def solvate(molecule, file_format, residues_added, solvent, box_x, box_y, box_z):
user = getuser()
# FILE MUST BE A PDB
if file_format.lower() != "pdb":
mol = FileReader.ReadFile(f"{molecule}.{file_format}")
mol.writePDBFile(f"{molecule}.pdb")
with open('packmol.inp', 'w') as f:
f.write(f"""tolerance 1.5
filetype pdb
output packmol.pdb
structure {molecule}.pdb
number 1
fixed 0. 0. 0. 0. 0. 0.
centerofmass
end structure
structure /home/{user}/zTeamVPScripts/solvents/{solvent}.pdb
number {residues_added}
inside box {round(box_x / -2.0)}. {round(box_y / -2.0)}. {round(box_z / -2.0)}. {round(box_x / 2.0)}. {round(box_y / 2.0)}. {round(box_z / 2.0)}.
radius 1.5
end structure
""")
run()
convertToMol2(molecule)
def run(substrates,
carbon_locations_file="carbon_locations.txt",
ATOM_NAME='C',
use_old=False,
run_multiple=False):
if run_multiple:
atom1, atom2, atom3 = getAtoms(carbon_locations_file)
if use_old:
atom1, atom2, atom3 = getContactAtom(atom1, ATOM_NAME, atom2,
ATOM_NAME, atom3, ATOM_NAME)
complex_file = FileReader.ReadFile('complex.mol2')
catalyst_contact_list, substrate1_contact_list, substrate2_contact_list = getAtomIndex(
complex_file, atom1, atom2, substrates)
else:
with open(carbon_locations_file, 'r') as f:
catalyst_contact_list = [f.readline().strip().replace('\n', '')]
substrate_contact_list = [f.readline().strip().replace('\n', '')]
return catalyst_contact_list, substrate_contact_list, []
return catalyst_contact_list, substrate1_contact_list, substrate2_contact_list
if arg in ['-h', '--help']:
usage()
sys.exit()
elif arg in ['-f', '--file']:
carbon_locations_file = ARGS[i + 1]
elif arg in ['-s', '--substrates']:
substrates = int(ARGS[i + 1])
elif arg in ['-d']:
ADD_ATOM_NAME = False
atom1, atom2, atom3 = getAtoms(carbon_locations_file)
if ADD_ATOM_NAME:
atom1, atom2, atom3 = getContactAtom(atom1, ATOM_NAME, atom2,
ATOM_NAME, atom3, ATOM_NAME)
complex_file = FileReader.ReadFile('complex.mol2')
catalyst_contact_list, substrate1_contact_list, substrate2_contact_list = getAtomIndex(
complex_file, atom1, atom2, substrates)
print()
print(f"Catalyst Contact Points: {', '.join(catalyst_contact_list)}")
print()
print(f"Substrate 1 Contact Points: {', '.join(substrate1_contact_list)}")
print()
print(f"Substrate 2 Contact Points: {', '.join(substrate2_contact_list)}")
print()
def convertToMol2(molecule):
call(["obabel", "packmol.pdb", "pdb", "-o", "mol2", "-O", f'{molecule}_solvated.mol2'])
mol = FileReader.ReadFile(f'{molecule}_solvated.mol2')
mol.writeMol2File(f'{molecule}_solvated.mol2')
