diffpy.structure 3.2.0__py3-none-any.whl

diffpy/Structure.py

@@ -0,0 +1,35 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# diffpy.structure  Complex Modeling Initiative
+#                   (c) 2017 Brookhaven Science Associates,
+#                   Brookhaven National Laboratory.
+#                   All rights reserved.
+#
+# File coded by:    Pavol Juhas
+#
+# See AUTHORS.txt for a list of people who contributed.
+# See LICENSE.txt for license information.
+#
+##############################################################################
+
+"""Support import of old camel-case module names with `DeprecationWarning`.
+
+The imported camel-case modules are aliases for the current module
+instances. Their `__name__` attributes are thus all in lower-case.
+
+Warning
+-------
+This module is deprecated and will be removed in the future.
+"""
+
+
+import sys
+
+# install legacy import hooks
+import diffpy.structure._legacy_importer
+
+# replace this module with the new one
+sys.modules["diffpy.Structure"] = diffpy.structure
+
+# End of file

diffpy/__init__.py

@@ -0,0 +1,23 @@
+#!/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.
+#
+##############################################################################
+
+"""Blank namespace package for module diffpy."""
+
+
+from pkgutil import extend_path
+
+__path__ = extend_path(__path__, __name__)
+
+# End of file

diffpy/structure/__init__.py

@@ -0,0 +1,93 @@
+#!/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.
+#
+##############################################################################
+
+"""
+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
+"""
+
+# Interface definitions ------------------------------------------------------
+
+from diffpy.structure.atom import Atom
+from diffpy.structure.lattice import Lattice
+from diffpy.structure.parsers import getParser
+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__
+
+# top level routines
+
+
+def loadStructure(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.
+    """
+
+    p = getParser(fmt, **kw)
+    rv = p.parseFile(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.py

@@ -0,0 +1,88 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# diffpy.structure  Complex Modeling Initiative
+#                   (c) 2017 Brookhaven Science Associates,
+#                   Brookhaven National Laboratory.
+#                   All rights reserved.
+#
+# File coded by:    Pavol Juhas
+#
+# See AUTHORS.txt for a list of people who contributed.
+# See LICENSE.txt for license information.
+#
+##############################################################################
+
+"""
+Support import of old camel-case module names with DeprecationWarning.
+
+The imported camel-case modules are aliases for the current module
+instances. Their `__name__` attributes are thus all in lower-case.
+
+Note
+----
+this module must be only imported from `diffpy.Structure`.
+
+Warning
+-------
+This module is deprecated and will be removed in the future.
+"""
+
+
+import importlib.abc
+import sys
+from warnings import warn
+
+WMSG = "Module {!r} is deprecated. Use {!r} instead."
+
+# ----------------------------------------------------------------------------
+
+
+class FindRenamedStructureModule(importlib.abc.MetaPathFinder):
+
+    prefix = "diffpy.Structure."
+
+    def find_spec(self, fullname, path=None, target=None):
+        # only handle submodules of diffpy.Structure
+        if not fullname.startswith(self.prefix):
+            return None
+        lcname = fullname.lower()
+        spec = importlib.util.find_spec(lcname)
+        if spec is not None:
+            spec.name = fullname
+            spec.loader = MapRenamedStructureModule()
+        return spec
+
+
+# end of class FindRenamedStructureModule
+
+# ----------------------------------------------------------------------------
+
+
+class MapRenamedStructureModule(importlib.abc.Loader):
+    """Loader for old camel-case module names.
+    Import the current module and alias it under the old name.
+    """
+
+    def create_module(self, spec):
+        lcname = spec.name.lower()
+        mod = importlib.import_module(lcname)
+        sys.modules[spec.name] = mod
+        warn(WMSG.format(spec.name, lcname), DeprecationWarning, stacklevel=2)
+        return mod
+
+    def exec_module(self, module):
+        return
+
+
+# end of class MapRenamedStructureModule
+
+# ----------------------------------------------------------------------------
+
+# show deprecation warning for diffpy.Structure
+warn(WMSG.format("diffpy.Structure", "diffpy.structure"), DeprecationWarning, stacklevel=2)
+
+# install meta path finder for diffpy.Structure submodules
+sys.meta_path.append(FindRenamedStructureModule())
+
+# End of file

