"""
Classes and functions for creating crystals by unit cell.
Copyright Schrodinger, LLC. All rights reserved."""
import typing
from collections import defaultdict
import numpy
# Please DO NOT add any dependencies, to prevent circular imports
from schrodinger.infra import mm
SYMMOP_ROUND = 2
# https://www.ruppweb.org/Xray/tutorial/enantio.htm
# https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Space_group_determination
SOHNCHKE_SPG_GROUPS = {
1, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 75, 76, 77, 78, 79, 80, 89,
90, 91, 92, 93, 94, 95, 96, 97, 98, 143, 144, 145, 146, 149, 150, 151, 152,
153, 154, 155, 168, 169, 170, 171, 172, 173, 177, 178, 179, 180, 181, 182,
195, 198, 207, 208, 212, 213, 196, 209, 210, 197, 199, 211, 214
} # yapf: disabled
# Global variable
_SPACE_GROUPS = None
[docs]def get_spacegroups():
"""
Get space groups object.
:rtype: SpaceGroups
:return: Cached space groups object, do not modify!!
"""
global _SPACE_GROUPS
if _SPACE_GROUPS is None:
_SPACE_GROUPS = SpaceGroups()
return _SPACE_GROUPS
[docs]def 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]
:type symm: dict of two keys: 'rotations': list of 3 x 3 matrices,
'translations': list of 1 x 3 matrices
:param symm: dictionary of list of rotations and translations
:return: list of 4x4 matrices
:rtype: list of symmetry operators
"""
ret = []
for rot, tran in zip(symm['rotations'], symm['translations']):
symm_op = numpy.zeros(shape=(4, 4))
symm_op[3, 3] = 1
symm_op[0:3, 0:3] = rot.copy()
# Sometime spglib has -1, -0, 1 in translations (which is the same as 0)
translations = numpy.round(tran, SYMMOP_ROUND)
translations[translations == 1.] = 0.
translations[translations == -1.] = 0.
translations[translations == -0.] = 0.
symm_op[0:3, 3] = translations
ret.append(symm_op)
return ret
[docs]class CrystalSystems(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'
[docs] class Triclinic(object):
"""
Manage the triclinic system.
"""
[docs] def __init__(self, name):
"""
Create an instance.
:type name: str
:param name: crystal system name
"""
self.name = name
[docs] class Monoclinic(object):
"""
Manage the monoclinic system.
"""
[docs] def __init__(self, name):
"""
Create an instance.
:type name: str
:param name: crystal system name
"""
self.name = name
[docs] class Orthorhombic(object):
"""
Manage the orthorhombic system.
"""
[docs] def __init__(self, name):
"""
Create an instance.
:type name: str
:param name: crystal system name
"""
self.name = name
[docs] class Tetragonal(object):
"""
Manage the tetragonal system.
"""
[docs] def __init__(self, name):
"""
Create an instance.
:type name: str
:param name: crystal system name
"""
self.name = name
[docs] class Trigonal(object):
"""
Manage the trigonal system.
"""
[docs] def __init__(self, name):
"""
Create an instance.
:type name: str
:param name: crystal system name
"""
self.name = name
[docs] class Hexagonal(object):
"""
Manage the hexagonal system.
"""
[docs] def __init__(self, name):
"""
Create an instance.
:type name: str
:param name: crystal system name
"""
self.name = name
[docs] class Cubic(object):
"""
Manage the cubic system.
"""
[docs] def __init__(self, name):
"""
Create an instance.
:type name: str
:param name: crystal system name
"""
self.name = name
[docs] def getCrystalSystem(self, name):
"""
Return the crystal system object for the crystem
system of the provided name.
:type name: str
:param name: crystal system name
:rtype: one of the seven crystal system objects
:return: crystal_system_obj
"""
name = name.lower()
if name == self.TRICLINIC_NAME:
crystal_system_obj = self.Triclinic(name)
elif name == self.MONOCLINIC_NAME:
crystal_system_obj = self.Monoclinic(name)
elif name == self.ORTHORHOMBIC_NAME:
crystal_system_obj = self.Orthorhombic(name)
elif name == self.TETRAGONAL_NAME:
crystal_system_obj = self.Tetragonal(name)
elif name == self.TRIGONAL_NAME:
crystal_system_obj = self.Trigonal(name)
elif name == self.HEXAGONAL_NAME:
crystal_system_obj = self.Hexagonal(name)
elif name == self.CUBIC_NAME:
crystal_system_obj = self.Cubic(name)
return crystal_system_obj
[docs]class SpaceGroup(typing.NamedTuple):
"""
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
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: typing.List
primary_opers: typing.List
symmetry_opers: typing.List
num_centering_opers: int
num_primary_opers: int
num_symmetry_opers: int
centering_opers_strs: typing.List
primary_opers_strs: typing.List
symmetry_opers_strs: typing.List
crystal_system: CrystalSystems
xyzasu: str
spg_setting: str
[docs] @classmethod
def fromData(self, 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.
