pymopac

PyMOPAC: A Python interface for MOPAC calculations.

This package provides tools and utilities for working with MOPAC, a semi-empirical quantum chemistry program.

class MopacInput(geometry, model: str = 'PM7', custom_header: str = '', comment: str = '#', path=False, addHs: bool = True, preopt: bool = True, verbose: bool = False, stream: bool = False, plot: bool = False, aux: bool = True)

Bases: BaseInput

Class that sets up the input file for a MOPAC calculation.

geometry:

• pure xyz block

• SMILES (str)

• rdkit Mol

model: str

all supported MOPAC keywords, e.g. AM1, PM6, …

custom_header: str

custom string that is attached to other header keywords

comment: str

second line in the input file

path:

if False, a dir is created under /tmp/, else under the given str

AddHs: bool

calls AddHs on the mol object

preopt: bool

uses MMFF to optimize the mol structure

verbose: bool

if True, prints additional class internal statements

stream: bool

if True, streams the outfile to stdout

plot: bool

if True, plots progress via matplotlib

+ run()

runs MOPAC as a subprocess

returns MopacOutput class

+ getInpFile()

returns the MOPAC input as a string

geoToXyz()

Helper function that tries to infer a geometry from any input and returns a xyz block

getAuxResult()

getInpFile()

getOutResult()

run()

runs MOPAC as a subprocess returns MopacOutput class

silentRun()

just runs MOPAC, no feedback or streaming

stream_run()

returns both the mopac process and the stream yielding lines

verboseRun()

Sets up the basics for a stream run and contains switches for being verbose and streaming. If plot is True, it creates a live-updating matplotlib figure of gradient values.

class MopacOutput(outfile: str, stdout=None, stderr=None, aux: str | None = None)

Bases: BaseOutput

Main Output class, calls parsers and structures outputs

Custom parsers can be written, inherinting from input.BaseParser. Every Output class has a list at self.parser which, custom parsers can simply be added. If a parser has been added after Output initialization, parsing can be redone using Output.parseAll() By convention, custom parsers are able to set attributes on the Ouput class by having the Output passed as an argument at parse time.

a .aux file is passed, as is standard when creating the output via the MopacInput.run() method. Using this, all properties can be parsed in an unsupervised manner. Results of this can be found under self.auxDict

keys()

toMol()

returns an rdkit.Chem mol object

get_mopac()

Checks if the MOPAC binary is within the path. looks for approximate alternatives. E.g., finds run_mopac7 on ubuntu22, but older MOPAC versions might parse files differently, thus being incompatible with this wrapper

API Module

class MopacProperties

Bases: Structure

Stores the calculated ground-state properties and job information.

heat

Heat of formation (kcal/mol).

Type:

float

dipole

Dipole moment vector (Debye).

Type:

float[3]

charge

Pointer to atomic partial charges array (size natom).

Type:

POINTER(c_double)

coord_update

Pointer to updated coordinates array (size 3*natom_move).

Type:

POINTER(c_double)

coord_deriv

Pointer to heat gradients array (size 3*natom_move).

Type:

POINTER(c_double)

freq

Pointer to vibrational frequencies array (size 3*natom_move).

Type:

POINTER(c_double)

disp

Pointer to displacement vectors array (size 3*natom_move, 3*natom_move).

Type:

POINTER(c_double)

bond_index

Pointer to CSC format bond matrix indices array (size natom+1).

Type:

POINTER(c_int)

bond_atom

Pointer to bonded atoms list (size bond_index[natom]).

Type:

POINTER(c_int)

bond_order

Pointer to bond orders array (size bond_index[natom]).

Type:

POINTER(c_double)

lattice_update

Pointer to updated lattice vectors array (size 3*nlattice_move).

Type:

POINTER(c_double)

lattice_deriv

Pointer to lattice gradients array (size 3*nlattice_move).

Type:

POINTER(c_double)

stress

Stress tensor in Voigt form.

Type:

float[6]

nerror

Number of error messages.

Type:

int

error_msg

Pointer to error messages array (size nerror).

Type:

POINTER(POINTER(c_char))

bond_atom

Structure/Union member

bond_index

Structure/Union member

bond_order

Structure/Union member

charge

Structure/Union member

coord_deriv

Structure/Union member

coord_update

Structure/Union member

dipole

Structure/Union member

disp

Structure/Union member

error_msg

Structure/Union member

freq

Structure/Union member

heat

Structure/Union member

lattice_deriv

Structure/Union member

lattice_update

Structure/Union member

nerror

Structure/Union member

stress

Structure/Union member

class MopacState

Bases: Structure

Represents an electronic state using standard molecular orbitals.

mpack

Number of packed matrix elements.

Type:

int

uhf

Unrestricted HF flag (0 = restricted, 1 = unrestricted).

Type:

int

pa

Pointer to alpha density matrix array (size mpack).

Type:

POINTER(c_double)

pb

Pointer to beta density matrix array (size mpack, NULL if uhf=0).

Type:

POINTER(c_double)

mpack

Structure/Union member

pa

Structure/Union member

pb

Structure/Union member

uhf

Structure/Union member

class MopacSystem

Bases: Structure

Defines the atomistic system and MOPAC job options.

natom

Number of atoms in the system.

Type:

int

natom_move

Number of atoms allowed to move.

