schrodinger.application.matsci.nano.xtal module

Classes and functions for creating crystals by unit cell.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.matsci.nano.xtal.AXIS(X, Y, Z)

Bases: tuple

X

Alias for field number 0

Y

Alias for field number 1

Z

Alias for field number 2

schrodinger.application.matsci.nano.xtal.find_furthest_atom_along_vector(struct, vector)

Find the atom in struct that is furthest in the direction of vector. For instance, if vector is the Z-axis, this will find the atom with the largest z coordinate

Parameters
Return type

schrodinger.structure._StructureAtom

Returns

The atom furthest in the vector direction

schrodinger.application.matsci.nano.xtal.find_origin_on_structure_exterior(struct, vector)

Find the point to originate the normal plane to the passed vector so that the passed structure is entirely behind the vector (i.e. the structure will be entirely on one side of the plane, and vector on the other side).

schrodinger.application.matsci.nano.xtal.is_infinite(astructure)

Return a boolean indicating whether the given structure is infinitely bonded, meaning that it has bonds that cross the periodic boundary which can not be eliminated by means of molecule contraction. If any molecule in the given structure is infinitely bonded then the structure itself is considered infinite. As examples of infinite systems consider graphene, gold, infinite polymer, etc.

Parameters

astructure (schrodinger.structure.Structure) – the structure whose infiniteness is in question, can be a unit cell or an ASU

Raises

ValueError – if there is an issue with the input

Return type

bool

Returns

True if infinite, False otherwise

schrodinger.application.matsci.nano.xtal.get_check_also_reg_bond(struct, pbc=None, is_cg=None)

Get the value of the check_also_reg_bond that is passed to is_pbc_bond based on the PBC cell lengths.

Parameters
  • astructure (schrodinger.structure.Structure) – Structure for which to check the value of check_also_reg_bond flag

  • pbc (schrodinger.infra.structure.PBC or None) – The infrastructure PBC created from the Chorus box properties

  • is_cg (bool or None) – True, if structure is CG, otherwise False. If None, this will be evaluated

Return type

bool

Returns

Flag value

schrodinger.application.matsci.nano.xtal.is_infinite2(astructure, check_also_reg_bond=None, is_cg=None, atom_indices=None)

Return a boolean indicating whether the given structure is infinitely bonded, meaning that it has bonds that cross the periodic boundary which can not be eliminated by means of molecule contraction. If any molecule in the given structure is infinitely bonded then the structure itself is considered infinite. As examples of infinite systems consider graphene, gold, infinite polymer, etc. Note that, correct bond information is expected in the input structure.

Parameters
  • astructure (schrodinger.structure.Structure) – the structure whose infiniteness is in question, can be a unit cell or an ASU

  • check_also_reg_bond (bool or None) – Deprecated. 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. If None, bool value will be decided automatically (preferred)

  • is_cg (bool) – Deprecated. True, if structure is CG, otherwise False. Needed if check_also_reg_bond is None. If None, this will be evaluated

Paran atom_indices

Atom indices to check from the structure. If None, entire stucture is checked

Return type

bool

Returns

True if infinite, False otherwise

schrodinger.application.matsci.nano.xtal.check_bond_vec_proj(xyz1, xyz2, unit_lattice_vectors, threshold)

Check if any of the bond vector projections on the lattice vectors is close to the half length of a lattice vector.

schrodinger.application.matsci.nano.xtal.has_pbc_bond(struct, pbc=None)

Check if structure has a PBC bond.

Parameters
  • struct (structure.Structure) – the structure to check

  • pbc (schrodinger.infra.structure.PBC) – PBC of the structure

Return type

bool

Returns

Whether the structure has a PBC bond

schrodinger.application.matsci.nano.xtal.store_chorus_box_props(struct, ax, ay=0.0, az=0.0, bx=0.0, by=None, bz=0.0, cx=0.0, cy=0.0, cz=None)

Add properties to the structure that define the periodic boundary condition in the way Desmond wants it defined.

Parameters
  • struct (schrodinger.structure.Structure) – The structure to add the properties to

  • ax (float) – The value of the ax box property

  • ay (float) – The value of the ay box property. Defaults to 0.

  • az (float) – The value of the az box property. Defaults to 0.

  • bx (float) – The value of the bx box property. Defaults to 0.

  • by (float) – The value of the by box property. If not given, this value is set the same as ax.

  • bz (float) – The value of the bz box property. Defaults to 0.

  • cx (float) – The value of the cx box property. Defaults to 0.

  • cy (float) – The value of the cy box property. Defaults to 0.

  • cz (float) – The value of the cz box property. If not given, this value is set the same as ax.

schrodinger.application.matsci.nano.xtal.copy_chorus_box_props(struct1, struct2)

Copy the Chorus box PBC properties from one struct to another if they exist. If no Chorus properties exist, no error is raised.

Parameters
schrodinger.application.matsci.nano.xtal.clear_asu_and_fractional_properties(struct)

Clear the atomic ASU and Fractional coordinate properties

Parameters

struct (schrodinger.structure.Structure) – The structure to clear the ASU and fractional properties from

schrodinger.application.matsci.nano.xtal.get_cov_radii()

Return a dictionary of atomic covalent radii.

Return type

dict

Returns

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

schrodinger.application.matsci.nano.xtal.get_cov_radius(st, idx, is_cg=None)

Return the covalent radius in Angstrom of the given atom or coarse grain particle index.

Parameters
  • st (schrodinger.structure.Structure) – the structure

  • idx (int) – the atom or coarse grain particle index

  • is_cg (bool or None) – True, if structure is CG, otherwise False. If None, structure will be evaluated (slow)

Return type

float

Returns

the covalent radius in Angstrom

schrodinger.application.matsci.nano.xtal.get_max_cov_radius(st, is_cg=None)

For atomic input return the maximum covalent radius in Angstrom over all atoms in the periodic table, for CG input return the same but over all particles in the given structure.

Parameters
  • st (schrodinger.structure.Structure) – the structure

  • is_cg (bool or None) – True, if structure is CG, otherwise False. If None, structure will be evaluated (slow)

Return type

float

Returns

the maximum covalent radius in Angstrom

schrodinger.application.matsci.nano.xtal.get_cov_parameter(st, atomistic_cov_param, is_cg=None)

Return the covalent parameter in Angstrom for the given structure.

Parameters
  • st (schrodinger.structure.Structure) – the structure

  • atomistic_cov_param (float) – the atomistic covalent parameter in Angstrom

  • is_cg (bool or None) – True, if structure is CG, otherwise False. If None, structure will be evaluated (slow)

Return type

float

Returns

the covalent parameter in Angstrom

schrodinger.application.matsci.nano.xtal.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

Return type

list

Returns

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

schrodinger.application.matsci.nano.xtal.get_lattice_vectors(a_param, b_param, c_param, alpha_param, beta_param, gamma_param)

Get the 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

Return type

numpy.array, numpy.array, numpy.array

Returns

the lattice vectors of the parallelepiped

class schrodinger.application.matsci.nano.xtal.ParserWrapper(args, scriptname, description)

Bases: object

Manages the argparse module to parse user command line arguments.

