def md_to_sp():
""" Creates gaussian sp inputs from the molecular dynamics"""
oniom_gaussian_example = gaussian.GaussianCom(GAUSSIAN_AMBER_EXAMPLE)
example_atoms_list = oniom_gaussian_example.atoms_list
## read single point charge inputs to know the geometries to create
charge_com_files = []
for charge_com_file in os.listdir(GAUSSIAN_CHARGE_FOLDER):
if charge_com_file.endswith(".com"):
charge_com_files.append(charge_com_file)
charge_com_files.sort()
## read geometries list and correct charges from log files
geometries_list = []
for charge_com_file in charge_com_files:
charge_com_file = "{}/{}".format(GAUSSIAN_CHARGE_FOLDER,
charge_com_file)
gaussian_charge_com = gaussian.GaussianCom(charge_com_file)
charge_com_atoms_list = gaussian_charge_com.atoms_list
############ read mulliken new charges
charge_log_name = charge_com_file.replace(".com", ".log")
mulliken_charges_list = gaussian.read_mulliken_charges(charge_log_name)
for no, charge in enumerate(mulliken_charges_list):
if charge != 0:
charge_com_atoms_list[no].charge = float(charge)
############# end of charges reading #########
geometries_list.append(charge_com_atoms_list)
# read numbers of important atoms
gaussian_amber_file = gaussian.GaussianCom(GAUSSIAN_AMBER_EXAMPLE)
gaussian_sp_file = gaussian.GaussianCom(GAUSSIAN_CHARGE_EXAMPLE)
amber_atoms_list = gaussian_amber_file.atoms_list
gaussian_atoms_list = gaussian_sp_file.atoms_list
amber_hl_no_atoms_list = []
gaussian_hl_no_atoms_list = []
for no, atom in enumerate(amber_atoms_list):
if 'H' in atom.oniom.layer:
amber_hl_no_atoms_list.append(no)
for no, atom in enumerate(gaussian_atoms_list):
if 'H' in atom.oniom.layer:
gaussian_hl_no_atoms_list.append(no)
for md_no in sorted(os.listdir(AMBER_FOLDER)):
if int(md_no) in range(LOG_POINTS[0][1],
LOG_POINTS[0][2] + 1,
LOG_POINTS[0][3]):
folder_name = "{}/{}".format(SP_ONIOM_FOLDER, md_no)
amber_folder_name = "{}/{}".format(AMBER_FOLDER, md_no)
os.makedirs(folder_name)
mdcrd_name = "{}/{}".format(amber_folder_name, "mdp.mdcrd")
sp_jobs_list = []
snapshots = amber.extract_many_from_mdcrd(mdcrd_name,
MD_NO_ATOMS, 0,1000,1) #TODO
for sp_no in range(0, 1000, 1): ####### TODO!!!!!!
