PyPI - yu-mcal - Versions diffs - 0.1.4__tar.gz → 0.1.5__tar.gz - Mend

yu-mcal 0.1.4tar.gz → 0.1.5tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (71) hide show

{yu_mcal-0.1.4 → yu_mcal-0.1.5}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: yu-mcal
-Version: 0.1.4
+Version: 0.1.5
 Summary: Program for the calculation of mobility tensor for organic semiconductor crystals
 Author: Koki Ozawa
 Author-email: Hiroyuki Matsui <h-matsui@yz.yamagata-u.ac.jp>

{yu_mcal-0.1.4 → yu_mcal-0.1.5}/docs/_modules/mcal/mcal.html RENAMED Viewed

@@ -377,7 +377,7 @@
     <span class="n">cif_path_without_ext</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">directory</span><span class="si">}</span><span class="s1">/</span><span class="si">{</span><span class="n">filename</span><span class="si">}</span><span class="s1">&#39;</span>
     <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;----------------------------------------&#39;</span><span class="p">)</span>
-    <span class="nb">print</span><span class="p">(</span><span class="s1">&#39; mcal 0.1.4 (2026/01/20) by Matsui Lab. &#39;</span><span class="p">)</span>
+    <span class="nb">print</span><span class="p">(</span><span class="s1">&#39; mcal 0.1.5 (2026/01/28) by Matsui Lab. &#39;</span><span class="p">)</span>
     <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;----------------------------------------&#39;</span><span class="p">)</span>
     <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">read_pickle</span><span class="p">:</span>
@@ -720,8 +720,8 @@
 <span class="sd">    Tuple[NDArray[np.float64], NDArray[np.float64]]</span>
 <span class="sd">        Eigenvalue(mobility value) and eigenvector(mobility vector)</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-    <span class="n">value</span><span class="p">,</span> <span class="n">vector</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">eig</span><span class="p">(</span><span class="n">mobility_tensor</span><span class="p">)</span>
-    <span class="k">return</span> <span class="n">value</span><span class="p">,</span> <span class="n">vector</span></div>
+    <span class="n">value</span><span class="p">,</span> <span class="n">vector</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">eigh</span><span class="p">(</span><span class="n">mobility_tensor</span><span class="p">)</span>
+    <span class="k">return</span> <span class="n">value</span><span class="p">[::</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="n">vector</span><span class="p">[:,</span> <span class="p">::</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span></div>

{yu_mcal-0.1.4 → yu_mcal-0.1.5}/docs/_modules/mcal/utils/cif_reader.html RENAMED Viewed