SPACE_GROUP = None
A_PARAM = None
B_PARAM = None
C_PARAM = None
ALPHA_PARAM = None
BETA_PARAM = None
GAMMA_PARAM = None
MIN_ANGLE = 0.0
MAX_ANGLE = 180.0
NCELLA = 1
NCELLB = 1
NCELLC = 1
ORIGIN = (0.0, 0.0, 0.0)
CHOICE_ON = 'on'
CHOICE_OFF = 'off'
BONDING_CHOICES = ['on', 'off']
BONDING_DEFAULT = 'off'
BOND_ORDERS_CHOICES = ['on', 'off']
BOND_ORDERS_DEFAULT = 'off'
TRANSLATE_CHOICES = ['on', 'off']
TRANSLATE_DEFAULT = 'off'
COV_MIN = 0.4
COV_OFFSET = 0.4
COV_FACTOR = 1.0
PRINT_INFO = False
PBC_BONDING = True
__init__(args, scriptname, description)

Create a ParserWrapper object and process it.

Parameters
  • args (tuple) – command line arguments

  • scriptname (str) – name of this script

  • description (str) – description of this script

loadIt()

Load ParserWrapper with options.

parseArgs(args)

Parse the command line arguments.

Parameters

args (tuple) – command line arguments

validate()

Validate parser options.

class schrodinger.application.matsci.nano.xtal.CheckInput

Bases: object

Check user input.

TITLE_KEY = 's_m_title'
ENTRY_NAME_KEY = 's_m_entry_name'
checkInputFile(input_file)

Check input file.

Parameters

input_file (str) – the name of the input file

checkASU(asu, logger=None)

Check the asymmetric unit structure object.

Parameters
  • asu (schrodinger.Structure.structure) – the structure object of the asymmetric unit

  • logger (logging.getLogger) – output logger

checkFractionalRedundancies(asu, logger=None)

Check the redundancy of fractional coordinate definitions.

Raises

ValueError – If redundancy is found

Parameters
  • asu (schrodinger.Structure.structure) – the structure object of the asymmetric unit

  • logger (logging.getLogger) – output logger

checkSpaceGroup(space_group, space_groups, logger=None)

Check the specified space group.

Parameters
  • space_group (str) – the specified space group

  • space_groups (space_groups.SpaceGroups) – SpaceGroups object

  • logger (logging.getLogger) – output logger

Raises

ValueError – If no space group is specified, or if the provided space group symbol is not valid

Return type

space_goups.SpaceGroup

Returns

Space group object

checkLatticeAngleValues(alpha, beta, gamma, logger=None)

Check the values of the specified lattice angles.

Parameters
  • alpha (float) – lattice angle alpha in degrees

  • beta (float) – lattice angle beta in degrees

  • gamma (float) – lattice angle gamma in degrees

  • logger (logging.getLogger) – output logger

Return type

float, float, float

Returns

alpha_new, beta_new, gamma_new, updated lattice angles

checkLatticeParameters(a_param, b_param, c_param, alpha_param, beta_param, gamma_param, logger=None)

Check the specified lattice parameters.

Parameters
  • a_param (float) – lattice vector a in Angstrom

  • b_param (float) – lattice vector b in Angstrom

  • c_param (float) – lattice vector c in Angstrom

  • alpha_param (float) – lattice angle alpha in degrees

  • beta_param (float) – lattice angle beta in degrees

  • gamma_param (float) – lattice angle gamma in degrees

  • logger (logging.getLogger) – output logger

Return type

six floats

Returns

a_param, b_param, c_param, alpha_param, beta_param, gamma_param

checkLatticeMaxVolume(a_param, b_param, c_param, logger=None)

Using the lattice lengths check the maximum volume.

Parameters
  • a_param (float) – lattice vector a in Angstrom

  • b_param (float) – lattice vector b in Angstrom

  • c_param (float) – lattice vector c in Angstrom

  • logger (logging.getLogger) – output logger

Raises

ValueError – If the lattice vector lengths result in a unit cell that has too small of a volume

checkNumUnitCellParams(ncella, ncellb, ncellc, logger=None)

Check the number of unit cells requested by the user.

Parameters
  • ncella (int) – number of unit cells along lattice vector a

  • ncellb (int) – number of unit cells along lattice vector b

  • ncellc (int) – number of unit cells along lattice vector c

  • logger (logging.getLogger) – output logger

Raises

ValueError – At least one of the ncell* parameters is not a positive integer

checkOrigin(origin)

Check the origin.

Parameters

origin (list or None) – the unit cell origin, list of three floats, in fractional coordinates or None if not provided

Raises

ValueError – The specified origin is invalid

Return type

list

Returns

the unit cell origin, list of three floats, in fractional coordintes

checkBondingAndTranslate(bonding, bond_orders, translate, logger=None)

Check the bonding and translate options.

Parameters
  • bonding (str) – specify how the bonding should be handled

  • bond_orders (str) – specify how the bond orders should be handled

  • translate (str) – specify how the translation to the first unit cell should be handled

  • logger (logging.getLogger) – output logger

Raises

ValueError – The bonding or translation options are invalid

schrodinger.application.matsci.nano.xtal.get_duplicate_atoms(struct, pbc=None, atoms_to_check=None, duplicate_thresh=0.25)

Get atoms to keep and atoms to delete from a structure that possibly contains duplicate atoms that are within the defined threshold. Of the redundant atoms that with the lowest index is kept.

Parameters
  • struct (schrodinger.Structure.structure) – the structure object to find duplicate atoms

  • pbc (schrodinger.infra.structure.PBC or None) – The infrastructure PBC created from the Chorus box properties, if None, system will be treated as finite

  • atoms_to_check (set) – indices of atoms that are to be checked for duplicate copies

  • 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

Return type

list, list

Returns

First list of atom indices to keep. Second is list of lists of atom indices to be removed. Each item in the list is a list of duplicated atom indices corresponding to the atom index from to_keep list

schrodinger.application.matsci.nano.xtal.delete_duplicate_atoms(astructure, atoms_to_check=None, duplicate_thresh=0.25, fract_offset=0.0001, preserve_bonding=False)

Delete duplicate atoms that are within the defined threshold. Of the redundant atoms that with the lowest index 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) – indices 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

  • fract_offset (float) – the threshold used to compare floating point fractional coordinate values and in particular those that are on the cell boundary

  • preserve_bonding (bool) – If True, preserve bonding between atoms (might be slow)

Return type

dict

Returns

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

schrodinger.application.matsci.nano.xtal.max_connect_distance(cov_rad_a, cov_rad_b, cov_factor=1.0, cov_offset=0.4)

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

Return type

float

Returns

the maximum bonding distance

schrodinger.application.matsci.nano.xtal.connect_atoms(astructure, atoms_to_connect=None, cov_min=0.4, cov_offset=0.4, cov_factor=1.0, delete_existing=True, cov_radii_props=False, pbc_bonding=True, only_pbc_bonds=False, check_also_reg_bond=None, max_valencies=None)

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 indices 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

  • cov_radii_props (bool) – set the atomic covalent radii used in the connectivity protocol as atom properties. Enabling this, causes a decrease in performance of approx. 10%.

  • 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 or None) – 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. If None, this will be evaluated

  • max_valencies (dict or None) – The maximum valencies to use for each element. If None, the valencies defined in get_max_valencies() will be used.