mdcrd_coordinates = snapshots[sp_no]
gaussian_atoms_list = []
# an example file is used to read the pdb info
for no, atom in enumerate(example_atoms_list):
atom.SetVector(float(mdcrd_coordinates[no][0]),
float(mdcrd_coordinates[no][1]),
float(mdcrd_coordinates[no][2]))
gaussian_atoms_list.append(atom)
#### high layer geometry and charges come from the
####charge single points
for position in [-1, 0, 1]:
hl_geometry_no = int(md_no)+position
if hl_geometry_no < 0:
continue
gaussian_path_file_name = "{}/{:03d}_on_{:03d}_{:03d}"\
.format(folder_name, hl_geometry_no, int(md_no), sp_no)
gaussian_name = "{}.com".format(gaussian_path_file_name)
try:
for index, no in enumerate(gaussian_hl_no_atoms_list):
gaussian_no = no
amber_no = amber_hl_no_atoms_list[index]
#gaussian_atoms_list[amber_no].charge =\
gaussian_atoms_list[amber_no].SetVector(
geometries_list[hl_geometry_no][gaussian_no].GetVector())
#geometries_list[hl_geometry_no][gaussian_no].charge
sp_jobs_list.append("{:03d}_on_{:03d}_{:03d}.com"\
.format(hl_geometry_no, int(md_no), sp_no))
oniom_gaussian_example.atoms_list = gaussian_atoms_list
oniom_gaussian_example.write_to_file(gaussian_name)
print("Using {} and md:{}".format(charge_com_files[int(md_no)+position],md_no ))
print("Saved {}".format(gaussian_name))
except IndexError:
print("Cannot save {}".format(gaussian_name))
sp_script = "{}/{}".format(folder_name, SP_ONIOM_RUN_SCRIPT)
with open(sp_script, 'w') as script_file:
for job in sp_jobs_list:
script_file.write("g09 {}\n".format(job))
def md_to_sp():
""" Creates gaussian sp inputs from the molecular dynamics"""
oniom_gaussian_example = gaussian.GaussianCom(GAUSSIAN_AMBER_EXAMPLE)
example_atoms_list = oniom_gaussian_example.atoms_list
## read single point charge inputs to know the geometries to create
charge_com_files = []
for charge_com_file in os.listdir(GAUSSIAN_CHARGE_FOLDER):
if charge_com_file.endswith(".com"):
charge_com_files.append(charge_com_file)
charge_com_files.sort()
## read geometries list and correct charges from log files
geometries_list = []
for charge_com_file in charge_com_files:
charge_com_file = "{}/{}".format(GAUSSIAN_CHARGE_FOLDER,
charge_com_file)
gaussian_charge_com = gaussian.GaussianCom(charge_com_file)
charge_com_atoms_list = gaussian_charge_com.atoms_list
############ read mulliken new charges
charge_log_name = charge_com_file.replace(".com", ".log")
mulliken_charges_list = gaussian.read_mulliken_charges(charge_log_name)
for no, charge in enumerate(mulliken_charges_list):
if charge != 0:
charge_com_atoms_list[no].charge = float(charge)
############# end of charges reading #########
geometries_list.append(charge_com_atoms_list)
# read numbers of important atoms
gaussian_amber_file = gaussian.GaussianCom(GAUSSIAN_AMBER_EXAMPLE)
gaussian_sp_file = gaussian.GaussianCom(GAUSSIAN_CHARGE_EXAMPLE)
amber_atoms_list = gaussian_amber_file.atoms_list
gaussian_atoms_list = gaussian_sp_file.atoms_list
amber_hl_no_atoms_list = []
gaussian_hl_no_atoms_list = []
for no, atom in enumerate(amber_atoms_list):
if 'H' in atom.oniom.layer:
amber_hl_no_atoms_list.append(no)
for no, atom in enumerate(gaussian_atoms_list):
if 'H' in atom.oniom.layer:
gaussian_hl_no_atoms_list.append(no)
for md_no in sorted(os.listdir(AMBER_FOLDER)):
if int(md_no) in range(LOG_POINTS[0][1], LOG_POINTS[0][2] + 1,
LOG_POINTS[0][3]):
folder_name = "{}/{}".format(SP_ONIOM_FOLDER, md_no)
amber_folder_name = "{}/{}".format(AMBER_FOLDER, md_no)
os.makedirs(folder_name)
mdcrd_name = "{}/{}".format(amber_folder_name, "mdp.mdcrd")
sp_jobs_list = []
snapshots = amber.extract_many_from_mdcrd(mdcrd_name, MD_NO_ATOMS,
0, 1000, 1) #TODO
for sp_no in range(0, 1000, 1): ####### TODO!!!!!!
