本文整理汇总了Python中molecule.Molecule.morphes方法的典型用法代码示例。如果您正苦于以下问题：Python Molecule.morphes方法的具体用法？Python Molecule.morphes怎么用？Python Molecule.morphes使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类molecule.Molecule的用法示例。
在下文中一共展示了Molecule.morphes方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: read_new_mtp_entry
# 需要导入模块: from molecule import Molecule [as 别名]
# 或者: from molecule.Molecule import morphes [as 别名]
def read_new_mtp_entry( entry, filename = 'mutres.mtp'):
if not hasattr(filename,"read"):
lst = open(filename).readlines()
else:
lst = filename.readlines()
lst = kickOutComments(lst,';')
key = '[ '+entry+' ]'
keyw = ('[ morphes ]', '[ atoms ]','[ impropers ]','[ dihedrals ]',\
'[ rotations ]','[ coords ]')
res = []
for i, line in enumerate(lst):
if line.startswith(key):
for line2 in lst[i+1:]:
if line2.startswith('[') and \
line2 not in keyw:
break
else:
res.append(line2)
morphes = {}
ml = readSection(res,'[ morphes ]','[')
for i, line in enumerate(ml):
entr = line.split()
n0 = entr[0]
t0 = entr[1]
n1 = entr[3]
t1 = entr[4]
morphes[n0] = {
't0':t0,
'n1':n1,
't1':t1,
}
atoms = []
al = readSection(res,'[ atoms ]','[')
for i, line in enumerate(al):
entr = line.split()
name = entr[0]
atomtype = entr[1]
q = float(entr[2])
cgnr = int(entr[3])
m = float(entr[4])
atomtypeB = entr[5]
qB = float(entr[6])
mB = float(entr[7])
a = Atom(name = name,id=i+1,\
atomtype=atomtype, q = q,\
m=m,cgnr=cgnr,atomtypeB=atomtypeB,\
qB = qB, mB = mB)
atoms.append(a)
mol = Molecule(atoms = atoms, unity = 'nm')
mol.set_resname(entry)
coords = readSection(res,'[ coords ]','[')
coords = parseList('fff',coords)
for i, atom in enumerate(mol.atoms):
atom.x = coords[i]
atom.unity = 'A'
il = readSection(res,'[ impropers ]','[')
imps = []
for line in il:
imps.append(line.split())
diheds = []
dl = readSection(res,'[ dihedrals ]','[')
for line in dl:
diheds.append(line.split())
rl = readSection(res,'[ rotations ]','[')
rots = []
for line in rl:
rots.append(line.split())
rotdic = {}
for rot in rots:
key = rot[0]
rotdic[key] = rot[1:]
mol.morphes = morphes
bonds = []
return mol, bonds, imps, diheds, rotdic