:type definition_id: int
:param definition_id: 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).
:type space_group_id: int
:param space_group_id: the id of the space group, i.e.
a number ranging from 1 to 230, which the number of
space groups.
:type ichoice: int
:param ichoice: the space group setting index
:type num_choices: int
:param num_choices: the number of different unit cell
settings for this space group. For example, a setting
may be a choice of axes, etc.
:type space_group_short_name: string
:param space_group_short_name: the short Hermann-Mauguin symbol
of the space group.
:type space_group_full_name: string
:param space_group_full_name: the full Hermann-Mauguin symbol
of the space group.
:type point_group_name: string
:param point_group_name: the name of the point group of the
space group.
:type centering_opers: list of numpy.array
:param centering_opers: contains the centering matricies
of the space group.
:type primary_opers: list of numpy.array
:param primary_opers: contains the primary matricies
of the space group.
:type symmetry_opers: list of numpy.array
:param symmetry_opers: contains the symmetry matricies
of the space group, i.e. the combinations of the centering
and primary matricies.
:type centering_opers_strs: list
:param centering_opers_strs: string representation of the
centering operators.
:type primary_opers_strs: list
:param primary_opers_strs: string representation of the
primary operators.
:type symmetry_opers_strs: list
:param symmetry_opers_strs: string representation of the
symmetry operators, i.e. the combination of the centering
and primary string representations.
:type crystal_system: one of the sevel crystal system objects
:param crystal_system: the crystal system.
:type xyzasu: str
:param xyzasu: the xyzasu descriptor which will be parsed but
not used
:type spg_setting: str
:param spgsetting: the setting of the space group
"""
return SpaceGroup(definition_id=definition_id,
space_group_id=space_group_id,
ichoice=ichoice,
num_choices=num_choices,
space_group_short_name=space_group_short_name,
space_group_full_name=space_group_full_name,
point_group_name=point_group_name,
centering_opers=centering_opers,
primary_opers=primary_opers,
symmetry_opers=symmetry_opers,
num_centering_opers=len(centering_opers),
num_primary_opers=len(primary_opers),
num_symmetry_opers=len(symmetry_opers),
centering_opers_strs=centering_opers_strs,
primary_opers_strs=primary_opers_strs,
symmetry_opers_strs=symmetry_opers_strs,
crystal_system=crystal_system,
xyzasu=xyzasu,
spg_setting=spg_setting)
[docs] def isSohnckeGroup(self):
"""
Return whether this group is Sohncke or not.
:rtype bool
:return: Whether this group is Sohncke or not.
"""
return self.space_group_id in SOHNCHKE_SPG_GROUPS
def __repr__(self):
"""
Representation of this class.
"""
spgrepr = '%s %s %s %s %s %s %s %s %s %s' % \
(str(self.definition_id).ljust(len(self.DEFINITION_ID)),
str(self.space_group_id).ljust(len(self.SPACE_GROUP_ID)),
str(self.crystal_system.name).rjust(len(self.CRYSTAL_SYSTEM)),
str(self.space_group_short_name).rjust( \
len(self.SHORT_HERMANN_MAUGUIN_SYMBOL)),
str(self.space_group_full_name).rjust( \
len(self.FULL_HERMANN_MAUGUIN_SYMBOL)),
str(self.point_group_name).rjust( \
len(self.POINT_GROUP_NAME)),
str(self.num_centering_opers).rjust( \
len(self.NUM_CENTERING_OPERS)),
str(self.num_primary_opers).rjust( \
len(self.NUM_PRIMARY_OPERS)),
str(self.num_symmetry_opers).rjust( \
len(self.NUM_SYMMETRY_OPERS)),
str(self.spg_setting).rjust( \
len(self.SPACE_GROUP_SETTING)))
return spgrepr
[docs] def printSymmetryOpers(self, logger=None):
"""
Log a formatted print of all of the symmetry operators for
this space group.
:type logger: logging.getLogger
:param logger: output logger
"""
if logger:
logger.info(self.space_group_full_name)
logger.info('-' * len(self.space_group_full_name))
logger.info('')
logger.info(self.CENTERING_OPERS)
logger.info('-' * len(self.CENTERING_OPERS))
logger.info('')
for oper_str, oper in zip(self.centering_opers_strs,
self.centering_opers):
logger.info(oper_str)
for row in oper:
logger.info(row)
logger.info('')
logger.info(self.PRIMARY_OPERS)
logger.info('-' * len(self.PRIMARY_OPERS))
logger.info('')
for oper_str, oper in zip(self.primary_opers_strs,
self.primary_opers):
logger.info(oper_str)
for row in oper:
logger.info(row)
logger.info('')
logger.info(self.SYMMETRY_OPERS)
logger.info('-' * len(self.SYMMETRY_OPERS))
logger.info('')
for oper_str, oper in zip(self.symmetry_opers_strs,
self.symmetry_opers):
logger.info(oper_str)
for row in oper:
logger.info(row)
logger.info('')
[docs] def printDatabaseEntry(self, logger=None):
"""
Print a space group object in mmspg/spgbase.dat format.
