schrodinger.application.matsci.nano.space_groups module¶

Classes and functions for creating crystals by unit cell.

schrodinger.application.matsci.nano.space_groups.get_spacegroups()¶

Get space groups object.

Return type: SpaceGroups
Returns: Cached space groups object, do not modify!!

schrodinger.application.matsci.nano.space_groups.get_symmops_from_spglib(symm)¶

Get set of symmetry operators from a set of rotations and translations. Symmetry operator is defined with a 4 x 4 matrix, top left 3 x 3 is rotation matrix, top right column 1 x 3 is translation, rest, bottom row is [0 0 0 1]

Parameters: symm (dict of two keys: 'rotations': list of 3 x 3 matrices, 'translations': list of 1 x 3 matrices) – dictionary of list of rotations and translations
Returns: list of 4x4 matrices
Return type: list of symmetry operators

class schrodinger.application.matsci.nano.space_groups.CrystalSystems¶

Bases: object

Manage the properties of the seven crystal systems.

TRICLINIC_NAME = 'triclinic'¶

MONOCLINIC_NAME = 'monoclinic'¶

ORTHORHOMBIC_NAME = 'orthorhombic'¶

TETRAGONAL_NAME = 'tetragonal'¶

TRIGONAL_NAME = 'trigonal'¶

HEXAGONAL_NAME = 'hexagonal'¶

CUBIC_NAME = 'cubic'¶

class Triclinic(name)¶

Bases: object

Manage the triclinic system.

__init__(name)¶

Create an instance.

Parameters: name (str) – crystal system name

class Monoclinic(name)¶

Bases: object

Manage the monoclinic system.

__init__(name)¶

Create an instance.

Parameters: name (str) – crystal system name

class Orthorhombic(name)¶

Bases: object

Manage the orthorhombic system.

__init__(name)¶

Create an instance.

Parameters: name (str) – crystal system name

class Tetragonal(name)¶

Bases: object

Manage the tetragonal system.

__init__(name)¶

Create an instance.

Parameters: name (str) – crystal system name

class Trigonal(name)¶

Bases: object

Manage the trigonal system.

__init__(name)¶

Create an instance.

Parameters: name (str) – crystal system name

class Hexagonal(name)¶

Bases: object

Manage the hexagonal system.

__init__(name)¶

Create an instance.

Parameters: name (str) – crystal system name

class Cubic(name)¶

Bases: object

Manage the cubic system.

__init__(name)¶

Create an instance.

Parameters: name (str) – crystal system name

getCrystalSystem(name)¶

Return the crystal system object for the crystem system of the provided name.

Parameters: name (str) – crystal system name
Return type: one of the seven crystal system objects
Returns: crystal_system_obj

class schrodinger.application.matsci.nano.space_groups.SpaceGroup(definition_id: int, space_group_id: int, ichoice: int, num_choices: int, space_group_short_name: str, space_group_full_name: str, point_group_name: str, centering_opers: List, primary_opers: List, symmetry_opers: List, num_centering_opers: int, num_primary_opers: int, num_symmetry_opers: int, centering_opers_strs: List, primary_opers_strs: List, symmetry_opers_strs: List, crystal_system: schrodinger.application.matsci.nano.space_groups.CrystalSystems, xyzasu: str, spg_setting: str)¶

Bases: tuple

Collect the properties of a space group.

