Package schrodinger :: Package application :: Package matsci :: Package nano :: Module xtal

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Module xtal

Classes

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ParserWrapper
Manages the argparse module to parse user command line arguments.

CheckInput
Check user input.

CrystalSystems
Manage the properties of the seven crystal systems.

SpaceGroup
Collect the properties of a space group.

SpaceGroups
Manage space group objects.

Crystal
Main class for generating crystals.

PBCBond
Class to manage a PBC bond, i.e.

PBCBonds
Class to manage a collection of PBC bonds.

Functions

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dict

get_cov_radii()
Return a dictionary of atomic covalent radii.

list

get_params_from_vectors(a_vec, b_vec, c_vec)
Return the lattice parameters from the given lattice vectors.

numpy.array, numpy.array, numpy.array, numpy.array

get_lattice_vectors(a_param, b_param, c_param, alpha_param, beta_param, gamma_param)
Get the origin and lattice vectors of the specified parallelepiped.

dict

delete_duplicate_atoms(astructure, atoms_to_check=None, duplicate_thresh=0.25, transform=None, fract_offset=FRACT_OFFSET)
Delete duplicate atoms that are within the defined threshold.

float

max_connect_distance(cov_rad_a, cov_rad_b, cov_factor=ParserWrapper.COV_FACTOR, cov_offset=ParserWrapper.COV_OFFSET)
Return the maximum bonding distance for the given covalent radii and distance equation parameters.

list, dict, dict

connect_atoms(astructure, atoms_to_connect=None, cov_min=ParserWrapper.COV_MIN, cov_offset=ParserWrapper.COV_OFFSET, cov_factor=ParserWrapper.COV_FACTOR, delete_existing=True, organic_structure=None, cov_radii_props=True, pbc_bonding=ParserWrapper.PBC_BONDING, only_pbc_bonds=False, check_also_reg_bond=False)
Connect the atoms in a structure.

bool

before_lower_edge(coord, lower_bound)
Return True if this fractional coordinate value is before the lower edge of the cell.

bool

on_lower_edge(coord, lower_bound, fract_offset=FRACT_OFFSET)
Return True if this fractional coordinate value is on the lower edge of the cell.

bool

inside_cell(coord, lower_bound, upper_bound, fract_offset=FRACT_OFFSET)
Return True if this fractional coordinate value is inside the cell.

bool

on_upper_edge(coord, lower_bound, fract_offset=FRACT_OFFSET)
Return True if this fractional coordinate value is on the upper edge of the cell.

bool

after_upper_edge(coord, lower_bound, fract_offset=FRACT_OFFSET)
Return True if this fractional coordinate value is after the upper edge of the cell.

translate_to_cell(astructure, fract_offset=FRACT_OFFSET, origin=ParserWrapper.ORIGIN, transform=None)
Translate the fractional coordinate definitions of the atoms of the given structure so that they are all in the cell defined with the given origin and optionally also actually transform the Cartesian coordinates of the atoms using the specified fractional-to-Cartesian transform.

trans_atoms_fract_to_cart(astructure, transform)
Transform the atoms in a structure from the fractional basis to the Cartesian basis.

trans_atoms_cart_to_fract(astructure, transform)
Transform the atoms in a structure from the Cartesian basis to the fractional basis.

int

get_gcd_list_ints(list_of_ints)
Return the greatest common divisor (GCD) of a list of integers.

bool

is_organic_structure(astructure, percent_metal_threshold=PERCENT_METAL_THRESHOLD)
Return True if the structure contains more than one type of element and no more than the given percentage of metal elements.

bool

is_closed_shell_organic_structure(astructure, percent_metal_threshold=PERCENT_METAL_THRESHOLD)
Return True if the structure is both organic and closed shell, i.e.

bool

has_organic_molecule(astructure, percent_metal_threshold=PERCENT_METAL_THRESHOLD)
Return True if the provided structure contains at least one organic molecule.

bool

has_closed_shell_organic_molecule(astructure, percent_metal_threshold=PERCENT_METAL_THRESHOLD)
Return True if the provided structure contains at least one closed-shell organic molecule.

bool

is_bonding_infinite(astructure, percent_metal_threshold=PERCENT_METAL_THRESHOLD)
Return True if the bonding is of infinite extent, i.e.

transfer_atom_bonds_and_props(index_a, index_b, astructure, props=None)
Transfer the bonds and specified properties of the atom indexed with index_b to the atom indexed with index_a.

