orto 1.14.0__tar.gz → 1.14.1__tar.gz

{orto-1.14.0 → orto-1.14.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.14.0
+Version: 1.14.1
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

orto-1.14.1/orto/__version__.py

@@ -0,0 +1 @@
+__version__ = '1.14.1'

{orto-1.14.0 → orto-1.14.1}/orto/extractor.py

@@ -380,6 +380,81 @@ class ExchangeCouplingExtractor(extto.BetweenExtractor):
         return _ext.data
 
 
+class AILFTOrbMatrixExtractor(extto.BetweenExtractor):
+    '''
+    Extracts AI-LFT orbital matrix from Orca output file
+    '''
+    # Regex Start Pattern
+    START_PATTERN = rb'(?<=Ligand field one-electron matrix VLFT \(a.u.\) : )' # noqa
+
+    # Regex End Pattern
+    END_PATTERN = rb'(?=-------------------------------------------------)'
+
+    MODIFIERS = [re.MULTILINE]
+
+    @property
+    def data(self) -> list[NDArray]:
+        '''
+        AI-LFT matrices, one per block, in atomic units
+        '''
+        return self._data
+
+    @staticmethod
+    def _process_block(block: str) -> NDArray:
+        '''
+        Converts single block into data entries described in self.data
+
+        Parameters
+        ----------
+        block: str
+            String block extracted from file
+
+        Returns
+        -------
+        ndarray of floats
+            Keys described in self.data
+        '''
+
+        # Find number of orbitals from header of matrix
+        orb_list = re.findall(
+            r'Orbital[\sxyzd2f3\-]+\n',
+            block
+        )
+        n_orbs = len(orb_list[0].split()) - 1
+
+        rows = re.findall(
+            rf'((?:\s+\-?\d\.\d{{6}}){{{n_orbs:d}}})', # noqa
+            block
+        )
+
+        matrix = np.array([
+            [float(ve) for ve in row.split()]
+            for row in rows
+        ])
+
+        return matrix
+
+    @classmethod
+    def extract(cls, file_name: str | pathlib.Path) -> list[NDArray]: # noqa
+        '''
+        Convenience method which instantiates class, extracts blocks, and
+        returns processed datasets
+
+        Parameters
+        ----------
+        file_name: str | pathlib.Path
+            File to parse
+
+        Returns
+        -------
+        list[ndarray of floats]
+            Each entry contains processed data, as defined in cls.data
+        '''
+        _ext = cls()
+        _ext(file_name, process=True)
+        return _ext.data
+
+
 class AILFTOrbEnergyExtractor(extto.BetweenExtractor):
     '''
     Extracts AI-LFT orbital energies from Orca output file
@@ -2292,7 +2367,7 @@ class StructureInputExtractor(extto.BetweenExtractor):
 
         # Get labels and coordinates
         all_info = re.findall(
-            r'([A-Za-z]+\s*-?\d\.\d*\s+-?\d\.\d*\s+-?\d\.\d*)',
+            r'([A-Za-z]+\s*-?\d*\.\d*\s+-?\d*\.\d*\s+-?\d*\.\d*)',
             block
         )
 

{orto-1.14.0 → orto-1.14.1}/orto.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.14.0
+Version: 1.14.1
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

{orto-1.14.0 → orto-1.14.1}/setup.py

@@ -8,7 +8,7 @@ Please see the `orto` documentation for more details.
 
 # DO NOT EDIT THIS NUMBER!
 # IT IS AUTOMATICALLY CHANGED BY python-semantic-release
-__version__ = '1.14.0'
+__version__ = '1.14.1'
 
 setuptools.setup(
     name='orto',

orto-1.14.0/orto/__version__.py

@@ -1 +0,0 @@
-__version__ = '1.14.0'