qmmmrebind.parameterize

Functions

copy_file(source, destination)	Copies a file from a source to the destination.
dihedral_energy(x, k1, k2, k3[, k4])	Expression for the dihedral energy.
dot_product(u_PA, eig_AB)	Returns the dot product of two vectors.
error_function(delta_qm, delta_mm)	Root Mean Squared Error.
error_function_boltzmann(delta_qm, delta_mm, T)	Boltzmann Root Mean Squared Error.
fit_params(qm_scan_file, load_topology, ...)	Optimization of the objective function.
force_angle_constant(atom_A, atom_B, atom_C, ...)	Calculates force constant according to Equation 14 of Seminario calculation paper; returns angle (in kcal/mol/rad^2) and equilibrium angle (in degrees).
force_angle_constant_special_case(atom_A, ...)	Calculates force constant according to Equation 14 of Seminario calculation paper when the vectors u_CB and u_AB are linearly dependent and u_N cannot be defined.
force_constant_bond(atom_A, atom_B, ...)	Calculates the bond force constant for the bonds in the molecule according to equation 10 of seminario paper, given the bond atoms' indices and the corresponding eigenvalues, eigenvectors and coordinates matrices.
gen_init_guess(qm_scan_file, load_topology, ...)	Initial guess for the torsional parameter.
generate_mm_pdbs(qm_scan_file, template_pdb)	Generate PDBs from the torsiondrive scan file based on a template PDB.
generate_xml_from_charged_pdb_sdf(...)	Generates an openforcefield xml file from the pdb file via SDF file and openforcefield.
generate_xml_from_pdb_sdf(system_pdb, ...)	Generates an openforcefield xml file from the pdb file.
get_dihedrals(qm_scan_file)	Returns dihedrals from the torsiondrive scan file.
get_mm_potential_energies(qm_scan_file, ...)	Returns potential energy of the system from the PDB file given the topology and the forcefield file.
get_non_torsion_mm_energy(system_pdb, ...)	Returns sum of all the non-torsional energies (that includes HarmonicBondForce, HarmonicAngleForce and NonBondedForce) of the system from the PDB file given the topology and the forcefield file.
get_qm_energies(qm_scan_file)	Returns QM optimized energies from the torsiondrive scan file.
get_tor_params(qm_scan_file, template_pdb, ...)	Returns the fitted torsional parameters.
get_torsional_lines(template_pdb, ...)	Returns the torsional lines for the XML forcefield file.
get_vibrational_scaling(functional, basis_set)	Returns vibrational scaling factor given the functional and the basis set for the QM engine.
list_diff(list_1, list_2)	Returns the difference between two lists as a list.
list_hartree_kcal(list_)	Convert the elements in the list from hartree units to kiloCalories units.
list_kJ_kcal(list_)	Convert the elements in the list from kiloJoules units to kiloCalories units.
list_to_dict(lst)	Converts an input list with mapped characters (every odd entry is the key of the dictionary and every even entry adjacent to the odd entry is its correponding value) to a dictionary.
objective_function(k_array, x, delta_qm)	Objective function for the torsional parameter fitting.
remove_mm_files(qm_scan_file)	Delete all generated PDB files.
reverse_list(lst)	Returns the reversed form of a given list.
scale_list(list_)	Returns a scaled list with the minimum value subtracted from each element of the corresponding list.
search_in_file(file, word)	Search for the given string in file and return lines containing that string along with line numbers.
torsiondrive_input_to_xyz(psi_input_file, ...)	Returns an xyz file from a torsiondrive formatted input file.
u_PA_from_angles(atom_A, atom_B, atom_C, coords)	Returns the vector in the plane A,B,C and perpendicular to AB.
uniq(input_)	Returns a list with only unique elements from a list containing duplicate / repeating elements.
unit_vector_N(u_BC, u_AB)	Calculates unit normal vector perpendicular to plane ABC.
xyz_to_pdb(xyz_file, coords_file, ...)	Converts a XYZ file to a PDB file.

Classes

GuestAmberXMLAmber([charge, ...])	A class used to generate a template force field XML file for the ligand in order regenerate the reparametrised forcefield XML file.
HostAmberXMLAmber([system_pdb, system_sdf, ...])	A class used to generate a template force field XML file for the receptor in order regenerate the reparametrised forcefield XML file.
MergeHostGuestTopology(host_prmtop, ...)	A class used to merge the host and guest topology and coordinate files.
ParameterizeGuest([xyz_file, ...])	A class used to obtain force field parameters for the ligand (bond, angle and charge parameters) from QM calculations.
ParameterizeHost([xyz_file, ...])	A class used to obtain force field parameters for the QM region of the receptor (bond, angle and charge parameters) from QM calculations.
PrepareGaussianGuest([charge, multiplicity, ...])	A class used to prepare the QM engine input file (Gaussian) for the ligand and run QM calculations with appropriate keywords.
PrepareGaussianHost([charge, multiplicity, ...])	A class used to prepare the QM engine input file (Gaussian) for the receptor and run QM calculations with appropriate keywords.
PrepareGaussianHostGuest([charge, ...])	A class used to prepare the QM engine input file (Gaussian) for the receptor - ligand complex and run the QM calculations with the appropriate keywords.
PrepareQMMM(init_pdb, distance, ...[, ...])	A class used to segregate the QM and MM regions.
PrepareSolvatedParams(init_pdb[, ...])	A class used to integrate the parameterized topology files of the receptor - ligand complex and the solvent.
RunOpenMMSims(system_prmtop, system_inpcrd, ...)	A class used to run the OpenMM simulation on any specified system.
TorsionDriveParams([num_charge_atoms, ...])	A class used to parameterize the torsional parameters of the ligand by fitting the torsional parameters obtained from torsiondrive calculations.
TorsionDriveSims([charge, multiplicity, ...])	A class used to create a filetree for torsion scan using torsionsdrive for the dihedral angles of the ligand.