Return type

list, dict, dict

Returns

maximally_bonded_atoms, contains the indices of any maximally bonded atoms, 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)

schrodinger.application.matsci.nano.xtal.translate_to_cell(astructure, fract_offset=0.0001, origin=(0.0, 0.0, 0.0), extents=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 given extents 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 in fractional coordinates

  • extents (list) – the number of cells along each lattice vector

schrodinger.application.matsci.nano.xtal.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

Return type

int

Returns

gcd, the GCD

schrodinger.application.matsci.nano.xtal.get_carts_from_center_string(center: str) list

Return the Cartesian coordinates from the given ‘s_mae_pbc_center’ string, i.e. ‘center_x_y_z’.

Parameters

center – the center string

Returns

the Cartesians floats

schrodinger.application.matsci.nano.xtal.get_carts_from_anchor_string(anchor)

Return the Cartesian coordinates from the given ‘s_mae_pbc_position’ anchor string, i.e. ‘anchor_x_y_z’.

Parameters

anchor (str) – the anchor string

Raises

ValueError – if the given string is not an anchor string

Return type

list

Returns

the Cartesians floats

class schrodinger.application.matsci.nano.xtal.Crystal(asymmetric_unit, space_group=None, a_param=None, b_param=None, c_param=None, alpha_param=None, beta_param=None, gamma_param=None, ncella=1, ncellb=1, ncellc=1, origin=None, bonding='off', bond_orders='off', translate='off', translate_centroids=False, cov_offset=0.4, fract_offset=0.0001, overlap_tresh=0.25, use_existing_pbc_bonds=False, logger=None, valency_exceptions=None)

Bases: object

Main class for generating crystals.

SPACE_GROUP_KEY = 's_pdb_PDB_CRYST1_Space_Group'
A_KEY = 'r_pdb_PDB_CRYST1_a'
B_KEY = 'r_pdb_PDB_CRYST1_b'
C_KEY = 'r_pdb_PDB_CRYST1_c'
ALPHA_KEY = 'r_pdb_PDB_CRYST1_alpha'
BETA_KEY = 'r_pdb_PDB_CRYST1_beta'
GAMMA_KEY = 'r_pdb_PDB_CRYST1_gamma'
SPACE_GROUP_ID_KEY = 'i_matsci_Space_Group_ID'
CHORUS_BOX_BASE_KEY = 'r_chorus_box_'
CHORUS_BOX_AX_KEY = 'r_chorus_box_ax'
CHORUS_BOX_AY_KEY = 'r_chorus_box_ay'
CHORUS_BOX_AZ_KEY = 'r_chorus_box_az'
CHORUS_BOX_BX_KEY = 'r_chorus_box_bx'
CHORUS_BOX_BY_KEY = 'r_chorus_box_by'
CHORUS_BOX_BZ_KEY = 'r_chorus_box_bz'
CHORUS_BOX_CX_KEY = 'r_chorus_box_cx'
CHORUS_BOX_CY_KEY = 'r_chorus_box_cy'
CHORUS_BOX_CZ_KEY = 'r_chorus_box_cz'
CHORUS_BOX_A_KEYS = ['r_chorus_box_ax', 'r_chorus_box_ay', 'r_chorus_box_az']
CHORUS_BOX_B_KEYS = ['r_chorus_box_bx', 'r_chorus_box_by', 'r_chorus_box_bz']
CHORUS_BOX_C_KEYS = ['r_chorus_box_cx', 'r_chorus_box_cy', 'r_chorus_box_cz']
CHORUS_BOX_KEYS = ['r_chorus_box_ax', 'r_chorus_box_ay', 'r_chorus_box_az', 'r_chorus_box_bx', 'r_chorus_box_by', 'r_chorus_box_bz', 'r_chorus_box_cx', 'r_chorus_box_cy', 'r_chorus_box_cz']
CHORUS_BOX_KEY_VECTORS = [['r_chorus_box_ax', 'r_chorus_box_ay', 'r_chorus_box_az'], ['r_chorus_box_bx', 'r_chorus_box_by', 'r_chorus_box_bz'], ['r_chorus_box_cx', 'r_chorus_box_cy', 'r_chorus_box_cz']]
NUM_DECIMAL_COORDS = 4
MSGWIDTH = 80
GENERAL_VEC_1 = array([1., 0., 0.])
GENERAL_VEC_2 = array([0., 1., 0.])
GENERAL_VEC_3 = array([0., 0., 1.])
SYMMETRY_LABEL_KEY = 'i_matsci_Symmetry_Label'
ASU_LABEL_KEY = 'b_matsci_ASU_Atom'
CM_TO_ANGSTROM = 100000000.0
UNIT_CELL_FORMULA_KEY = 's_m_Unit_Cell_Formula'
UNIT_CELL_VOLUME_KEY = 'r_m_Unit_Cell_Volume/Ang.^3'
UNIT_CELL_DENSITY_KEY = 'r_m_Unit_Cell_Density/g/cm^3'
__init__(asymmetric_unit, space_group=None, a_param=None, b_param=None, c_param=None, alpha_param=None, beta_param=None, gamma_param=None, ncella=1, ncellb=1, ncellc=1, origin=None, bonding='off', bond_orders='off', translate='off', translate_centroids=False, cov_offset=0.4, fract_offset=0.0001, overlap_tresh=0.25, use_existing_pbc_bonds=False, logger=None, valency_exceptions=None)

Create an instance.

Parameters
  • asymmetric_unit (schrodinger.Structure.structure) – the ASU

  • space_group (str) – the full or short Hermann-Mauguin symbol of the space group

  • a_param (float) – the lattice parameter a in Angstrom

  • b_param (float) – the lattice parameter b in Angstrom

  • c_param (float) – the lattice parameter c in Angstrom

  • alpha_param (float) – the lattice parameter alpha in degrees

  • beta_param (float) – the lattice parameter beta in degrees

  • gamma_param (float) – the lattice parameter gamma in degrees

  • ncella (int) – the number of unit cells to generate along lattice vector a

  • ncellb (int) – the number of unit cells to generate along lattice vector b

  • ncellc (int) – the number of unit cells to generate along lattice vector c

  • origin (list or None) – the origin of the unit cell, i.e. list of three floats, in fractional coordinates or None if one is not provided

  • bonding (str) – specifies how the bonding should be handled, takes a string in BONDING_CHOICES

  • bond_orders (str) – specifies how the bond orders should be handled, takes a string in BOND_ORDERS_CHOICES

  • translate (str) – specifies how the translation to the first unit cell should be handled, takes a string in TRANSLATE_CHOICES

  • translate_centroids (bool) – If True, after the cell is built, entire molecules are moved into the first cell. Cannot be used together with translate

  • cov_offset (float) – the maximum distance for drawn bonds is the sum of the covalent radii of the two atoms plus this offset in angstrom

  • fract_offset (float) – the threshold used to compare floating point fractional coordinate values and in particular those that are on the cell boundary

  • overlap_tresh (float) – distance used to define overlapping atoms. If 0, no atoms will be deleted

  • use_existing_pbc_bonds (bool) – rather than recalculating PBC bonds use existing PBC bonds

  • logger (logging.getLogger) – output logger

  • valency_exceptions (dict) – The exceptions to update default valencies with.

handleSettings()

Handle the settings of this crystal build.

doBonding()

Determine if this script should handle the bonding both inside and between unit cells.