diffpy/structure/apps/__init__.py

@@ -0,0 +1,17 @@
+#!/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.
+#
+##############################################################################
+
+"""Script applications that use the `diffpy.structure` package.
+"""

diffpy/structure/apps/anyeye.py

@@ -0,0 +1,284 @@
+#!/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.
+#
+##############################################################################
+
+"""
+Anyeye view structure file in atomeye.
+
+Usage: ``anyeye [options] strufile``
+
+Anyeye understands more `Structure` formats than atomeye. It converts `strufile`
+to a temporary XCFG file which is opened in atomeye. See supported file formats:
+``inputFormats``
+
+Options:
+  -f, --formula
+      Override chemical formula in `strufile`. The formula defines
+      elements in the same order as in `strufile`, e.g., ``Na4Cl4``.
+
+  -w, --watch
+      Watch input file for changes.
+
+  --viewer=VIEWER
+      The structure viewer program, by default "atomeye".
+      The program will be executed as "VIEWER structurefile".
+
+  --formats=FORMATS
+      Comma-separated list of file formats that are understood
+      by the VIEWER, by default ``"xcfg,pdb"``. Files of other
+      formats will be converted to the first listed format.
+
+  -h, --help
+      Display this message and exit.
+
+  -V, --version
+      Show script version and exit.
+"""
+
+from __future__ import print_function
+
+import os
+import re
+import signal
+import sys
+
+from diffpy.structure.structureerrors import StructureFormatError
+
+# parameter dictionary
+pd = {
+    "formula": None,
+    "watch": False,
+    "viewer": "atomeye",
+    "formats": ["xcfg", "pdb"],
+}
+
+
+def usage(style=None):
+    """Show usage info, for ``style=="brief"`` show only first 2 lines."""
+    import os.path
+
+    myname = os.path.basename(sys.argv[0])
+    msg = __doc__.replace("anyeye", myname)
+    if style == "brief":
+        msg = msg.split("\n")[1] + "\n" + "Try `%s --help' for more information." % myname
+    else:
+        from diffpy.structure.parsers import inputFormats
+
+        fmts = [f for f in inputFormats() if f != "auto"]
+        msg = msg.replace("inputFormats", " ".join(fmts))
+    print(msg)
+    return
+
+
+def version():
+    from diffpy.structure import __version__
+
+    print("anyeye", __version__)
+    return
+
+
+def loadStructureFile(filename, format="auto"):
+    """Load structure from specified file.
+
+    Parameters
+    ----------
+    filename : str
+        Path to the structure file.
+    format : str, Optional
+        File format, by default "auto".
+
+    Returns
+    -------
+    tuple
+        A tuple of (Structure, fileformat).
+    """
+    from diffpy.structure import Structure
+
+    stru = Structure()
+    p = stru.read(filename, format)
+    fileformat = p.format
+    return (stru, fileformat)
+
+
+def convertStructureFile(pd):
+    # make temporary directory on the first pass
+    if "tmpdir" not in pd:
+        from tempfile import mkdtemp
+
+        pd["tmpdir"] = mkdtemp()
+    strufile = pd["strufile"]
+    tmpfile = os.path.join(pd["tmpdir"], os.path.basename(strufile))
+    pd["tmpfile"] = tmpfile
+    # speed up file processing in the watch mode
+    fmt = pd.get("format", "auto")
+    stru = None
+    if fmt == "auto":
+        stru, fmt = loadStructureFile(strufile)
+        pd["fmt"] = fmt
+    # if fmt is recognized by the viewer, use as is
+    if fmt in pd["formats"] and pd["formula"] is None:
+        import shutil
+
+        shutil.copyfile(strufile, tmpfile + ".tmp")
+        os.rename(tmpfile + ".tmp", tmpfile)
+        return
+    # otherwise convert to the first recognized viewer format
+    if stru is None:
+        stru = loadStructureFile(strufile, fmt)[0]
+    if pd["formula"]:
+        formula = pd["formula"]
+        if len(formula) != len(stru):
+            emsg = "Formula has %i atoms while structure %i" % (len(formula), len(stru))
+            raise RuntimeError(emsg)
+        for a, el in zip(stru, formula):
+            a.element = el
+    elif format == "rawxyz":
