A library of Python modules for chemistry on the Cornell Chemical Engineering system.

lammps.py: parse_opls_parameters(parameter_file) guess_opls_parameters(atoms, bonds, angles, dihedrals, opls_parameter_file) write_data_file(atoms, bonds, angles, dihedrals, starting_params, run_name) write_data_file_general(atoms, bonds, angles, dihedrals, box_size, run_name, pair_coeffs_included=True, atom_types=None) write_data_file2(atoms, bonds, angles, dihedrals, run_name) run_anneal(run_name, run_on='none') run_minimize(run_name, restrained=None, restraint_value=None) anneal(atoms, bonds, angles, dihedrals, params, name='') minimize(atoms, bonds, angles, dihedrals, params, name='', restrained=None, restraint_value=None) minimize2(atoms, bonds, angles, dihedrals, name='', restrained=None, restraint_value=None) get_dihedral_values(atoms, bonds, angles, dihedrals) set_internal_coordinates_BROKEN(atoms, bonds, angles, dihedrals, strong_dihedral=None) dynamics(atoms, bonds, angles, dihedrals, params, name='') opls_energy(coords, atoms, bonds, angles, dihedrals, params) opls_hbond_energy(coords, atoms, bonds, angles, dihedrals) minimize_rigid(atoms, rigid_groups) evaluate(mol_atoms, mol_bonds, mol_angles, mol_dihedrals, N=1)

jsub.py: wait(run_names)

filetypes.py: get_bonds(atoms) get_angles_and_dihedrals(atoms, bonds) parse_tinker_arc(molecule_file, parameter_file=None) parse_sdf(molecule_file) compare_structures(molecule_files) write_xyz(name, atoms, f=None) parse_xyz(name) write_arc(name, atoms, index_offset=0) gaussian_to_xyz(input_file, output_file)

utils.py: frange(low, high, step) quat_to_mat(quat): #quat = [w i j k quat_to_mat(q): #quat = [w i j k quat_to_mat(q): #quat = [w i j k transform_difference(P, Q): #two sets of points on a rigid bod matvec(m,v) matmat(a,b) rand_rotation(): #http://tog.acm.org/resources/GraphicsGems/, Ed II unique_filename(directory, name, filetype) dist_squared(a,b) dist(a,b) angle_size(a,center,b) dihedral_angle(a,b,c,d) rotate_about_dihedral(atoms, dihedral, angle): #dihedral = a struct containing a quad of atom lj_energy(atoms, bonds, angles, dihedrals, bonded=None, angled=None, dihedraled=None, lj_eps=None) opls_energy(coords, atoms, bonds, angles, dihedrals, bonded=None, angled=None, dihedraled=None, no_bonds=False, no_angles=False, no_dihedrals=False, dihedrals_only=False, list_components=False) energy_compare(coords, atoms, bonds, angles, dihedrals, params) residual_E_coeffs(coords, atoms, bonds, angles, dihedrals, dihedral_types_list=None, coeffs_per_dihedral=3) add_lone_pairs(atoms)

gaussian.py: job(atoms, basis, queue, run_name, job_type, extra_section='', procs=None, alternate_coords=None, charge_and_multiplicity='0,1') restart_job(old_run_name, job_type='ChkBasis Opt=Restart', queue='batch', procs=None) parse_coords(input_file, get_modredundant=False, get_energy=True) scan_modredundant(starting_atoms, basis, run_name_base, modredundant_section, param_starts, param_ends, n_steps) parse_atoms(input_file, get_energy=True, check_convergence=True, get_time=False, counterpoise=False) parse_starting_coords(input_file) parse_scan(input_file) parse_chelpg(input_file) minimize(atoms, theory, queue='batch', name='', restrained=None, async=False): #blocks until don chelpg(atoms, theory, queue='batch', chkfile_run_name=None, name='') energy(atoms, theory, queue='batch', chkfile=None, async=False, name='', alternate_coords=None) bond_energy(atoms, bond, theory, queue, chkfile, async=False, inc=None, name='') angle_energy(atoms, angle, theory, queue, chkfile, async=False, inc=3.0, name='') dihedral_energy(atoms, dihedral, theory, queue, chkfile, async=False, inc=None, name='')