vtkmodules.util.molecule

Pythonic API for vtkMolecule.

Adds iteration, len, array properties, and interop with ASE and RDKit::

from vtkmodules.vtkCommonDataModel import vtkMolecule

# Construction from arrays:
mol = vtkMolecule(atomic_numbers=[1, 1, 8],
                  positions=[[0, 0, 0], [1, 0, 0], [0.5, 0.8, 0]])
mol = vtkMolecule(symbols=['H', 'H', 'O'],
                  positions=[[0, 0, 0], [1, 0, 0], [0.5, 0.8, 0]])

# Sequence protocol:
len(mol)                 # atom count
mol[0]                   # vtkAtom proxy
for atom in mol: ...     # iterate atoms

# Array properties:
mol.positions            # (N, 3) float32 numpy array
mol.atomic_numbers       # (N,) uint16 numpy array
mol.bond_orders          # (N_bonds,) uint16 numpy array

# Views:
mol.atoms[2]             # indexable atom view
mol.bonds[0]             # indexable bond view

# Data:
mol.atom_data            # vtkDataSetAttributes
mol.bond_data            # vtkDataSetAttributes

# Interop:
ase_atoms = mol.to_ase()
mol2 = vtkMolecule().from_ase(ase_atoms)
rdmol = mol.to_rdkit()
mol3 = vtkMolecule().from_rdkit(rdmol)

Module Contents

Classes

_AtomView	Indexable, iterable view of atoms in a vtkMolecule.
_BondView	Indexable, iterable view of bonds in a vtkMolecule.
_MoleculeMixin
Molecule

Functions

_get_periodic_table

Return a lazily-created singleton vtkPeriodicTable.

Data

_periodic_table
_RDKIT_BOND_TYPE_TO_VTK_ORDER
_VTK_ORDER_TO_RDKIT_BOND_TYPE

API

vtkmodules.util.molecule._periodic_table

None

vtkmodules.util.molecule._get_periodic_table()

Return a lazily-created singleton vtkPeriodicTable.

vtkmodules.util.molecule._RDKIT_BOND_TYPE_TO_VTK_ORDER

None

vtkmodules.util.molecule._VTK_ORDER_TO_RDKIT_BOND_TYPE

None

class vtkmodules.util.molecule._AtomView(mol)

Indexable, iterable view of atoms in a vtkMolecule.

Initialization

__slots__

(‘_mol’,)

__len__()

__getitem__(key)

__iter__()

__repr__()

class vtkmodules.util.molecule._BondView(mol)

Indexable, iterable view of bonds in a vtkMolecule.

Initialization

__slots__

(‘_mol’,)

__len__()

__getitem__(key)

__iter__()

__repr__()

class vtkmodules.util.molecule._MoleculeMixin(*args, atomic_numbers=None, symbols=None, positions=None, **kwargs)

Initialization

__len__()

__getitem__(key)

__iter__()

property atoms

Indexable, iterable view of atoms.

property bonds

Indexable, iterable view of bonds.

property positions

Atom positions as an (N, 3) float32 numpy array.

This is a live view into VTK memory; mutating it changes the molecule in place (call Modified() afterwards to notify the pipeline). The view is invalidated if the atom array is reallocated (e.g. by AppendAtom), so do not hold onto it across mutations. Use the positions setter for a safe, length-checked bulk assignment.

property atomic_numbers

Atomic numbers as an (N,) uint16 numpy array.

This is a live view into VTK memory; mutating it changes the molecule in place (call Modified() afterwards to notify the pipeline). The view is invalidated if the atom array is reallocated (e.g. by AppendAtom), so do not hold onto it across mutations. Use the atomic_numbers setter for a safe, length-checked bulk assignment.

property bond_orders

Bond orders as an (N_bonds,) uint16 numpy array.

This is a live view into VTK memory; mutating it changes the molecule in place (call Modified() afterwards to notify the pipeline). The view is invalidated if the bond array is reallocated (e.g. by AppendBond), so do not hold onto it across mutations.

property symbols

Element symbols as a list of strings.

Requires vtkDomainsChemistry.

property formula

Molecular formula in Hill system order.

Requires vtkDomainsChemistry.

property atom_data

Atom data arrays (vtkDataSetAttributes).

property bond_data

Bond data arrays (vtkDataSetAttributes).

append(atomic_number_or_symbol, position)

Append an atom and return the vtkAtom proxy.

Parameters

atomic_number_or_symbol : int or str Atomic number or element symbol. position : sequence of 3 floats (x, y, z) position.

add_bond(atom1, atom2, order=1)

Add a bond between two atoms.

Parameters

atom1, atom2 : int Atom indices. order : int Bond order (1=single, 2=double, 3=triple).

property lattice

Unit cell lattice as a 3x3 numpy array, or None if not set.

VTK stores lattice vectors as columns of a 3x3 matrix.

property lattice_origin

Lattice origin as a (3,) numpy array, or None if no lattice is set.

The origin is only meaningful together with a lattice, so this mirrors lattice and returns None when HasLattice() is false.

__repr__()

to_ase()

Convert to an ASE Atoms object.

Positions and atomic numbers are copied. If a lattice is set, it is transferred as the ASE cell (transposed, since VTK stores vectors as columns and ASE as rows) and pbc=True.

Bonds are not transferred (ASE does not store bonds).

from_ase(atoms)

Populate this molecule from an ASE Atoms object.

Existing atoms and bonds are cleared first. Bonds are not set (use vtkSimpleBondPerceiver to infer them). Returns self so it can be chained, e.g. vtkMolecule().from_ase(atoms).

to_rdkit(sanitize=False)

Convert to an RDKit Mol object.

Atoms, bonds, and 3D coordinates (as a conformer) are transferred. Bond order mapping: 1→SINGLE, 2→DOUBLE, 3→TRIPLE, 4→AROMATIC.

Parameters

sanitize : bool If True, run Chem.SanitizeMol on the result. The returned mol is otherwise unsanitized: perception of rings, valence, and aromaticity has not been run, and some downstream RDKit operations require a sanitized mol. Sanitization is off by default because molecules derived from geometry or bond perceivers need not satisfy RDKit’s valence model, and SanitizeMol would raise on them.

from_rdkit(rdkit_mol, conformer_id=-1)

Populate this molecule from an RDKit Mol object.

Existing atoms and bonds are cleared first. Returns self so it can be chained, e.g. vtkMolecule().from_rdkit(rdmol).

Parameters

rdkit_mol : rdkit.Chem.Mol Source molecule. conformer_id : int Which conformer to use for positions (-1 = first/default). If no conformer exists, positions default to (0, 0, 0).

class vtkmodules.util.molecule.Molecule(*args, atomic_numbers=None, symbols=None, positions=None, **kwargs)

Bases: vtkmodules.util.molecule._MoleculeMixin, vtkmodules.vtkCommonDataModel.vtkMolecule

Initialization