shnitsel.bridges

This submodule contains functions used to interface with other packages and programs, especially RDKit.

Functions

to_xyz(da[, comment, units])

Convert an xr.DataArray of molecular geometry to an XYZ string

traj_to_xyz(traj_atXYZ[, units])

Convert an entire trajectory's worth of geometries to an XYZ string

to_mol(atXYZ_frame[, charge, covFactor, to2D, ...])

Convert a single frame's geometry to an RDKit Mol object

numbered_smiles_to_mol(smiles)

Convert a numbered SMILES-string to a analogically-numbered Mol object

default_mol(obj)

Try many ways to get a representative Mol object for an ensemble:

smiles_map(atXYZ_frame[, charge, covFactor])

Convert a geometry to a SMILES-string, retaining atom order

Module Contents

to_xyz(da, comment='#', units='angstrom')

Convert an xr.DataArray of molecular geometry to an XYZ string

Parameters:

  • da (shnitsel.core.typedefs.AtXYZ) – A molecular geometry – should have dimensions ‘atom’ and ‘direction’

  • comment – The comment line for the XYZ, by default ‘#’

  • units – The units to which to convert before creating the XYZ string

Return type:

The XYZ data as a string

Notes

The units of the outputs will be the same as the array; consider converting to angstrom first, as most tools will expect this.

traj_to_xyz(traj_atXYZ, units='angstrom')

Convert an entire trajectory’s worth of geometries to an XYZ string

Parameters:

  • traj_atXYZ (shnitsel.core.typedefs.AtXYZ) – Molecular geometries – should have dimensions ‘atom’ and ‘direction’; should also be groupable by ‘time’ (i.e. either have a ‘time’ dimension or a ‘time’ coordinate)

  • units – The units to which to convert before creating the XYZ string

Return type:

The XYZ data as a string, with time indicated in the comment line of each frame

Notes

The units of the outputs will be the same as the array; consider converting to angstrom first, as most tools will expect this.

to_mol(atXYZ_frame, charge=None, covFactor=1.2, to2D=True, molAtomMapNumber=None, atomNote=None, atomLabel=None)

Convert a single frame’s geometry to an RDKit Mol object

Parameters:

  • atXYZ_frame (shnitsel.core.typedefs.AtXYZ) – The xr.DataArray object to be converted; must have ‘atom’ and ‘direction’ dims, must not have ‘frame’ dim.

  • charge (int | None) – Charge of the molecule, used by RDKit to determine bond orders; if None (the default), this function will try charge=0 and leave the bond orders undetermined if that causes an error; otherwise failure to determine bond order will raise an error.

  • covFactor (float) – Scales the distance at which atoms are considered bonded, by default 1.2

  • to2D (bool) – Discard 3D information and generate 2D conformer (useful for displaying), by default True

  • molAtomMapNumber (list | Literal[True] | None) – Set the molAtomMapNumber properties to values provided in a list, or (if True is passed) set the properties to the respective atom indices

  • atomNote (list | Literal[True] | None) – Behaves like the molAtomMapNumber parameter above, but for the atomNote properties

  • atomLabel (list | Literal[True] | None) – Behaves like the molAtomMapNumber parameter above, but for the atomLabel properties

Return type:

An RDKit Mol object

Raises:

ValueError – If charge is not None and bond order determination fails

numbered_smiles_to_mol(smiles)

Convert a numbered SMILES-string to a analogically-numbered Mol object

Parameters:

smiles (str) – A SMILES string in which each atom is associated with a mapping index, e.g. ‘[H:3][C:1]#[C:0][H:2]’

Returns:

  • An rdkit.Chem.Mol() object with atom indices numbered according

  • to the indices from the SMILES-string

Return type:

rdkit.Chem.Mol

default_mol(obj)

Try many ways to get a representative Mol object for an ensemble:

  1. Use the mol attr (of either obj or obj[‘atXYZ’]) directly

2. Feed the smiles_map attr (of either obj or obj['atXYZ']) to shnitsel.bridges.default_mol() 3. Take the geometry from the first frame of the molecule and the charge specified in the charge attr (charge=0 assumed if not specified) and feed these to shnitsel.bridges.to_mol()

Parameters:

obj – An ‘atXYZ’ xr.DataArray with molecular geometries or an xr.Dataset containing the above as one of its variables

Return type:

An rdkit.Chem.Mol object

Raises:

ValueError – If the final approach fails

smiles_map(atXYZ_frame, charge=0, covFactor=1.5)

Convert a geometry to a SMILES-string, retaining atom order

Parameters:

  • atXYZ_frame – An xr.DataArray of molecular geometry

  • charge – The charge of the molcule, by default 0

  • optional – The charge of the molcule, by default 0

  • covFactor – Scales the distance at which atoms are considered bonded, by default 1.5

  • optional – Scales the distance at which atoms are considered bonded, by default 1.5

Returns:

  • A SMILES-string in which the mapping number indicates the order in which the

  • atoms appeared in the input matrix, e.g. ‘[H (3][C:1]#[C:0][H:2]’)

Return type:

str