diffpy.structure 3.4.0rc1__tar.gz → 3.5.0__tar.gz

{diffpy_structure-3.4.0rc1 → diffpy_structure-3.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: diffpy.structure
-Version: 3.4.0rc1
+Version: 3.5.0
 Summary: Crystal structure container and parsers for structure formats.
 Author-email: Simon Billinge <sbillinge@ucsb.edu>
 Maintainer-email: Simon Billinge <sbillinge@ucsb.edu>
@@ -49,8 +49,8 @@ Dynamic: license-file
 .. |Black| image:: https://img.shields.io/badge/code_style-black-black
         :target: https://github.com/psf/black
 
-.. |CI| image:: https://github.com/diffpy/diffpy.structure/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg
-        :target: https://github.com/diffpy/diffpy.structure/actions/workflows/matrix-and-codecov-on-merge-to-main.yml
+.. |CI| image:: https://github.com/diffpy/diffpy.structure/actions/workflows/matrix-and-codecov.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.structure/actions/workflows/matrix-and-codecov.yml
 
 .. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.structure/branch/main/graph/badge.svg
         :target: https://codecov.io/gh/diffpy/diffpy.structure

{diffpy_structure-3.4.0rc1 → diffpy_structure-3.5.0}/README.rst

@@ -15,8 +15,8 @@
 .. |Black| image:: https://img.shields.io/badge/code_style-black-black
         :target: https://github.com/psf/black
 
-.. |CI| image:: https://github.com/diffpy/diffpy.structure/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg
-        :target: https://github.com/diffpy/diffpy.structure/actions/workflows/matrix-and-codecov-on-merge-to-main.yml
+.. |CI| image:: https://github.com/diffpy/diffpy.structure/actions/workflows/matrix-and-codecov.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.structure/actions/workflows/matrix-and-codecov.yml
 
 .. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.structure/branch/main/graph/badge.svg
         :target: https://codecov.io/gh/diffpy/diffpy.structure

{diffpy_structure-3.4.0rc1 → diffpy_structure-3.5.0}/src/diffpy/structure/__init__.py

@@ -33,7 +33,6 @@ Exceptions:
     * SymmetryError
 """
 
-
 import os
 import sys
 
@@ -102,10 +101,10 @@ def load_structure(filename, fmt="auto", **kw):
         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.
+        one of the formats listed by the `parsers.input_formats` function.
         When 'auto', all supported formats are tried in a sequence.
     kw : Optional
-        Extra keyword arguments that are passed to `parsers.getParser`
+        Extra keyword arguments that are passed to `parsers.get_parser`
         function. These configure the dedicated Parser object that
         is used to read content in filename.
 

{diffpy_structure-3.4.0rc1 → diffpy_structure-3.5.0}/src/diffpy/structure/_legacy_importer.py

@@ -27,7 +27,6 @@ Warning
 This module is deprecated and will be removed in the future.
 """
 
-
 import importlib.abc
 import sys
 from warnings import warn

{diffpy_structure-3.4.0rc1 → diffpy_structure-3.5.0}/src/diffpy/structure/apps/anyeye.py

@@ -187,7 +187,7 @@ def convert_structure_file(pd):
     fmt = pd.get("format", "auto")
     stru = None
     if fmt == "auto":
-        stru, fmt = loadStructureFile(strufile)
+        stru, fmt = load_structure_file(strufile)
         pd["fmt"] = fmt
     # if fmt is recognized by the viewer, use as is
     if fmt in pd["formats"] and pd["formula"] is None:

{diffpy_structure-3.4.0rc1 → diffpy_structure-3.5.0}/src/diffpy/structure/apps/vesta_viewer.py

@@ -72,12 +72,13 @@ pd = {
 
 
 def usage(style=None):
-    """Show usage info. for ``style=="brief"`` show only first 2 lines.
+    """Show usage info.
 
