schrodinger.comparison.struc module

schrodinger.comparison.struc.align_pos(pos, fit_pos, fit_ref_pos, weights=None, return_trans_rot=False, allow_improper_rotation=False, is_precentered=False)

Align pos using transformations (rotation and translation) derived from converting fit_pos to fit_ref_pos. Weighted Kabsch algorithm is used to obtain the transformations.

Parameters

  • allow_improper_rotation – If not set, only proper rotation is allowed.

  • is_precentered (bool) – True if all position arrays, i.e., pos, fit_pos, and fit_ref_pos, have been properly centered. Note that pos and fit_pos should be centered to the origin with respect to weights.

Returns

aligned pos and optionally the transformation matrices if return_trans_rot is set to be True

Return type

Nx3 numpy.ndarray if return_trans is False. Otherwise (numpy.ndarray, (1x3 numpy.ndarray, 3x3 numpy.ndarray)) where the 1x3 array is the translation vector, and the 3x3 array is the rotation matrix. The aligned position is calculated as numpy.dot(pos - trans_vec, rot_mat).

schrodinger.comparison.struc.chorus_to_lower_triangle(struct)

Update chorus properties and with the atom coordinates so that upper triangle of the lattice vectors are all zeros. This is needed so that maestro displays structure correctly.

Parameters

struct (structure.Structure) – Structure to update

Return type

structure.Structure

Returns

Updated structure (not a copy!!)

schrodinger.comparison.struc.atom_indices_are_contiguous(st: schrodinger.structure._structure.Structure) → bool

Determine if atom indices of each molecule are contiguous. This is to guard against DFT making hydrogen transfers.

schrodinger.comparison.struc.get_pymatgen_mol(ct)
schrodinger.comparison.struc.get_pointgroup_symmetry_ops(st, mol_index=1, include_H=False)

Determine point group symmetry ops using pymatgen. These symmetry operations are given at the origin.

Parameters

  • st – Structure

  • mol_index – index of molecule to perform point group analysis on assumed to be the ASU

  • include_H – if True include hydrogens

Returns

list of SymmOp instances representing symmetry operations

schrodinger.comparison.struc.rotate_pointgroup_symmetry_ops(symmetry_ops, U)

transform point group symmetry ops due to a rotation of the molecule for which the symmetry operations belong

Parameters

  • symmetry_ops – list of SymmOp

  • U – 3x3 unitary transformation

:return list of SymmOp

schrodinger.comparison.struc.apply_pointgroup_symmetry_op(op, st, asu_atom_indices)

Apply point group symmetry operation to structure. This will translate the asu to the origin, apply the symmetry operation and translate back

Parameters

  • op – SymmOp

  • st – Structure to transform

  • asu_atom_indices – list of atom indices of the asu

Returns

transformed cartesian coordinates

schrodinger.comparison.struc.get_op_trans_idx(op, st, asu_atom_indices)

calculates the transformation of indices that occurs under the application of the given symmetry operation

Parameters

  • op – SymmOp

  • st – Structure to transform

  • asu_atom_indices – list of atom indices of the asu

Returns

0-based indices for coordinates after the transformation

schrodinger.comparison.struc.is_better_match(n_matched, rmsd, best_n, best_rmsd, n_thresh=20)

is a new rmsd N better?

schrodinger.comparison.struc.center_com(st: schrodinger.structure._structure.Structure)

Move center of mass to origin.

schrodinger.comparison.struc.align_st_by_mol(st: schrodinger.structure._structure.Structure, st_indices: numpy.ndarray, ref_st: schrodinger.structure._structure.Structure, ref_indices: numpy.ndarray, allow_reflection=False) → Tuple[numpy.ndarray, numpy.ndarray]

Transform st such that its molecule mol_id is aligned to molecule ref_mol_id in ref_st. Only heavy atoms are considered.

Parameters

  • st – test structure to align

  • st_indices – list of atom indices to align (zero based)

  • ref_st – reference structure to align on

  • ref_indices – list of atom indices to align on (zero based)

  • allow_reflection – allow improper rotations in alignment

Returns

translation vector and rotation matrix for the alignment

schrodinger.comparison.struc.reorder_cluster_atoms(st, ref, allow_reflection, align_structures=True, use_chirality=False) → schrodinger.structure._structure.Structure

Re-order atoms in st to match ref. New order is generated by matching the first molecule in st and ref and applied to all other molecules in st.