Return type

bool

Returns

True if this script should handle the bonding, False otherwise.

doBondOrders()

Determine if this script should handle the assignment of bond orders both inside and between unit cells.

Return type

bool

Returns

True if this script should handle the assignment, False otherwise.

doTranslation()

Determine if a translation to the first unit cell should be performed.

Return type

bool

Returns

True if this translation should be performed, False otherwise.

getLatticeParameters()

Get lattice parameters.

checkInputParams()

Check input parameters.

updateLatticeProperties()

Update the lattice properties for the asymmetric unit structure.

setCrystalSymmetry()

Set the crystal symmetry.

determineBasisVectors()

Determine the lattice vectors in the cartesian basis and the cartesian vectors in the lattice basis. Also determine the reciprocal lattice vectors.

buildCrystalUnitCell(mmcrystal_handle)

Build a crystal unit cell.

Parameters

mmcrystal_handle (handle) – the mmcrystal handle

labelSymEquivPos()

Label the symmetry equivalent positions.

labelAsuAtoms(astructure)

Label the atoms that make up an ASU, i.e. the symmetry unique atoms.

Parameters

astructure (schrodinger.Structure.structure) – the structure whose atoms will be labeled

doPropertyEvaluation()

Compute some properties of the unit cell. In order for the properties to be consistent with their standard definitions the provided unit cell must be void of the redundant edge, meaning that the fractionals must be defined on n < f < n + 1 rather than n < f <= n + 1, as well as any other redundancies.

setStructureProperties()

Set some structure properties.

setChorusProperties(astructure, ncella=1, ncellb=1, ncellc=1)

Set the chorus structure properties on the given structure.

Parameters
  • astructure (schrodinger.structure.Structure) – the structure that needs the chorus properties

  • ncella (int) – the number of cells along a

  • ncellb (int) – the number of cells along b

  • ncellc (int) – the number of cells along c

printCrystalParams()

Print some crystal parameters.

setAsuAtomsFalse(astructure)

Set the ASU atom labels to false for this structure.

Parameters

astructure (schrodinger.Structure.structure) – the structure object to be updated

buildCrystalSuperCell(ncella, ncellb, ncellc)

Build a crystal super cell.

Parameters
  • ncella (int) – the number of unit cells to generate along lattice vector a

  • ncellb (int) – the number of unit cells to generate along lattice vector b

  • ncellc (int) – the number of unit cells to generate along lattice vector c

setOrigin()

Set the origin.

orchestrate()

Orchestrate the construction of the crystal.

schrodinger.application.matsci.nano.xtal.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

Return type

numpy.array

Returns

the three reciprocal lattice vectors

schrodinger.application.matsci.nano.xtal.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

Return type

int

Returns

the number of integers traversed

schrodinger.application.matsci.nano.xtal.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

Return type

int

Returns

the signal

schrodinger.application.matsci.nano.xtal.assign_bond_orders(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

Return type

schrodinger.Structure.structure

Returns

a copy of the input structure with the bond orders assigned

schrodinger.application.matsci.nano.xtal.fix_metal_bonding(astructure)

Fix metal bonding in the given structure.

Parameters

astructure (schrodinger.Structure.structure) – the structure object for which metal bonding will be fixed

schrodinger.application.matsci.nano.xtal.assign_bond_orders_w_mmlewis(astructure, fix_metals=True, 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

  • fix_metals (bool) – fix metals coming from mmlewis

  • logger (logging.getLogger or None) – output logger or None if there isn’t one

Return type

schrodinger.Structure.structure

Returns

a copy of the input structure with the bond orders assigned

schrodinger.application.matsci.nano.xtal.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

Return type

tuple

Returns

contains the nine chorus properties

schrodinger.application.matsci.nano.xtal.extract_chorus_lattice_vector(struct, letter)

Extract the lattice vector from the chorus box properties. Each vector is comprised of 3 properites ending in mx, my, and mz, where m is either a, b or c. For instance, the a vector properties end in ax, ay and az.

Parameters
  • struct (schrodinger.structure.Structure) – The structure with the periodic boundary information

  • letter (str) – The single letter, a, b or c, that indicates which of the three vectors is desired

Return type

np.array

Returns

Numpy array of chrous for the given lattice letter (direction).

schrodinger.application.matsci.nano.xtal.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

Return type

list

Returns

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

schrodinger.application.matsci.nano.xtal.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

Return type

list

Returns

contains the nine chorus properties

schrodinger.application.matsci.nano.xtal.get_volume_from_params(params)

Return cell volume (in Angstrom^3) from cell parameters.

Parameters

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

Return type

float

Returns

Cell volume in Angstrom^3

schrodinger.application.matsci.nano.xtal.get_volume_from_vecs(vecs)

Return cell volume (in Angstrom^3) from lattice vectors.

Parameters

params (list) – lattice vectors parameters

Return type

float

Returns

Cell volume in Angstrom^3

schrodinger.application.matsci.nano.xtal.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

Return type

list

Returns

contains tuples of unique atom index pairs within the specified distance

class schrodinger.application.matsci.nano.xtal.PBCBond(atom1, atom2, order, also_reg_bond)

Bases: object

Class to manage a PBC bond, i.e. a long bond connecting two real atoms on opposite sides of a unit cell that is used in lieu of the bond between the real and image atoms.

PBC_BOND_THRESHOLD = 0.001
PBC_BOND_KEY = 'b_matsci_PBC_bond'
ALSO_REG_BOND_KEY = 'b_matsci_also_reg_bond'
PBC_BOND_COLOR_KEY = 'i_m_color'
PBC_BOND_COLOR = 4
AHEAD = 'ahead'
BEHIND = 'behind'
__init__(atom1, atom2, order, also_reg_bond)

Create an instance.

Parameters
  • atom1 (int) – the first atom index of the bond

  • atom2 (int) – the second atom index of the bond

  • order (int) – the bond order

  • also_reg_bond (bool) – indicates whether this 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

setDeltasToNeighboringCells(atom1_vec, atom2_vec, spanning_vectors)

Set two dictionaries, one for moving to neighboring cells ahead and one for moving behind. Keys are tuples of integer cell deltas and values are (tail, head) tuples giving a directionality of this PBC bond along the given direction.

Parameters
  • atom1_vec (numpy.array) – vector to the first atom of the PBC bond

  • atom2_vec (numpy.array) – vector to the second atom of the PBC bond

  • spanning_vectors (dict) – keys are tuples of cell index triples, values are tuples of normalized spanning vectors for the cell and their original lengths

getNeighborPBCBond(cell_indices, ncella, ncellb, ncellc, cell_size, cell_delta, tail_head)

Return a (tail, head) ordered tuple of atom indices for the neighboring PBC bond in the cell given by the cell delta. If this cell is the first or last cell then it will wrap around to the ending or beginning cell, respectively.

Parameters
  • cell_indices (tuple) – a triple of cell indices

  • ncella (int) – the number of cells along a

  • ncellb (int) – the number of cells along b

  • ncellc (int) – the number of cells along c

  • cell_size (int) – the number of atoms in a cell

  • cell_delta (tuple) – a triple of cell deltas which provide the neighboring cells location

  • tail_head (tuple) – provides the tail and head atom indices for this PBC bond given the cell delta

Return type

tuple

Returns

atom indices for the neighboring PBC bond

offsetAtomData(offset)

Offset the atom data of this instance.

