Constructed Molecule

class ConstructedMolecule(topology_graph)[source]

Bases: stk.molecular.molecules.molecule.molecule.Molecule

Represents constructed molecules.

Examples

Initialization

A ConstructedMolecule is initialized from a TopologyGraph, which is typically initialized from some BuildingBlock instances.

import stk

bb1 = stk.BuildingBlock('NCCCN', [stk.PrimaryAminoFactory()])
bb2 = stk.BuildingBlock(
    smiles='O=CC(C=O)CC=O',
    functional_groups=[stk.AldehydeFactory()],
)
tetrahedron = stk.cage.FourPlusSix((bb1, bb2))
cage = stk.ConstructedMolecule(tetrahedron)

Hierarchical Construction

A ConstructedMolecule may be used to construct other ConstructedMolecule instances, though you will probably have to convert it to a BuildingBlock first

import stk

bb1 = stk.BuildingBlock('NCCCN', [stk.PrimaryAminoFactory()])
bb2 = stk.BuildingBlock(
    smiles='O=CC(C=O)CC=O',
    functional_groups=[stk.AldehydeFactory()],
)
tetrahedron = stk.cage.FourPlusSix((bb1, bb2))
cage = stk.ConstructedMolecule(tetrahedron)

benzene = stk.host_guest.Guest(stk.BuildingBlock('c1ccccc1'))
cage_complex = stk.host_guest.Complex(
    host=stk.BuildingBlock.init_from_molecule(cage),
    guests=benzene,
)
cage_complex = stk.ConstructedMolecule(cage_complex)

Obviously, the initialization of the ConstructedMolecule depends mostly on the specifics of the TopologyGraph used, and the documentation of those classes should be examined for more examples.

Methods

clone()

Return a clone.

get_atom_infos([atom_ids])

Yield data about atoms in the molecule.

get_atomic_positions([atom_ids])

Yield the positions of atoms.

get_atoms([atom_ids])

Yield the atoms in the molecule, ordered by id.

get_bond_infos()

Yield data about bonds in the molecule.

get_bonds()

Yield the bond in the molecule.

get_building_blocks()

Yield the building blocks of the constructed molecule.

get_canonical_atom_ids()

Map the id of each atom to its id under canonical ordering.

get_centroid([atom_ids])

Return the centroid.

get_direction([atom_ids])

Return a vector of best fit through the atoms.

get_maximum_diameter([atom_ids])

Return the maximum diameter.

get_num_atoms()

Return the number of atoms in the molecule.

get_num_bonds()

Return the number of bonds in the molecule.

get_num_building_block(building_block)

Get the number of times building_block is present.

get_plane_normal([atom_ids])

Return the normal to the plane of best fit.

get_position_matrix()

Return a matrix holding the atomic positions.

init(atoms, bonds, position_matrix, …)

Initialize a ConstructedMolecule from its components.

init_from_construction_result(…)

Initialize a ConstructedMolecule.

to_rdkit_mol()

Return an rdkit representation.

with_canonical_atom_ordering()

Return a clone, with canonically ordered atoms.

with_centroid(position[, atom_ids])

Return a clone with its centroid at position.

with_displacement(displacement)

Return a displaced clone.

with_position_matrix(position_matrix)

Return a clone with atomic positions set by position_matrix.

with_rotation_about_axis(angle, axis, origin)

Return a rotated clone.

with_rotation_between_vectors(start, target, …)

Return a rotated clone.

with_rotation_to_minimize_angle(start, …)

Return a rotated clone.

with_structure_from_file(path[, extension])

Return a clone, with its structure taken from a file.

write(path[, atom_ids])

Write the structure to a file.

__init__(topology_graph)[source]

Initialize a ConstructedMolecule.

Parameters

topology_graph (TopologyGraph) – The topology graph of the constructed molecule.

clone()[source]

Return a clone.

Returns

The clone. Has the same type as the original molecule.

Return type

Molecule

get_atom_infos(atom_ids=None)[source]

Yield data about atoms in the molecule.

Parameters

atom_ids (iterable of int, optional) – The ids of atoms whose data is desired. If None, data on all atoms will be yielded. Can be a single int, if data on a single atom is desired.

Yields

AtomInfo – Data about an atom.

get_atomic_positions(atom_ids=None)

Yield the positions of atoms.

Parameters

atom_ids (iterable of int, optional) – The ids of the atoms whose positions are desired. If None, then the positions of all atoms will be yielded. Can be a single int, if the position of a single atom is desired.