@@ -233,7 +233,7 @@
         </div>
         <article role="main" id="furo-main-content">
           <h1>Source code for mcal.utils.cif_reader</h1><div class="highlight"><pre>
-<span></span><span class="sd">&quot;&quot;&quot;CifReader beta (2025/10/30)&quot;&quot;&quot;</span>
+<span></span><span class="sd">&quot;&quot;&quot;CifReader beta (2026/01/28)&quot;&quot;&quot;</span>
 <span class="kn">import</span><span class="w"> </span><span class="nn">os</span>
 <span class="kn">import</span><span class="w"> </span><span class="nn">re</span>
 <span class="kn">from</span><span class="w"> </span><span class="nn">itertools</span><span class="w"> </span><span class="kn">import</span> <span class="n">product</span>
@@ -304,13 +304,16 @@
         <span class="bp">self</span><span class="o">.</span><span class="n">_make_adjacency_mat</span><span class="p">()</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_split_mols</span><span class="p">()</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_put_unit_cell</span><span class="p">()</span>
+        <span class="c1"># Remove duplicates again as they may occur when moving atoms into the unit cell</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">sym_symbols</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">sym_coords</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_duplicates</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sym_symbols</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">sym_coords</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_make_adjacency_mat</span><span class="p">()</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_split_mols</span><span class="p">()</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_calc_z_value</span><span class="p">()</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_ref_z_value</span> <span class="o">!=</span> <span class="mi">0</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">z_value</span> <span class="o">!=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_ref_z_value</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="n">ZValueIsNotMatchError</span><span class="p">(</span><span class="s1">&#39;Z value is not match.&#39;</span><span class="p">)</span>
+            <span class="k">raise</span> <span class="n">ZValueIsNotMatchError</span><span class="p">(</span>
+                <span class="sa">f</span><span class="s1">&#39;Z value is not match. Z value in cif file is </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_ref_z_value</span><span class="si">}</span><span class="s1">, but calculated Z value is </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">z_value</span><span class="si">}</span><span class="s1">.&#39;</span>
+            <span class="p">)</span>
     <span class="k">def</span><span class="w"> </span><span class="nf">_calc_lattice</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Calculate lattice.&quot;&quot;&quot;</span>
@@ -530,10 +533,11 @@
                         <span class="k">if</span> <span class="s1">&#39;?&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">tmp_atom_data</span><span class="p">[</span><span class="n">atom_data_index</span><span class="p">[</span><span class="s1">&#39;_atom_site_label&#39;</span><span class="p">]]:</span>
                             <span class="k">if</span> <span class="n">atom_data_index</span><span class="p">[</span><span class="s1">&#39;_atom_site_type_symbol&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
                                 <span class="n">symbol_label</span> <span class="o">=</span> <span class="n">tmp_atom_data</span><span class="p">[</span><span class="n">atom_data_index</span><span class="p">[</span><span class="s1">&#39;_atom_site_label&#39;</span><span class="p">]]</span>
-                                <span class="n">symbol</span> <span class="o">=</span> <span class="n">symbol_label</span>
-                                <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">&#39;A&#39;</span><span class="p">,</span> <span class="s1">&#39;B&#39;</span><span class="p">,</span> <span class="s1">&#39;C&#39;</span><span class="p">]:</span>
-                                    <span class="n">symbol</span> <span class="o">=</span> <span class="n">symbol</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="n">s</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
-                                <span class="n">symbol</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\d+&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">symbol</span><span class="p">)</span>
+                                <span class="n">symbol</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[A-Z][a-z]?&#39;</span><span class="p">,</span> <span class="n">symbol_label</span><span class="p">)</span>
+                                <span class="k">if</span> <span class="n">symbol</span><span class="p">:</span>
+                                    <span class="n">symbol</span> <span class="o">=</span> <span class="n">symbol</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+                                <span class="k">else</span><span class="p">:</span>
+                                    <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Symbol label </span><span class="si">{</span><span class="n">symbol_label</span><span class="si">}</span><span class="s1"> is not valid.&#39;</span><span class="p">)</span>
                             <span class="k">else</span><span class="p">:</span>
                                 <span class="n">symbol_label</span> <span class="o">=</span> <span class="n">tmp_atom_data</span><span class="p">[</span><span class="n">atom_data_index</span><span class="p">[</span><span class="s1">&#39;_atom_site_label&#39;</span><span class="p">]]</span>
                                 <span class="n">symbol</span> <span class="o">=</span> <span class="n">tmp_atom_data</span><span class="p">[</span><span class="n">atom_data_index</span><span class="p">[</span><span class="s1">&#39;_atom_site_type_symbol&#39;</span><span class="p">]]</span>
@@ -547,11 +551,10 @@
                     <span class="c1"># get symmetry operation information</span>
                     <span class="k">elif</span> <span class="n">is_read_sym</span><span class="p">:</span>
                         <span class="k">if</span> <span class="s2">&quot;&#39;&quot;</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span>
-                            <span class="n">line</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39; &#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">),</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;&#39;&quot;</span><span class="p">)))</span>
-                            <span class="bp">self</span><span class="o">.</span><span class="n">symmetry_pos</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="n">symmetry_data_index</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">())</span>
+                            <span class="n">line</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39; &#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;&#39;&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">),</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()))</span>
                         <span class="k">else</span><span class="p">:</span>
                             <span class="n">line</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39; &#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">),</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()))</span>
-                            <span class="bp">self</span><span class="o">.</span><span class="n">symmetry_pos</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="n">symmetry_data_index</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">())</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">symmetry_pos</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="n">symmetry_data_index</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">())</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">symbols</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">symbols</span><span class="p">)</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">coordinates</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">coordinates</span><span class="p">)</span>