three numpy.array

get_reciprocal_lattice_vectors(a_vec, b_vec, c_vec)
Return the reciprocal lattice vectors.

int

get_collapsed_index(abc, alimit, blimit, climit)
Given a three dimensional grid of integers defined on [1, limit] for the given a, b, and c limits and a traversal path of c then b then a return the number of integers traversed in order to reach the given abc integer index triple.

int

modified_sawtooth(n, x)
Given a positive integer variable x in [0, n+1] return a signal from a modified sawtooth function.

schrodinger.Structure.structure

assign_bond_orders(astructure)
Return a copy of the input structure that has bond orders assigned.

schrodinger.Structure.structure

assign_bond_orders_w_mmlewis(astructure, logger=None)
Return a copy of the input structure that has bond orders assigned.

tuple

get_chorus_properties(astructure)
Return a tuple containing the nine chorus properties of the given structure.

list

get_params_from_chorus(chorus_properties)
Return the a, b, c, alpha, beta, and gamma lattice properties from the nine chorus properties.

list

get_chorus_from_params(params)
Return the nine chorus properties, i.e.

set

get_cell_pairs(astructure, cell_distance, pbc_bonding=True, atom_indices=None, chorus_properties=None)
Using a distance cell that optionally honors a PBC return a list of tuples of atom index pairs that are within the specified distance.

add_labeled_pbc_bond(astructure, atom1, atom2, order, is_pbc_bond=False, also_reg_bond=False, color=PBCBond.PBC_BOND_COLOR)
Add the specified bond to the provided structure and label it depending on if it is a PBC bond.

int

get_natom_btw_two_cells(cell1, cell2, extents, size)
Using a traversal path of c then b then a, return the number of atoms between two cells, of the given size, in a super cell with the given extents.

delete_pbc_bonds(astructure)
Delete any PBC bonds from the given structure.

tuple

is_pbc_bond(astructure, atom1, atom2, check_also_reg_bond=False, unit_lattice_vectors=None)
Return a (is_pbc_bond, also_reg_bond, bond_distance) tuple that indicates (1) whether the specified bond is a PBC bond, (2) if checked whether that PBC bond is also a regular bond, and (3) the bond length.

tuple

get_lattice_param_properties(astructure)
Return a tuple containing the six lattice parameter properties of the given structure.

dict

get_normalized_spanning_vectors(lattice_vectors)
Return the thirteen unique normalized spanning vectors for the cell.

str

get_unit_cell_formula(unit_cell)
Return the formatted unit cell formula of the given unit cell.

numpy.array

trans_cart_to_fract(cart_vec, a_param, b_param, c_param, alpha_param, beta_param, gamma_param)
Transform the given vector in the Cartesian basis to the fractional basis.

numpy.array

trans_fract_to_cart(fract_vec, a_param, b_param, c_param, alpha_param, beta_param, gamma_param)
Transform the given vector in the fractional basis to the Cartesian basis.

schrodinger.structure.Structure

get_cell(asu, space_group=None, lattice_params=None, extents=None, xtal_kwargs=None)
Build and return a crystalline cell using the given asymmetric unit, space group, lattice parameters, and extents.

Variables

[hide private]

__doc__ = ...

_version = '$Revision 0.0 $'

BC_BOX_SHAPE_KEY = 's_m_BC_Box_Shape'

BC_BOX_A_KEY = 'r_m_BC_Box_A'

BC_BOX_B_KEY = 'r_m_BC_Box_B'

BC_BOX_C_KEY = 'r_m_BC_Box_C'

BC_BOX_ALPHA_KEY = 'r_m_BC_Box_Alpha'

BC_BOX_BETA_KEY = 'r_m_BC_Box_Beta'

BC_BOX_GAMMA_KEY = 'r_m_BC_Box_Gamma'

BC_BOX_SHAPE = 'Triclinic'

PRESERVE_BONDING_KEY = 'b_matsci_Preserve_Bonding'

P1_SPACE_GROUP_SYMBOL = 'P 1'

COV_RADIUS_KEY = 'r_matsci_COV_radius/Ang.'

FRACT_OFFSET = 0.0001

PERCENT_METAL_THRESHOLD = 25.0

METAL_ASL = 'metals'

PROTEIN_ASL = 'protein'

MMPDB_MAX_ELEMENTS = 103

AHEAD_BASE_TRIPLES = [(1, 0, 0), (0, 1, 0), (0, 0, 1)]

AHEAD_TRIPLES = AHEAD_BASE_TRIPLES+ [(0, 1, 1), (0, 1,-1), (1,...

