tscode - pypi Package Compare versions

Comparing version 0.4.15 to 0.4.16

CHANGELOG.md

@@ -8,2 +8,6 @@ ## TSCoDe Changelog
 
+## 0.4.16 (April 2, 2024)
+- Solved bugfix in check_objects_compenetration.
+- Updated compenetration_check warning printouts, specifying the number of compenetrations found.
+
 ## 0.4.15 (March 23, 2024)
@@ -10,0 +14,0 @@ - Reinstated the only_refined option at the end of optimization_refining.

PKG-INFO

 Metadata-Version: 2.1
 Name: tscode
-Version: 0.4.15
+Version: 0.4.16
 Summary: Computational chemistry general purpose transition state builder and ensemble optimizer
@@ -43,2 +43,6 @@ Home-page: https://www.github.com/ntampellini/tscode
 
+## 0.4.16 (April 2, 2024)
+- Solved bugfix in check_objects_compenetration.
+- Updated compenetration_check warning printouts, specifying the number of compenetrations found.
+
 ## 0.4.15 (March 23, 2024)
@@ -45,0 +49,0 @@ - Reinstated the only_refined option at the end of optimization_refining.

tscode.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: tscode
-Version: 0.4.15
+Version: 0.4.16
 Summary: Computational chemistry general purpose transition state builder and ensemble optimizer
@@ -43,2 +43,6 @@ Home-page: https://www.github.com/ntampellini/tscode
 
+## 0.4.16 (April 2, 2024)
+- Solved bugfix in check_objects_compenetration.
+- Updated compenetration_check warning printouts, specifying the number of compenetrations found.
+
 ## 0.4.15 (March 23, 2024)
@@ -45,0 +49,0 @@ - Reinstated the only_refined option at the end of optimization_refining.

tscode/__main__.py

@@ -26,3 +26,3 @@ # coding=utf-8
 
-__version__ = '0.4.15'
+__version__ = '0.4.16'
 
@@ -29,0 +29,0 @@ if __name__ == '__main__':

tscode/numba_functions.py

@@ -50,2 +50,12 @@ # coding=utf-8
 @njit
+def count_clashes(coords):
+    '''
+    '''
+    return np.count_nonzero(
+                            (all_dists(coords,coords) < 0.5) & (
+                             all_dists(coords,coords) > 0)
+                            )
+
+
+@njit
 def compenetration_check(coords, ids=None, thresh=1.5, max_clashes=0) -> bool:
@@ -59,9 +69,7 @@ '''
     returns True if the molecule shows less than max_clashes
+    
     '''
 
     if ids is None:
-        return 0 if np.count_nonzero(
-                                     (all_dists(coords,coords) < 0.5) & (
-                                      all_dists(coords,coords) > 0)
-                                    ) > max_clashes else 1
+        return 0 if count_clashes(coords) > max_clashes else 1
 
@@ -68,0 +76,0 @@ if len(ids) == 2:

tscode/operators.py

@@ -454,3 +454,4 @@ # coding=utf-8
     logfunction(f'--> {filename}: Geometry optimization pre-mtd_search ({embedder.options.theory_level} via {embedder.options.calculator})')
-    logfunction(f'    {len(constrained_indices)} constraints applied{": "+constrained_indices if len(constrained_indices) > 0 else ""}')
+    return_char = "\n"
+    logfunction(f'    {len(constrained_indices)} constraints applied{": "+str(constrained_indices).replace(return_char, " ") if len(constrained_indices) > 0 else ""}')
     
@@ -491,2 +492,4 @@ for c, coords in enumerate(mol.atomcoords.copy()):
 
+    logfunction()
+
     # update mol and embedder graph after optimization 
@@ -493,0 +496,0 @@ mol.graph = graphize(mol.atomcoords[0], mol.atomnos)

tscode/utils.py

@@ -355,3 +355,3 @@ # coding=utf-8
 
-def scramble_check(TS_structure, TS_atomnos, excluded_atoms, mols_graphs, max_newbonds=0, logfunction=False, title=None) -> bool:
+def scramble_check(TS_structure, TS_atomnos, excluded_atoms, mols_graphs, max_newbonds=0, logfunction=None, title=None) -> bool:
     '''
@@ -358,0 +358,0 @@ Check if a multimolecular arrangement has scrambled during some optimization

Alert delta unavailable

Currently unable to show alert delta for PyPI packages.

Improved metrics

Total package byte prevSize

1373258

0.04%

Lines of code

18948

0.04%