Type:

int

charge

Net charge of the system.

Type:

int

spin

Number of spin excitations.

Type:

int

model

Semiempirical model (PM7=0, PM6-D3H4=1, etc.).

Type:

int

epsilon

Dielectric constant for COSMO solvent.

Type:

float

atom

Pointer to atomic numbers array (size natom).

Type:

POINTER(c_int)

coord

Pointer to atomic coordinates array (size 3*natom).

Type:

POINTER(c_double)

nlattice

Number of lattice vectors.

Type:

int

nlattice_move

Number of moveable lattice vectors.

Type:

int

pressure

External hydrostatic pressure (GPa).

Type:

float

lattice

Pointer to lattice vectors array (size 3*nlattice).

Type:

POINTER(c_double)

tolerance

Relative numerical tolerance.

Type:

float

max_time

Time limit in seconds.

Type:

int

atom

Structure/Union member

charge

Structure/Union member

coord

Structure/Union member

epsilon

Structure/Union member

lattice

Structure/Union member

max_time

Structure/Union member

model

Structure/Union member

natom

Structure/Union member

natom_move

Structure/Union member

nlattice

Structure/Union member

nlattice_move

Structure/Union member

pressure

Structure/Union member

spin

Structure/Union member

tolerance

Structure/Union member

class MozymeState

Bases: Structure

Represents an electronic state using localized molecular orbitals.

numat

Number of real atoms.

Type:

int

nbonds

Pointer to Lewis bonds per atom array (size numat).

Type:

POINTER(c_int)

ibonds

Pointer to Lewis-bonded atoms array (size 9*numat).

Type:

POINTER(c_int)

iorbs

Pointer to orbitals per atom array (size numat).

Type:

POINTER(c_int)

noccupied

Number of occupied molecular orbitals.

Type:

int

ncf

Pointer to atoms in occupied localized molecular orbitals (size noccupied).

Type:

POINTER(c_int)

nvirtual

Number of virtual molecular orbitals.

Type:

int

nce

Pointer to atoms in virtual localized molecular orbitals (size nvirtual).

Type:

POINTER(c_int)

icocc_dim

Size of icocc array.

Type:

int

icocc

Pointer to atom indices in occupied LMOs array (size icocc_dim).

Type:

POINTER(c_int)

icvir_dim

Size of icvir array.

Type:

int

icvir

Pointer to atom indices in virtual LMOs array (size icvir_dim).

Type:

POINTER(c_int)

cocc_dim

Size of cocc array.

Type:

int

cocc

Pointer to occupied LMO coefficients array (size cocc_dim).

Type:

POINTER(c_double)

cvir_dim

Size of cvir array.

Type:

int

cvir

Pointer to virtual LMO coefficients array (size cvir_dim).

Type:

POINTER(c_double)

cocc

Structure/Union member

cocc_dim

Structure/Union member

cvir

Structure/Union member

cvir_dim

Structure/Union member

ibonds

Structure/Union member

icocc

Structure/Union member

icocc_dim

Structure/Union member

icvir

Structure/Union member

icvir_dim

Structure/Union member

iorbs

Structure/Union member

nbonds

Structure/Union member

nce

Structure/Union member

ncf

Structure/Union member

noccupied

Structure/Union member

numat

Structure/Union member

nvirtual

Structure/Union member

calculate_frequencies(system: MopacSystem, state: MopacState | None = None, properties: MopacProperties | None = None)

Perform MOPAC vibrational analysis

calculate_mozyme_frequencies(system: MopacSystem, state: MozymeState | None = None, properties: MopacProperties | None = None)

Perform MOZYME vibrational analysis

calculate_mozyme_scf(system: MopacSystem, state: MozymeState | None = None, properties: MopacProperties | None = None)

Perform MOZYME electronic ground state calculation

calculate_scf(system: MopacSystem, state: MopacState | None = None, properties: MopacProperties | None = None)

Perform MOPAC electronic ground state calculation

mol_to_system(mol, charge=0, spin=0, model=0, preopt=True, add_Hs=True, optimize_geometry=True)

Convert an RDKit molecule to a MOPAC system

Parameters:

• mol – RDKit molecule object

• preopt – if the mol object should by pre-optimized via MMFF

• assHs – if hydrogens should be substituted at empty spots

• charge – Net molecular charge (default: 0)

• spin – Number of unpaired electrons (default: 0)

• model – Semiempirical model (default: 0/PM7)

• optimize_geometry – Whether atoms can move in calculation (default: True)

Returns:

MopacSystem object ready for calculation

optimize_geometry(system: MopacSystem, state: MopacState | None = None, properties: MopacProperties | None = None)

Perform MOPAC geometry optimization

optimize_mozyme_geometry(system: MopacSystem, state: MozymeState | None = None, properties: MopacProperties | None = None)

Perform MOZYME geometry optimization

run_from_file(filepath: str) → int

Run MOPAC calculation from input file

system_to_mol(system, sanitize=True, charge=0, cov_factor=1.3)

Convert a MOPAC system to an RDKit molecule

Parameters:

• system – MopacSystem object

• sanitize – Whether to sanitize the molecule (default: True)

• charge – Molecular charge (default: 0)

• cov_factor – Factor to multiply covalent radii (default: 1.3)

Returns:

RDKit Mol object