LATTICE_PARAMS_KEYS = ['a_param', 'b_param', 'c_param', 'alpha...

EXTENTS_KEYS = ['ncella', 'ncellb', 'ncellc']

MMPDB_COV_RADII = get_cov_radii()

MAX_MMPDB_COV_RADIUS = max(MMPDB_COV_RADII.values())

Function Details

[hide private]

get_cov_radii()

Return a dictionary of atomic covalent radii.

Returns: dict: dictionary where keys are atomic numbers and values are atomic covalent radii in Angstrom

get_params_from_vectors(a_vec, b_vec, c_vec)

Return the lattice parameters from the given lattice vectors.

Parameters:

a_vec (numpy.array) - the a lattice vector
b_vec (numpy.array) - the b lattice vector
c_vec (numpy.array) - the c lattice vector

Returns: list

contains the a, b, c, alpha, beta, and gamma parameters

get_lattice_vectors(a_param, b_param, c_param, alpha_param, beta_param, gamma_param)

Get the origin and lattice vectors of the specified parallelepiped.

Parameters:

a_param (float) - the length of the parallelepiped along edge a
b_param (float) - the length of the parallelepiped along edge b
c_param (float) - the length of the parallelepiped along edge c
alpha_param (float) - the angle between edges b and c
beta_param (float) - the angle between edges a and c
gamma_param (float) - the angle between edges a and b

Returns: numpy.array, numpy.array, numpy.array, numpy.array

the origin and lattice vectors of the parallelepiped

delete_duplicate_atoms(astructure, atoms_to_check=None, duplicate_thresh=0.25, transform=None, fract_offset=FRACT_OFFSET)

Delete duplicate atoms that are within the defined threshold. Of the redundant atoms that with the lowest index is kept. Prior to deleteing the duplicates transfer the bonds and some atom properties of at least one of the duplicate atoms to the single atom that is kept. If transform is not None then this function will use the periodic boundary conditions defined in transform when determining redundant atoms.

Parameters:

astructure (schrodinger.Structure.structure) - the structure object from which the duplicate atoms will be deleted
atoms_to_check (set) - indicies of atoms that are to be checked for duplicate copies, for a given redundant set of atoms any index can be passed in
duplicate_thresh (float) - distance used to define duplicate atoms, conservatively chosen based on considering the resolutions of some crystal structures and the wavelengths of light used to obtain the diffraction patterns
transform (numpy.array or None) - if not None then specifies that the Cartesians also be transformed using this fractional-to-Cartesian transformation matrix
fract_offset (float) - the threshold used to compare floating point fractional coordinate values and in particular those that are on the cell boundary

Returns: dict

renumber_map, keys are original indicies, values are new indicies or None if the atom was deleted

max_connect_distance(cov_rad_a, cov_rad_b, cov_factor=ParserWrapper.COV_FACTOR, cov_offset=ParserWrapper.COV_OFFSET)

Return the maximum bonding distance for the given covalent radii and distance equation parameters.

Parameters:

cov_rad_a (float) - covalent radii for atom a
cov_rad_b (float) - covalent radii for atom b
cov_factor (float) - the maximum distance for a connection is the sum of the covalent radii of the two atoms weighted by this factor plus the cov_offset in angstrom, increasing this value will increase the number of connections, this value is unit-less
cov_offset (float) - the maximum distance for a connection is the sum of the covalent radii of the two atoms weighted by cov_factor plus this offset in angstrom, increasing this value will increase the number of connections

Returns: float

the maximum bonding distance

connect_atoms(astructure, atoms_to_connect=None, cov_min=ParserWrapper.COV_MIN, cov_offset=ParserWrapper.COV_OFFSET, cov_factor=ParserWrapper.COV_FACTOR, delete_existing=True, organic_structure=None, cov_radii_props=True, pbc_bonding=ParserWrapper.PBC_BONDING, only_pbc_bonds=False, check_also_reg_bond=False)

Connect the atoms in a structure.