Parameters

offset (int) – the offset to use

class schrodinger.application.matsci.nano.xtal.PBCBonds(cell_indices=None, pbc_bonds_dict=None, cell_size=None, cov_offset=0.4)

Bases: object

Class to manage a collection of PBC bonds.

FIRST_CELL = (1, 1, 1)
__init__(cell_indices=None, pbc_bonds_dict=None, cell_size=None, cov_offset=0.4)

Create an instance.

Parameters
  • cell_indices (tuple or None) – a triple of cell indices indicating to which cell the given PBC bonds belong, if None then the first cell will be used

  • pbc_bonds_dict (dict or None) – used to create a dictionary of PBCBond objects, keys are tuples of PBC bond atom index pairs, values are tuples of bond orders and booleans indicating whether the PBC bond is also a regular bond, if None then the dictionary of PBCBond ojects will be empty

  • cell_size (int) – the number of atoms in a cell

  • 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

setPBCBonds(pbc_bonds_dict)

Create a dictionary of PBCBond objects from a dictionary containing PBC bonds.

Parameters

pbc_bonds_dict (dict) – keys are tuples of PBC bond atom index pairs, values are tuples of bond orders and booleans indicating whether the PBC bond is also a regular bond

updatePBCBondOrders(astructure)

Update the bond orders in this instance given a structure with updated PBC bond orders.

Parameters

astructure (schrodinger.Structure.structure) – the structure with the updated PBC bond orders

setDeltasToNeighboringCells(astructure, lattice_vectors)

For each PBC bond in this cell determine the cell deltas that are needed to move ahead and behind to relevant neighboring cells.

Parameters
  • astructure (schrodinger.Structure.structure) – the structure with the PBC bonds

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

cleanUpPBCBonds(astructure, pairs, delete)

Clean up the specified PBC bonds in the structure.

Parameters
  • astructure (schrodinger.Structure.structure) – the structure with the PBC bonds

  • pairs (list) – tuples of PBC bonding atom index pairs

  • delete (bool) – if True then the PBC bonds will be deleted

getOffsetPBCBonds(cell_indices, offset)

Return a PBCBonds instance for the provided cell indices in which the atom indices have been offset by the given amount.

Parameters
  • cell_indices (tuple) – a triple of cell indices indicating to which cell the offset PBC bonds belong

  • offset (int) – the offset to use in setting the atom indices

Return type

PBCBonds

Returns

a PBCBonds object for the given cell containing the offset atoms

connectToCells(astructure, ncella, ncellb, ncellc, direction)

Connect the PBC bonds in this cell with those relevant neighboring cells ahead of or behind this one so as to create real bonds from pairs of PBC bonds or new PBC bonds. If this cell is the first or last along a given direction then if possible it will create new PBC bonds by wrapping around to ending or beginning cells, respectively.

Parameters
  • astructure (schrodinger.Structure.structure) – the structure for which the connections are sought

  • ncella (int) – the number of cells along a

  • ncellb (int) – the number of cells along b

  • ncellc (int) – the number of cells along c

  • direction (str) – the direction in which to go for the next PBC bond, either PBCBond.AHEAD or PBCBond.BEHIND

schrodinger.application.matsci.nano.xtal.add_labeled_pbc_bond(astructure, atom1, atom2, order, is_pbc_bond=False, also_reg_bond=False, color=4)

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

schrodinger.application.matsci.nano.xtal.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

Return type

int

Returns

the number of atoms between the two cells

schrodinger.application.matsci.nano.xtal.delete_all_pbc_bonds(astructure)

Delete all PBC bonds from the given structure.

Parameters

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

schrodinger.application.matsci.nano.xtal.is_pbc_bond(astructure, atom1, atom2, check_also_reg_bond=False, unit_lattice_vectors=None, pbc=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

  • pbc (schrodinger.infra.structure.PBC or None) – The infrastructure PBC created from the Chorus box properties, if None, pbc object will be created

Return type

tuple

Returns

a (is_pbc_bond, also_reg_bond, bond_distance) tuple

schrodinger.application.matsci.nano.xtal.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

Return type

tuple

Returns

contains the six lattice parameter properties

schrodinger.application.matsci.nano.xtal.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

Return type

dict

Returns

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

schrodinger.application.matsci.nano.xtal.get_element_priority(pair)

Return the formula ordering priority of the element in the given pair.

Parameters

pair (tuple) – (element, number) tuple

Return type

int

Returns

the element priority

schrodinger.application.matsci.nano.xtal.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

Return type

str

Returns

the formatted unit cell formula

schrodinger.application.matsci.nano.xtal.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

Return type

numpy.array

Returns

the given vector in the fractional basis

schrodinger.application.matsci.nano.xtal.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

Return type

numpy.array

Returns

the given vector in the Cartesian basis

schrodinger.application.matsci.nano.xtal.trans_cart_to_frac_from_vecs(coords, a_vec, b_vec, c_vec, rec=False)

Transform coordinates from (reciprocal) Cartesian to (reciprocal) fractional using lattice vectors.

Parameters
  • coords (numpy.array) – a list of Cartesian coordinates

  • a_vec (list of 3 floats) – ‘a’ lattice vector

  • b_vec (list of 3 floats) – ‘b’ lattice vector

  • c_vec (list of 3 floats) – ‘c’ lattice vector

  • rec (bool) – If True, work in reciprocal space

Return type

numpy array

Returns

Coordinates in fractional coordinates

schrodinger.application.matsci.nano.xtal.trans_frac_to_cart_from_vecs(coords, a_vec, b_vec, c_vec, rec=False)

Transform coordinates from (reciprocal) fractional to (reciprocal) Cartesian using lattice vectors.

Parameters
  • coords (numpy.array) – a list of fractional coordinates

  • a_vec (list of 3 floats) – ‘a’ lattice vector

  • b_vec (list of 3 floats) – ‘b’ lattice vector

  • c_vec (list of 3 floats) – ‘c’ lattice vector

  • rec (bool) – If True, work in reciprocal space

Return type

numpy array

Returns

Coordinates in Cartesian coordinates

schrodinger.application.matsci.nano.xtal.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

Return type

schrodinger.structure.Structure

Returns

the built cell

schrodinger.application.matsci.nano.xtal.get_vectors_from_chorus(astructure)

Return the three lattice vectors from the nine lattice chorus properties.

Parameters

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

Raises

ValueError – if any chorus property is missing

Return type

numpy.array

Returns

the three lattice vectors

schrodinger.application.matsci.nano.xtal.get_conv_from_vecs(a_vec, b_vec, c_vec)

Generate matrices to convert from fractional to Cartesian and back.

Parameters
  • a_vec (list of 3 floats) – ‘a’ lattice vector

  • b_vec (list of 3 floats) – ‘b’ lattice vector

  • c_vec (list of 3 floats) – ‘c’ lattice vector

Return type

tuple of matrices

Returns

Matrices that convert fractional atomic coordinates to Cartesian and back

schrodinger.application.matsci.nano.xtal.create_new_box(struct, minval=0.0, buffer=2)

Create a new box that is large enough to encompass the X, Y and Z lengths of the system

Parameters
  • struct (schrodinger.structure.Structure) – The structure to work on

  • minval (float) – Minimum length of the cell edge or 0. if vdW is fine

  • buffer (float) – The buffer to add to all PBC lengths. We add 2.0 as the default vdw buffer to make sure atoms at the boundary don’t clash with their mirror images.

schrodinger.application.matsci.nano.xtal.set_lattice_properties(astructure, lattice_properties)

Set the given lattice properties on the structure.