+        for a in stru:
+            if a.element == "":
+                a.element = "C"
+    stru.write(tmpfile + ".tmp", pd["formats"][0])
+    os.rename(tmpfile + ".tmp", tmpfile)
+    return
+
+
+def watchStructureFile(pd):
+    from time import sleep
+
+    strufile = pd["strufile"]
+    tmpfile = pd["tmpfile"]
+    while pd["watch"]:
+        if os.path.getmtime(tmpfile) < os.path.getmtime(strufile):
+            convertStructureFile(pd)
+        sleep(1)
+    return
+
+
+def cleanUp(pd):
+    if "tmpfile" in pd:
+        os.remove(pd["tmpfile"])
+        del pd["tmpfile"]
+    if "tmpdir" in pd:
+        os.rmdir(pd["tmpdir"])
+        del pd["tmpdir"]
+    return
+
+
+def parseFormula(formula):
+    """Parse chemical formula and return a list of elements"""
+    # remove all blanks
+    formula = re.sub(r"\s", "", formula)
+    if not re.match("^[A-Z]", formula):
+        raise RuntimeError("InvalidFormula '%s'" % formula)
+    elcnt = re.split("([A-Z][a-z]?)", formula)[1:]
+    ellst = []
+    try:
+        for i in range(0, len(elcnt), 2):
+            el = elcnt[i]
+            cnt = elcnt[i + 1]
+            cnt = (cnt == "") and 1 or int(cnt)
+            ellst.extend(cnt * [el])
+    except ValueError:
+        emsg = "Invalid formula, %r is not valid count" % elcnt[i + 1]
+        raise RuntimeError(emsg)
+    return ellst
+
+
+def die(exit_status=0, pd={}):
+    cleanUp(pd)
+    sys.exit(exit_status)
+
+
+def signalHandler(signum, stackframe):
+    # revert to default handler
+    signal.signal(signum, signal.SIG_DFL)
+    if signum == signal.SIGCHLD:
+        pid, exit_status = os.wait()
+        exit_status = (exit_status >> 8) + (exit_status & 0x00FF)
+        die(exit_status, pd)
+    else:
+        die(1, pd)
+    return
+
+
+def main():
+    import getopt
+
+    # default parameters
+    pd["watch"] = False
+    try:
+        opts, args = getopt.getopt(
+            sys.argv[1:], "f:whV", ["formula=", "watch", "viewer=", "formats=", "help", "version"]
+        )
+    except getopt.GetoptError as errmsg:
+        print(errmsg, file=sys.stderr)
+        die(2)
+    # process options
+    for o, a in opts:
+        if o in ("-f", "--formula"):
+            try:
+                pd["formula"] = parseFormula(a)
+            except RuntimeError as msg:
+                print(msg, file=sys.stderr)
+                die(2)
+        elif o in ("-w", "--watch"):
+            pd["watch"] = True
+        elif o == "--viewer":
+            pd["viewer"] = a
+        elif o == "--formats":
+            pd["formats"] = [w.strip() for w in a.split(",")]
+        elif o in ("-h", "--help"):
+            usage()
+            die()
+        elif o in ("-V", "--version"):
+            version()
+            die()
+    if len(args) < 1:
+        usage("brief")
+        die()
+    elif len(args) > 1:
+        print("too many structure files", file=sys.stderr)
+        die(2)
+    pd["strufile"] = args[0]
+    # trap the following signals
+    signal.signal(signal.SIGHUP, signalHandler)
+    signal.signal(signal.SIGQUIT, signalHandler)
+    signal.signal(signal.SIGSEGV, signalHandler)
+    signal.signal(signal.SIGTERM, signalHandler)
+    signal.signal(signal.SIGINT, signalHandler)
+    env = os.environ.copy()
+    if os.path.basename(pd["viewer"]).startswith("atomeye"):
+        env["XLIB_SKIP_ARGB_VISUALS"] = "1"
+    # try to run the thing:
+    try:
+        convertStructureFile(pd)
+        spawnargs = (pd["viewer"], pd["viewer"], pd["tmpfile"], env)
+        # load strufile in atomeye
+        if pd["watch"]:
+            signal.signal(signal.SIGCLD, signalHandler)
+            os.spawnlpe(os.P_NOWAIT, *spawnargs)
+            watchStructureFile(pd)
+        else:
+            status = os.spawnlpe(os.P_WAIT, *spawnargs)
+            die(status, pd)
+    except IOError as e:
+        print("%s: %s" % (args[0], e.strerror), file=sys.stderr)
+        die(1, pd)
+    except StructureFormatError as e:
+        print("%s: %s" % (args[0], e), file=sys.stderr)
+        die(1, pd)
+    return
+
+
+if __name__ == "__main__":
+    main()

