diffpy.structure 3.2.0__py3-none-any.whl

diffpy/structure/utils.py

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+#!/usr/bin/env python
+##############################################################################
+#
+# diffpy.structure  by DANSE Diffraction group
+#                   Simon J. L. Billinge
+#                   (c) 2006 trustees of the Michigan State University.
+#                   All rights reserved.
+#
+# File coded by:    Pavol Juhas
+#
+# See AUTHORS.txt for a list of people who contributed.
+# See LICENSE_DANSE.txt for license information.
+#
+##############################################################################
+
+"""Small shared functions.
+"""
+
+from collections.abc import Iterable as _Iterable
+
+import numpy
+
+
+def isiterable(obj):
+    """``True`` if argument is iterable."""
+    rv = isinstance(obj, _Iterable)
+    return rv
+
+
+def isfloat(s):
+    """``True`` if argument can be converted to float."""
+    try:
+        float(s)
+        return True
+    except ValueError:
+        pass
+    return False
+
+
+def atomBareSymbol(smbl):
+    """Remove atom type string stripped of isotope and ion charge symbols.
+
+    This function removes any blank, isotope numbers (0-9), leading hyphens (-), and ion charge
+    symbols (1-9)(+-) from the given atom type string, returning only the bare element symbol.
+
+    Parameters
+    ----------
+    smbl : str
+        Atom type string that may include isotope numbers, ion charges, or hyphens.
+
+    Returns
+    -------
+    str
+        The bare element symbol.
+
+    Examples
+    --------
+    >>> atomBareSymbol("Cl-")
+    'Cl'
+    >>> atomBareSymbol("Ca2+")
+    'Ca'
+    >>> atomBareSymbol("12-C")
+    'C'
+    """
+
+    rv = smbl.strip().lstrip("0123456789-").rstrip("123456789+-")
+    return rv
+
+
+# Helpers for the Structure class --------------------------------------------
+
+
+def _linkAtomAttribute(attrname, doc, toarray=numpy.array):
+    """Create property wrapper that maps the specified atom attribute.
+
+    The returned property object provides convenient access to atom
+    attributes from the owner `Structure` class.
+
+    Parameters
+    ----------
+    attrname : str
+        The string name of the `Atom` class attribute to be mapped.
+    doc : str
+        The docstring for the property wrapper.
+    toarray : callable, Optional
+        Factory function that converts list of attributes to `numpy.ndarray`.
+        Use `numpy.char.array` for string attributes.
+
+    Return a property object.
+    """
+    from itertools import repeat
+    from operator import setitem
+
+    _all = slice(None)
+
+    def fget(self):
+        va = toarray([getattr(a, attrname) for a in self])
+        return va
+
+    def fset(self, value):
+        n = len(self)
+        if n == 0:
+            return
+        v0 = getattr(self[0], attrname)
+        # replace scalar values, but change array attributes in place
+        if numpy.isscalar(v0):
+
+            def setvalue(a, v):
+                return setattr(a, attrname, v)
+
+        else:
+
+            def setvalue(a, v):
+                return setitem(getattr(a, attrname), _all, v)
+
+        # avoid broadcasting if the new value is a scalar
+        if numpy.isscalar(value):
+            genvalues = repeat(value)
+        else:
+            genvalues = numpy.broadcast_to(value, (n,) + numpy.shape(v0))
+        for a, v in zip(self, genvalues):
+            setvalue(a, v)
+        return
+
+    rv = property(fget, fset, doc=doc)
+    return rv

diffpy/structure/version.py

@@ -0,0 +1,26 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2024 The Trustees of Columbia University in the City of New York.
+# All rights reserved.
+#
+# File coded by: Billinge Group members and community contributors.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.structure/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################
+
+"""Definition of __version__."""
+
+#  We do not use the other three variables, but can be added back if needed.
+#  __all__ = ["__date__", "__git_commit__", "__timestamp__", "__version__"]
+
+# obtain version information
+from importlib.metadata import version
+
+__version__ = version("diffpy.structure")
+
+# End of file

diffpy.structure-3.2.0.dist-info/AUTHORS.rst

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+Authors
+=======
+
+Pavol Juhas,
+Christopher L. Farrow,
+Xiaohao Yang,
+Simon J.L. Billinge
+
+Contributors
+------------
+
+For a list of contributors, visit
+https://github.com/diffpy/diffpy.structure/graphs/contributors

