def add_mol_itp(self, mol_itp_file):
"""Add a molecule itp in the topologie itp_list.
"""
fullname = (mol_itp_file.split("/")[-1])
include = fullname.split(".")[0]
path = os_command.full_path_and_check(mol_itp_file)
mol_itp = Itp(name=include, fullname=fullname, path=path)
# 1. Get new mol name:
mol_name_list = []
for top_mol in mol_itp.top_mol_list:
mol_name_list.append(top_mol.name)
# 2. Check if it already present
present = False
for itp in self.itp_list:
for top_mol in itp.top_mol_list:
if top_mol.name in mol_name_list:
present = True
break
if present:
break
# Add the itp if not present
if not present:
self.itp_list.append(mol_itp)
def extract_itp_atomtypes(itp_in, itp_atomtypes_out):
field = None
atom_types_list = "[ atomtypes ]\n"
with open(itp_in) as itpfile:
for line in itpfile:
if line.startswith("["):
# Remove space and [ ]
field = line.strip()[1:-1].strip()
# print(field)
continue
if field == 'atomtypes':
atom_types_list += line
filout = open(itp_atomtypes_out, "w")
filout.write(atom_types_list)
filout.close()
# Read and write itp to remove the [ atomtypes ] part
fullname = (itp_in.split("/")[-1])
include = fullname.split(".")[0]
path = os_command.full_path_and_check(itp_in)
top_mol = gmx.Itp(name=include, fullname=fullname, path=path)
top_mol.write_file(path)
def make_amber_top_mol_rdkit(pdb_in,
res_name,
smile,
charge_model="bcc",
atom_type="gaff",
remove_h=True):
full_coor = pdb_manip.Coor(pdb_in)
# Select coor:
mol_coor = full_coor.select_part_dict(selec_dict={'res_name': [res_name]})
# Change first residue to 1, as it is the res from rdkit output
res_list = mol_coor.get_attribute_selection(attribute='res_num')
index_list = mol_coor.get_index_selection(
selec_dict={'res_num': [res_list[0]]})
mol_coor.change_index_pdb_field(index_list, change_dict={'res_num': 1})
# Remove hydrogens:
if remove_h:
to_del_list = []
for atom_num, atom in mol_coor.atom_dict.items():
if atom['name'].startswith('H'):
to_del_list.append(atom_num)
mol_coor.del_atom_index(to_del_list)
mol_coor.write_pdb(res_name + '.pdb', check_file_out=False)
# Add hydrogens:
# add_hydrogen(res_name+'.pdb', res_name+'_h.pdb')
charge = add_hydrogen_rdkit(res_name + '.pdb', smile, res_name + '_h.pdb')
# Get only one molecule
mol_h_coor = pdb_manip.Coor(res_name + '_h.pdb')
res_list = mol_h_coor.get_attribute_selection(attribute='uniq_resid')
mol_uniq_coor = mol_h_coor.select_part_dict(
selec_dict={'uniq_resid': [res_list[0]]})
# Save coordinates:
mol_uniq_coor.write_pdb(res_name + '_h_unique.pdb', check_file_out=False)
# Compute topologie with acpype:
gmxsys = acpype(res_name + '_h_unique.pdb',
res_name,
net_charge=charge,
charge_model="bcc",
atom_type="gaff")
return ({
'GmxSys': gmxsys,
'coor': os_command.full_path_and_check(res_name + '_h.pdb'),
'num': len(res_list)
})
def make_amber_top_mol(pdb_in,
res_name,
charge,
charge_model="bcc",
atom_type="gaff",
remove_h=True):
full_coor = pdb_manip.Coor(pdb_in)
# Select coor:
mol_coor = full_coor.select_part_dict(selec_dict={'res_name': [res_name]})
# Remove hydrogens:
if remove_h:
to_del_list = []
for atom_num, atom in mol_coor.atom_dict.items():
if atom['name'][0] == 'H':
to_del_list.append(atom_num)
mol_coor.del_atom_index(to_del_list)
mol_coor.write_pdb(res_name + '.pdb')
# Add hydrogens:
add_hydrogen(res_name + '.pdb', res_name + '_h.pdb')
# Get only one molecule
mol_h_coor = pdb_manip.Coor(res_name + '_h.pdb')
res_list = mol_h_coor.get_attribute_selection(attribute='uniq_resid')
mol_uniq_coor = mol_h_coor.select_part_dict(
selec_dict={'uniq_resid': [res_list[0]]})
# Save coordinates:
mol_uniq_coor.write_pdb(res_name + '_h_unique.pdb')
# Compute topologie with acpype:
gmxsys = acpype(res_name + '_h_unique.pdb',
res_name,
net_charge=charge,
charge_model="bcc",
atom_type="gaff")
return ({
'GmxSys': gmxsys,
'coor': os_command.full_path_and_check(res_name + '_h.pdb'),
'num': len(res_list)
})
def __init__(self, top_in):
self.path = os_command.full_path_and_check(top_in)
self.forcefield = None
self.itp_list = []
self.mol_comp = []
self.name = ""
self.folder = os_command.get_directory(top_in)
self.include_itp = False
# Intermolecular restraints (only for Free ener):
self.inter_interact = False
self.inter_bond_list = []
self.inter_angl_list = []
self.inter_dihe_list = []
self.read_file(top_in)
if self.include_itp:
logger.info("Rewrite topologie: {}".format(top_in))
self.write_file(top_in)
def add_atomtypes(self, new_atomtypes):
""" Add atomtypes in a topologie.