:type logger: logging.getLogger
:param logger: output logger
"""
spg_id = self.ID_TAG + str(self.space_group_id)
spg_short_name = self.SHORT_NAME_TAG + self.space_group_short_name
spg_full_name = self.FULL_NAME_TAG + self.space_group_full_name
spg_point_group = self.POINT_GROUP_TAG + self.point_group_name
spg_crystal_system = self.CRYSTAL_SYSTEM_TAG + self.crystal_system.name
spg_setting = self.SETTING_TAG + self.spg_setting
spg_xyzasu = self.ASU_TAG + self.xyzasu
spg_eod = self.END_OF_DEF_TAG
logger.info(spg_id)
logger.info(spg_short_name)
logger.info(spg_full_name)
logger.info(spg_point_group)
logger.info(spg_crystal_system)
logger.info(spg_setting)
logger.info(spg_xyzasu)
for oper in self.primary_opers_strs:
logger.info(self.PRIMARY_OPERATIONS_TAG + oper)
for oper in self.centering_opers_strs:
logger.info(self.CENTERING_OPERATIONS_TAG + oper)
logger.info(spg_eod)
logger.info('')
[docs]class SpaceGroups(object):
"""
Manage space group objects.
"""
NUM_SPACE_GROUPS = 230
CRYSTAL_SYSTEMS = CrystalSystems()
CENTERING = 'centering'
PRIMARY = 'primary'
SYMMETRY = 'symmetry'
[docs] def __init__(self):
"""
Create an instance.
"""
self.getAllSpaceGroups()
[docs] def getAllSpaceGroups(self):
"""
Make a list of all SpaceGroup objects each of which contains
some space group parameters from mmspg/spgbase.dat.
"""
def unpack_symmetry_opers(symtype):
# get the number of operators and the operators themselves
if symtype == self.CENTERING:
nsym = mm.mmspg_num_cent_oper_get(handle)
symlist = mm.mmspg_cent_oper_get(handle, nsym)
elif symtype == self.PRIMARY:
nsym = mm.mmspg_num_prim_oper_get(handle)
symlist = mm.mmspg_prim_oper_get(handle, nsym)
elif symtype == self.SYMMETRY:
nsym = mm.mmspg_num_symmetry_oper_get(handle)
symlist = mm.mmspg_symmetry_oper_get(handle, nsym)
symlist = numpy.array(symlist)
symlist = numpy.reshape(symlist, (nsym, 4, 4))
# collect the operators and string representations thereof
symopers = []
symopersstrs = []
for oper in symlist:
symopers.append(tuple(tuple(row) for row in oper))
operstr = mm.mmspg_get_string_oper_by_matrix(
oper.flatten().tolist())
symopersstrs.append(operstr)
return tuple(symopers), tuple(symopersstrs)
# initialize and load the spgbase.dat file contents
definition_id = 0
mm.mmspg_initialize()
mm.mmspg_load_spgbase()
all_spg_objs = []
self.spg_objs = defaultdict(list)
all_spg_full_symbols = []
all_spg_short_symbols = []
# loop over space group ids 1..230 and loop over the different
# settings for each space group id, this includes the standard
# setting any non-standard settings as well as some alias space
# group symbols
for spgid in range(1, self.NUM_SPACE_GROUPS + 1):
nchoices = mm.mmspg_nchoices_get(spgid)
for ichoice in range(1, nchoices + 1):
definition_id += 1
# get the mm handle
handle = mm.mmspg_spg_of_choice_get(spgid, ichoice)
# collect short names
spgshortname = mm.mmspg_short_spgname_get(handle)
all_spg_short_symbols.append(spgshortname)
# collect full names
spgfullname = mm.mmspg_full_spgname_get(handle)
all_spg_full_symbols.append(spgfullname)
# get the point group name
pgname = mm.mmspg_pgname_get(handle)
# for each type of symmetry operator, (1) centering, (2) primary,
# and (3) the "real" final symmetry operator (centering*primary),
# get the operators themselves as well as their string
# representations
centopers, centopers_strs = unpack_symmetry_opers(
self.CENTERING)
primopers, primopers_strs = unpack_symmetry_opers(self.PRIMARY)
symopers, symopers_strs = unpack_symmetry_opers(self.SYMMETRY)
# get the crystal system name and object
crysys = mm.mmspg_crystal_system_name_get(handle)
crysys = self.CRYSTAL_SYSTEMS.getCrystalSystem(crysys)
# get the xyz ASU descriptor even though it is never used anywhere
# in our suite
xyzasu = mm.mmspg_get_xyzasu(handle)
# get the space group setting label
spgsetting = mm.mmspg_get_setting(handle)
# make and collect the SpaceGroup object
spgobj = SpaceGroup.fromData(
definition_id, spgid, ichoice, nchoices, spgshortname,
spgfullname, pgname, centopers, primopers, symopers,
centopers_strs, primopers_strs, symopers_strs, crysys,
xyzasu, spgsetting)
all_spg_objs.append(spgobj)
self.spg_objs[spgid].append(spgobj)
# Convert to immutable tuples
self.all_spg_objs = tuple(all_spg_objs)
self.all_spg_full_symbols = tuple(all_spg_full_symbols)
self.all_spg_short_symbols = tuple(all_spg_short_symbols)
# Convert values from list to tuple
self.spg_objs = {k: tuple(v) for k, v in self.spg_objs.items()}
# clean up
mm.mmspg_terminate()
[docs] def getSpgObjByName(self, name, first=True):
"""
Get a space group object by name.