mdcrd_coordinates = snapshots[sp_no]
gaussian_atoms_list = []
# an example file is used to read the pdb info
for no, atom in enumerate(example_atoms_list):
atom.SetVector(float(mdcrd_coordinates[no][0]),
float(mdcrd_coordinates[no][1]),
float(mdcrd_coordinates[no][2]))
gaussian_atoms_list.append(atom)
#### high layer geometry and charges come from the
####charge single points
for position in [-1, 0, 1]:
hl_geometry_no = int(md_no) + position
if hl_geometry_no < 0:
continue
gaussian_path_file_name = "{}/{:03d}_on_{:03d}_{:03d}"\
.format(folder_name, hl_geometry_no, int(md_no), sp_no)
gaussian_name = "{}.com".format(gaussian_path_file_name)
try:
for index, no in enumerate(gaussian_hl_no_atoms_list):
gaussian_no = no
amber_no = amber_hl_no_atoms_list[index]
#gaussian_atoms_list[amber_no].charge =\
gaussian_atoms_list[amber_no].SetVector(
geometries_list[hl_geometry_no]
[gaussian_no].GetVector())
#geometries_list[hl_geometry_no][gaussian_no].charge
sp_jobs_list.append("{:03d}_on_{:03d}_{:03d}.com"\
.format(hl_geometry_no, int(md_no), sp_no))
oniom_gaussian_example.atoms_list = gaussian_atoms_list
oniom_gaussian_example.write_to_file(gaussian_name)
print("Using {} and md:{}".format(
charge_com_files[int(md_no) + position], md_no))
print("Saved {}".format(gaussian_name))
except IndexError:
print("Cannot save {}".format(gaussian_name))
sp_script = "{}/{}".format(folder_name, SP_ONIOM_RUN_SCRIPT)
with open(sp_script, 'w') as script_file:
for job in sp_jobs_list:
script_file.write("g09 {}\n".format(job))
def sp_to_md():
""" Reads gaussian charge single points and writes the md inputs with it"""
#read model files
model_coordinates = amber.read_crd_file(MODEL_INPCRD)
model_charges = amber.read_prmtop_charges(MODEL_PRMTOP)
# read single point charge inputs to know the geometries to create
charge_com_files = []
for charge_com_file in os.listdir(GAUSSIAN_CHARGE_FOLDER):
if charge_com_file.endswith(".com"):
charge_com_files.append(charge_com_file)
charge_com_files.sort()
geometries_list = []
for charge_com_file in charge_com_files:
charge_com_file = "{}/{}".format(GAUSSIAN_CHARGE_FOLDER,
charge_com_file)
gaussian_charge_com = gaussian.GaussianCom(charge_com_file)
geometries_list.append(gaussian_charge_com.atoms_list)
# read numbers of important atoms
gaussian_amber_file = gaussian.GaussianCom(GAUSSIAN_AMBER_EXAMPLE)
gaussian_sp_file = gaussian.GaussianCom(GAUSSIAN_CHARGE_EXAMPLE)
amber_atoms_list = gaussian_amber_file.atoms_list
gaussian_atoms_list = gaussian_sp_file.atoms_list
amber_h_no_atoms_list = []
amber_l_no_atoms_list = []
amber_hl_no_atoms_list = []
gaussian_h_no_atoms_list = []
gaussian_l_no_atoms_list = []
gaussian_hl_no_atoms_list = []
amber_hl_atoms_list = []
for no, atom in enumerate(amber_atoms_list):
if atom.oniom.link_atom:
amber_l_no_atoms_list.append(no)
amber_hl_no_atoms_list.append(no)
amber_hl_atoms_list.append(atom)
if 'H' in atom.oniom.layer:
amber_h_no_atoms_list.append(no)
amber_hl_no_atoms_list.append(no)
amber_hl_atoms_list.append(atom)
for no, atom in enumerate(gaussian_atoms_list):
if atom.oniom.link_atom:
gaussian_l_no_atoms_list.append(no)
gaussian_hl_no_atoms_list.append(no)
if 'H' in atom.oniom.layer:
gaussian_h_no_atoms_list.append(no)
gaussian_hl_no_atoms_list.append(no)
restraint_mask = amber.create_restraint_mask(amber_hl_no_atoms_list)
### write coordinates
for step, atoms_list in enumerate(geometries_list):
folder_name = "{}/{:03d}".format(AMBER_FOLDER, step)
try:
os.makedirs(folder_name)
except OSError:
print("\n{0} folder already exists".format(folder_name))
if OVERWRITE:
print("--overwrite is on. I will write over the old files\n")
else:
print("Exiting without writing anything.")