Parameters:

astructure (schrodinger.Structure.structure) - the structure object for which the connections are wanted
atoms_to_connect (list) - atom indicies to consider connecting, if None then all atoms will be considered
cov_min (float) - the minimum distance for a connection in angstrom
cov_offset (float) - the maximum distance for a connection is the sum of the covalent radii of the two atoms weighted by cov_factor plus this offset in angstrom, increasing this value will increase the number of connections
cov_factor (float) - the maximum distance for a connection is the sum of the covalent radii of the two atoms weighted by this factor plus the cov_offset in angstrom, increasing this value will increase the number of connections, this value is unit-less
delete_existing (bool) - indicates whether existing connections should first be deleted, i.e. any bonds to atoms in atoms_to_connect will be deleted
organic_structure (bool or None) - True if this structure is known to be organic, False if this structure is known to not be organic, and None if it is unknown in which case it will be determined, this information is used to assign single, rather than zero-order, bonds for metal atoms in non-organic structures
cov_radii_props (bool) - set the atomic covalent radii used in the connectivity protocol as atom properties
pbc_bonding (bool) - if True and if the input structure has the chorus properties defined, then PBC bonds will be created
only_pbc_bonds (bool) - if True then only PBC bonds will be created, i.e. regular bonds will not be created
check_also_reg_bond (bool) - if True then PBC bonds will be checked to see if they are also regular bonds, meaning that one of the atoms of the PBC bond is covalently bound to two copies of the other atom, one inside the cell and one outside the cell

Returns: list, dict, dict

maximally_bonded_atoms, contains the indicies of any maximally bonded atoms, there is currently a hard coded limit on the number of bonds an atom can have according to mm.MMCT_MAXBOND which has a value of 16, and two dictionaries (one for regular bonds and one for PBC bonds) where keys are tuples of bonding atom indices and values are bond orders (for regular bonds) or tuples of bond orders and booleans indicating whether the PBC bond is also a regular bond (for PBC bonds)

before_lower_edge(coord, lower_bound)

Return True if this fractional coordinate value is before the lower edge of the cell.

Parameters:

coord (float) - the fractional coordinate being tested
lower_bound (float) - the lower bound for this fractional coordinate

Returns: bool

True if the coordinate is before the lower edge, False otherwise

on_lower_edge(coord, lower_bound, fract_offset=FRACT_OFFSET)

Return True if this fractional coordinate value is on the lower edge of the cell.

Parameters:

coord (float) - the fractional coordinate being tested
lower_bound (float) - the lower bound for this fractional coordinate
fract_offset (float) - used to make floating point comparisons

Returns: bool

True if the coordinate is on the lower edge, False otherwise

inside_cell(coord, lower_bound, upper_bound, fract_offset=FRACT_OFFSET)

Return True if this fractional coordinate value is inside the cell.

Parameters:

coord (float) - the fractional coordinate being tested
lower_bound (float) - the lower bound for this fractional coordinate
upper_bound (float) - the upper bound for this fractional coordinate
fract_offset (float) - used to make floating point comparisons

Returns: bool

True if the coordinate is inside the cell, False otherwise

on_upper_edge(coord, lower_bound, fract_offset=FRACT_OFFSET)

Return True if this fractional coordinate value is on the upper edge of the cell.

Parameters:

coord (float) - the fractional coordinate being tested
lower_bound (float) - the lower bound for this fractional coordinate
fract_offset (float) - used to make floating point comparisons

Returns: bool

True if the coordinate is on the upper edge, False otherwise

after_upper_edge(coord, lower_bound, fract_offset=FRACT_OFFSET)

Return True if this fractional coordinate value is after the upper edge of the cell.

Parameters:

coord (float) - the fractional coordinate being tested
lower_bound (float) - the lower bound for this fractional coordinate
fract_offset (float) - used to make floating point comparisons

Returns: bool

True if the coordinate is after the upper edge, False otherwise

translate_to_cell(astructure, fract_offset=FRACT_OFFSET, origin=ParserWrapper.ORIGIN, transform=None)

Translate the fractional coordinate definitions of the atoms of the given structure so that they are all in the cell defined with the given origin and optionally also actually transform the Cartesian coordinates of the atoms using the specified fractional-to-Cartesian transform.

Parameters:

astructure (schrodinger.Structure.structure) - the structure object whose atoms will be translated
fract_offset (float) - the threshold used to compare floating point fractional coordinate values and in particular those that are on the cell boundary
origin (list) - the origin of the cell to which to translate
transform (numpy.array or None) - if not None then specifies that the Cartesians also be transformed using this fractional-to-Cartesian transformation matrix

trans_atoms_fract_to_cart(astructure, transform)

Transform the atoms in a structure from the fractional basis to the Cartesian basis.

