pymatgen.io.babel module

OpenBabel interface module, which opens up access to the hundreds of file formats supported by OpenBabel. Requires openbabel with python bindings to be installed. Please consult the openbabel documentation.

class BabelMolAdaptor(mol)[source]

Bases: object

Adaptor serves as a bridge between OpenBabel’s Molecule and pymatgen’s Molecule.

Initializes with pymatgen Molecule or OpenBabel’s OBMol.

Parameters:

mol – pymatgen’s Molecule/IMolecule or OpenBabel OBMol

add_hydrogen()[source]

Add hydrogens (make all hydrogen explicit).

confab_conformers(forcefield='mmff94', freeze_atoms=None, rmsd_cutoff=0.5, energy_cutoff=50.0, conf_cutoff=100000, verbose=False)[source]

Conformer generation based on Confab to generate all diverse low-energy conformers for molecules. This is different from rotor_conformer or gen3d_conformer as it aims to not simply to find a low energy conformation but to generate several different conformations.

Parameters:

  • forcefield (str) – Default is mmff94. Options are ‘gaff’, ‘ghemical’, ‘mmff94’, ‘mmff94s’, and ‘uff’.

  • freeze_atoms ([int]) – index of atoms to be freezed when performing conformer search, default is None.

  • rmsd_cutoff (float) – rmsd_cufoff, default is 0.5 Angstrom.

  • energy_cutoff (float) – energy_cutoff, default is 50.0 kcal/mol.

  • conf_cutoff (float) – max number of conformers to test, default is 1 million.

  • verbose (bool) – whether to display information on torsions found, default is False.

Returns:

list of pymatgen Molecule objects for generated conformers.

Return type:

(list)

static from_file(filename, file_format='xyz', return_all_molecules=False)[source]

Uses OpenBabel to read a molecule from a file in all supported formats.

Parameters:

  • filename – Filename of input file

  • file_format – String specifying any OpenBabel supported formats.

  • return_all_molecules – If True, will return a list of BabelMolAdaptor instances, one for each molecule found in the file. If False, will return only the first molecule.

Returns:

BabelMolAdaptor object or list thereof

static from_molecule_graph(mol)[source]

Read a molecule from a pymatgen MoleculeGraph object.

Parameters:

mol – pymatgen MoleculeGraph object.

Returns:

BabelMolAdaptor object

static from_string(string_data, file_format='xyz')[source]

Uses OpenBabel to read a molecule from a string in all supported formats.

Parameters:

  • string_data – String containing molecule data.

  • file_format – String specifying any OpenBabel supported formats.

Returns:

BabelMolAdaptor object

gen3d_conformer()[source]

A combined method to first generate 3D structures from 0D or 2D structures and then find the minimum energy conformer:

  1. Use OBBuilder to create a 3D structure using rules and ring templates

  2. Do 250 steps of a steepest descent geometry optimization with the MMFF94 forcefield

  3. Do 200 iterations of a Weighted Rotor conformational search (optimizing each conformer with 25 steps of a steepest descent)

  4. Do 250 steps of a conjugate gradient geometry optimization.

Warning from openbabel docs: For many applications where 100s if not 1000s of molecules need to be processed, gen3d is rather SLOW. Sometimes this function can cause a segmentation fault. A future version of Open Babel will provide options for slow/medium/fast 3D structure generation which will involve different compromises between speed and finding the global energy minimum.

localopt(forcefield='mmff94', steps=500)[source]

A wrapper to pybel’s localopt method to optimize a Molecule.

Parameters:

  • forcefield – Default is mmff94. Options are ‘gaff’, ‘ghemical’, ‘mmff94’, ‘mmff94s’, and ‘uff’.

  • steps – Default is 500.

make3d(forcefield='mmff94', steps=50)[source]

A wrapper to pybel’s make3D method generate a 3D structure from a 2D or 0D structure. The 3D structure is made very quickly using a combination of rules (e.g. sp3 atoms should have four bonds arranged in a tetrahedron) and ring templates (e.g. cyclohexane is shaped like a chair). Once 3D coordinates are generated, hydrogens are added and a quick local optimization is carried out as default.

The generated 3D structure can have clashes or have high energy structures due to some strain. Please consider to use the conformer search or geometry optimization to further optimize the structure.

Parameters:

  • forcefield – Default is mmff94. Options are ‘gaff’, ‘ghemical’, ‘mmff94’, ‘mmff94s’, and ‘uff’.

  • steps – Default is 50.

property openbabel_mol[source]

Returns OpenBabel’s OBMol.

property pybel_mol[source]

Returns Pybel’s Molecule object.

property pymatgen_mol[source]

Returns pymatgen Molecule object.

remove_bond(idx1, idx2)[source]

Remove a bond from an openbabel molecule

Parameters:

  • idx1 – The atom index of one of the atoms participating the in bond

  • idx2 – The atom index of the other atom participating in the bond

rotor_conformer(*rotor_args, algo='WeightedRotorSearch', forcefield='mmff94')[source]

Conformer search based on several Rotor Search algorithms of openbabel. If the input molecule is not 3D, make3d will be called (generate 3D structure, add hydrogen, a quick localopt). All hydrogen atoms need to be made explicit.

Parameters:

  • rotor_args – pass args to Rotor Search in openbabel. for “WeightedRotorSearch”: (conformers, geomSteps, sampleRingBonds-default False) for “SystematicRotorSearch”: (geomSteps-default 2500, sampleRingBonds-default False) for “RandomRotorSearch”: (conformers, geomSteps-default 2500, sampleRingBonds-default False)

  • algo (str) – Default is “WeightedRotorSearch”. Options are “SystematicRotorSearch”, “RandomRotorSearch”, and “WeightedRotorSearch”.

  • forcefield (str) – Default is mmff94. Options are ‘gaff’, ‘ghemical’, ‘mmff94’, ‘mmff94s’, and ‘uff’.

write_file(filename, file_format='xyz')[source]

Uses OpenBabel to output all supported formats.

Parameters:

  • filename – Filename of file to output

  • file_format – String specifying any OpenBabel supported formats.