Parameters
  • astructure (schrodinger.structure.Structure) – the structure on which to set the lattice properties

  • lattice_properties (list) – a, b, c, alpha, beta, and gamma lattice properties

schrodinger.application.matsci.nano.xtal.make_p1(astructure, logger=None, in_place=False)

Make a P1 cell.

Parameters
  • astructure (schrodinger.structure.Structure) – the structure to make P1

  • logger (logging.Logger or None) – if not None then the logger for printing

  • in_place (bool) – if True then operate directly on the given structure as opposed to a copy of it

Return type

schrodinger.structure.Structure

Returns

the P1 cell

schrodinger.application.matsci.nano.xtal.sync_pbc(st, create_pbc=False, in_place=False)

Return the given structure with a synchronized PBC, if create_pbc is True and the structure lacks a PBC then one will be created, otherwise this function will return False if there is no PBC.

Parameters
  • st (structure.Structure) – the structure with the PBC to be synchronized

  • create_pbc (bool) – if True and the given structure lacks a PBC then a minimal PBC will be created, if False and if the given structure lacks a PBC then this function will return False

  • in_place (bool) – if True then operate directly on the given structure as opposed to a copy of it

Return type

structure.Structure or bool

Returns

the structure with a synchronized PBC or False if there was no PBC and one wasn’t created

schrodinger.application.matsci.nano.xtal.sync_pbc2(struct, lattice_params=None, chorus_params=None, prioritize_cparams=True)

Sync PBC properties in place (without creating a new structure) for struct. If all PBC properties are absent (both chorus and PDB) return False. It is possible to provide new lattice or chorus parameters and to prioritize one of the sets.

Type

schrodinger.structure.Structure

Param

Structure to be modified

Parameters
  • lattice_params (list or numpy.array or None) – contains the a, b, c, alpha, beta, and gamma lattice parameters or None. These will be used instead of ones possibly obtained from the struct

  • chorus_params (list or numpy.array or None) – contains the nine chorus properties, i.e. ax, ay, az, bx, …, cz or None. These will be used instead of ones possibly obtained from the struct

Param

Prioritize chorus params over lattice params if True. If False, lattice params have priority

Return type

bool

Returns

True on syncing success, False if both sets were not provided or empty

schrodinger.application.matsci.nano.xtal.get_pbc_bonds_dict(astructure)

Return a PBC bonds dict for the given structure.

Parameters

astructure (schrodinger.structure.Structure) – the structure with the PBC bonds from which to create the dict

Return type

dict

Returns

keys are tuples of PBC bond atom index pairs, values are tuples of bond orders and booleans indicating whether the PBC bond is also a regular bond

schrodinger.application.matsci.nano.xtal.set_representation_bond(abond)

Set the representation of the given bond.

Parameters

abond (schrodinger.structure._StructureBond) – the bond to set the representation for

schrodinger.application.matsci.nano.xtal.set_pbc_properties(astructure, chorus_properties)

Set the chorus and PDB properties on the given structure using the given chorus properties.

Parameters
  • astructure (schrodinger.structure.Structure) – the structure on which the properties are set

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

schrodinger.application.matsci.nano.xtal.transform_pbc(struct_in, supercell_matrix, scale_only=False, cell_only=False, origin_shift=None, overlap_threshold=0.25)

Create a new structure based on the transformation matrix. If both ‘scale_only’ and ‘cell_only’ are False (default behavior), atoms will be added or subtracted based on the expansion/contraction of the PBC.

Parameters
  • struct_in (schrodinger.structure.Structure) – Structure to which transformation will be applied

  • supercell_matrix (3 x 3 floats) – Transformation matrix

  • scale_only (bool) – If True, scale atoms to the new cell defined by supercell_matrix, this keeps constant fractional coordinates and number of atoms from the original ‘struct’

  • cell_only (bool) – If True, change cell frame to a new cell. This keeps constant Cartesian coordinates and number of atoms from the original ‘struct’. Note that if supercell cell is smaller than original cell, atoms could be cut by the new smaller cell frame

  • origin_shift (list of 3 floats) – Origin shift in fractional coordinates

  • overlap_threshold (float) – (Ang) distance used to define overlapping atoms

  • struct – Transformed structure

Rtype struct

schrodinger.structure.Structure

schrodinger.application.matsci.nano.xtal.get_simple_supercell_matrix(supercell_matrix)

Get minimal diagonal elements of a simple supercell matrix starting from (non)-diagonal supercell matrix. Supercell matrix can be: -1, 1, 1 2, -3, 4 -5, 6, 7 Resulting simple supercell (described by the matrix) must be able to hold the supercell above.

In the case of a smaller lattice, for example: 0.5 0 0 0 0.5 0 0 0 0.5

[1, 1, 1] will be returned

Parameters

supercell_matrix (3 x 3 list of floats) – Supercell matrix

Return type

list of three ints

Returns

Diagonal elements of the simple supercell matrix (must be positive nonzero integers)

schrodinger.application.matsci.nano.xtal.get_transformed_vectors(vecs, tmatrix)

Get new lattice vectors based on the original vectors and the transformation matrix.

Parameters
  • vecs (numpy.array) – Input lattice vectors (3x3)

  • tmatrix (numpy.array) – Transformation matrix

Return type

tuple

Returns

Transformed vectors (3x3), extents for the original vecs (3), trimmed transformation matrix (3x3)

schrodinger.application.matsci.nano.xtal.get_simple_supercell(struct, supercell_matrix)

Get supercell structure.

Parameters
  • struct (structure.Structure) – Input structure

  • supercell_matrix (List of 3 floats) – Diagonal elements of the supercell matrix

Return type

structure.Structure

Returns

Supercell structure

schrodinger.application.matsci.nano.xtal.get_transformation_matrix(vecs, new_vecs)

Get transformation matrix between old and new set of lattice vectors.

Parameters
  • vecs (3 x 3 float list) – Old lattice vectors

  • new_vecs (3 x 3 float list) – New lattice vectors

Return type

3 x 3 float list

Returns

Transformation matrix

schrodinger.application.matsci.nano.xtal.get_physical_properties(struct, vecs=None)

Get cell formula, volume and density of a struct.

Type

structure.Structure

Param

Input structure

Parameters

vecs (list(list) or None) – Lattice vectors. If None, will be obtained from structure

Return type

float, float, float

Returns

formula, volume and density

schrodinger.application.matsci.nano.xtal.set_physical_properties(struct)

Set cell formula, volume and density to struct.

Type

structure.Structure

Param

Input structure

schrodinger.application.matsci.nano.xtal.pdist_vec_row_col(d, i)

Convert from triangular indices of distance matrix to indices of the square form.

Parameters
  • d (int) – row length of the original triangular matrix

  • i (numpy.array(int)) – Condensed triangular indices, 0-indexed

Return type

numpy.array(int), numpy.array(int)

Returns

row and column indices (0-indexed) from the corresponding square form

schrodinger.application.matsci.nano.xtal.preserve_bonds(struct, to_keep, to_remove)

Try to preserve bonding during the remove of the duplicates atoms.