:param str name: 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.
:param bool first: If True, returns the first occurrence based on the
symmetry operators
:rtype: SpaceGroup or None
:return: Space group object or None if not found
"""
name_ns = name.replace(' ', '')
for spgid, spgobjs in self.spg_objs.items():
for spgobj in spgobjs:
if (name_ns in [
spgobj.space_group_short_name.replace(' ', ''),
spgobj.space_group_full_name.replace(' ', '')
]):
break
else:
spgobj = None
if spgobj:
break
else:
return
if not first:
return spgobj
for aspgobj in self.spg_objs[spgid]:
if equal_rotations(spgobj.symmetry_opers, aspgobj.symmetry_opers):
return aspgobj
[docs] def printAllSpgInfo(self, verbose, logger):
"""
Print all space group information.
:type verbose: bool
:param verbose: verbose log
:type logger: logging.getLogger
:param logger: output logger
"""
HEADER = 'Space group parameters'
logger.info(HEADER)
logger.info('-' * len(HEADER))
logger.info('')
defid = SpaceGroup.DEFINITION_ID
spid = SpaceGroup.SPACE_GROUP_ID
crysys = SpaceGroup.CRYSTAL_SYSTEM
short = SpaceGroup.SHORT_HERMANN_MAUGUIN_SYMBOL
full = SpaceGroup.FULL_HERMANN_MAUGUIN_SYMBOL
pgname = SpaceGroup.POINT_GROUP_NAME
ncent = SpaceGroup.NUM_CENTERING_OPERS
nprim = SpaceGroup.NUM_PRIMARY_OPERS
nsym = SpaceGroup.NUM_SYMMETRY_OPERS
setting = SpaceGroup.SPACE_GROUP_SETTING
HEADER = '%s %s %s %s %s %s %s %s %s %s' % (defid, spid, \
crysys, short, full, pgname, ncent, nprim, nsym, setting)
logger.info(HEADER)
logger.info('-' * len(HEADER))
current_spg_id = 1
for spgobj in self.all_spg_objs:
if spgobj.space_group_id != current_spg_id:
logger.info('')
current_spg_id = spgobj.space_group_id
logger.info(spgobj)
if verbose:
logger.info('')
HEADER = 'Symmetry operators by space group name'
logger.info(HEADER)
logger.info('-' * len(HEADER))
logger.info('')
for spgobj in self.all_spg_objs:
spgobj.printSymmetryOpers(logger)
[docs]def equal_rotations(rotations1, rotations2):
"""
Check if rotations are equal.
:type rotations1: 3D numpy.array
:param rotations1: Array of rotation matrices (2D arrays) associated with a
space group
:type rotations2: 3D numpy.array
:param rotations2: Array of rotation matrices (2D arrays) associated with a
space group
:rtype: bool
:return: True, if rotations are the same, otherwise False
"""
rotations1 = numpy.asarray(rotations1)
rotations2 = numpy.asarray(rotations2)
shape1 = numpy.shape(rotations1)
shape2 = numpy.shape(rotations2)
if not (shape1 == shape2):
return False
rots1_1d = []
rots2_1d = []
for idx, (rot1, rot2) in enumerate(zip(rotations1, rotations2)):
rots1_1d.append(''.join(map(str, numpy.round(rot1.flat, SYMMOP_ROUND))))
rots2_1d.append(''.join(map(str, numpy.round(rot2.flat, SYMMOP_ROUND))))
# Rotations 1 and 2 are not necessarily listed in the same order
return not len(set(rots1_1d).symmetric_difference(rots2_1d))