def bonds_from_ff(atoms, linkers, ff):
ff_bonds = []
found = False
for line in read_file(ff):
if "BONDS" in line:
found = True
if "ANGLES" in line:
break
if found and not re.search("^\s*$", line):
line = line.split()
if all(x in atoms for x in line[:2]):
ff_bonds.append(line[:2] + line[3:5])
# add on linkers by copying lines that include the type after forming
# the bond
additional = []
for linker, newtype in linkers.items():
for bond in ff_bonds:
if newtype in bond[:2]:
tmp = bond.copy()
for ind, i in enumerate(tmp):
if i == newtype:
tmp[ind] = linker
additional.append(tmp)
break
# only want to replace one instance of C3, so we have C3, LC1
ff_bonds += additional
ret = []
for i in ff_bonds:
if i not in ret:
ret.append(i)
return ret
def params_from_initial_datafile(datafile):
params = {}
params["atoms"] = []
params["pairs"] = []
params["bonds"] = []
params["angles"] = []
params["dihs"] = []
params["imps"] = []
atoms = False
pairs = False
bonds = False
angles = False
dihs = False
imps = False
for line in read_file(datafile):
if "Masses" in line:
atoms = True
continue
if "Pair Coeffs" in line:
atoms = False
pairs = True
continue
if "Bond Coeffs" in line:
pairs = False
bonds = True
continue
if "Angle Coeffs" in line:
bonds = False
angles = True
continue
if "Dihedral Coeffs" in line:
angles = False
dihs = True
continue
# improps not always present
if re.search("^\s*[A-Z]", line):
dihs = False
if "Improper Coeffs" in line:
imps = True
continue
if "Atoms" in line:
break
if re.search("^\s*$", line):
continue
line = line.split()
if atoms and re.search("^\s*[0-9]", line[0]):
params["atoms"].append(line[-1])
if pairs and re.search("^\s*[0-9]", line[0]):
params["pairs"].append(line[-1])
if bonds and re.search("^\s*[0-9]", line[0]):
params["bonds"].append(line[-1])
if angles and re.search("^\s*[0-9]", line[0]):
params["angles"].append(line[-1])
if dihs and re.search("^\s*[0-9]", line[0]):
params["dihs"].append(line[-1])
if imps and re.search("^\s*[0-9]", line[0]):
params["imps"].append(line[-1])
return params
def change_datafile(charges, datafile, output):
b4_atoms = []
atoms = []
after_atoms = []
b4_atoms_bool = True
found_atoms_bool = False
after_atoms_bool = False
for line in read_file(datafile):
if re.search('\s*Atoms', line):
b4_atoms_bool = False
found_atoms_bool = True
if re.search('^\s*Bonds', line):
found_atoms_bool = False
after_atoms_bool = True
if b4_atoms_bool:
b4_atoms.append(line)
if found_atoms_bool:
atoms.append(line)
if after_atoms_bool:
after_atoms.append(line)
newatoms = []
for line, charge in zip(atoms[2:-1], charges):
line = line.split()
line[3] = str(charge) # change column
newatoms.append(' '.join(line) + '\n')
atoms = atoms[:2] + newatoms + [atoms[-1]]
with open(output, 'w') as f:
f.writelines(b4_atoms)
f.writelines(atoms)
f.writelines(after_atoms)
def main():
file = 'gaff.lt'
file = read_file(file)
find_masses(file, atoms)
pair_coeffs(file, atoms)
bond_coeffs(file, bonds)
angle_coeffs(file, angles)
dihedral_coeffs(file, dihs)
improper_coeffs(file, imps)
write_file(atoms, bonds, angles, dihs, imps)
def linker_atom_types(datafile, polym="polym.in", ff="gaff.ff"):
atoms_to_consider = []
linkers = {}
for line in read_file(polym):
if "link" in line:
tmp = line.split()[1:]
for i in tmp:
atoms_to_consider += i.split(",")
linker, after_bond = i.split(",")
linkers[linker] = after_bond
atoms_to_consider = list(set(atoms_to_consider))
atom_types = []
# find atom types of each atom label,
# then just add all possible parameters
for line in read_file(ff):
if "BONDS" in line:
break
line = line.split()
if len(line) > 6:
if line[0] in atoms_to_consider:
atom_types.append(line[1])