Parameters
  • struct (structure.Structure) – Structure to preserve bonding for

  • to_keep (list) – List of atom indices to keep

  • to_remove (list(list)) – List of lists of atom indices to be removed. Each item in the list is a list of duplicated atom indices corresponding to the atom index from to_keep list

schrodinger.application.matsci.nano.xtal.translate_to_1st_cell(coords, vecs, is_cartesian=True, fract_offset=0.0001, axes=None, origin=(0.0, 0.0, 0.0))

Translate coordinates to the 1st cell (in range [0, 1). If it is a supercell with original vectors, overlap atoms are expected.

Parameters
  • coords (list) – Coordinates (can be Cartesian or fractional, see is_cartesian)

  • vecs (list) – Lattice vectors

  • is_cartesian (bool) – Whether input coordinates are Cartesian or fractional

  • fract_offset (float) – DEPRECATED. The threshold used to compare floating point fractional coordinate values and in particular those that are on the cell boundary

  • axes (iterable or None) – List of axes to use

  • origin (tuple) – the origin of the cell to which to translate in fractional coordinates

Returns

Translated Cartesian coordinates

schrodinger.application.matsci.nano.xtal.coords_outside_1st_cell(coords, vecs, is_cartesian=True, axes=None, above=False, below=False, is_hb=False)

Returns coordinate indices (atom indices - 1) of the atoms outside of the cell defined with vecs.

Parameters
  • coords (list) – Coordinates (can be Cartesian or fractional, see is_cartesian)

  • vecs (list) – Lattice vectors

  • is_cartesian (bool) – Whether input coordinates are Cartesian or fractional

  • fract_offset (float) – The threshold used to compare floating point fractional coordinate values and in particular those that are on the cell boundary

  • axes (iterable or None) – List of axes to use

  • above (bool) – Whether to return indices that are “above” the first cell separately

  • below (bool) – Whether to return indices that are “below” the first cell separately

  • is_hb (bool) – Whether system is located in the cell around origin (between -0.5 and 0.5) or between 0 and 1

Return type

numpy.array

Returns

Indices outside the first cell

schrodinger.application.matsci.nano.xtal.is_normal_surface(vecs=None, pbc=None)

Checks if C-axis is normal to the a-b plane from lattice vectors or pbc object

Parameters
  • vecs (numpy.array) – Lattice vectors

  • pbc (schrodinger.infra.structure.PBC) – The structure pbc object

Return type

bool

Returns

Whether C-axis is normal to the a-b plane

schrodinger.application.matsci.nano.xtal.are_c_and_z_parallel(pbc, tolerance=0.98)

Return whether c vector is parallel to Z axis within a tolerance

Parameters

pbc (schrodinger.infra.structure.PBC) – The pbc object

Return type

bool

Returns

Whether C and Z are parallel

schrodinger.application.matsci.nano.xtal.move_atoms_into_cell(struct, frac_coords=None, overlap_tresh=0.25, fract_offset=0.0001, preserve_bonding=False)

Get structure with all the atoms moved into the first cell.

Type

structure.Structure

Param

Input structure

Parameters
  • frac_coords (numpy arrays of arrays of 3 floats or None) – Fractional coordinates

  • overlap_tresh (float) – Distance between two atoms, such that they are considered overlapping

  • fract_offset (float) – The threshold used to compare floating point fractional coordinate values and in particular those that are on the cell boundary

  • preserve_bonding (bool) – If True, preserve bonding between atoms (might be slow)

Return type

structure.Structure

Returns

Structure with all the atoms moved inside first unit cell

schrodinger.application.matsci.nano.xtal.get_unit_lattice_vector_info(astructure)

Return a list of tuples containing unit lattice vector information, i.e. the unit lattice vectors and their original lengths.

Parameters

astructure (schrodinger.structure.Structure) – the structure with lattice vectors defined by chorus box properties

Return type

list of tuples

Returns

each (numpy.array, float) tuple contains (1) the unit lattice vector and (2) the length of the original vector

schrodinger.application.matsci.nano.xtal.label_pbc_bonds(astructure, pbc=None, check_also_reg_bond=None, is_cg=None)

Label PBC bonds.

Parameters
  • astructure (schrodinger.structure.Structure) – the structure with the bonds to label

  • pbc (schrodinger.infra.structure.PBC or None) – The infrastructure PBC created from the Chorus box properties, if None, pbc object will be created

  • check_also_reg_bond (bool or None) – 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. If None, this will be evaluated

  • is_cg (bool or None) – True, if structure is CG, otherwise False. If None, structure will be evaluated (slow)

  • pbc – The infrastructure PBC created from the Chorus box properties, if None, pbc object will be created

schrodinger.application.matsci.nano.xtal.label_pbc_bond(abond, also_reg_bond=False, color=4)

Label this PBC bond.

Parameters
  • abond (schrodinger.structure._StructureBond) – the PBC bond to label

  • 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 a PBC bond, that is not also a regular bond, should be colored with this color, if None then no coloring is performed

schrodinger.application.matsci.nano.xtal.get_primitive_cell(struct_in, set_space_group=False)

Get primitive cell.

Parameters

struct (schrodinger.structure.Structure) – Original structure

Return type

schrodinger.structure.Structure

Returns

Primitive cell with the space group set, if requested

schrodinger.application.matsci.nano.xtal.get_std_cell_from_spglib_dataset(struct, dataset)

Get standardized cell (structure) from spglib dataset and copy all the structure properties (except symmetry related) from struct_in.

Parameters
Return type

schrodinger.structure.Structure

Returns

Standardized cell with the space group set

schrodinger.application.matsci.nano.xtal.assign_space_group(struct_in, symprec=0.01, search_alt_cells=False)

Set space group and space group id to the input structure. An error message is returned on failure.

Type

schrodinger.structure.Structure

Param

Input structure that will be modified

Parameters
  • symprec (float) – Symmetry tolerance used for atomic coordinates to assign space group

  • search_alt_cells (bool) – If True, search for alternative cells

Return type

list

Returns

If search_alt_cells is True, conventional and primitive cells are returned. Otherwise, empty list.

schrodinger.application.matsci.nano.xtal.get_normal_surf(struct, restore_vacuum=True, overlap_threshold=0.25)

Enforce system to have C-axis normal to the a-b plane. This is done by straining the structure.

Parameters
  • struct (schrodinger.structure.Structure) – Input structure

  • restore_vacuum (bool) – If True, set vacuum value in Z direction to the original value, before the surface is “normalized”. Should be set to True for infinite systems. If False, don’t modify cell after normalization

  • overlap_threshold (float) – (Ang) distance used to define overlapping atoms

Return type

schrodinger.structure.Structure

Returns

Output structure with C-axis normal to the a-b plane

schrodinger.application.matsci.nano.xtal.get_normal_surf_from_HKL(hkl, vecs, max_normal_search=10)

Calculate transformation matrix with c-axis most normal to a-b plane from HKL plane indices and lattice vectors.

Parameters
  • hkl (list of 3 integers) – Miller plane indices

  • vecs (list of 3 lists of floats) – Lattice vectors

  • max_normal_search (int) – Maximum number of linear combinations of lattice vectors to be considered when search most normal surface

Return type

bool, numpy.array 3 x 3 of integers

Returns

True, if normal is found, otherwise False and transformation matrix

schrodinger.application.matsci.nano.xtal.lcm(numbers)

Get the lowest common multiple of a sequence of numbers.