diffpy/structure/apps/transtru.py

@@ -0,0 +1,126 @@
+#!/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.
+#
+##############################################################################
+
+"""Translate structure file to different format.
+
+Usage: ``transtru INFMT..OUTFMT strufile``
+
+Translates structure file strufile from `INFMT` to `OUTFMT` format and prints it
+to the screen. Use "-" as `strufile` to read from standard input. To save the
+translated file, use
+
+    ``transtru INFMT..OUTFMT strufile > strufile.out``
+
+Supported input and output structure formats are
+    * `INFMT`: ``inputFormats``
+    * `OUTFMT`: ``outputFormats``
+
+Options:
+  -h, --help
+    Display this message.
+
+  -V, --version
+    Show script version.
+"""
+
+from __future__ import print_function
+
+import sys
+
+from diffpy.structure import Structure
+from diffpy.structure.structureerrors import StructureFormatError
+
+
+def usage(style=None):
+    """Show usage info, for ``style=="brief"`` show only first 2 lines."""
+    import os.path
+
+    myname = os.path.basename(sys.argv[0])
+    msg = __doc__.replace("transtru", myname)
+    if style == "brief":
+        msg = msg.split("\n")[1] + "\n" + "Try `%s --help' for more information." % myname
+    else:
+        from diffpy.structure.parsers import inputFormats, outputFormats
+
+        msg = msg.replace("inputFormats", " ".join(inputFormats()))
+        msg = msg.replace("outputFormats", " ".join(outputFormats()))
+    print(msg)
+    return
+
+
+def version():
+    from diffpy.structure import __version__
+
+    print("diffpy.structure", __version__)
+    return
+
+
+def main():
+    import getopt
+
+    # default parameters
+    try:
+        opts, args = getopt.getopt(sys.argv[1:], "hV", ["help", "version"])
+    except getopt.GetoptError as errmsg:
+        print(errmsg, file=sys.stderr)
+        sys.exit(2)
+    # process options
+    for o, a in opts:
+        if o in ("-h", "--help"):
+            usage()
+            sys.exit()
+        elif o in ("-V", "--version"):
+            version()
+            sys.exit()
+    if len(args) < 1:
+        usage("brief")
+        sys.exit()
+    # process arguments
+    from diffpy.structure.parsers import inputFormats, outputFormats
+
+    try:
+        infmt, outfmt = args[0].split("..", 1)
+        if infmt not in inputFormats():
+            print("'%s' is not valid input format" % infmt, file=sys.stderr)
+            sys.exit(2)
+        if outfmt not in outputFormats():
+            print("'%s' is not valid output format" % outfmt, file=sys.stderr)
+            sys.exit(2)
+    except ValueError:
+        print("invalid format specification '%s' does not contain .." % args[0], file=sys.stderr)
+        sys.exit(2)
+    # ready to do some real work
+    try:
+        strufile = args[1]
+        stru = Structure()
+        if args[1] == "-":
+            stru.readStr(sys.stdin.read(), infmt)
+        else:
+            stru.read(strufile, infmt)
+        sys.stdout.write(stru.writeStr(outfmt))
+    except IndexError:
+        print("strufile not specified", file=sys.stderr)
+        sys.exit(2)
+    except IOError as e:
+        print("%s: %s" % (strufile, e.strerror), file=sys.stderr)
+        sys.exit(1)
+    except StructureFormatError as e:
+        print("%s: %s" % (strufile, e), file=sys.stderr)
+        sys.exit(1)
+    return
+
+
+if __name__ == "__main__":
+    main()