def write_to_file(self, name):
self.additional_input_dict['modred'] = [
m.write() for m in self.modreds
]
with open(name, 'w') as gaussian_com_file:
for line in self.link_0_commands:
gaussian_com_file.write(line)
gaussian_com_file.write(self.route_section.write().replace(
'\n ', '\n')) # FIXME
gaussian_com_file.write("\n")
gaussian_com_file.write(self.title_line)
gaussian_com_file.write("\n")
gaussian_com_file.write(self.multiplicity_line)
for atom in self.atoms_list:
line = iolines.atom2zmat(atom)
gaussian_com_file.write(line)
for section in self.additional_input_dict:
if self.additional_input_dict[section]:
gaussian_com_file.write("\n")
if section == 'first' and 'soft' in self.route_section.text:
gaussian_com_file.write("\n")
elif section == 'dftb=read' and 'dftb=read' in self.route_section.text:
gaussian_com_file.write("\n")
for line in self.additional_input_dict[section]:
gaussian_com_file.write(line)
gaussian_com_file.write("\n\n\n\n\n")
def _gen_zmat(self, inpcrd_name):
text = ''
chargelist = self.read_flag('CHARGE')
if 'ATOMIC_NUMBER' in self._flags: # old amboniom_elements.py (glycam)
elements = self._guess_elements()
else:
elements = self._read_elements()
total_charge = 0
X, Y, Z = self._coords_from_inpcrd(inpcrd_name)
j = 0
for i in self.atom_sel_idx:
name = self.pdb_atom_name[i].replace('-', '').replace('+', '')
residue_name = self.pdb_resname[i].replace('-',
'').replace('+', '')
residue_number = self.pdb_resid[i]
mm_type = self.upper_atom_types[i]
charge = chargelist[i] / 18.2223
total_charge += charge
mask = '0'
x = X[i]
y = Y[i]
z = Z[i]
chain = ''
layer = 'L'
element = elements[j]
j += 1
link_element = link_mm_type = link_bound_to = link_scale1 = None
# create atom
this_atom = atoms.Atom(element, (x, y, z))
resinfo = atoms.RESinfo(name, residue_name, residue_number, chain)
this_atom.set_resinfo(resinfo)
oniominfo = atoms.Oniom(mask, layer)
this_atom.set_oniom(oniominfo)
mm = atoms.MM(mm_type, charge)
this_atom.set_mm(mm)
# print z-matrix for atom
text += iolines.atom2zmat(this_atom)
# Add stuff to text
header = ''
#header += '%nproc=4\n'
#header += '%mem=2GB\n'
#header += '%chk=chk.chk\n'
header += '# amber=softonly geom=connectivity\n\n'
header += 'Se amanha nao chover vai estar um lindo dia de sol\n\n'
header += 'Sum of partial charges: %f\n' % (total_charge)
return header + text
def _gen_zmat(self, inpcrd_name):
text = ''
chargelist = self.read_flag('CHARGE')
if 'ATOMIC_NUMBER' in self._flags: # old amboniom_elements.py (glycam)
elements = self._guess_elements()
else:
elements = self._read_elements()
total_charge = 0
X,Y,Z = self._coords_from_inpcrd(inpcrd_name)
j = 0
for i in self.atom_sel_idx:
name = self.pdb_atom_name[i].replace('-','').replace('+','')
residue_name = self.pdb_resname[i].replace('-','').replace('+','')
residue_number = self.pdb_resid[i]
mm_type = self.upper_atom_types[i]
charge = chargelist[i] / 18.2223
total_charge += charge
mask = '0'
x = X[i]
y = Y[i]
z = Z[i]
chain = ''
layer = 'L'
element = elements[j]
j += 1
link_element = link_mm_type = link_bound_to = link_scale1 = None
# create atom
this_atom = atoms.Atom(element, (x, y, z))
resinfo = atoms.RESinfo(name, residue_name, residue_number, chain)
this_atom.set_resinfo(resinfo)
oniominfo = atoms.Oniom(mask, layer)
this_atom.set_oniom(oniominfo)
mm = atoms.MM(mm_type, charge)
this_atom.set_mm(mm)
# print z-matrix for atom
text += iolines.atom2zmat(this_atom)
# Add stuff to text
header = ''
#header += '%nproc=4\n'
#header += '%mem=2GB\n'
#header += '%chk=chk.chk\n'
header += '# amber=softonly geom=connectivity\n\n'
header += 'Se amanha nao chover vai estar um lindo dia de sol\n\n'
header += 'Sum of partial charges: %f\n' % (total_charge)
return header + text
def write_to_file(self,name):
self.additional_input_dict['modred'] = [m.write() for m in self.modreds]
with open(name, 'w') as gaussian_com_file:
for line in self.link_0_commands:
gaussian_com_file.write(line)
gaussian_com_file.write(self.route_section.write().replace('\n ','\n')) # FIXME
gaussian_com_file.write("\n")
gaussian_com_file.write(self.title_line)
gaussian_com_file.write("\n")
gaussian_com_file.write(self.multiplicity_line)
for atom in self.atoms_list:
line = iolines.atom2zmat(atom)
gaussian_com_file.write(line)
for section in self.additional_input_dict:
if self.additional_input_dict[section]:
gaussian_com_file.write("\n")
if section == 'first' and 'soft' in self.route_section.text:
gaussian_com_file.write("\n")
elif section == 'dftb=read' and 'dftb=read' in self.route_section.text:
gaussian_com_file.write("\n")
for line in self.additional_input_dict[section]:
gaussian_com_file.write(line)
gaussian_com_file.write("\n\n\n\n\n")
