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Utilities

qcio.json_dumps 

json_dumps(obj: Union[BaseModel, list[BaseModel]]) -> str

Serialization helper for lists of pydantic objects.

Source code in qcio/utils.py 
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def json_dumps(obj: Union[BaseModel, list[BaseModel]]) -> str:
    """Serialization helper for lists of pydantic objects."""
    if isinstance(obj, list):
        return json.dumps([o.model_dump() for o in obj])
    return obj.model_dump_json()

qcio.rmsd 

rmsd(struct1: Structure, struct2: Structure, symmetry: bool = True, numthreads: int = 1, use_hueckel: bool = True, use_vdw: bool = False, cov_factor: float = 1.3, length_unit: LengthUnit = LengthUnit.BOHR) -> float

Calculate the root mean square deviation between two structures in Bohr or Angstrom.

May lead to a 'combinatorial explosion' especially if many molecule symmetries (e.g., many hydrogens) are present.If this function is taking a long time to compute, consider passing symmetry=False to disable symmetry consideration. Or pass numthreads=an_integer to increase the number of threads used for the symmetry consideration step.

Parameters:

Name Type Description Default
struct1 Structure

The first structure.

 required
struct2 Structure

The second structure.

 required
symmetry bool

Whether to consider symmetries in the structures before calculating the RMSD, i.e., to allow atom renumbering. This relies on the RDKit DetermineConnectivity and GetBestRMS functions. If False, the RMSD is calculated with alignment but without considering symmetry, i.e., naively assuming the atoms are already correctly indexed across structures.

 True
numthreads int

The number of threads to use for the RMSD calculation. Applies only to the alignment step if symmetry=True.

 1
use_hueckel bool

Whether to use Hueckel method when determining connectivity. Applies only to symmetry=True.

 True
use_vdw bool

Whether to use Van der Waals radii when determining connectivity. Applies only to symmetry=True.

 False
cov_factor float

The scaling factor for the covalent radii when determining connectivity. Applies only to symmetry=True.

 1.3
length_unit LengthUnit

The unit of length to use for the RMSD calculation. Default is "bohr". If "angstrom", the RMSD will be in Angstroms.

 BOHR

Returns:

Type Description
float

The RMSD between the two structures in Angstroms.
Source code in qcio/models/utils.py 
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def rmsd(
    struct1: "Structure",
    struct2: "Structure",
    symmetry: bool = True,
    numthreads: int = 1,
    use_hueckel: bool = True,
    use_vdw: bool = False,
    cov_factor: float = 1.3,
    length_unit: LengthUnit = LengthUnit.BOHR,
) -> float:
    """
    Calculate the root mean square deviation between two structures in Bohr or Angstrom.

    May lead to a 'combinatorial explosion' especially if many molecule symmetries
    (e.g., many hydrogens) are present.If this function is taking a long time to
    compute, consider passing `symmetry=False` to disable symmetry consideration. Or
    pass `numthreads=an_integer` to increase the number of threads used for the
    symmetry consideration step.

    Args:
        struct1: The first structure.
        struct2: The second structure.
        symmetry: Whether to consider symmetries in the structures before calculating
            the RMSD, i.e., to allow atom renumbering. This relies on the  RDKit
            `DetermineConnectivity` and `GetBestRMS` functions. If False, the RMSD is
            calculated with alignment but without considering symmetry, i.e., naively
            assuming the atoms are already correctly indexed across structures.
        numthreads: The number of threads to use for the RMSD calculation. Applies only
            to the alignment step if `symmetry=True`.
        use_hueckel: Whether to use Hueckel method when determining connectivity.
            Applies only to `symmetry=True`.
        use_vdw: Whether to use Van der Waals radii when determining connectivity.
            Applies only to `symmetry=True`.
        cov_factor: The scaling factor for the covalent radii when determining
            connectivity. Applies only to `symmetry=True`.
        length_unit: The unit of length to use for the RMSD calculation. Default is
            "bohr". If "angstrom", the RMSD will be in Angstroms.