diffpy.structure-3.2.0.dist-info/LICENSE.rst

@@ -0,0 +1,141 @@
+OPEN SOURCE LICENSE AGREEMENT
+=============================
+
+Copyright (c) 1989, 1991 Free Software Foundation, Inc.
+
+Copyright (c) 2006, The Regents of the University of California through Lawrence Berkeley National Laboratory
+
+Copyright (c) 2006-2007, Board of Trustees of Michigan State University
+
+Copyright (c) 2008-2012, The Trustees of Columbia University in the City of New York
+
+Copyright (c) 2009-2011, University of Tennessee
+
+Copyright (c) 2014, Australian Synchrotron Research Program Inc., ("ASRP")
+
+Copyright (c) 2014-2019, Brookhaven Science Associates, Brookhaven National Laboratory
+
+Copyright (c) 2024, The Trustees of Columbia University in the City of New York. 
+All rights reserved.
+
+The "DiffPy-CMI" is distributed subject to the following license conditions:
+
+.. code-block:: text
+
+    SOFTWARE LICENSE AGREEMENT
+
+    Software: DiffPy-CMI
+
+
+    (1) The "Software", below, refers to the aforementioned DiffPy-CMI (in either
+    source code, or binary form and accompanying documentation).
+
+    Part of the software was derived from the DANSE, ObjCryst++ (with permission),
+    PyCifRW, Python periodictable, CCTBX, and SasView open source projects, of
+    which the original Copyrights are contained in each individual file.
+
+    Each licensee is addressed as "you" or "Licensee."
+
+
+    (2) The copyright holders shown above and their third-party Licensors hereby
+    grant licensee a royalty-free nonexclusive license, subject to the limitations
+    stated herein and U.S. Government license rights.
+
+
+    (3) You may modify and make a copy or copies of the software for use within
+    your organization, if you meet the following conditions:
+
+        (a) Copies in source code must include the copyright notice and this
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+        (b) Copies in binary form must include the copyright notice and this
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+            provided with the copy.
+
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+    (4) You may modify a copy or copies of the Software or any portion of it, thus
+    forming a work based on the Software, and distribute copies of such work
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+
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+    (5) Portions of the Software resulted from work developed under a U.S.
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+
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+    THEIR EMPLOYEES: (1) DISCLAIM ANY WARRANTIES, EXPRESS OR IMPLIED, INCLUDING
+    BUT NOT LIMITED TO ANY IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
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+
+
+Brookhaven National Laboratory Notice
+=====================================
+
+Acknowledgment of sponsorship
+-----------------------------
+
+This software was produced by the Brookhaven National Laboratory, under
+Contract DE-AC02-98CH10886 with the Department of Energy.
+
+
+Government disclaimer of liability
+----------------------------------
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+Neither the United States nor the United States Department of Energy, nor
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+Brookhaven disclaimer of liability
+----------------------------------
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+
+
+Maintenance of notice
+---------------------
+
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+maintain this notice affixed to any distribution by the recipient that
+contains a copy or derivative of this software.
+
+END OF LICENSE

diffpy.structure-3.2.0.dist-info/LICENSE_DANSE.rst

@@ -0,0 +1,50 @@
+LICENSE
+=======
+
+This program is part of the DiffPy and DANSE open-source projects
+and is available subject to the conditions and terms laid out below.
+
+Copyright 2006-2007, Board of Trustees of Michigan State University,
+
+Copyright 2008-2012, The Trustees of Columbia University in the
+City of New York.  (Copyright holder indicated in each source file).
+
+Copyright (c) 2024, The Trustees of Columbia University in the City of New York. 
+All rights reserved.
+
+For more information please visit the project web-page:
+
+    http://www.diffpy.org/
+    
+or email Prof. Simon Billinge at sb2896@columbia.edu
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions
+are met:
+
+- Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+
+- Redistributions in binary form must reproduce the above copyright
+    notice, this list of conditions and the following disclaimer in the
+    documentation and/or other materials provided with the distribution.
+
+- Neither the name of the copyright holder nor the names of its
+    contributors may be used to endorse or promote products derived from
+    this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY COPYRIGHT HOLDER "AS IS".  COPYRIGHT HOLDER
+EXPRESSLY DISCLAIMS ANY AND ALL WARRANTIES AND CONDITIONS, EITHER
+EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY, TITLE, FITNESS, ADEQUACY OR SUITABILITY
+FOR A PARTICULAR PURPOSE, AND ANY WARRANTIES OF FREEDOM FROM
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+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
+THIS SOFTWARE OR RELATING TO THIS AGREEMENT, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.

diffpy.structure-3.2.0.dist-info/LICENSE_pymmlib.rst

@@ -0,0 +1,203 @@
+.. code-block:: text
+        
+                        The Artistic License 2.0
+
+                Copyright (c) 2000-2006, The Perl Foundation.
+
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