Parameters

  • st – Structure to re-order atoms of

  • ref – Reference Structure

  • allow_reflection – whether or not to allow reflection when optimizing rmsd in scoring method

  • align – if True align for rmsd in scoring atom maps

Returns

the renumbered structure

schrodinger.comparison.struc.resolve_conflict(test: List[int], ref: List[int]) → Iterator[Tuple[numpy.ndarray, numpy.ndarray]]

Return all valid mappings even if ref has repeats

schrodinger.comparison.struc.get_mappings(choices: Dict[int, List[int]]) → Iterator[Tuple[List[int], List[int]]]

Return mappings without duplicates in values

schrodinger.comparison.struc.get_xyz_matches(xyz1: numpy.ndarray, xyz2: numpy.ndarray, matching_cutoff, matched_cutoff) → Iterator[Tuple[List[int], List[int]]]

Yield coordinates mappings

schrodinger.comparison.struc.get_xyz_RMSDn(xyz1: numpy.ndarray, xyz2: numpy.ndarray, matching_cutoff: float = 2, matched_cutoff=15) → Tuple[int, float]

Return number of matched coordinates, and sum of square differences

schrodinger.comparison.struc.get_potential_alignment(centroids1, centroids2, rdv1, rdv2, match_thresh, n_max=5) → Iterator[numpy.ndarray]

Return potential alignment

Parameters

n_max – max number of centroids for alignment check, in addition to the origin

schrodinger.comparison.struc.get_centroid_RMSDn(st: schrodinger.structure._structure.Structure, ref: schrodinger.structure._structure.Structure, matching_cutoff: float = 2, matched_cutoff=15, allow_reflection=True, n_maybe=5, n_nb=3, parity_seen=None) → Iterator[Tuple[int, float, schrodinger.structure._structure.Structure]]

Return number of molecules matched, their RMSD, and the aligned st with respect to ref. The st and ref are assumed to be spherical clusters centered about the first molecule.

Parameters

  • n_maybe – number of small radius centroids for maybe-inlier test

  • n_nb – number of neighboring centroids (besides the central one) for maybe-inlier test

  • parity_seen – Only attempt centroid alignment if the corresponding parity has not been tried (proper or improper rotations)

schrodinger.comparison.struc.get_spherical_cluster_RMSDn(st: schrodinger.structure._structure.Structure, ref: schrodinger.structure._structure.Structure, matching_cutoff: float = 2, matched_cutoff=15, align_cluster=True, include_H=False, renumber_rmsd_thresh=0.8, allow_reflection=True, pg_symmetry_ops=()) → Tuple[int, float, schrodinger.structure._structure.Structure]

Return number of molecules matched, their RMSD, and the aligned st with respect to ref. The st and ref are assumed to be spherical clusters centered about the first molecule.

Parameters

  • st – test Structure to align

  • ref – reference Structure (unmoved)

  • matching_cutoff – If the centroid of a molecule is within the radius of another molecule from a different cluster, it is considered as matched.

  • matched_cutoff – If the number of matched centroids is less than this number, abort further computation

  • align_cluster – If not set, only align on the central molecules, i.e., the first molecules of the input structures; otherwise further align on all molecules

  • include_H – if False using heavy atom rmsd, else use all atom rmsd

  • renumber_rmsd_thresh – only attempt atom renumber if rmsd for 1st molecule is greater than this

  • allow_reflection – whether or not to allow reflection when optimizing rmsd in scoring method

  • pg_symmetry_ops – iterable of SymmOp instances, each representing a point group symmetry operation. If the iterable is not empty each operation is applied to the test cluster RMSD N analysis is performed. The best RMSD N is returned.

Returns

three-tuple: N matched, rmsd of match, st after renumbering/alignment A new structure is returned

schrodinger.comparison.struc.load_cif(fname: str, neutralize=True, mmjag=True) → schrodinger.structure._structure.Structure
Parameters

fname – input file name

schrodinger.comparison.struc.replicate(st: schrodinger.structure._structure.Structure, multiplicity: Union[int, fractions.Fraction], copy_cc=True) → schrodinger.structure._structure.Structure
Parameters

  • multiplicity – number of st in the returned structure

  • copy_cc – copy over custom charge if True

schrodinger.comparison.struc.get_niggli_params(lattice_params: List[float]) → List[float]

Niggli reduction of the lattice parameters (a, b, c, alpha, beta, gamma)

schrodinger.comparison.struc.get_standard_cell(cell: schrodinger.structure._structure.Structure, to_primitive=False, no_idealize=False, symprec=1e-05) → schrodinger.structure._structure.Structure

Fix skewed cell definition Note the new structure won’t carry over bonding information (reassigned), or any CT and atom level properties.

Parameters

  • symprec – distance tolerance in Cartesian coordinates

  • no_idealize – whether to idealize cell lengths and angles according to crystal symmetry

schrodinger.comparison.struc.niggli_reduce_cell(cell: schrodinger.structure._structure.Structure) → schrodinger.structure._structure.Structure

Transform cell with Niggli reduced lattice parameters. Note the new cell may not be in the original space group. It seems only to make sense for triclinic lattices (space groups).

schrodinger.comparison.struc.get_cell_fast(st: schrodinger.structure._structure.Structure, symm_ops: Tuple[numpy.ndarray], lattice_params: Optional[Tuple[float]] = None, copy_cc=True, extents: Tuple[int, ...] = (1, 1, 1), asu_input=False, asu_template=None) → schrodinger.structure._structure.Structure

The first molecule in st is used as ASU. Supercell box and unit cell lattice parameters are stored in the output structure.