-    Parameters
-    ----------
-    style : str, optional
-        The usage display style.
+    for ``style=="brief"`` show only first 2 lines.
+        Parameters
+        ----------
+        style : str, optional
+            The usage display style.
     """
     myname = Path(sys.argv[0]).name
     msg = __doc__.replace("vestaview", myname)

{diffpy_structure-3.4.0rc1 → diffpy_structure-3.5.0}/src/diffpy/structure/atom.py

@@ -42,7 +42,7 @@ msdCart_deprecation_msg = build_deprecation_message(
 
 
 class Atom(object):
-    """Storage of structure information relevant for a single atom.
+    """The storage of structure information relevant for a single atom.
 
     This class manages atom information such as element symbol, position
     in fractional and Cartesian coordinates, atomic displacement parameters
@@ -55,10 +55,10 @@ class Atom(object):
         By default an empty string. When of the `Atom` type, create
         a copy of `atype` and adjust it per other arguments.
     xyz : numpy.ndarray, Optional
-        Fractional coordinates within the associated `lattice`.
+        The fractional coordinates within the associated `lattice`.
         By default ``[0, 0, 0]``.
     label : str, Optional
-        A unique string `label` for referring to this `Atom`.
+        The unique string `label` for referring to this `Atom`.
         By default an empty string.
     occupancy : float, Optional
         The initial `occupancy` of this atom, by default ``1``.
@@ -76,25 +76,25 @@ class Atom(object):
         *Uisoequiv* arguments may be provided at the same time. Assume
         zero atomic displacements when *U* and *Uisoequiv* are unset.
     lattice : Lattice, Optional
-        Coordinate system for the fractional coordinates `xyz`.
+        The coordinate system for the fractional coordinates `xyz`.
         Use the absolute Cartesian system when ``None``.
 
     Attributes
     ----------
     element : str
-        The string type of the atom. An element or ion symbol.
+        The string type of the atom. An element or ion symbol, default "".
     xyz : numpy.ndarray
         The fractional coordinates in the associated `lattice`.
     label : str
-        A unique string label referring to this atom, for example, "C_1".
+        The unique string label referring to this atom, for example, "C_1".
         The *label* can be used to reference this atom when contained in
-        a `Structure` object.
+        a `Structure` object, default "".
     occupancy : float
-        The fractional occupancy of this atom.
+        The fractional occupancy of this atom, default 1.0.
     lattice : Lattice
-        Coordinate system for the fractional coordinates `xyz` and
+        The coordinate system for the fractional coordinates `xyz` and
         the tensor of atomic displacement parameters `U`.
-        Use the absolute Cartesian coordinates when ``None``.
+        Use the absolute Cartesian coordinates when ``None`` as the default.
 
     Note
     ----
@@ -104,21 +104,17 @@ class Atom(object):
     # Private attributes
     #
     #   _U : 3-by-3 ndarray
-    #       Internal storage of the displacement parameters.
+    #       The internal storage of the displacement parameters.
 
     # instance attributes that have immutable default values
     element = ""
-    """str: Default values of `element`."""
 
     label = ""
-    """str: Default values of `label`."""
 
     occupancy = 1.0
-    """float: Default values of `occupancy`."""
 
     _anisotropy = False
     lattice = None
-    """None: Default values of `lattice`."""
 
     def __init__(
         self,
@@ -232,7 +228,7 @@ class Atom(object):
         return msd
 
     def __repr__(self):
-        """String representation of this Atom."""
+        """The string representation of this Atom."""
         xyz = self.xyz
         s = "%-4s %8.6f %8.6f %8.6f %6.4f" % (
             self.element,
@@ -273,29 +269,29 @@ class Atom(object):
     x = property(
         lambda self: self.xyz[0],
         lambda self, val: self.xyz.__setitem__(0, val),
-        doc="float : fractional coordinate *x*, same as ``xyz[0]``.",
+        doc="The fractional coordinate *x*, same as ``xyz[0]``, as a float",
     )
     y = property(
         lambda self: self.xyz[1],
         lambda self, val: self.xyz.__setitem__(1, val),
-        doc="float : fractional coordinate *y*, same as ``xyz[1]``.",
+        doc="The fractional coordinate *y*, same as ``xyz[1]``, as a float",
     )
     z = property(
         lambda self: self.xyz[2],
         lambda self, val: self.xyz.__setitem__(2, val),
-        doc="float : fractional coordinate *z*, same as ``xyz[2]``.",
+        doc="The fractional coordinate *z*, same as ``xyz[2]``, as a float",
     )
 