{yu_mcal-0.1.4 → yu_mcal-0.1.5}/docs/mcal.utils.html RENAMED Viewed

@@ -246,7 +246,7 @@
 </section>
 <section id="module-mcal.utils.cif_reader">
 <span id="mcal-utils-cif-reader-module"></span><h2>mcal.utils.cif_reader module<a class="headerlink" href="#module-mcal.utils.cif_reader" title="Link to this heading">¶</a></h2>
-<p>CifReader beta (2025/10/30)</p>
+<p>CifReader beta (2026/01/28)</p>
 <dl class="py class">
 <dt class="sig sig-object py" id="mcal.utils.cif_reader.CifReader">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">mcal.utils.cif_reader.</span></span><span class="sig-name descname"><span class="pre">CifReader</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cif_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/mcal/utils/cif_reader.html#CifReader"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#mcal.utils.cif_reader.CifReader" title="Link to this definition">¶</a></dt>

{yu_mcal-0.1.4 → yu_mcal-0.1.5}/docs/searchindex.js RENAMED Viewed

	@@ -1 +1 @@
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"print_transfer_integr": [1, 4], "process": 0, "produc": 3, "project": 0, "properti": 3, "protactinium": 3, "pseudo": 2, "pt": 3, "pu": 3, "py": [1, 2], "python": [0, 1], "quantum": 0, "r": 1, "ra": 3, "rais": [2, 3], "rang": [0, 1], "rate": 2, "rb": 3, "rcal": [1, 4], "rcond": 2, "re": 3, "read": [1, 2, 3], "read_pickl": [1, 4], "reader": 3, "rel": 3, "releas": 0, "remov": 3, "remove_dupl": [1, 3], "remove_radical_flag": 3, "reorg_energi": 1, "reorgan": [0, 1, 2], "replac": 0, "repres": 3, "research": 0, "reset": 3, "reset_vari": [1, 3], "resourc": 1, "result": 1, "resum": 1, "return": [1, 2, 3], "reversed_readlin": [1, 3], "rf": 3, "rg": 3, "rh": 3, "rn": 3, "roel": 0, "root": 3, "row": 3, "rp": 1, "ru": 3, "run": [0, 1], "rwf": 3, "sampl": 3, "save": [0, 1, 3], "save_dir": [1, 3], "sb": 3, "sc": 3, "se": 3, "search": 0, "see": 0, "semiconductor": [0, 1, 2], "set": [1, 3], "set_charge_spin": [1, 3], "set_coordin": [1, 3], "set_funct": [1, 3], "set_resourc": [1, 3], "set_symbol": [1, 3], "set_titl": [1, 3], "sg": 3, "shape": 3, "should": 2, "si": 3, "significantli": 0, "sim_typ": 1, "simul": [1, 2], "singular": 2, "size": [0, 2], "skip": [1, 2], "skip_cal": 2, "skip_specified_c": 2, "sm": 3, "small": 2, "smaller": 0, "sn": 3, "solut": 2, "sourc": [1, 2, 3], "specifi": [0, 2], "speedup": [0, 1], "spin": 3, "sr": 3, "src": 3, "static": 2, "step": 2, "str": [1, 2, 3], "structur": [0, 3], "subaru": 3, "submodul": 4, "subpackag": 4, "suffici": 0, "supercel": [0, 1], "support": 