Yields

numpy.ndarray – The x, y and z coordinates of an atom.

get_atoms(atom_ids=None)

Yield the atoms in the molecule, ordered by id.

Parameters

atom_ids (iterable of int, optional) – The ids of atoms to yield. Can be a single int if a single atom is wanted, or None if all atoms are wanted.

Yields

Atom – An atom in the molecule.

get_bond_infos()[source]

Yield data about bonds in the molecule.

Yields

BondInfo – Data about a bond.

get_bonds()

Yield the bond in the molecule.

Yields

Bond – A bond in the molecule.

get_building_blocks()[source]

Yield the building blocks of the constructed molecule.

Building blocks are yielded in an order based on their position in the constructed molecule. For two topologically equivalent constructed molecules, but with different building blocks, equivalently positioned building blocks will be yielded at the same time.

Yields

Molecule – A building block of the constructed molecule.

get_canonical_atom_ids()

Map the id of each atom to its id under canonical ordering.

Returns

Maps the id of each atom in the molecule to the id it would have under canonical ordering.

Return type

dict

get_centroid(atom_ids=None)

Return the centroid.

Parameters

atom_ids (iterable of int, optional) – The ids of atoms which are used to calculate the centroid. Can be a single int, if a single atom is to be used, or None if all atoms are to be used.

Returns

The centroid of atoms specified by atom_ids.

Return type

numpy.ndarray

Raises

ValueError – If atom_ids has a length of 0.

get_direction(atom_ids=None)

Return a vector of best fit through the atoms.

Parameters

atom_ids (iterable of int, optional) – The ids of atoms which should be used to calculate the vector. Can be a single int, if a single atom is to be used, or None, if all atoms are to be used.

Returns

The vector of best fit.

Return type

numpy.ndarray

Raises

ValueError – If atom_ids has a length of 0.

get_maximum_diameter(atom_ids=None)

Return the maximum diameter.

This method does not account for the van der Waals radius of atoms.

Parameters

atom_ids (iterable of int, optional) – The ids of atoms which are considered when looking for the maximum diameter. Can be a single int, if a single atom is to be used, or None, if all atoms are to be used.

Returns

The maximum diameter in the molecule.

Return type

float

Raises

ValueError – If atom_ids has a length of 0.

get_num_atoms()

Return the number of atoms in the molecule.

Returns

The number of atoms in the molecule.

Return type

int

get_num_bonds()

Return the number of bonds in the molecule.

Returns

The number of bonds in the molecule.

Return type

int

get_num_building_block(building_block)[source]

Get the number of times building_block is present.

Parameters

building_block (Molecule) – The building block whose frequency in the constructed molecule is desired.

Returns

The number of times building_block was used in the construction of the constructed molecule.

Return type

int

get_plane_normal(atom_ids=None)

Return the normal to the plane of best fit.

Parameters

atom_ids (iterable of int, optional) – The ids of atoms which should be used to calculate the plane. Can be a single int, if a single atom is to be used, or None, if all atoms are to be used.

Returns

Vector orthonormal to the plane of the molecule.

Return type

numpy.ndarray

Raises

ValueError – If atom_ids has a length of 0.

get_position_matrix()

Return a matrix holding the atomic positions.

Returns

The array has the shape (n, 3). Each row holds the x, y and z coordinates of an atom.

Return type

numpy.ndarray

classmethod init(atoms, bonds, position_matrix, atom_infos, bond_infos, num_building_blocks)[source]

Initialize a ConstructedMolecule from its components.

Parameters
  • atoms (tuple of Atom) – The atoms of the molecule.

  • bond (tuple of Bond) – The bonds of the molecule.

  • position_matrix (numpy.ndarray) – A (n, 3) position matrix of the molecule.

  • atom_infos (tuple of AtomInfo) – The atom infos of the molecule.

  • bond_infos (tuple of BondInfo) – The bond infos of the molecule.

  • num_building_blocks (dict) – Maps each building block of the constructed molecule to the number of times it is present in it.

Returns

The constructed molecule.

Return type

ConstructedMolecule

classmethod init_from_construction_result(construction_result)[source]

Initialize a ConstructedMolecule.

Parameters

construction_result (ConstructionResult) – The result of a construction, from which the ConstructedMolecule should be initialized.

Returns

The constructed molecule.

Return type

ConstructedMolecule

to_rdkit_mol()

Return an rdkit representation.

Returns

The molecule in rdkit format.

