rmgpy.qm.molecule

class rmgpy.qm.molecule.Geometry(settings, unique_id, molecule, unique_id_long=None)

A geometry, used for quantum calculations.

Created from a molecule. Geometry estimated by RDKit.

The attributes are:

Attribute

Type

Description

settings

QMSettings

Settings for QM calculations

unique_id

str

A short ID such as an augmented InChI Key

molecule

Molecule

RMG Molecule object

unique_id_long

str

A long, truly unique ID such as an augmented InChI

generate_rdkit_geometries()

Use RDKit to guess geometry.

Save mol files of both crude and refined. Saves coordinates on atoms.

get_crude_mol_file_path()

Returns the path of the crude mol file.

get_file_path(extension, scratch=True)

Returns the path to the file with the given extension.

The provided extension should include the leading dot. If called with scratch=False then it will be in the fileStore directory, else scratch=True is assumed and it will be in the scratchDirectory directory.

get_refined_mol_file_path()

Returns the path the the refined mol file.

rd_build()

Import rmg molecule and create rdkit molecule with the same atom labeling.

rd_embed(rdmol, num_conf_attempts)

Embed the RDKit molecule and create the crude molecule file.

save_coordinates_from_qm_data(qmdata)

Save geometry info from QMData (eg CCLibData)

unique_id

A short unique ID such as an augmented InChI Key.

unique_id_long

Long, truly unique, ID, such as the augmented InChI.

class rmgpy.qm.molecule.QMMolecule(molecule, settings)

A base class for QM Molecule calculations.

Specific programs and methods should inherit from this and define some extra attributes and methods:

  • outputFileExtension

  • inputFileExtension

  • generate_qm_data() …and whatever else is needed to make this method work.

The attributes are:

Attribute

Type

Description

molecule

Molecule

RMG Molecule object

settings

QMSettings

Settings for QM calculations

unique_id

str

A short ID such as an augmented InChI Key

unique_id_long

str

A long, truly unique ID such as an augmented InChI

calculate_chirality_correction()

Returns the chirality correction to entropy (R*ln(2) if chiral) in J/mol/K.

calculate_thermo_data()

Calculate the thermodynamic properties.

Stores and returns a ThermoData object as self.thermo. self.qm_data and self.point_group need to be generated before this method is called.

check_paths()

Check the paths in the settings are OK. Make folders as necessary.

check_ready()

Check that it’s ready to run calculations.

create_geometry()

Creates self.geometry with RDKit geometries

determine_point_group()

Determine point group using the SYMMETRY Program

Stores the resulting PointGroup in self.point_group

generate_qm_data()

Calculate the QM data somehow and return a CCLibData object, or None if it fails.

generate_thermo_data()

Generate Thermo Data via a QM calc.

Returns None if it fails.

get_augmented_inchi_key()

Returns the augmented InChI from self.molecule

get_file_path(extension, scratch=True)

Returns the path to the file with the given extension.

The provided extension should include the leading dot. If called with scratch=False then it will be in the fileStore directory, else scratch=True is assumed and it will be in the scratchDirectory directory.

get_mol_file_path_for_calculation(attempt)

Get the path to the MOL file of the geometry to use for calculation attempt.

If attempt <= self.script_attempts then we use the refined coordinates, then we start to use the crude coordinates.

get_thermo_file_path()

Returns the path the thermo data file.

initialize()

Do any startup tasks.

property input_file_path

Get the input file name.

load_thermo_data()

Try loading a thermo data from a previous run.

property max_attempts

The total number of attempts to try

property output_file_path

Get the output file name.

parse()

Parses the results of the Mopac calculation, and returns a QMData object.

save_thermo_data()

Save the generated thermo data.

property script_attempts

The number of attempts with different script keywords