print("Delete the folder or use --overwrite to"\
"write over the old files\n")
sys.exit(0)
# write coordinate file
coordinates_list = [(atom.GetX(), atom.GetY(), atom.GetZ()) for atom in atoms_list]
all_coordinates_list = model_coordinates[:]
for index, no in enumerate(gaussian_hl_no_atoms_list):
gaussian_no = no
amber_no = amber_hl_no_atoms_list[index]
all_coordinates_list[amber_no] = coordinates_list[gaussian_no]
crd_name = "{0}/inpcrd.inpcrd".format(folder_name)
amber.write_crd_file(crd_name, all_coordinates_list, box_info=True,
velocities=False)
#read new charges and write them to model prmtop
charge_log_name = charge_com_files[step].replace(".com", ".log")
charge_log_name = "{0}/{1}".format(GAUSSIAN_CHARGE_FOLDER,
charge_log_name)
mulliken_charges_list = gaussian.read_mulliken_charges(charge_log_name)
hl_charges_list = []
for charge in mulliken_charges_list:
if charge != 0:
hl_charges_list.append(charge)
new_charges_list = []
for atom in amber_hl_atoms_list:
if 'H' in atom.oniom.layer:
new_charges_list.append(hl_charges_list.pop(0))
else:
new_charges_list.append(atom.mm.charge)
new_charge_amber_hl_atoms_list = amber.give_resp_charges(\
amber_hl_atoms_list, new_charges_list)
all_charges_list = model_charges[:]
for index, no in enumerate(amber_hl_no_atoms_list):
all_charges_list[no] = new_charge_amber_hl_atoms_list[index].mm.charge
# write these charges to a new prmtop
new_prmtop_name = "{0}/prmtop.prmtop".format(folder_name)
amber.write_prmtop_charges(MODEL_PRMTOP, new_prmtop_name,
all_charges_list)
# read and write amber in files
for amber_in_name in AMBER_INPUT_FILES:
with open(amber_in_name, 'r') as model_in_file:
model_file_str = model_in_file.read()
new_file_str = model_file_str.replace("XXXX", restraint_mask)
new_file_name = "{}/{}".format(folder_name,
amber_in_name.split("/")[-1])
with open(new_file_name, 'w') as new_in_file:
new_in_file.write(new_file_str)
def sp_to_md():
""" Reads gaussian charge single points and writes the md inputs with it"""
#read model files
model_coordinates = amber.read_crd_file(MODEL_INPCRD)
model_charges = amber.read_prmtop_charges(MODEL_PRMTOP)
# read single point charge inputs to know the geometries to create
charge_com_files = []
for charge_com_file in os.listdir(GAUSSIAN_CHARGE_FOLDER):
if charge_com_file.endswith(".com"):
charge_com_files.append(charge_com_file)
charge_com_files.sort()
geometries_list = []
for charge_com_file in charge_com_files:
charge_com_file = "{}/{}".format(GAUSSIAN_CHARGE_FOLDER,
charge_com_file)
gaussian_charge_com = gaussian.GaussianCom(charge_com_file)
geometries_list.append(gaussian_charge_com.atoms_list)
# read numbers of important atoms
gaussian_amber_file = gaussian.GaussianCom(GAUSSIAN_AMBER_EXAMPLE)
gaussian_sp_file = gaussian.GaussianCom(GAUSSIAN_CHARGE_EXAMPLE)
amber_atoms_list = gaussian_amber_file.atoms_list
gaussian_atoms_list = gaussian_sp_file.atoms_list
amber_h_no_atoms_list = []
amber_l_no_atoms_list = []
amber_hl_no_atoms_list = []
