypes(self, file):
format = FortranFormat('A2,1X,F10.2')
while 1:
l = FortranLine(file.readline()[:-1], format)
if l.isBlank(): break
name = _normalizeName(l[0])
self.atom_types[name] = AmberAtomType(name, l[1])
def _readHbondParameters(self, file):
format = FortranFormat('2X,A2,2X,A2,2X,2F10.2')
while True:
l = FortranLine(file.readline()[:-1], format)
if l.isBlank(): break
name1 = _normalizeName(l[0])
name2 = _normalizeName(l[1])
name1, name2 = _sort(name1, name2)
self.hbonds[(name1, name2)] = \
AmberHbondParameters(self.atom_types[name1],
self.atom_types[name2],
l[2], l[3])
def _readHbondParameters(self, file):
format = FortranFormat('2X,A2,2X,A2,2X,2F10.2')
while 1:
l = FortranLine(file.readline()[:-1], format)
if l.isBlank(): break
name1 = _normalizeName(l[0])
name2 = _normalizeName(l[1])
name1, name2 = _sort(name1, name2)
self.hbonds[(name1, name2)] = \
AmberHbondParameters(self.atom_types[name1],
self.atom_types[name2],
l[2], l[3])
def _readAngleParameters(self, file):
format = FortranFormat('A2,1X,A2,1X,A2,2F10.2')
while True:
l = FortranLine(file.readline()[:-1], format)
if l.isBlank(): break
name1 = _normalizeName(l[0])
name2 = _normalizeName(l[1])
name3 = _normalizeName(l[2])
name1, name3 = _sort(name1, name3)
self.bond_angles[(name1, name2, name3)] = \
AmberBondAngleParameters(self.atom_types[name1],
self.atom_types[name2],
self.atom_types[name3],
l[3], l[4])
def _readAngleParameters(self, file):
format = FortranFormat('A2,1X,A2,1X,A2,2F10.2')
while 1:
l = FortranLine(file.readline()[:-1], format)
if l.isBlank(): break
name1 = _normalizeName(l[0])
name2 = _normalizeName(l[1])
name3 = _normalizeName(l[2])
name1, name3 = _sort(name1, name3)
self.bond_angles[(name1, name2, name3)] = \
AmberBondAngleParameters(self.atom_types[name1],
self.atom_types[name2],
self.atom_types[name3],
l[3], l[4])
def __init__(self, file, modifications=[]):
if isinstance(file, basestring):
file = TextFile(file)
title = file.readline()[:-1]
self.atom_types = DictWithDefault(None)
self._readAtomTypes(file)
format = FortranFormat('20(A2,2X)')
done = False
while not done:
l = FortranLine(file.readline()[:-1], format)
for entry in l:
name = _normalizeName(entry)
if len(name) == 0:
done = True
break
try: # ignore errors for now
self.atom_types[name].hydrophylic = True
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 True:
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 True:
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, basestring):
file = TextFile(mod)
else:
file = mod
title = file.readline()[:-1]
blank = file.readline()[:-1]
while True:
keyword = file.readline()
if not keyword: break
keyword = keyword.strip()[: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])
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])