0, "sure": 0, "symbol": [1, 3], "symbols1": 1, "symbols2": 1, "symmetri": 3, "symmetryisnotdefinederror": [1, 3], "system": 0, "t": [2, 3], "ta": 3, "tb": 3, "tc": 3, "tcal": 0, "te": 3, "temperatur": 2, "tennessin": 3, "tensor": [0, 1, 2], "term": 2, "termin": [0, 1, 2, 3], "th": [2, 3], "thi": [0, 2, 3], "thorium": 3, "ti": 3, "tight": 3, "timestamp": 2, "titl": 3, "tl": 3, "tm": 3, "tol": 3, "toler": 3, "tool": 0, "total": 2, "transfer": [0, 1, 2], "true": [1, 2, 3], "tupl": [1, 2, 3], "two": 1, "txt": 3, "type": [0, 1, 2, 3], "u": [0, 3], "under": 0, "union": 1, "uniqu": [1, 3], "unique_mol": 1, "unit": [0, 3], "univers": 0, "uranium": 3, "us": [0, 1, 2, 3], "usag": 1, "user": 3, "util": [1, 4], "v": 3, "valu": [1, 2, 3], "valueerror": 2, "vari": 0, "variabl": 3, "vdw_radiu": 3, "vector": [1, 2], "w": 3, "wa": [0, 2], "weight": [0, 1, 3], "when": 3, "while": 3, "widen": [0, 1], "within": 3, "without": [0, 1], "work": 0, "x": 3, "xe": 3, "xxx": [0, 1], "xxx_result": [0, 1], "xyz": 3, "y": 3, "yamagata": 0, "yb": 3, "you": 0, "your": 0, "yu": 0, "yz": 0, "z": 3, "zero": 2, "zn": 3, "zr": 3, "zvalueisnotmatcherror": [1, 3]}, "titles": ["mcal Documentation", "mcal package", "mcal.calculations package", "mcal.utils package", "mcal"], "titleterms": {"If": 0, "To": 0, "acknowledg": 0, "api": 0, "argument": 0, "author": 0, "basic": 0, "c": 0, "calcul": [0, 2], "cellsiz": 0, "cif_read": 3, "coeffici": 0, "compar": 0, "content": [1, 2, 3], "control": 0, "cpu": 0, "diffus": 0, "document": 0, "error": 0, "exampl": 0, "featur": 0, "fullcal": 0, "g": 0, "g09": 0, "gaus_log_read": 3, "gjf_maker": 3, "high": 0, "hopping_mobility_model": 2, "indic": 0, "instal": 0, "licens": 0, "m": 0, "manual": 0, "mc": 0, "mcal": [0, 1, 2, 3, 4], "mem": 0, "memori": 0, "method": 0, "midwai": 0, "modul": [1, 2, 3], "note": 0, "number": 0, "od": 0, "option": 0, "output": 0, "overview": 0, "p": 0, "packag": [1, 2, 3], "pickl": 0, "practic": 0, "precis": 0, "r": 0, "rcal": 2, "read": 0, "read_pickl": 0, "reduc": 0, "refer": 0, "requir": 0, "result": 0, "resum": 0, "reus": 0, "rp": 0, "set": 0, "shortag": 0, "standard": 0, "stop": 0, "submodul": [1, 2, 3], "subpackag": 1, "tabl": 0, "time": 0, "troubleshoot": 0, "usag": 0, "util": 3, "verifi": 0}})

{yu_mcal-0.1.4 → yu_mcal-0.1.5}/pyproject.toml RENAMED Viewed

@@ -1,6 +1,6 @@
 [project]
 name = "yu-mcal"
-version = "0.1.4"
+version = "0.1.5"
 description = "Program for the calculation of mobility tensor for organic semiconductor crystals"
 requires-python = ">=3.9"
 dependencies = [