DEFINITION_ID = 'Def. ID'¶

SPACE_GROUP_ID = 'Space Group ID'¶

CRYSTAL_SYSTEM = 'Crystal System'¶

SHORT_HERMANN_MAUGUIN_SYMBOL = 'Short H.-M. Symbol'¶

FULL_HERMANN_MAUGUIN_SYMBOL = 'Full H.-M. Symbol'¶

POINT_GROUP_NAME = 'Point Group'¶

NUM_CENTERING_OPERS = 'N Centering Ops.'¶

NUM_PRIMARY_OPERS = 'N Primary Ops.'¶

NUM_SYMMETRY_OPERS = 'N Symmetry Ops.'¶

CENTERING_OPERS = 'Centering Operators'¶

PRIMARY_OPERS = 'Primary Operators'¶

SYMMETRY_OPERS = 'Symmetry Operators'¶

SPACE_GROUP_SETTING = 'Space Group Setting'¶

ID_TAG = 'spgid '¶

SHORT_NAME_TAG = 'sspgname '¶

FULL_NAME_TAG = 'fspgname '¶

POINT_GROUP_TAG = 'pgname '¶

CRYSTAL_SYSTEM_TAG = 'crysym '¶

SETTING_TAG = 'setting '¶

ASU_TAG = 'xyzasu '¶

PRIMARY_OPERATIONS_TAG = 'primoper '¶

CENTERING_OPERATIONS_TAG = 'centoper '¶

END_OF_DEF_TAG = 'endofdef'¶

definition_id: int¶: Alias for field number 0

space_group_id: int¶: Alias for field number 1

ichoice: int¶: Alias for field number 2

num_choices: int¶: Alias for field number 3

space_group_short_name: str¶: Alias for field number 4

space_group_full_name: str¶: Alias for field number 5

point_group_name: str¶: Alias for field number 6

centering_opers: List¶: Alias for field number 7

primary_opers: List¶: Alias for field number 8

symmetry_opers: List¶: Alias for field number 9

num_centering_opers: int¶: Alias for field number 10

num_primary_opers: int¶: Alias for field number 11

num_symmetry_opers: int¶: Alias for field number 12

centering_opers_strs: List¶: Alias for field number 13

primary_opers_strs: List¶: Alias for field number 14

symmetry_opers_strs: List¶: Alias for field number 15

crystal_system: schrodinger.application.matsci.nano.space_groups.CrystalSystems¶: Alias for field number 16

xyzasu: str¶: Alias for field number 17

spg_setting: str¶: Alias for field number 18

classmethod fromData(definition_id, space_group_id, ichoice, num_choices, space_group_short_name, space_group_full_name, point_group_name, centering_opers, primary_opers, symmetry_opers, centering_opers_strs, primary_opers_strs, symmetry_opers_strs, crystal_system, xyzasu, spg_setting)¶

Create an instance.

Parameters

definition_id (int) – the id of the definition, i.e. a number ranging from 1 to 291 (some of the 230 space groups have more than a single unit cell definition).
space_group_id (int) – the id of the space group, i.e. a number ranging from 1 to 230, which the number of space groups.
ichoice (int) – the space group setting index
num_choices (int) – the number of different unit cell settings for this space group. For example, a setting may be a choice of axes, etc.
space_group_short_name (string) – the short Hermann-Mauguin symbol of the space group.
space_group_full_name (string) – the full Hermann-Mauguin symbol of the space group.
point_group_name (string) – the name of the point group of the space group.
centering_opers (list of numpy.array) – contains the centering matricies of the space group.
primary_opers (list of numpy.array) – contains the primary matricies of the space group.
symmetry_opers (list of numpy.array) – contains the symmetry matricies of the space group, i.e. the combinations of the centering and primary matricies.
centering_opers_strs (list) – string representation of the centering operators.
primary_opers_strs (list) – string representation of the primary operators.
symmetry_opers_strs (list) – string representation of the symmetry operators, i.e. the combination of the centering and primary string representations.
crystal_system (one of the sevel crystal system objects) – the crystal system.
xyzasu (str) – the xyzasu descriptor which will be parsed but not used
spgsetting – the setting of the space group

isSohnckeGroup()¶

Return whether this group is Sohncke or not.

:rtype bool :return: Whether this group is Sohncke or not.

printSymmetryOpers(logger=None)¶

Log a formatted print of all of the symmetry operators for this space group.

Parameters: logger (logging.getLogger) – output logger

printDatabaseEntry(logger=None)¶

Print a space group object in mmspg/spgbase.dat format.

Parameters: logger (logging.getLogger) – output logger

__contains__(key, /)¶: Return key in self.

__len__()¶: Return len(self).

count(value, /)¶: Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)¶

Return first index of value.

Raises ValueError if the value is not present.

class schrodinger.application.matsci.nano.space_groups.SpaceGroups¶

Bases: object

Manage space group objects.

NUM_SPACE_GROUPS = 230¶

CRYSTAL_SYSTEMS = <schrodinger.application.matsci.nano.space_groups.CrystalSystems object>¶

CENTERING = 'centering'¶

PRIMARY = 'primary'¶

SYMMETRY = 'symmetry'¶

__init__()¶: Create an instance.

getAllSpaceGroups()¶: Make a list of all SpaceGroup objects each of which contains some space group parameters from mmspg/spgbase.dat.

getSpgObjByName(name, first=True)¶

Get a space group object by name.

Parameters

name (str) – short name (HM symbol) checked first. If short_only=False, long symbol checked second. The first space group encountered with such a name is returned.
first (bool) – If True, returns the first occurrence based on the symmetry operators

Return type

SpaceGroup or None

Returns

Space group object or None if not found

printAllSpgInfo(verbose, logger)¶

Print all space group information.

Parameters

verbose (bool) – verbose log
logger (logging.getLogger) – output logger

schrodinger.application.matsci.nano.space_groups.equal_rotations(rotations1, rotations2)¶

Check if rotations are equal.

Parameters

rotations1 (3D numpy.array) – Array of rotation matrices (2D arrays) associated with a space group
rotations2 (3D numpy.array) – Array of rotation matrices (2D arrays) associated with a space group

Return type

bool

Returns

True, if rotations are the same, otherwise False