Return type

rdkit.Mol

with_canonical_atom_ordering()

Return a clone, with canonically ordered atoms.

Returns

The clone. Has the same type as the original molecule.

Return type

Molecule

with_centroid(position, atom_ids=None)

Return a clone with its centroid at position.

Parameters
  • position (numpy.ndarray) – This array holds the position on which the centroid of the clone is going to be placed.

  • atom_ids (iterable of int, optional) – The ids of atoms which should have their centroid set to position. Can be a single int, if a single atom is to be used, or None, if all atoms are to be used.

Returns

A clone with its centroid at position. Has the same type as the original molecule.

Return type

Molecule

with_displacement(displacement)

Return a displaced clone.

Parameters

displacement (numpy.ndarray) – The displacement vector to be applied.

Returns

A displaced clone. Has the same type as the original molecule.

Return type

Molecule

with_position_matrix(position_matrix)

Return a clone with atomic positions set by position_matrix.

Parameters

position_matrix (numpy.ndarray) – The position matrix of the clone. The shape of the matrix is (n, 3).

Returns

The clone. Has the same type as the original molecule.

Return type

Molecule

with_rotation_about_axis(angle, axis, origin)

Return a rotated clone.

The clone is rotated by angle about axis on the origin.

Parameters
  • angle (float) – The size of the rotation in radians.

  • axis (numpy.ndarray) – The axis about which the rotation happens. Must have unit magnitude.

  • origin (numpy.ndarray) – The origin about which the rotation happens.

Returns

A rotated clone. Has the same type as the original molecule.

Return type

Molecule

with_rotation_between_vectors(start, target, origin)

Return a rotated clone.

The rotation is equal to a rotation from start to target.

Given two direction vectors, start and target, this method applies the rotation required transform start to target onto the clone. The rotation occurs about the origin.

For example, if the start and target vectors are 45 degrees apart, a 45 degree rotation will be applied to the clone. The rotation will be along the appropriate direction.

The great thing about this method is that you as long as you can associate a geometric feature of the molecule with a vector, then the clone can be rotated so that this vector is aligned with target. The defined vector can be virtually anything. This means that any geometric feature of the molecule can be easily aligned with any arbitrary direction.

Parameters
  • start (numpy.ndarray) – A vector which is to be rotated so that it transforms into the target vector.

  • target (numpy.ndarray) – The vector onto which start is rotated.

  • origin (numpy.ndarray) – The point about which the rotation occurs.

Returns

A rotated clone. Has the same type as the original molecule.

Return type

Molecule

with_rotation_to_minimize_angle(start, target, axis, origin)

Return a rotated clone.

The clone is rotated by the rotation required to minimize the angle between start and target.

Note that this function will not necessarily overlay the start and target vectors. This is because the possible rotation is restricted to the axis.

Parameters
  • start (numpy.ndarray) – The vector which is rotated.

  • target (numpy.ndarray) – The vector which is stationary.

  • axis (numpy.ndarray) – The vector about which the rotation happens. Must have unit magnitude.

  • origin (numpy.ndarray) – The origin about which the rotation happens.

Returns

A rotated clone. Has the same type as the original molecule.

Return type

Molecule

Raises

ValueError – If target has a magnitude of 0. In this case it is not possible to calculate an angle between start and target.

with_structure_from_file(path, extension=None)

Return a clone, with its structure taken from a file.

Multiple file types are supported, namely:

  1. .mol, .sdf - MDL V2000 and V3000 files

  2. .xyz - XYZ files

  3. .mae - Schrodinger Maestro files

  4. .coord - Turbomole files

  5. .pdb - PDB files

Parameters
  • path (str) – The path to a molecular structure file holding updated coordinates for the Molecule.

  • extension (str, optional) – If you want to treat the file as though it has a particular extension, put it here. Include the dot.

Returns

A clone with atomic positions found in path. Has the same type as the original molecule.

Return type

Molecule

write(path, atom_ids=None)

Write the structure to a file.

This function will write the format based on the extension of path.

  1. .mol, .sdf - MDL V3000 MOL file

  2. .xyz - XYZ file

  3. .pdb - PDB file

Parameters
  • path (str) – The path to which the molecule should be written.

  • atom_ids (iterable of int, optional) – The atom ids of atoms to write. Can be a single int, if a single atom is to be used, or None, if all atoms are to be used. If you use this parameter, the atom ids in the file may not correspond to the atom ids in the molecule.

Returns

The molecule.

Return type

Molecule