gaussian_h_no_atoms_list = []
gaussian_l_no_atoms_list = []
gaussian_hl_no_atoms_list = []
amber_hl_atoms_list = []
for no, atom in enumerate(amber_atoms_list):
if atom.oniom.link_atom:
amber_l_no_atoms_list.append(no)
amber_hl_no_atoms_list.append(no)
amber_hl_atoms_list.append(atom)
if 'H' in atom.oniom.layer:
amber_h_no_atoms_list.append(no)
amber_hl_no_atoms_list.append(no)
amber_hl_atoms_list.append(atom)
for no, atom in enumerate(gaussian_atoms_list):
if atom.oniom.link_atom:
gaussian_l_no_atoms_list.append(no)
gaussian_hl_no_atoms_list.append(no)
if 'H' in atom.oniom.layer:
gaussian_h_no_atoms_list.append(no)
gaussian_hl_no_atoms_list.append(no)
restraint_mask = amber.create_restraint_mask(amber_hl_no_atoms_list)
### write coordinates
for step, atoms_list in enumerate(geometries_list):
folder_name = "{}/{:03d}".format(AMBER_FOLDER, step)
try:
os.makedirs(folder_name)
except OSError:
print("\n{0} folder already exists".format(folder_name))
if OVERWRITE:
print("--overwrite is on. I will write over the old files\n")
else:
print("Exiting without writing anything.")
print("Delete the folder or use --overwrite to"\
"write over the old files\n")
sys.exit(0)
# write coordinate file
coordinates_list = [(atom.GetX(), atom.GetY(), atom.GetZ())
for atom in atoms_list]
all_coordinates_list = model_coordinates[:]
for index, no in enumerate(gaussian_hl_no_atoms_list):
gaussian_no = no
amber_no = amber_hl_no_atoms_list[index]
all_coordinates_list[amber_no] = coordinates_list[gaussian_no]
crd_name = "{0}/inpcrd.inpcrd".format(folder_name)
amber.write_crd_file(crd_name,
all_coordinates_list,
box_info=True,
velocities=False)
#read new charges and write them to model prmtop
charge_log_name = charge_com_files[step].replace(".com", ".log")
charge_log_name = "{0}/{1}".format(GAUSSIAN_CHARGE_FOLDER,
charge_log_name)
mulliken_charges_list = gaussian.read_mulliken_charges(charge_log_name)
hl_charges_list = []
for charge in mulliken_charges_list:
if charge != 0:
hl_charges_list.append(charge)
new_charges_list = []
for atom in amber_hl_atoms_list:
if 'H' in atom.oniom.layer:
new_charges_list.append(hl_charges_list.pop(0))
else:
new_charges_list.append(atom.mm.charge)
new_charge_amber_hl_atoms_list = amber.give_resp_charges(\
amber_hl_atoms_list, new_charges_list)
all_charges_list = model_charges[:]
for index, no in enumerate(amber_hl_no_atoms_list):
all_charges_list[no] = new_charge_amber_hl_atoms_list[
index].mm.charge
# write these charges to a new prmtop
new_prmtop_name = "{0}/prmtop.prmtop".format(folder_name)
amber.write_prmtop_charges(MODEL_PRMTOP, new_prmtop_name,
all_charges_list)
# read and write amber in files
for amber_in_name in AMBER_INPUT_FILES:
with open(amber_in_name, 'r') as model_in_file:
model_file_str = model_in_file.read()
new_file_str = model_file_str.replace("XXXX", restraint_mask)
new_file_name = "{}/{}".format(folder_name,
amber_in_name.split("/")[-1])
with open(new_file_name, 'w') as new_in_file:
new_in_file.write(new_file_str)
