pyxtal.molecule module

Module for handling molecules.

class pyxtal.molecule.Box(dims)

Bases: object

Class for storing the binding box for a molecule.

Parameters:

dims – [length, width, height]

operate(rot=array([[1., 0., 0.], [0., 1., 0.], [0., 0., 1.]]), center=array([0., 0., 0.]))

Perform operation on the box:

Parameters:

• rot – 3*3 rotation matrix

• center – center position

class pyxtal.molecule.Orientation(matrix=None, degrees=2, axis=None)

Bases: object

Stores orientations for molecules based on vector constraints. Can be stored to regenerate orientations consistent with a given constraint vector, without re-calling orientation_in_wyckoff_position. Allows for generating orientations which differ only in their rotation about a given axis.

Parameters:

• matrix – a 3x3 rotation matrix describing the orientation (and/or inversion) to store

• degrees – the number of degrees of freedom… 0 - The orientation refers to a single rotation matrix 1 - The orientation can be rotated about a single axis 2 - The orientation can be any pure rotation matrix

• axis – an optional axis about which the orientation can rotate. Only used if degrees is equal to 1

change_orientation(angle='random', flip=False)

Allows for specification of an angle (possibly random) to rotate about the constraint axis.

Parameters:

• angle (only apply on) – an angle to rotate about the constraint axis.

• "random" (If)

• angle. (chooses a random rotation)

• self.degrees==2 (If)

• matrix. (chooses a random rotation)

• self.degrees==1 (If)

• angle

• self.degrees==0 (If)

• change (no)

copy()

get_Euler_angles()

get the Euler angles

get_matrix(angle='random')

Generate a 3x3 rotation matrix consistent with the orientation’s constraints. Allows for specification of an angle (possibly random) to rotate about the constraint axis.

Parameters:

angle – an angle to rotate about the constraint axis. If “random”, chooses a random rotation angle. If self.degrees==2, chooses a random 3d rotation matrix to multiply by. If the original matrix is wanted, set angle=0, or call self.matrix

Returns:

a 3x3 rotation (and/or inversion) matrix (numpy array)

get_op()

Generate a SymmOp object consistent with the orientation’s constraints. Allows for specification of an angle (possibly random) to rotate about the constraint axis.

Parameters:

angle – an angle to rotate about the constraint axis. If “random”, chooses a random rotation angle. If self.degrees==2, chooses a random 3d rotation matrix to multiply by. If the original matrix is wanted, set angle=0, or call self.matrix

Returns:

pymatgen.core.structure. SymmOp object

classmethod load_dict(dicts)

random_orientation()

Applies random rotation (if possible) and returns a new orientation with the new base matrix.

Returns:

a new orientation object with a different base rotation matrix

reset_matrix(matrix)

rotate_by_matrix(matrix, ignore_constraint=True)

rotate

Parameters:

matrix – 3*3 rotation matrix

save_dict()

pyxtal.molecule.compare_mol_connectivity(mol1, mol2, ignore_name=False)

Compare two molecules by connectivity

pyxtal.molecule.find_rotor_from_smile(smile)

Find the positions of rotatable bonds in the molecule.

pyxtal.molecule.generate_molecules(smile, wps=None, N_iter=5, N_conf=10, tol=0.5)

generate pyxtal_molecules from smiles codes.

Parameters:

• smile – smiles code

• wps – list of wps

• N_iter – rdkit parameter

• N_conf – number of conformers

• tol – rdkit parameter

Returns:

a list of pyxtal molecules

pyxtal.molecule.get_inertia_tensor(coords, weights=None)

Calculate the symmetric inertia tensor for a molecule.

Parameters:

coords – [N, 3] array of coordinates

Returns:

a 3x3 numpy array representing the inertia tensor

pyxtal.molecule.has_non_aromatic_ring(smiles)

Determine if a molecule has a non-aromatic ring. Mainly used to check if a cyclic ring exists.

Parameters:

smiles – smiles string

Returns:

True or False

pyxtal.molecule.is_compatible_symmetry(mol, wp)

Tests if a molecule meets the symmetry requirements of a Wyckoff position

Parameters:

• mol – a pymatgen Molecule object.

• wp – a pyxtal.symmetry.Wyckoff_position object

pyxtal.molecule.make_graph(mol, tol=0.2)

make graph object for the input molecule

class pyxtal.molecule.pyxtal_molecule(mol=None, symmetrize=True, fix=False, torsions=None, seed=None, tm=<pyxtal.tolerance.Tol_matrix object>, symtol=0.3)

Bases: object

Extended molecule class based on pymatgen.core.structure.Molecule The added features include: 0, parse the input 1, estimate volume/tolerance/radii 2, find and store symmetry 3, get the principle axis 4, re-align the molecule

The molecule is always centered at (0, 0, 0).

