def gettorsbytype(mol, types):
types = [molparam.torsion_uni(type_) for type_ in types]
result = {}
for typ in types:
result[typ] = []
mol.confirmconnect()
tors = relalist.genD(relalist.genconns(mol.connect))
for tor in tors:
typ = molparam.torsion_uni(gettortype(mol, tor))
if typ in types:
result[typ].append(tor)
return result
def readtorsionprm(prmfname, i, j, k, l):
toridx = molparam.torsion_uni((i, j, k, l))
ifile = file(prmfname)
for line in ifile:
words = line.split()
if (
len(words) in [14, 17, 20, 23]
and words[0] == "torsion"
and molparam.torsion_uni([int(x) for x in words[1:5]]) == toridx
):
fold = (len(words) - 5) // 3
result = []
for idx in range(fold):
data = words[5 + 3 * idx : 8 + 3 * idx]
if idx % 2 == 0:
assert float(data[1]) == 0.0
else:
assert float(data[1]) == 180.0
assert int(data[2]) == idx + 1
result.append(float(data[0]))
ifile.close()
return result
return None
def readidx(idxfname):
idxs = []
folds = []
for line in file(idxfname):
words = line.split()
if not words:
continue
assert 4 <= len(words) <= 5
idx = tuple([int(x) for x in words[:4]])
if len(words) == 5:
fold = int(words[-1])
else:
fold = 3
idxs.append(molparam.torsion_uni(idx))
folds.append(fold)
return (idxs, folds)
def getmoldata(molfname):
mol = read.readxyz(file(molfname))
types = tools.gettypes(mol)
result = {}
result['atomtypes'] = set(types)
subtypes = list(result['atomtypes'])
typepairs = []
for i, type_1 in enumerate(subtypes):
for type_2 in subtypes[i:]:
typepairs.append(molparam.bond_uni([type_1, type_2]))
result['typepairs'] = set(typepairs)
rela = relalist.Relalist(mol)
result['bondtypes'] = set([molparam.bond_uni(gettype(bond, types))
for bond in rela.bonds])
result['angletypes'] = set([molparam.angle_uni(gettype(angle, types))
for angle in rela.angles])
result['torsiontypes'] = set([molparam.torsion_uni(gettype(torsion, types))
for torsion in rela.torsions])
return result
def checktorsiontypes(words, moldata):
key = molparam.torsion_uni([int(words[1]), int(words[2]),
int(words[3]), int(words[4])])
if key in moldata['torsiontypes']:
return True
return False