Parameters

numbers (list of integers) – Sequence of integers

Return type

int

Returns

Lowest common multiple

schrodinger.application.matsci.nano.xtal.reduce_vector(vector)

Get reduced vector of a transformation matrix.

Parameters

vector (list of integers) – Components of a vector of transformation matrix

Return type

list of integers

Returns

Components of a reduced vector of transformation matrix

schrodinger.application.matsci.nano.xtal.get_struct_from_CIF(cif_fn)

Get structure from CIF file.

Parameters

cif_fn (str) – CIF file name

Return type

schrodinger.structure.Structure

Returns

Structure from CIF file

Raises

ValueError – If file doesn’t exist or the structure could not be read

schrodinger.application.matsci.nano.xtal.translate_atoms(cell, origin=None)

Translate all atoms to the first unit cell.

Parameters
  • cell (schrodinger.structure.Structure) – the structure to translate, must have chorus properties defined

  • origin (list or None) – the list with origin of the cell to which to translate in fractional coordinates. If none it will be set to [-0.5, -0.5, -0.5] for system with s_ffio_ct_type set and ParserWrapper.ORIGIN for others.

schrodinger.application.matsci.nano.xtal.translate_molecules(cell, centroids=False, maxes=False, fract_offset=0.0001)

Translate all molecules to the first unit cell.

Parameters
  • cell (schrodinger.structure.Structure) – the structure to translate, must have chorus properties defined

  • centroids (bool) – If True, translation is using molecular centroid

  • maxes (bool) – If True, translation is using maximum in x, y, z direction for each molecule. Cannot be used together with centroids option

  • fract_offset (float) – The threshold used to compare floating point fractional coordinate values and in particular those that are on the cell boundary

schrodinger.application.matsci.nano.xtal.get_cell_fast(asu, symm_ops)

Get crystal cell with all applied symmetry operators on the ASU.

Parameters
  • asu (structure.Structure) – Asymmetric unit

  • symm_ops (list) – List of symmetry operations (4 x 4 matrices)

Return type

structure.Structure

Returns

Crystal cell

schrodinger.application.matsci.nano.xtal.create_nonbonded_extents(struct, extents=None)

Place the given structure in the middle of extents, adding one cell in each of the +/- directions of the indicated vectors. No bonding is performed - the structure created this way is only good for representing atom locations/sterics. If struct has no pbc, a copy of it will be returned.

The atoms from the given structure will retain their order and be the first atoms in the returned structure.

The diagram below demonstrates what the structure looks like if extents=[1,1,0] is given. “o” represents an added extent image, “x” represents the given system, and the lines are just there for visual reference:

 o | o | o
-----------
 o | x | o
-----------
 o | o | o
Parameters
  • struct (structure.Structure) – The original structure to extend

  • extents (list) – Which vectors should be extended and by how many images in the + and - directions. For instance, [1, 1, 1] indicates to extend by 1 cell each in the + and - a, b and c directions. [2, 1, 0] extend by 2 cells in +/- a, 1 cell in +/- b, and will not extend in the c direction. The default is [1, 1, 1].

Return type

schrodinger.structure.Structure

Returns

The extended structure

schrodinger.application.matsci.nano.xtal.get_pbc_origin(st)

Return the PBC origin in Angstrom from the given structure.

Parameters

st (structure.Structure) – the structure

Raises

KeyError – if no PBC exists

Return type

numpy.array

Returns

the origin in Angstrom

schrodinger.application.matsci.nano.xtal.get_pbc_bonded_atom_pairs(st, along_vector_idxs=None, exclusive=False, only_infinite=False)

Return a dictionary of PBC bonded atom pairs along the specified directions.

Parameters
  • st (structure.Structure) – the structure

  • along_vector_idxs (list or None) – the directions to consider, 0 for a-vector, 1 for b-vector, and/or 2 for c-vector, if None then the c-vector is used by default

  • exclusive (bool) – if True then consider PBC bonds that wrap only the specified directions, if False then must wrap the specified directions but can also wrap other directions

  • only_infinite (bool) – if True then consider only PBC bonds that are responsible for the system being infinite (meaning that breaking such bonds makes the infinite system finite)

Return type

dict

Returns

contains atom index pairs for PBC bonds, keys are direction indices, values are lists of atom index (near, far) pair tuples where the fractional coordinate along the keyed direction is near < far

schrodinger.application.matsci.nano.xtal.delete_pbc_bonds(st, along_vector_idxs=None, exclusive=False, only_infinite=False)

Delete PBC bonds from the given structure along the specified directions.

Parameters
  • st (structure.Structure) – the structure

  • along_vector_idxs (list or None) – the directions to consider, 0 for a-vector, 1 for b-vector, and/or 2 for c-vector, if None then the c-vector is used by default

  • exclusive (bool) – if True then consider PBC bonds that wrap only the specified directions, if False then must wrap the specified directions but can also wrap other directions

  • only_infinite (bool) – if True then consider only PBC bonds that are responsible for the system being infinite (meaning that breaking such bonds makes the infinite system finite)

Return type

dict

Returns

contains atom index pairs for PBC bonds, keys are direction indices, values are lists of atom index (near, far) pair tuples where the fractional coordinate along the keyed direction is near < far

schrodinger.application.matsci.nano.xtal.has_pbc(st)

Return True if the given structure has a PBC.

Parameters

st (schrodinger.structure.Structure) – the structure

Return type

bool

Returns

True if the given structure has a PBC

schrodinger.application.matsci.nano.xtal.scale_cell(vecs, new_volume)

Return a new Lattice with volume new_volume by performing a scaling of the lattice vectors so that length proportions and angles are preserved.

Parameters
  • vecs (numpy.array) – Original lattice vectors

  • new_volume (float) – New volume

Return type

numpy.array

Returns

New lattice vectors with the desired volume

schrodinger.application.matsci.nano.xtal.both_bond_types_exist(st)

Raise a ValueError if the given structure does not have at least both a single regular bond and a single PBC bond, otherwise return sample atom indices for both.

Parameters

st (schrodinger.structure.Structure) – the structure to check

Raises

ValueError – if both bond types do not exist

Return type

tuple

Returns

pair tuple containing two pair tuples, one for a regular bond and one for a PBC bond

schrodinger.application.matsci.nano.xtal.get_strained_cell(pos, vecs, new_vecs, remap=True)

Strain cell using the vectors and atom coordinates are scaled proportionally if remap is True.

Parameters
  • pos (list) – Atomic positions

  • vecs (list[3x3]) – Lattice vectors

  • new_vecs (list[3x3]) – New lattice vectors

  • remap (bool) – whether to strain the atom coordinates in the cell

Return type

list, list[3x3]

Returns

Updated positions, updated lattice vectors

schrodinger.application.matsci.nano.xtal.is_valid_lower_triangle(pbc_vecs)

Check if vectors obey lower triangle right hand-side convention. Valid vecs have zeros in the upper triangle and positive along the diagonal.

Parameters

pbc_vecs (list or PBC) – Lattice vectors or a PBC object

Return type

bool

Returns

Whether vectors obey lower triangle right hand-side convention

schrodinger.application.matsci.nano.xtal.chorus_to_lower_triangle(struct)

Update chorus properties and with them 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!!)