+

+ +

Source code for diffpy.structure

+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2024-2026 The Trustees of Columbia University in the City of New York.
+# All rights reserved.
+#
+# File coded by: Chris Farrow, Pavol Juhas,  Simon Billinge, Billinge Group members.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.structure/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################
+"""Crystal structure container and parsers for structure formats.
+
+Classes related to the structure of materials:
+    * Atom
+    * Lattice
+    * Structure
+    * PDFFitStructure
+
+Other classes:
+    * SpaceGroup
+    * SymOp
+    * ExpandAsymmetricUnit
+    * GeneratorSite
+    * SymmetryConstraints
+
+Exceptions:
+    * StructureFormatError
+    * LatticeError
+    * SymmetryError
+"""
+
+
+import os
+import sys
+
+import diffpy.structure as _structure
+from diffpy.structure.atom import Atom
+from diffpy.structure.lattice import Lattice
+from diffpy.structure.parsers import get_parser
+from diffpy.structure.pdffitstructure import PDFFitStructure
+from diffpy.structure.structure import Structure
+from diffpy.structure.structureerrors import LatticeError, StructureFormatError, SymmetryError
+
+# package version
+from diffpy.structure.version import __version__
+from diffpy.utils._deprecator import build_deprecation_message, deprecated
+
+# Deprecations -------------------------------------------------------
+base = "diffpy.structure"
+removal_version = "4.0.0"
+loadStructure_deprecation_msg = build_deprecation_message(
+    base,
+    "loadStructure",
+    "load_structure",
+    removal_version,
+)
+
+
+# @deprecated
+# custom deprecator for diffpy.Structure module
+
+[docs]
+class DeprecatedStructureModule:
+    """Proxy for backward compatibility of diffpy.Structure."""
+
+    def __getattr__(self, name):
+        import warnings
+
+        warnings.warn(
+            "Module 'diffpy.Structure' is deprecated and will be removed in version 4.0. "
+            "Use 'diffpy.structure' instead.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        return getattr(_structure, name)
+
+
+
+sys.modules["diffpy.Structure"] = DeprecatedStructureModule()
+
+# top level routines
+
+
+@deprecated(loadStructure_deprecation_msg)
+def loadStructure(filename, fmt="auto", **kw):
+    """This function has been deprecated and will be removed in version
+    4.0.0.
+
+    Please use diffpy.structure.load_structure instead.
+    """
+    return load_structure(filename, fmt, **kw)
+
+
+
+[docs]
+def load_structure(filename, fmt="auto", **kw):
+    """Load new structure object from the specified file.
+
+    Parameters
+    ----------
+
+    filename : str
+        Path to the file to be loaded.
+    fmt : str, Optional
+        Format of the structure file such as 'cif' or 'xyz'. Must be
+        one of the formats listed by the `parsers.inputFormats` function.
+        When 'auto', all supported formats are tried in a sequence.
+    kw : Optional
+        Extra keyword arguments that are passed to `parsers.getParser`
+        function. These configure the dedicated Parser object that
+        is used to read content in filename.
+
+    Returns
+    -------
+    stru : `Structure`, `PDFFitStructure`
+        The new Structure object loaded from the specified file.
+        Return a more specific PDFFitStructure type for 'pdffit'
+        and 'discus' formats.
+    """
+    filename = os.fspath(filename)
+    p = get_parser(fmt, **kw)
+    rv = p.parse_file(filename)
+    return rv
+
+
+
+# silence pyflakes checker
+assert StructureFormatError and LatticeError and SymmetryError
+assert Atom
+assert Lattice
+assert Structure
+assert PDFFitStructure
+
+# silence the pyflakes syntax checker
+assert __version__ or True
+
+# End of file
+