    Returns:
        The RMSD between the two structures in Angstroms.
    """
    _assert_module_installed("rdkit")
    from rdkit.Chem import rdMolAlign  # type: ignore

    # Create RDKit molecules
    mol1 = _rdkit_mol_from_structure(struct1)
    mol2 = _rdkit_mol_from_structure(struct2)

    # Compute RMSD
    if symmetry:
        # Determine connectivity
        _rdkit_determine_connectivity(
            mol1,
            charge=struct1.charge,
            use_hueckel=use_hueckel,
            use_vdw=use_vdw,
            cov_factor=cov_factor,
        )

        _rdkit_determine_connectivity(
            mol2,
            charge=struct2.charge,
            use_hueckel=use_hueckel,
            use_vdw=use_vdw,
            cov_factor=cov_factor,
        )
        # Take symmetry into account, align the two molecules, compute RMSD
        try:
            rmsd = rdMolAlign.GetBestRMS(mol2, mol1, numThreads=numthreads)
        except RuntimeError as e:  # Possible failure to make substructure match
            try:  # Swap the order of the molecules and try again.
                rmsd = rdMolAlign.GetBestRMS(mol1, mol2, numThreads=numthreads)
            except RuntimeError:  # If it fails again, raise the original error
                raise e

    else:  # Do not take symmetry into account. Structs aligned by atom index.
        rmsd, _ = rdMolAlign.GetAlignmentTransform(mol2, mol1)

    return rmsd * ANGSTROM_TO_BOHR if length_unit == LengthUnit.BOHR else rmsd

qcio.align 

align(struct: Structure, refstruct: Structure, symmetry: bool = True, use_hueckel: bool = True, use_vdw: bool = False, cov_factor: float = 1.3, length_unit: LengthUnit = LengthUnit.BOHR) -> tuple[Structure, float]

Return a new structure that is optimally aligned to the reference structure and the RMSD between the two structures in Bohr or Angstroms.

May lead to a 'combinatorial explosion' especially if many molecule symmetries (e.g., many hydrogens) are present.If this function is taking a long time to compute, consider passing symmetry=False to disable symmetry consideration.

Parameters:

Name Type Description Default
struct Structure

The structure to align.

 required
refstruct Structure

The reference structure.

 required
symmetry bool

Whether to consider symmetries in the structures before aligning and calculating the RMSD, i.e., to allow atom renumbering. This relies on the RDKit's GetBestAlignmentTransform method and GetBestRMS functions. If False, the RMSD is calculated with alignment but without considering symmetry, i.e., naively assuming the atoms are already correctly indexed across structures.

 True
use_hueckel bool

Whether to use Hueckel method when determining connectivity. Applies only to best=True.

 True
use_vdw bool

Whether to use Van der Waals radii when determining connectivity. Applies only to best=True.

 False
cov_factor float

The scaling factor for the covalent radii when determining connectivity. Applies only to best=True.

 1.3
length_unit LengthUnit

The unit of length to use for the RMSD calculation. Default is "bohr". If "angstrom", the RMSD will be in Angstroms.

 BOHR

Returns:

Type Description
tuple[Structure, float]

Tuple of the aligned structure and the RMSD in Angstroms.
Source code in qcio/utils.py 
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def align(
    struct: Structure,
    refstruct: Structure,
    symmetry: bool = True,
    use_hueckel: bool = True,
    use_vdw: bool = False,
    cov_factor: float = 1.3,
    length_unit: LengthUnit = LengthUnit.BOHR,
) -> tuple[Structure, float]:
    """
    Return a new structure that is optimally aligned to the reference structure and
    the RMSD between the two structures in Bohr or Angstroms.

    May lead to a 'combinatorial explosion' especially if many molecule symmetries
    (e.g., many hydrogens) are present.If this function is taking a long time to
    compute, consider passing `symmetry=False` to disable symmetry consideration.