     # xyz_cartn
 
     @property
     def xyz_cartn(self):
-        """numpy.ndarray: Atom position in absolute Cartesian
-        coordinates.
+        """Atom position in absolute Cartesian coordinates, as a
+        numpy.ndarray.
 
         This is computed from fractional coordinates `xyz` and the
-        current `lattice` setup. Assignment to *xyz_cartn* or
-        its components is applied on fractional coordinates `xyz`.
+        current `lattice` setup. Assignment to *xyz_cartn* or its
+        components is applied on fractional coordinates `xyz`.
         """
         if not self.lattice:
             rv = self.xyz
@@ -315,7 +311,8 @@ class Atom(object):
 
     @property
     def anisotropy(self):
-        """bool : Flag for allowing anisotropic displacement parameters.
+        """The flag for allowing anisotropic displacement parameters, as
+        a bool.
 
         When ``False`` the tensor of thermal displacement parameters `U`
         must be isotropic and only its diagonal elements are taken into
@@ -340,8 +337,8 @@ class Atom(object):
 
     @property
     def U(self):
-        """numpy.ndarray : The 3x3 matrix of anisotropic atomic
-        displacements.
+        """The 3x3 matrix of anisotropic atomic displacements, as a
+        ndarray.
 
         For isotropic displacements (when `anisotropy` is ``False``)
         assignment to *U* uses only the first ``Unew[0, 0]`` element
@@ -387,7 +384,7 @@ class Atom(object):
     # _doc_uii, _doc_uij are temporary local variables.
 
     _doc_uii = """
-        float : The ``U[{0}, {0}]`` component of the displacement tensor `U`.
+        The ``U[{0}, {0}]`` component of the displacement tensor `U`, as a float
 
         When `anisotropy` is ``False`` setting a new value updates entire
         tensor *U*.
@@ -410,7 +407,7 @@ class Atom(object):
     )
 
     _doc_uij = """
-        float : The ``U[{0}, {1}]`` element of the displacement tensor `U`.
+        The ``U[{0}, {1}]`` element of the displacement tensor `U`, as a float
 
         Sets ``U[{1}, {0}]`` together with ``U[{0}, {1}]``. Assignment
         has no effect when `anisotropy` is ``False``.
@@ -439,7 +436,8 @@ class Atom(object):
 
     @property
     def Uisoequiv(self):
-        """float : The isotropic displacement parameter or an equivalent value.
+        """The isotropic displacement parameter or an equivalent value,
+        as a float.
 
         Setting a new value rescales tensor `U` so it yields equivalent
         direction-averaged displacements.
@@ -481,14 +479,14 @@ class Atom(object):
     # _doc_bii, _doc_bij are local variables.
 
     _doc_bii = """
-        float : The ``B{0}{0}`` element of the Debye-Waller matrix.
+        The ``B{0}{0}`` element of the Debye-Waller matrix, as a float
 
         This is equivalent to ``8 * pi**2 * U{0}{0}``. When `anisotropy`
         is ``False`` setting a new value updates entire tensor `U`.
         """
 
     _doc_bij = """
-        float : The ``B{0}{1}`` element of the Debye-Waller matrix.
+        The ``B{0}{1}`` element of the Debye-Waller matrix, as a float
 
         This is equivalent to ``8 * pi**2 * U{0}{1}``. Setting a new
         value updates `U` in a symmetric way. Assignment has no effect
@@ -533,7 +531,8 @@ class Atom(object):
 
     @property
     def Bisoequiv(self):
-        """float : The Debye-Waller isotropic displacement or an equivalent value.
+        """The Debye-Waller isotropic displacement or an equivalent
+        value, as a float.
 