:param new_atomtypes: path of the atomtype itp file
:type new_atomtypes: str
"""
# check if and atomtypes file exists:
# self.display()
atom_type = False
for itp_file in self.get_include_no_posre_file_list():
if itp_file.split("/")[-1].endswith('atomtypes.itp'):
# print('atomtypes file present', itp_file)
atom_type = True
atomtype_path = itp_file
break
# If it doesn't exist create it
if not atom_type:
fullname = (new_atomtypes.split("/")[-1])
include = fullname.split(".")[0]
path = os_command.full_path_and_check(new_atomtypes)
atomtype_itp = Itp(name=include, fullname=fullname, path=path)
self.itp_list = [atomtype_itp] + self.itp_list
# If it does exist add the new atomtypes in the first one:
else:
# First extract old atom types:
field = None
atom_dict = {}
name_list = []
with open(atomtype_path) as file:
for line in file:
if line.strip().startswith("["):
# Remove space and [ ], remove also comments
field = line.replace(" ", "").split("]")[0][1:]
continue
if (line[0] != ";" and line[0] != "#"
and line.strip() != ""):
# Remove commentary in the line
line_comment = line.split(';')
line_list = line_comment[0].split()
if field == 'atomtypes':
name_list.append(line_list[0])
name, bond_type, mass, charge, ptype, sigma, \
epsilon = line_list[:7]
atom_dict[name] = {
'bond_type': bond_type,
'mass': float(mass),
'charge': float(charge),
'ptype': ptype,
'sigma': float(sigma),
'epsilon': float(epsilon)
}
name_list.append(name)
# Second extract new atom types and
# check if they are already present:
field = None
new_atom_dict = {}
with open(new_atomtypes) as file:
for line in file:
if line.strip().startswith("["):
# Remove space and [ ], remove also comments
field = line.replace(" ", "").split("]")[0][1:]
continue
if (line[0] != ";" and line[0] != "#"
and line.strip() != ""):
# Remove commentary in the line
line_comment = line.split(';')
line_list = line_comment[0].split()
if field == 'atomtypes':
name, bond_type, mass, charge, ptype, sigma, \
epsilon = line_list[:7]
local_dict = {
'bond_type': bond_type,
'mass': float(mass),
'charge': float(charge),
'ptype': ptype,
'sigma': float(sigma),
'epsilon': float(epsilon)
}
if name not in name_list:
new_atom_dict[name] = local_dict
else:
# Check if the new values are the same:
if local_dict != atom_dict[name]:
logger.warning(
'Atom types parameters for {} are '
'different in {} and {}. Only one '
'version is kept !!!'.format(
name, atomtype_path,
new_atomtypes))
# Finally append the new param in the old one
with open(atomtype_path, 'a') as file:
for name, atom_dict in new_atom_dict.items():
file.write(' {:3} {:3} {:.5f} {:.5f}'
' {} {:.5e} {:.5e}\n'.format(
name, atom_dict['bond_type'],
atom_dict['mass'], atom_dict['charge'],
atom_dict['ptype'], atom_dict['sigma'],
atom_dict['epsilon']))