Parameters:

astructure (schrodinger.Structure.structure) - the structure object to be transformed
transform (numpy.array) - the fractional-to-Cartesian transformation matrix

trans_atoms_cart_to_fract(astructure, transform)

Transform the atoms in a structure from the Cartesian basis to the fractional basis.

Parameters:

astructure (schrodinger.Structure.structure) - the structure object to be transformed
transform (numpy.array) - the Cartesian-to-fractional transformation

get_gcd_list_ints(list_of_ints)

Return the greatest common divisor (GCD) of a list of integers.

Parameters:

list_of_ints (list) - the list of ints for which the GCD is desired

Returns: int

gcd, the GCD

is_organic_structure(astructure, percent_metal_threshold=PERCENT_METAL_THRESHOLD)

Return True if the structure contains more than one type of element and no more than the given percentage of metal elements.

Parameters:

astructure (schrodinger.Structure.structure) - the structure object to be tested
percent_metal_threshold (float) - a structure can contain up to this percentage of metal elements and still be considered organic

Returns: bool

True if organic, False otherwise

is_closed_shell_organic_structure(astructure, percent_metal_threshold=PERCENT_METAL_THRESHOLD)

Return True if the structure is both organic and closed shell, i.e. all non-metal atoms have complete valencies. Note that proteins are automatically considered closed-shell to safeguard against the possible lack of hydrogens.

Parameters:

astructure (schrodinger.Structure.structure) - the structure object to be tested
percent_metal_threshold (float) - a structure can contain up to this percentage of metal elements and still be considered organic

Returns: bool

True if closed shell organic, False otherwise

has_organic_molecule(astructure, percent_metal_threshold=PERCENT_METAL_THRESHOLD)

Return True if the provided structure contains at least one organic molecule.

Parameters:

astructure (schrodinger.Structure.structure) - the structure object to be tested
percent_metal_threshold (float) - a structure can contain up to this percentage of metal elements and still be considered organic

Returns: bool

True if the structure has an organic molecule

has_closed_shell_organic_molecule(astructure, percent_metal_threshold=PERCENT_METAL_THRESHOLD)

Return True if the provided structure contains at least one closed-shell organic molecule.

Parameters:

astructure (schrodinger.Structure.structure) - the structure object to be tested
percent_metal_threshold (float) - a structure can contain up to this percentage of metal elements and still be considered organic

Returns: bool

True if the structure has a closed-shell organic molecule

is_bonding_infinite(astructure, percent_metal_threshold=PERCENT_METAL_THRESHOLD)

Return True if the bonding is of infinite extent, i.e. the real and image cells are covalently bound along at least a single lattice vector.

Parameters:

astructure (schrodinger.Structure.structure) - the structure object to be tested
percent_metal_threshold (float) - a structure can contain up to this percentage of metal elements and still be considered organic

Returns: bool

True if the bonding is of infinite extent

transfer_atom_bonds_and_props(index_a, index_b, astructure, props=None)

Transfer the bonds and specified properties of the atom indexed with index_b to the atom indexed with index_a.

Parameters:

index_a (int) - the index of the atom to be updated
index_b (int) - the index of the atom with the data that is to be transfered
astructure (schrodinger.Structure.structure) - the structure containing these two atoms
props (list or None) - a list of keys of atom properties to be transferred, if None then some default keys are set

get_reciprocal_lattice_vectors(a_vec, b_vec, c_vec)

Return the reciprocal lattice vectors.

Parameters:

a_vec (numpy.array) - the a lattice vector
b_vec (numpy.array) - the b lattice vector
c_vec (numpy.array) - the c lattice vector

Returns: three numpy.array

the three reciprocal lattice vectors

get_collapsed_index(abc, alimit, blimit, climit)

Given a three dimensional grid of integers defined on [1, limit] for the given a, b, and c limits and a traversal path of c then b then a return the number of integers traversed in order to reach the given abc integer index triple.

Parameters:

abc (tuple) - the integer indices
alimit (int) - the upper bound on a (unused)
blimit (int) - the upper bound on b
climit (int) - the upper bound on c

Returns: int

the number of integers traversed

modified_sawtooth(n, x)

Given a positive integer variable x in [0, n+1] return a signal from a modified sawtooth function. This function is linear on [1, n] but is n for x = 0 and is 1 for x = n+1.