         This equals ``8 * pi**2 * Uisoequiv``. Setting a new value
         rescales `U` tensor to yield equivalent direction-average of
@@ -553,7 +552,8 @@ class Atom(object):
 
 
 class _AtomCartesianCoordinates(numpy.ndarray):
-    """Specialized `numpy.ndarray` for accessing Cartesian coordinates.
+    """The specialized `numpy.ndarray` for accessing Cartesian
+    coordinates.
 
     Inplace assignments to this array are applied on the *xyz* position
     position of owner `Atom` as per the associated `Atom.lattice`.
@@ -561,7 +561,7 @@ class _AtomCartesianCoordinates(numpy.ndarray):
     Parameters
     ----------
     atom : Atom
-        `Atom` instance to be linked to these coordinate array.
+       The `Atom` instance to be linked to these coordinate array.
     """
 
     def __new__(self, atom):
@@ -575,7 +575,7 @@ class _AtomCartesianCoordinates(numpy.ndarray):
 
     @property
     def asarray(self):
-        """ndarray : This array viewed as standard numpy array."""
+        """This array viewed as standard numpy array."""
         return self.view(numpy.ndarray)
 
     def __setitem__(self, idx, value):

{diffpy_structure-3.4.0rc1 → diffpy_structure-3.5.0}/src/diffpy/structure/expansion/shapeutils.py

@@ -24,6 +24,8 @@ findCenter_deprecation_msg = build_deprecation_message(
 )
 """Utilities for making shapes."""
 
+# FIXME: remove this line when `docformatter` fixes the blank line bug
+
 
 @deprecated(findCenter_deprecation_msg)
 def findCenter(S):

{diffpy_structure-3.4.0rc1 → diffpy_structure-3.5.0}/src/diffpy/structure/lattice.py

@@ -18,7 +18,7 @@ lattice coordinate system.
 Attributes
 ----------
 cartesian : Lattice
-    Constant instance of Lattice, default Cartesian system.
+    The default Cartesian lattice with a=b=c=1 and alpha=beta=gamma=90 degrees.
 """
 
 import math
@@ -159,8 +159,8 @@ class Lattice(object):
     Note
     ----
     The array attributes are read-only. They get updated by changing
-    some lattice parameters or by calling the `setLatPar()` or
-    `setLatBase()` methods.
+    some lattice parameters or by calling the `set_latt_parms()` or
+    `set_new_latt_base_vec()` methods.
 
     Examples
     --------
@@ -757,13 +757,13 @@ class Lattice(object):
         I3 = numpy.identity(3, dtype=float)
         rotbaseI3diff = max(numpy.reshape(numpy.fabs(self.baserot - I3), 9))
         cartlatpar = numpy.array([1.0, 1.0, 1.0, 90.0, 90.0, 90.0])
-        latpardiff = cartlatpar - self.abcABG()
+        latpardiff = cartlatpar - self.cell_parms()
         if rotbaseI3diff > self._epsilon:
             s = "Lattice(base=%r)" % self.base
         elif numpy.fabs(latpardiff).max() < self._epsilon:
             s = "Lattice()"
         else:
-            s = "Lattice(a=%g, b=%g, c=%g, alpha=%g, beta=%g, gamma=%g)" % self.abcABG()
+            s = "Lattice(a=%g, b=%g, c=%g, alpha=%g, beta=%g, gamma=%g)" % self.cell_parms()
         return s
 
 

{diffpy_structure-3.4.0rc1 → diffpy_structure-3.5.0}/src/diffpy/structure/parsers/__init__.py

@@ -16,7 +16,7 @@
 
 The recognized structure formats are defined by subclassing `StructureParser`,
 by convention these classes are named `P_<format>.py`. The parser classes should
-to override the `parseLines()` and `toLines()` methods of `StructureParser`.
+to override the `parse_lines()` and `to_lines()` methods of `StructureParser`.
 Any structure parser needs to be registered in `parser_index` module.
 