If the smile format is used, the center is defined as in https://www.rdkit.org/docs/source/rdkit.Chem.rdMolTransforms.html

Otherwise, the center is just the mean of atomic positions

Parameters:

• mol – a string to reprent the molecule

• tm – tolerance matrix

align(conf, reflect=False, torsionlist=None)

Align the molecule and return the xyz The default CanonicalizeConformer function may also include inversion

apply_inversion()

reset the coordinates

copy()

simply copy the structure

get_box(padding=None)

Given a molecule, find a minimum orthorhombic box containing it. Size is calculated using min and max x, y, and z values, plus the padding defined by the vdw radius For best results, call oriented_molecule first.

Parameters:

padding – float (default is 3.4 according to the vdw radius of C)

Returns:

a Box object

Return type:

box

get_box_coordinates(xyz, padding=0, resolution=1.0)

create the points cloud to describe the molecular box

Parameters:

• center – molecular center position

• orientation – orientation matrix

• padding – padding of the box

• resolution – float in angstrom

Returns:

box axis vertices: [N, 3] array, Cartesian coordinates to describe the box. center: box center

Return type:

cell

get_center(xyz, geometry=False)

get the molecular center for a transformed xyz

get_coefs_matrix(mol2=None, ignore_error=True)

Get the Atom-Atom potential parameters E = A*exp(-B*R) - C*R^(-6) according to Gavezotti, Acc. Chem. Res., 27, 1994 in Kcal/mol and angstrom

Parameters:

• mol2 – the 2nd pyxtal_molecule object

• tm – tolerance class

Returns:

a 3D matrix for computing the intermolecular energy

get_energy(xyz1, xyz2)

Get packing energy between two neighboring molecules

get_orientation(xyz, rtol=0.15)

For the given xyz, compute the orientation

Parameters:

xyz – molecular xyz

get_orientations_in_wp(wp, rtol=0.01)

Compute the valid orientations from a given Wyckoff site symmetry.

Parameters:

wp – a pyxtal.symmetry.Wyckoff_position object

Returns:

a list of pyxtal.molecule.Orientation objects

get_orientations_in_wps(wps=None, rtol=0.01)

Compute the valid orientations from a given Wyckoff site symmetry.

Parameters:

wp – a pyxtal.symmetry.Wyckoff_position object

Returns:

a list of operations.Orientation objects

get_principle_axes(xyz, rdmt=True)

get the principle axis for a rotated xyz, sorted by the moments

get_radius()

get the radius of a molecule

get_rmsd(xyz, debug=False)

Compute the rmsd with another 3D xyz coordinates

Parameters:

xyz – 3D coordinates

Returns:

rmsd values transition matrix: 4*4 matrix match: True or False

Return type:

rmsd (float)

get_rmsd2(xyz0, xyz1)

Compute the rmsd with another 3D xyz coordinates

Parameters:

xyz – 3D coordinates

Returns:

transition matrix:

Return type:

rmsd

get_symbols()

get_symmetry(xyz=None, symmetrize=False, rtol=0.3)

Set the molecule’s point symmetry.

• pga: pymatgen.symmetry.analyzer.PointGroupAnalyzer object

• pg: pyxtal.symmetry.Group object

• symops: a list of SymmOp objects

Parameters:

symmetrize – boolean, whether or not symmetrize the coordinates

get_tols_matrix(mol2=None, tm=None)

Compute the 2D tolerance matrix between the current and other molecules

Parameters:

• mol2 – the 2nd pyxtal_molecule object

• tm – tolerance class

Returns:

a 2D matrix which is used internally for distance checking.

get_torsion_angles(xyz=None, torsionlist=None)

get the torsion angles

list_molecules()

list the internally supported molecules

classmethod load_str(string)

load the molecule from a dictionary

perturb_torsion(xyz)

slightly perturb the torsion

rdkit_mol(N_confs=1)

initialize the mol xyz and torsion list

rdkit_mol_init(smile, fix, torsions)

initialize the mol xyz and torsion list

Parameters:

• smile – smile string

• fix – whether or not fix the seed

• torsions – None or list

relax(xyz, align=False)

Relax the input xyz coordinates with rdit MMFF

Parameters:

• xyz – 3D coordinates

• align – whether or not align the xyz

Returns:

new xyz eng: energy value

Return type:

xyz

reset_positions(coors)

reset the coordinates

save_str()

save the object as a dictionary

set_labels()

Set atom labels for the given molecule for H-bond caculation. Needs to identify the following: - (O)N-H - acid-O - amide-O - alcohol-O - N with NH2 - N with NH

set_torsion_angles(conf, angles, reflect=False, torsionlist=None)

reset the torsion angles and update molecular xyz

show()

show the molecule

show_box(center=array([0., 0., 0.]), orientation=None)

show the molecule

swap_axis(ax)

swap the molecular axis

to_ase()

Convert to ase atoms

pyxtal.molecule.random() → x in the interval [0, 1).

pyxtal.molecule.reoriented_molecule(mol)

Allign a molecule so that its principal axes is the identity matrix.

Parameters:

mol – a Molecule object

Returns:

a reoriented copy of the original molecule. P: the 3x3 rotation matrix used to obtain it.

Return type:

new_mol