Parameters:

n (int) - the period
x (int) - the variable

Returns: int

the signal

assign_bond_orders(astructure)

Return a copy of the input structure that has bond orders assigned.

Parameters:

astructure (schrodinger.Structure.structure) - the structure object for which bond orders will be assigned

Returns: schrodinger.Structure.structure

a copy of the input structure with the bond orders assigned

assign_bond_orders_w_mmlewis(astructure, logger=None)

Return a copy of the input structure that has bond orders assigned.

Parameters:

astructure (schrodinger.Structure.structure) - the structure object for which bond orders will be assigned
logger (logging.getLogger or None) - output logger or None if there isn't one

Returns: schrodinger.Structure.structure

a copy of the input structure with the bond orders assigned

get_chorus_properties(astructure)

Return a tuple containing the nine chorus properties of the given structure.

Parameters:

astructure (schrodinger.Structure.structure) - the structure that has the chorus properties defined

Returns: tuple

contains the nine chorus properties

get_params_from_chorus(chorus_properties)

Return the a, b, c, alpha, beta, and gamma lattice properties from the nine chorus properties.

Parameters:

chorus_properties (list) - contains the nine chorus properties, i.e. ax, ay, az, bx, ..., cz

Returns: list

a, b, c, alpha, beta, and gamma lattice properties

get_chorus_from_params(params)

Return the nine chorus properties, i.e. [ax, ay, az, bx, ..., cz], from the six lattice parameters a, b, c, alpha, beta, and gamma.

Parameters:

params (list) - contains the a, b, c, alpha, beta, and gamma lattice parameters

Returns: list

contains the nine chorus properties

get_cell_pairs(astructure, cell_distance, pbc_bonding=True, atom_indices=None, chorus_properties=None)

Using a distance cell that optionally honors a PBC return a list of tuples of atom index pairs that are within the specified distance.

Parameters:

astructure (schrodinger.Structure.structure) - the structure containing the pairs
cell_distance (float) - the distance used in the distance cell, if using a PBC then min([cell_distance, a, b, c]) is actually what is used
pbc_bonding (bool) - if True and the chorus box properties exist on the incoming structure then the distance cell will honor the PBC, otherwise any PBC is not considered
atom_indices (list or None) - a list of atom indices to search for pairs, each atom is searched for pairs that may or may not already be in this list, if None then all atoms are searched
chorus_properties (list or None) - contains the nine chorus box properties that define a PBC, i.e. [ax, ay, az, bx, ..., cz], if None then the chorus structure properties will be used if available and if not available then no PBC will be used in the DistanceCell

Returns: set

contains tuples of unique atom index pairs within the specified distance

add_labeled_pbc_bond(astructure, atom1, atom2, order, is_pbc_bond=False, also_reg_bond=False, color=PBCBond.PBC_BOND_COLOR)

Add the specified bond to the provided structure and label it depending on if it is a PBC bond.

Parameters:

astructure (schrodinger.Structure.structure) - the structure to which the bond will be added
atom1 (int) - the first atom index of the bond
atom2 (int) - the second atom index of the bond
order (int) - the bond order
is_pbc_bond (bool) - if True then the specified bond is a PBC bond so we will label it as so
also_reg_bond (bool) - if True indicates that the given PBC bond is also a regular bond, meaning that one of the atoms of the PBC bond is covalently bound to two copies of the other atom, one inside the cell and one outside the cell
color (int or None) - if integer specifies that PBC bonds, that are not also regular bonds, should be colored with this color

get_natom_btw_two_cells(cell1, cell2, extents, size)

Using a traversal path of c then b then a, return the number of atoms between two cells, of the given size, in a super cell with the given extents.

Parameters:

cell1 (tuple) - a triple of cell indices for the first cell
cell2 (tuple) - a triple of cell indices for the second cell
extents (list) - contains the number of cells along a, b, and c lattice vectors in the super cell
size (int) - the number of atoms in a cell

Returns: int

the number of atoms between the two cells

delete_pbc_bonds(astructure)

Delete any PBC bonds from the given structure.

Parameters:

astructure (schrodinger.Structure.structure) - the structure from which the bonds will be deleted

is_pbc_bond(astructure, atom1, atom2, check_also_reg_bond=False, unit_lattice_vectors=None)

Return a (is_pbc_bond, also_reg_bond, bond_distance) tuple that indicates (1) whether the specified bond is a PBC bond, (2) if checked whether that PBC bond is also a regular bond, and (3) the bond length.