 For normal usage it should be sufficient to use the routines provided
@@ -25,9 +25,9 @@ in this module.
 Content:
     * StructureParser: base class for a concrete Parser
     * parser_index: dictionary of known structure formats
-    * getParser: factory for Parser at given format
-    * inputFormats: list of available input formats
-    * outputFormats: list of available output formats
+    * get_parser: factory for Parser at given format
+    * input_formats: list of available input formats
+    * output_formats: list of available output formats
 """
 
 from diffpy.structure.parsers.parser_index_mod import parser_index

{diffpy_structure-3.4.0rc1 → diffpy_structure-3.5.0}/src/diffpy/structure/parsers/p_auto.py

@@ -14,7 +14,7 @@
 ##############################################################################
 """Parser for automatic file format detection.
 
-This Parser does not provide the the `toLines()` method.
+This Parser does not provide the the `to_lines()` method.
 """
 
 import os
@@ -55,10 +55,10 @@ class P_auto(StructureParser):
     Attributes
     ----------
     format : str
-        Detected structure format. Initially set to "auto" and updated
+        The detected structure format. Initially set to "auto" and updated
         after successful detection of the structure format.
     pkw : dict
-        Keyword arguments passed to the parser.
+        The keyword arguments passed to the parser.
     """
 
     def __init__(self, **kw):

{diffpy_structure-3.4.0rc1 → diffpy_structure-3.5.0}/src/diffpy/structure/parsers/p_cif.py

@@ -17,9 +17,9 @@
 Attributes
 ----------
 rx_float : re.Pattern
-    Constant regular expression for `leading_float()`.
+    The constant regular expression for `leading_float()`.
 symvec : dict
-    Helper dictionary for `getSymOp()`.
+    The helper dictionary for `get_symop()`.
 
 Note
 ----
@@ -79,26 +79,26 @@ class P_cif(StructureParser):
     Attributes
     ----------
     format : str
-        Structure format name.
+        The structure format name.
     ciffile : CifFile
-        Instance of `CifFile` from `PyCifRW`.
+        The instance of `CifFile` from `PyCifRW`.
     stru : Structure
-        `Structure` instance used for CIF input or output.
+        The `Structure` instance used for CIF input or output.
     spacegroup : SpaceGroup
-        Instance of `SpaceGroup` used for symmetry expansion.
+        The instance of `SpaceGroup` used for symmetry expansion.
     eps : float
-        Resolution in fractional coordinates for non-equal positions.
+        The resolution in fractional coordinates for non-equal positions.
         Used for expansion of asymmetric unit.
     eau : ExpandAsymmetricUnit
-        Instance of `ExpandAsymmetricUnit` from `SymmetryUtilities`.
+        The instance of `ExpandAsymmetricUnit` from `SymmetryUtilities`.
     asymmetric_unit : list
-        List of `Atom` instances for the original asymmetric unit in the CIF file.
+        The list of `Atom` instances for the original asymmetric unit in the CIF file.
     labelindex : dict
-        Dictionary mapping unique atom label to index of `Atom` in `self.asymmetric_unit`.
+        The dictionary mapping unique atom label to index of `Atom` in `self.asymmetric_unit`.
     anisotropy : dict
-        Dictionary mapping unique atom label to displacement anisotropy resolved at that site.
+        The dictionary mapping unique atom label to displacement anisotropy resolved at that site.
     cif_sgname : str or None
-        Space group name obtained by looking up the value of
+        The space group name obtained by looking up the value of
         `_space_group_name_Hall`,
         `_symmetry_space_group_name_Hall`,
         `_space_group_name_H-M_alt`,
@@ -151,8 +151,8 @@ class P_cif(StructureParser):
         _atom_setters[k] = _atom_setters[k.lower()] = k
     del k
 
