def read_nbitp(fn):
l = open(fn, "r").readlines()
l = kickOutComments(l, ";")
l = kickOutComments(l, "#")
l = readSection(l, "[ atomtypes ]", "[")
l = parseList("ssiffsff", l)
dic = {}
for entry in l:
dic[entry[0]] = entry[1:]
return dic
def read_nbitp(fn):
l = open(fn,'r').readlines()
l = kickOutComments(l,';')
l = kickOutComments(l,'#')
l = readSection(l,'[ atomtypes ]','[')
l = parseList('ssiffsff',l)
dic = {}
for entry in l:
dic[entry[0]]=entry[1:]
return dic
def read_from_file(self,filename,nodeDeg):
fp = open(filename,'r')
lines = fp.readlines()
fp.close()
lines = pmxparser.kickOutComments( lines, comment = '#')
for l in lines:
l = l.rstrip()
l = l.lstrip()
foo = l.split()
foo[-1] = foo[-1].replace("'","")
foo[-1] = foo[-1].replace("\"","")
if 'None' == foo[-1]:
self.opt[foo[0]] = None
continue
if 'False' == foo[-1]:
self.opt[foo[0]] = None
continue
if 'True' == foo[-1]:
self.opt[foo[0]] = True
continue
self.opt[foo[0]] = foo[-1]
if ('Size' in foo[0]) or ('min' in foo[0]) or ('max' in foo[0]) or ('Transp' in foo[0]) or ('Width' in foo[0]) or ('Pos' in foo[0]) or ('Offset' in foo[0]):
self.opt[foo[0]] = float(foo[-1])
# some options need adjustment
if self.opt['nodeColor']=='var':
self.opt['nodeColor']=nodeDeg
def assign_mass_atp(r1, r2, ffatomtypes):
fp = open(ffatomtypes, "r")
lst = fp.readlines()
lst = kickOutComments(lst, ";")
fp.close()
mass = {}
for l in lst:
foo = l.split()
mass[foo[0]] = float(foo[1])
for atom in r1.atoms + r2.atoms:
atom.m = mass[atom.atomtype]