    Args:
        struct: The structure to align.
        refstruct: The reference structure.
        symmetry: Whether to consider symmetries in the structures before aligning and
            calculating the RMSD, i.e., to allow atom renumbering. This relies on the
            RDKit's `GetBestAlignmentTransform` method and `GetBestRMS` functions. If False, the RMSD is
            calculated with alignment but without considering symmetry, i.e., naively
            assuming the atoms are already correctly indexed across structures.
        use_hueckel: Whether to use Hueckel method when determining connectivity.
            Applies only to `best=True`.
        use_vdw: Whether to use Van der Waals radii when determining connectivity.
            Applies only to `best=True`.
        cov_factor: The scaling factor for the covalent radii when determining
            connectivity. Applies only to `best=True`.
        length_unit: The unit of length to use for the RMSD calculation. Default is
            "bohr". If "angstrom", the RMSD will be in Angstroms.

    Returns:
        Tuple of the aligned structure and the RMSD in Angstroms.
    """
    _assert_module_installed("rdkit")
    from rdkit.Chem import rdMolAlign  # type: ignore

    # Create RDKit molecules
    mol = _rdkit_mol_from_structure(struct)
    refmol = _rdkit_mol_from_structure(refstruct)

    # Determine connectivity
    _rdkit_determine_connectivity(
        mol,
        charge=struct.charge,
        use_hueckel=use_hueckel,
        use_vdw=use_vdw,
        cov_factor=cov_factor,
    )
    _rdkit_determine_connectivity(
        refmol,
        charge=refstruct.charge,
        use_hueckel=use_hueckel,
        use_vdw=use_vdw,
        cov_factor=cov_factor,
    )

    # Compute RMSD and align mol to refmol
    if symmetry:
        rmsd_val, trnsfm_matrix, atm_map = rdMolAlign.GetBestAlignmentTransform(
            mol, refmol
        )  # type: ignore # noqa: E501
    else:
        rmsd_val, trnsfm_matrix = rdMolAlign.GetAlignmentTransform(mol, refmol)

    # Convert to homogeneous coordinates in Angstroms
    coords_homogeneous = np.hstack(
        [struct.geometry_angstrom, np.ones((struct.geometry.shape[0], 1))]
    )

    # Apply the transformation matrix
    transformed_coords_homogeneous = coords_homogeneous @ trnsfm_matrix.T

    # Extract the transformed 3D coordinates and convert to Bohr
    transformed_coords = transformed_coords_homogeneous[:, :3] * ANGSTROM_TO_BOHR

    # Reorder the atoms to match the reference structure
    if symmetry:
        if Counter(struct.symbols) != Counter(refstruct.symbols):
            raise ValueError(
                "Structures must have the same number and type of atoms for "
                "`reorder_atoms=True` at this time. Pass "
                "`reorder_atoms=False` to align structures with different atom "
                "counts."
            )
        symbols = refstruct.symbols
        geometry = np.zeros((len(atm_map), 3))

        for probe_idx, ref_idx in atm_map:
            geometry[ref_idx] = transformed_coords[probe_idx]

    # Otherwise, keep the original atom order
    else:
        symbols = struct.symbols
        geometry = transformed_coords

    return (
        Structure(
            symbols=symbols,
            geometry=geometry,
            charge=struct.charge,
            multiplicity=struct.multiplicity,
            connectivity=struct.connectivity,
            identifiers=struct.identifiers,
        ),
        rmsd_val * ANGSTROM_TO_BOHR if length_unit == LengthUnit.BOHR else rmsd_val,
    )

qcio.to_multi_xyz 

to_multi_xyz(structures: Iterable[Structure]) -> str

Create a multi-structure XYZ string from a list of structures.

Parameters:

Name Type Description Default
structures Iterable[Structure]

An Iterable of Structure objects.

 required

Returns:

Type Description
str

The multi-structure XYZ string.
Source code in qcio/models/utils.py 
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def to_multi_xyz(structures: Iterable["Structure"]) -> str:
    """Create a multi-structure XYZ string from a list of structures.

    Args:
        structures: An Iterable of Structure objects.

    Returns:
        The multi-structure XYZ string.
    """
    return "".join(struct.to_xyz() for struct in structures)