+    # Conversion factor from B values to U values, as a float
     BtoU = 1.0 / (8 * numpy.pi**2)
-    """float: Conversion factor from B values to U values."""
 
     def _tr_ignore(a, value):
         return
@@ -362,7 +362,6 @@ class P_cif(StructureParser):
         """
         return self.parse_lines(lines)
 
-    @deprecated(parseLines_deprecation_msg)
     def parse_lines(self, lines):
         """Parse list of lines in CIF format.
 

{diffpy_structure-3.4.0rc1 → diffpy_structure-3.5.0}/src/diffpy/structure/parsers/p_discus.py

@@ -39,23 +39,24 @@ toLines_deprecation_msg = build_deprecation_message(
 
 
 class P_discus(StructureParser):
-    """Parser for DISCUS structure format. The parser chokes on molecule
-    and generator records.
+    """Parser for DISCUS structure format.
+
+    The parser chokes on molecule and generator records.
 
     Attributes
     ----------
     format : str
-        File format name, default "discus".
+        The file format name, default "discus".
     nl : int
-        Line number of the current line being parsed.
+        The line number of the current line being parsed.
     lines : list of str
-        List of lines from the input file.
+        The list of lines from the input file.
     line : str
-        Current line being parsed.
+        The current line being parsed.
     stru : PDFFitStructure
-        Structure being parsed.
+        The structure being parsed.
     ignored_lines : list of str
-        List of lines that were ignored during parsing.
+        The list of lines that were ignored during parsing.
     cell_read : bool
         ``True`` if cell record processed.
     ncell_read : bool
@@ -139,7 +140,7 @@ class P_discus(StructureParser):
                 raise StructureFormatError(emsg)
             # take care of superlattice
             if self.stru.pdffit["ncell"][:3] != [1, 1, 1]:
-                latpars = list(self.stru.lattice.abcABG())
+                latpars = list(self.stru.lattice.cell_parms())
                 superlatpars = [latpars[i] * self.stru.pdffit["ncell"][i] for i in range(3)] + latpars[3:]
                 superlattice = Lattice(*superlatpars)
                 self.stru.place_in_lattice(superlattice)
@@ -214,7 +215,7 @@ class P_discus(StructureParser):
                 raise StructureFormatError(emsg)
             # take care of superlattice
             if self.stru.pdffit["ncell"][:3] != [1, 1, 1]:
-                latpars = list(self.stru.lattice.abcABG())
+                latpars = list(self.stru.lattice.cell_parms())
                 superlatpars = [latpars[i] * self.stru.pdffit["ncell"][i] for i in range(3)] + latpars[3:]
                 superlattice = Lattice(*superlatpars)
                 self.stru.place_in_lattice(superlattice)
@@ -267,7 +268,7 @@ class P_discus(StructureParser):
         if stru_pdffit.get("stepcut", 0.0) > 0.0:
             line = "shape   stepcut, %g" % stru_pdffit["stepcut"]
             lines.append(line)
-        lines.append("cell   %9.6f, %9.6f, %9.6f, %9.6f, %9.6f, %9.6f" % self.stru.lattice.abcABG())
+        lines.append("cell   %9.6f, %9.6f, %9.6f, %9.6f, %9.6f, %9.6f" % self.stru.lattice.cell_parms())
         lines.append("ncell  %9i, %9i, %9i, %9i" % (1, 1, 1, len(self.stru)))
         lines.append("atoms")
         for a in self.stru:

{diffpy_structure-3.4.0rc1 → diffpy_structure-3.5.0}/src/diffpy/structure/parsers/p_pdb.py