Parameters:

astructure (schrodinger.Structure.structure) - the structure that has the bond
atom1 (schrodinger.structure._StructureAtom) - the first atom of the bond
atom2 (schrodinger.structure._StructureAtom) - the second atom of the bond
check_also_reg_bond (bool) - check if the PBC bond is also a regular bond, meaning that one of the atoms of the PBC bond is covalently bound to two copies of the other atom, one inside the cell and one outside the cell
unit_lattice_vectors (list of (numpy.array, float) tuples or None) - contains normalized a, b, and c lattice vectors and their original lengths, is None if no check for PBC bonds that are also regular bonds is being performed

Returns: tuple

a (is_pbc_bond, also_reg_bond, bond_distance) tuple

get_lattice_param_properties(astructure)

Return a tuple containing the six lattice parameter properties of the given structure.

Parameters:

astructure (schrodinger.Structure.structure) - the structure that has the lattice parameter properties defined

Returns: tuple

contains the six lattice parameter properties

get_normalized_spanning_vectors(lattice_vectors)

Return the thirteen unique normalized spanning vectors for the cell.

Parameters:

lattice_vectors (list of numpy.array) - the lattice a, b, and c vectors

Returns: dict

keys are tuples of cell index triples, values are tuples of normalized spanning vectors and their original lengths

get_unit_cell_formula(unit_cell)

Return the formatted unit cell formula of the given unit cell.

Parameters:

unit_cell (schrodinger.Structure.structure) - the structure object for the unit cell

Returns: str

the formatted unit cell formula

trans_cart_to_fract(cart_vec, a_param, b_param, c_param, alpha_param, beta_param, gamma_param)

Transform the given vector in the Cartesian basis to the fractional basis.

Parameters:

cart_vec (numpy.array) - the vector to be transformed from the Cartesian basis to the fractional basis
a_param (float) - the lattice a parameter
b_param (float) - the lattice b parameter
c_param (float) - the lattice c parameter
alpha_param (float) - the lattice alpha parameter
beta_param (float) - the lattice beta parameter
gamma_param (float) - the lattice gamma parameter

Returns: numpy.array

the given vector in the fractional basis

trans_fract_to_cart(fract_vec, a_param, b_param, c_param, alpha_param, beta_param, gamma_param)

Transform the given vector in the fractional basis to the Cartesian basis.

Parameters:

fract_vec (numpy.array) - the vector to be transformed from the fractional basis to the Cartesian basis
a_param (float) - the lattice a parameter
b_param (float) - the lattice b parameter
c_param (float) - the lattice c parameter
alpha_param (float) - the lattice alpha parameter
beta_param (float) - the lattice beta parameter
gamma_param (float) - the lattice gamma parameter

Returns: numpy.array

the given vector in the Cartesian basis

get_cell(asu, space_group=None, lattice_params=None, extents=None, xtal_kwargs=None)

Build and return a crystalline cell using the given asymmetric unit, space group, lattice parameters, and extents.

Parameters:

asu (schrodinger.structure.Structure) - the asymmetric unit
space_group (str or None) - the full or short Hermann-Mauguin symbol of the space group or None in which case the asu structure property Crystal.SPACE_GROUP_KEY will be used
lattice_params (list or None) - the six lattice parameters or None in which case the asu structure properties Crystal.A_KEY, Crystal.B_KEY, Crystal.C_KEY, Crystal.ALPHA_KEY, Crystal.BETA_KEY, and Crystal.GAMMA_KEY will be used
extents (list or None) - the integer extents along the a, b, and c lattice vectors or None if there are none
xtal_kwargs (dict or None) - extra xtal.Crystal kwargs or None if there are none

Returns: schrodinger.structure.Structure

the built cell

Variables Details

[hide private]

doc

Value:

"""
Classes and functions for creating crystals by unit cell.

Copyright Schrodinger, LLC.  All rights reserved."""

AHEAD_TRIPLES

Value:

AHEAD_BASE_TRIPLES+ [(0, 1, 1), (0, 1,-1), (1, 0, 1), (1, 1, 0), (1, 1
, 1), (1, 1,-1), (1, 0,-1), (1,-1, 0), (1,-1,-1), (1,-1, 1)]

LATTICE_PARAMS_KEYS

Value:

['a_param', 'b_param', 'c_param', 'alpha_param', 'beta_param', 'gamma_
param']