def __read_rtp_impropers(self, resname, lines ):
improps = []
for line in lines:
entr = line.split()
if entr[0] not in ['+','-']:
if _aliases.has_key( resname ) :
if _aliases[resname].has_key(entr[0]):
entr[0] = _aliases[resname][entr[0]]
if entr[1] not in ['+','-']:
if _aliases.has_key( resname ) :
if _aliases[resname].has_key(entr[1]):
entr[1] = _aliases[resname][entr[1]]
if entr[2] not in ['+','-']:
if _aliases.has_key( resname ) :
if _aliases[resname].has_key(entr[2]):
entr[2] = _aliases[resname][entr[2]]
if entr[3] not in ['+','-']:
if _aliases.has_key( resname ) :
if _aliases[resname].has_key(entr[3]):
entr[3] = _aliases[resname][entr[3]]
if len(entr) == 5:
improps.append(entr)
else:
improps.append(entr+[''])
return improps
def __read_rtp_impropers(self, resname, lines ):
improps = []
for line in lines:
entr = line.split()
if entr[0] not in ['+','-']:
if _aliases.has_key( resname ) :
if _aliases[resname].has_key(entr[0]):
entr[0] = _aliases[resname][entr[0]]
if entr[1] not in ['+','-']:
if _aliases.has_key( resname ) :
if _aliases[resname].has_key(entr[1]):
entr[1] = _aliases[resname][entr[1]]
if entr[2] not in ['+','-']:
if _aliases.has_key( resname ) :
if _aliases[resname].has_key(entr[2]):
entr[2] = _aliases[resname][entr[2]]
if entr[3] not in ['+','-']:
if _aliases.has_key( resname ) :
if _aliases[resname].has_key(entr[3]):
entr[3] = _aliases[resname][entr[3]]
if len(entr) == 5:
improps.append(entr)
else:
improps.append(entr+[''])
return improps
def __read_rtp_bonds(self, resname, lines ):
bonds = []
for line in lines:
entr = line.split()
if entr[0] not in ['+','-']:
if _aliases.has_key( resname ) :
if _aliases[resname].has_key(entr[0]):
entr[0] = _aliases[resname][entr[0]]
if entr[1] not in ['+','-']:
if _aliases.has_key( resname ) :
if _aliases[resname].has_key(entr[1]):
entr[1] = _aliases[resname][entr[1]]
bonds.append(entr)
return bonds
def __read_rtp_bonds(self, resname, lines ):
bonds = []
for line in lines:
entr = line.split()
if entr[0] not in ['+','-']:
if _aliases.has_key( resname ) :
if _aliases[resname].has_key(entr[0]):
entr[0] = _aliases[resname][entr[0]]
if entr[1] not in ['+','-']:
if _aliases.has_key( resname ) :
if _aliases[resname].has_key(entr[1]):
entr[1] = _aliases[resname][entr[1]]
bonds.append(entr)
return bonds
def __read_rtp_atoms(self, resname, lines ):
atoms = []
for line in lines:
entr = line.split()
if _aliases.has_key( resname ) :
if _aliases[resname].has_key(entr[0]):
entr[0] = _aliases[resname][entr[0]]
entr[2] = float(entr[2])
entr[3] = int(entr[3])
atoms.append(entr)
return atoms
def __read_rtp_atoms(self, resname, lines ):
atoms = []
for line in lines:
entr = line.split()
if _aliases.has_key( resname ) :
if _aliases[resname].has_key(entr[0]):
entr[0] = _aliases[resname][entr[0]]
entr[2] = float(entr[2])
entr[3] = int(entr[3])
atoms.append(entr)
return atoms