# Add atom types of atoms bonded to the linker atoms.
# To do this, need to create the original monomer system,
# and read in bond types
found = False
for line in read_file(datafile):
if "Bond Coeffs" in line:
found = True
continue
if "Atom Coeffs" in line:
break
line = line.split()
if len(line) < 5:
continue
if any(x in line[-1] for x in atoms_to_consider):
atom_types += line[-1].split("-")
return list(set(atom_types)), linkers
def dihs_from_ff(atoms, linkers, ff, params_in_original_datafile):
all_combos, with_types_that_exist = find_combos(
atoms, linkers, params_in_original_datafile)
ff_dihs = []
found = False
for line in read_file(ff):
if "DIHEDRALS" in line:
found = True
continue
if re.search("^\s*$", line) and len(ff_dihs) > 0:
break
if found and not re.search("^\s*$", line):
ff_dihs.append(line.split())
return compare_db(ff_dihs, all_combos, with_types_that_exist)
def atoms_from_ff(atoms, ff):
ff_atoms = []
ff_pairs = []
found = False
for line in read_file(ff):
if "ATOMS" in line:
found = True
continue
if "BONDS" in line:
break
if found and not re.search("^\s*$", line):
line = line.split()
if line[0] in atoms:
ff_atoms.append([line[0], line[2]])
ff_pairs.append([line[0]] + line[5:7])
return ff_atoms, ff_pairs
def imps_from_ff(atoms, linkers, ff, params_in_original_datafile):
"""
Same as dihs from ff, just changing the values in the force field
to search for
"""
all_combos, with_types_that_exist = find_combos(
atoms, linkers, params_in_original_datafile)
ff_dihs = []
found = False
for line in read_file(ff):
if "IMPROPERS" in line:
found = True
continue
if found and not re.search("^\s*$", line):
ff_dihs.append(line.split())
return compare_db(ff_dihs, all_combos, with_types_that_exist)
mol_id = []
mol_count = 1
for s in structs:
for _ in range(mols[s]['number']):
for _ in range(mols[s]["length"]):
mol_id.append(mol_count)
mol_count += 1
# now change data file
b4_atoms = []
atoms = []
after_atoms = []
b4_atoms_bool = True
found_atoms_bool = False
after_atoms_bool = False
for line in read_file(lammps):
if re.search('\s*Atoms', line):
b4_atoms_bool = False
found_atoms_bool = True
if re.search('^\s*Bonds', line):
found_atoms_bool = False
after_atoms_bool = True
if b4_atoms_bool:
b4_atoms.append(line)
if found_atoms_bool:
atoms.append(line)
if after_atoms_bool:
after_atoms.append(line)
newatoms = []
for line, molid in zip(atoms[2:-1], mol_id):
charge_regex = '^\s[A-Za-z]{1,2}(\s*-?[0-9]*.[0-9]*){2}$'
results = []
files = get_files('.', ['log', 'out'])
for logfile in files:
if file_is_gamess(logfile):
path, filename = os.path.split(logfile)
print(path)
inpfile = logfile[:-3] + 'inp'
res = []
assigned = []
for line in read_file(inpfile):
if re.search(atom_regex, line):
sym, atnum, x, y, z = line.split()
x, y, z = map(float, (x, y, z))
res.append([path,
Atom(sym,
coords=(x, y, z))]) # new key for each coord
found = False
counter = 0
for line in read_file(logfile):
if 'NET CHARGES:' in line:
found = True
if 'RMS DEVIATION' in line:
break
if found:
if re.search(charge_regex, line):
def angles_from_ff(atoms, linkers, ff, params_in_original_datafile):
ff_angles = []
found = False
for line in read_file(ff):
if "ANGLES" in line:
found = True
if "DIHEDRALS" in line:
break
if found and not re.search("^\s*$", line):
line = line.split()
if all(x in atoms for x in line[:3]):
ff_angles.append(line[:3] + line[4:6])
orig_atoms = []
for ang in params_in_original_datafile:
for atom in ang.split("-"):
if atom not in orig_atoms:
orig_atoms.append(atom)
all_atoms = []
for atom in atoms + orig_atoms:
if atom not in all_atoms:
all_atoms.append(atom)
all_combos = list(list(i) for i in itertools.product(all_atoms, repeat=3))
with_types_that_exist = []
for combo in all_combos:
with_types_that_exist.append(
[linkers[i] if i in linkers else i for i in combo])
# add on linkers by copying lines that include the type after forming
# the angle
angles_with_params = []
for line in ff_angles:
for combo, types_that_exist in zip(all_combos, with_types_that_exist):
if line[:3] == types_that_exist:
params = line[3:]
angles_with_params.append(combo + params)
angles_with_params.append(types_that_exist + params)
possibility = []
tmpval = combo
# find each possible different combination,
# i.e. for combo = [LC1, LC2, CA] and
# types_that_exist = [C3, C3, CA],
# also include LC1, C3, CA and
# C3, LC2, CA
for idx, data in enumerate(zip(combo, types_that_exist)):
with_linker, without_linker = data
if with_linker != without_linker:
# change one value and add it
to_add = tmpval.copy()
to_add[idx] = without_linker
possibility.append(to_add)
for p in possibility:
angles_with_params.append(p + params)
# prevent duplicates...
checked = []
ret = []
for angle in angles_with_params:
if angle[:3] not in checked:
checked.append(angle[:3])
ret.append(angle)
return ret
ff_angles = initial + additional
ret = []
for i in ff_angles:
if i not in ret:
ret.append(i)
return ret
cm5_results = []
files = get_files('.', ['.log', '.out'])
regex = "\s*[0-9]{1,3}\s*[A-Za-z]{1,2}(\s*\D?[0-9]{1,3}\.[0-9]{1,10}){6}"
inp_regex = '^[A-Z][a-z]?(\s*-?[0-9]*.[0-9]*){3}'
found = False
for file in files:
path, f = os.path.split(file)
print(path)
inputfile = file.replace('out', 'inp')
data = []
coords = []
parsed = []
lines = read_file(file)
for line in lines:
if 'Q-H S-H Dx Dy Dz Q-CM5' in line:
found = True
elif 'Tot' in line:
found = False
if found:
# index, sym, hirshfeld charge, spin density, dipole_x, dipole_y, dipole_z, cm5 charge
if re.search(regex, line):
res = line.split()
data.append([path] + res[:3] + res[4:])
# need coords
for line in read_file(inputfile):
if re.search(inp_regex, line):
sym, x, y, z = line.split()