+ +

+


	+ .
	+ `diffpy.structure._legacy_importer`	+
	+ `diffpy.structure.apps`	+
	+ `diffpy.structure.apps.anyeye`	+
	+ `diffpy.structure.apps.transtru`	+
	+ `diffpy.structure.apps.vesta_viewer`	+
	+ `diffpy.structure.atom`	+
	+ `diffpy.structure.expansion`	+
	+ `diffpy.structure.expansion.makeellipsoid`	+
	+ `diffpy.structure.expansion.shapeutils`	+
	+ `diffpy.structure.expansion.supercell_mod`	+
	+ `diffpy.structure.lattice`	+
	+ `diffpy.structure.mmlibspacegroups`	+
	+ `diffpy.structure.parsers`	+
	+ `diffpy.structure.parsers.p_auto`	+
	+ `diffpy.structure.parsers.p_cif`	+
	+ `diffpy.structure.parsers.p_discus`	+
	+ `diffpy.structure.parsers.p_pdb`	+
	+ `diffpy.structure.parsers.p_pdffit`	+
	+ `diffpy.structure.parsers.p_rawxyz`	+
	+ `diffpy.structure.parsers.p_vesta`	+
	+ `diffpy.structure.parsers.p_xcfg`	+
	+ `diffpy.structure.parsers.p_xyz`	+
	+ `diffpy.structure.parsers.parser_index_mod`	+
	+ `diffpy.structure.parsers.structureparser`	+
	+ `diffpy.structure.pdffitstructure`	+
	+ `diffpy.structure.sgtbxspacegroups`	+
	+ `diffpy.structure.spacegroupmod`	+
	+ `diffpy.structure.spacegroups`	+
	+ `diffpy.structure.structure`	+
	+ `diffpy.structure.structure_app`	+
	+ `diffpy.structure.structureerrors`	+
	+ `diffpy.structure.symmetryutilities`	+
	+ `diffpy.structure.utils`	+

	+ d
	+ `diffpy`	+
	+ `diffpy.structure`	+

Source code for diffpy.structure

Source code for diffpy.structure._legacy_importer

Source code for diffpy.structure.apps.anyeye

Source code for diffpy.structure.apps.transtru

Source code for diffpy.structure.apps.vesta_viewer

Source code for diffpy.structure.atom

Source code for diffpy.structure.expansion.makeellipsoid

Source code for diffpy.structure.expansion.shapeutils

Source code for diffpy.structure.expansion.supercell_mod

Source code for diffpy.structure.lattice

Source code for diffpy.structure.parsers

Source code for diffpy.structure.parsers.p_auto

Source code for diffpy.structure.parsers.p_cif

Source code for diffpy.structure.parsers.p_discus

Source code for diffpy.structure.parsers.p_pdb

Source code for diffpy.structure.parsers.p_pdffit

Source code for diffpy.structure.parsers.p_rawxyz

Source code for diffpy.structure.parsers.p_vesta

Source code for diffpy.structure.parsers.p_xcfg

Source code for diffpy.structure.parsers.p_xyz

Source code for diffpy.structure.parsers.structureparser

Source code for diffpy.structure.pdffitstructure

Source code for diffpy.structure.spacegroupmod

Source code for diffpy.structure.spacegroups

Source code for diffpy.structure.structure

Source code for diffpy.structure.structure_app

Source code for diffpy.structure.structureerrors

Source code for diffpy.structure.symmetryutilities

Source code for diffpy.structure.utils

All modules for which code is available

diffpy.structure.apps package

Submodules

diffpy.structure.apps.transtru module

diffpy.structure.apps.anyeye module

diffpy.structure.apps.vesta_viewer module

diffpy.structure.expansion package

Submodules

diffpy.structure.expansion.shapeutils module

diffpy.structure.expansion.makeellipsoid module

diffpy.structure.expansion.supercell_mod module

diffpy.structure package

Subpackages

Submodules

diffpy.structure.structure_app module

diffpy.structure.spacegroups module

diffpy.structure._legacy_importer module

diffpy.structure.structureerrors module

diffpy.structure.spacegroupmod module

diffpy.structure.utils module

diffpy.structure.lattice module

diffpy.structure.structure module

diffpy.structure.mmlibspacegroups module

diffpy.structure.symmetryutilities module

diffpy.structure.atom module

diffpy.structure.pdffitstructure module

diffpy.structure.sgtbxspacegroups module

diffpy.structure.parsers package

Submodules

diffpy.structure.parsers.p_rawxyz module

diffpy.structure.parsers.structureparser module

diffpy.structure.parsers.p_cif module

diffpy.structure.parsers.p_auto module

diffpy.structure.parsers.p_pdffit module

diffpy.structure.parsers.p_xcfg module

diffpy.structure.parsers.parser_index_mod module

diffpy.structure.parsers.p_pdb module

diffpy.structure.parsers.p_discus module

diffpy.structure.parsers.p_vesta module

diffpy.structure.parsers.p_xyz module

diffpy.structure.apps package

Submodules

diffpy.structure.apps.anyeye module

diffpy.structure.apps.transtru module

Module contents

diffpy.structure.expansion package

Submodules

diffpy.structure.expansion.makeellipsoid module

diffpy.structure.expansion.shapeutils module

diffpy.structure.expansion.supercell_mod module

Module contents