Parameters

  • st – Its first molecule is ASU

  • symm_ops – Each symmetry operator is a 4x4 numpy array

  • lattice_params – if None, read from CT level properties of st

  • copy_cc – copy custom charge to the supercell if set

  • extents – 3D extension of the unit cell

  • asu_input – If False, extract ASU

  • asu_template – ASU template

schrodinger.comparison.struc.has_clash(cell, cutoff=0.5, use_pbc=True) → bool

Clash detection

Maestro preferences: ugly is <0.75, bad is <0.89, and good is <1.3

Here cutoff := d_{ab} / (R_a + R_b)

schrodinger.comparison.struc.extract_supercell(r: schrodinger.comparison.results.Result, spg_name: str, extents=(1, 1, 1), copy_cc=True, asu_template=None) → schrodinger.structure._structure.Structure

Extract supercell from packing search result.

Parameters

  • r – packing search result

  • spg_name – space group name

  • copy_cc – copy over custom charge if True

  • extents – 3D extension of the unit cell

  • asu_template – example of ASU

schrodinger.comparison.struc.get_inscribe_extents(lattice_params: List[float], d: float) → numpy.array

Return supercell extents to inscribe a sphere of diameter d.

Parameters

  • lattice_params – a, b, c, alpha, beta, gamma

  • d – diameter

schrodinger.comparison.struc.get_ASU_RMSD(st1: schrodinger.structure._structure.Structure, st2: schrodinger.structure._structure.Structure, *, allow_improper_rotation=True, include_H=False, include_polar_H=True, reorder_atoms=True) → Tuple[float, schrodinger.structure._structure.Structure]

Return RMSD between st1 and st2 and aligned st1, with potential atom index rearrangement. Here st2 is used as reference.

schrodinger.comparison.struc.get_volume_and_density(st: schrodinger.structure._structure.Structure, vecs=None) → Tuple[float, float]

Return density in unit of g/cm^-3. The input st should be a supercell.

schrodinger.comparison.struc.is_chiral(st: schrodinger.structure._structure.Structure) → bool
schrodinger.comparison.struc.get_conformer_radial_distance_vector(st: schrodinger.structure._structure.Structure) → Tuple[numpy.ndarray, numpy.ndarray]

Return heavy atom coordinates. Origin is set at centroid

schrodinger.comparison.struc.get_centroid_radial_distance_vector(cluster: schrodinger.structure._structure.Structure, include_H=False, mol_aids=None) → Tuple[numpy.ndarray, numpy.ndarray]

Return the RDV of the centroids and the centroids excluding the 1st molecule, in sorted ordering in terms RDV.

Origin is set at the centroid of the 1st molecules.

schrodinger.comparison.struc.get_torsion_atoms(a2: schrodinger.structure._structure.StructureAtom, a3: schrodinger.structure._structure.StructureAtom) → Tuple[int, int, int, int]

Return the atom indices of a torsion angle

schrodinger.comparison.struc.get_torsions(st, indices=None) → Tuple[numpy.ndarray, List]

Return torsion angles

schrodinger.comparison.struc.get_max_torsion_deviation(st1, st2, ref_tors=None)

The input structures should have the SAME AID ordering

schrodinger.comparison.struc.regenerate_with_box_fix(cell: schrodinger.structure._structure.Structure, old_ext: numpy.ndarray, symm_ops, new_ext=(1, 1, 1)) → schrodinger.structure._structure.Structure

Regenerate supercell with potential box convention change

schrodinger.comparison.struc.remove_H_atoms(st: schrodinger.structure._structure.Structure) → schrodinger.structure._structure.Structure

Return a structure without H atoms

schrodinger.comparison.struc.is_dilute(cell: schrodinger.structure._structure.Structure, asu_v: float) → Tuple[bool, float]

Check packing_coeff if possible. asu_v == 0 means it’s not available, then check cell density

schrodinger.comparison.struc.get_asu_volume(idx: str, vfname: str) → float
schrodinger.comparison.struc.asu_iter(supercell: schrodinger.structure._structure.Structure, n=None, asu_template: Optional[schrodinger.structure._structure.Structure] = None) → schrodinger.structure._structure.Structure

Yield ASUs in supercell

Parameters

  • n – number of ASU copies in supercell

  • asu_template – asu template

schrodinger.comparison.struc.preprocess_st(st: schrodinger.structure._structure.Structure, *, remove_hydrogens=True, remove_asl='water', copy=False) → schrodinger.structure._structure.Structure

Return preprocessed structure

schrodinger.comparison.struc.rotate_xyz(xyz: numpy.ndarray, w: numpy.ndarray) → numpy.ndarray

Rotate the input coordinates using axis-angle parametrization.

Parameters

w – Rodrigues vectors in Radians