{yu_mcal-0.1.4 → yu_mcal-0.1.5}/src/mcal/mcal.py RENAMED Viewed

@@ -140,7 +140,7 @@ def main():
     cif_path_without_ext = f'{directory}/{filename}'
     print('----------------------------------------')
-    print(' mcal 0.1.4 (2026/01/20) by Matsui Lab. ')
+    print(' mcal 0.1.5 (2026/01/28) by Matsui Lab. ')
     print('----------------------------------------')
     if args.read_pickle:
@@ -471,8 +471,8 @@ def cal_eigenvalue_decomposition(mobility_tensor: NDArray[np.float64]) -> Tuple[
     Tuple[NDArray[np.float64], NDArray[np.float64]]
         Eigenvalue(mobility value) and eigenvector(mobility vector)
     """
-    value, vector = np.linalg.eig(mobility_tensor)
-    return value, vector
+    value, vector = np.linalg.eigh(mobility_tensor)
+    return value[::-1], vector[:, ::-1]
 def cal_min_distance(

{yu_mcal-0.1.4 → yu_mcal-0.1.5}/src/mcal/utils/cif_reader.py RENAMED Viewed

@@ -1,4 +1,4 @@
-"""CifReader beta (2025/10/30)"""
+"""CifReader beta (2026/01/28)"""
 import os
 import re
 from itertools import product
@@ -67,13 +67,16 @@ class CifReader:
         self._make_adjacency_mat()
         self._split_mols()
         self._put_unit_cell()
+        # Remove duplicates again as they may occur when moving atoms into the unit cell
         self.sym_symbols, self.sym_coords = self.remove_duplicates(self.sym_symbols, self.sym_coords)
         self._make_adjacency_mat()
         self._split_mols()
         self._calc_z_value()
         if self._ref_z_value != 0 and self.z_value != self._ref_z_value:
-            raise ZValueIsNotMatchError('Z value is not match.')
+            raise ZValueIsNotMatchError(
+                f'Z value is not match. Z value in cif file is {self._ref_z_value}, but calculated Z value is {self.z_value}.'
+            )
     def _calc_lattice(self):
         """Calculate lattice."""
@@ -293,10 +296,11 @@ class CifReader:
                         if '?' not in tmp_atom_data[atom_data_index['_atom_site_label']]:
                             if atom_data_index['_atom_site_type_symbol'] is None:
                                 symbol_label = tmp_atom_data[atom_data_index['_atom_site_label']]
-                                symbol = symbol_label
-                                for s in ['A', 'B', 'C']:
-                                    symbol = symbol.replace(s, '')
-                                symbol = re.sub(r'\d+', '', symbol)
+                                symbol = re.match(r'[A-Z][a-z]?', symbol_label)
+                                if symbol:
+                                    symbol = symbol.group(0)
+                                else:
+                                    raise ValueError(f'Symbol label {symbol_label} is not valid.')
                             else:
                                 symbol_label = tmp_atom_data[atom_data_index['_atom_site_label']]
                                 symbol = tmp_atom_data[atom_data_index['_atom_site_type_symbol']]
@@ -310,11 +314,10 @@ class CifReader:
                     # get symmetry operation information
                     elif is_read_sym:
                         if "'" in line:
-                            line = list(map(lambda x: x.strip().replace(' ', ''), line.split("'")))
-                            self.symmetry_pos.append(line[symmetry_data_index].lower())
+                            line = list(map(lambda x: x.strip().replace(' ', '').replace("'", ""), line.split()))
                         else:
                             line = list(map(lambda x: x.strip().replace(' ', ''), line.split()))
-                            self.symmetry_pos.append(line[symmetry_data_index].lower())
+                        self.symmetry_pos.append(line[symmetry_data_index].lower())
             self.symbols = np.array(self.symbols)
             self.coordinates = np.array(self.coordinates)

{yu_mcal-0.1.4 → yu_mcal-0.1.5}/uv.lock RENAMED Viewed

@@ -1244,7 +1244,7 @@ wheels = [
 [[package]]
 name = "yu-mcal"
-version = "0.1.4"
+version = "0.1.5"
 source = { editable = "." }
 dependencies = [
     { name = "numpy", version = "2.0.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" },