@@ -74,7 +74,11 @@ class P_pdb(StructureParser):
     Attributes
     ----------
     format : str
-        Format name, default "pdb".
+        The format name, default "pdb".
+    orderOfRecords : list
+        The ordered list of PDB record labels.
+    validRecords : dict
+        The set of valid PDB record labels.
     """
 
     # Static data members
@@ -135,10 +139,8 @@ class P_pdb(StructureParser):
         "MASTER",
         "END",
     ]
-    """list: Ordered list of PDB record labels."""
 
     validRecords = dict.fromkeys(orderOfRecords)
-    """dict: Dictionary of PDB record labels."""
 
     def __init__(self):
         StructureParser.__init__(self)
@@ -213,9 +215,9 @@ class P_pdb(StructureParser):
                     sc[2, :] = [float(x) for x in line[10:40].split()]
                     scaleU[2] = float(line[45:55])
                     base = numpy.transpose(numpy.linalg.inv(sc))
-                    abcABGcryst = numpy.array(stru.lattice.abcABG())
+                    abcABGcryst = numpy.array(stru.lattice.cell_parms())
                     stru.lattice.set_new_latt_base_vec(base)
-                    abcABGscale = numpy.array(stru.lattice.abcABG())
+                    abcABGscale = numpy.array(stru.lattice.cell_parms())
                     reldiff = numpy.fabs(1.0 - abcABGscale / abcABGcryst)
                     if not numpy.all(reldiff < 1.0e-4):
                         emsg = "%d: " % p_nl + "SCALE and CRYST1 are not consistent."

{diffpy_structure-3.4.0rc1 → diffpy_structure-3.5.0}/src/diffpy/structure/parsers/p_pdffit.py

@@ -40,11 +40,11 @@ class P_pdffit(StructureParser):
     Attributes
     ----------
     format : str
-        Format name, default "pdffit".
+        The format name, default "pdffit".
     ignored_lines : list
-        List of lines ignored during parsing.
+        The list of lines ignored during parsing.
     stru : PDFFitStructure
-        Structure instance used for cif input or output.
+        The structure instance used for cif input or output.
     """
 
     def __init__(self):

{diffpy_structure-3.4.0rc1 → diffpy_structure-3.5.0}/src/diffpy/structure/parsers/p_rawxyz.py

@@ -48,7 +48,7 @@ class P_rawxyz(StructureParser):
     Attributes
     ----------
     format : str
-        Format name, default "rawxyz".
+        The format name, default "rawxyz".
     """
 
     def __init__(self):

{diffpy_structure-3.4.0rc1 → diffpy_structure-3.5.0}/src/diffpy/structure/parsers/p_vesta.py

@@ -22,7 +22,7 @@ VESTA is the actively maintained successor viewer.
 Attributes
 ----------
 AtomicMass : dict
-    Dictionary of atomic masses for elements.
+    The dictionary of atomic masses for elements.
 """
 
 import re
@@ -47,8 +47,9 @@ class P_vesta(StructureParser):
     Attributes
     ----------
     format : str
-        Format name, default "vesta".
-
+        The format name, default "vesta".
+    cluster_boundary : int
+        The width of boundary around corners of non-periodic cluster, default 2.
     Notes
     -----
     The ``cluster_boundary`` attribute is retained from the original
@@ -57,10 +58,6 @@ class P_vesta(StructureParser):
     """
 
     cluster_boundary = 2
-    """int: Width of boundary around corners of non-periodic cluster.
-    Retained from the original AtomEye/XCFG parser for API compatibility.
-    VESTA handles periodicity natively so this value has no effect on output.
-    """
 
     def __init__(self):
         StructureParser.__init__(self)
@@ -187,7 +184,7 @@ class P_vesta(StructureParser):
                 emsg = "VESTA file is missing STRUC lattice parameters"
                 raise StructureFormatError(emsg)
 
-            stru.lattice.setLatPar(
+            stru.lattice.set_latt_parms(
                 a=latt_abc[0],
                 b=latt_abc[1],
                 c=latt_abc[2],