adds brief description to the pypi package, corrects naming, updates …

…version

HSR.egg-info/PKG-INFO

@@ -1,6 +1,7 @@
 Metadata-Version: 2.1
 Name: hsr
-Version: 0.1.11
+Version: 0.1.13
+Summary: Hypershape recognition (HSR): a general framework for moment-based similarity measures
 Author: Marcello Costamagna
 License: AGPL-3.0
 Description-Content-Type: text/markdown
@@ -9,7 +10,7 @@ Requires-Dist: numpy
 Requires-Dist: scipy
 Requires-Dist: rdkit
 
-# Hyper Shape recognition (HSR): a general framework for moment-based similarity measures
+# Hypershape recognition (HSR): a general framework for moment-based similarity measures
 
  HSR is a versatile, moment-based similarity measure tailored for three-dimensional (3D) chemical representations annotated with atomic features. It enhances the robustness and versatility of the Ultrafast Shape Recognition (USR) method by incorporating multidimensional features for each atom, such as protons, neutrons, and formal charges.
 

ReadME.md

@@ -1,4 +1,4 @@
-# Hyper Shape recognition (HSR): a general framework for moment-based similarity measures
+# Hypershape recognition (HSR): a general framework for moment-based similarity measures
 
  HSR is a versatile, moment-based similarity measure tailored for three-dimensional (3D) chemical representations annotated with atomic features. It enhances the robustness and versatility of the Ultrafast Shape Recognition (USR) method by incorporating multidimensional features for each atom, such as protons, neutrons, and formal charges.
 

build/lib/hsr/hsr_cli.py

@@ -33,8 +33,9 @@ def parse_dict_or_none(argument):
     parser.add_argument('-chirality', action='store_true', help='Consider chirality')
     parser.add_argument('-features', default='DEFAULT_FEATURES', type=parse_dict_or_none,
                         help="Defines the use of additional features for the comparison. "
-                             "Available options: '6D' for 6D representation (default), 'None' for only spatial coordinates. "
-                             "For different features, it is necessary to define new ones in the package.")
+                             "Available options: DEFAULT_FEATURES for 6D representation (default), 'None' for only spatial coordinates, and"
+                             "PROTON_FEATURES for 4D representation including proton feature besides spatial coordinates. "
+                             "For different features, it is necessary to define new ones in the package (see documentation).")
     parser.add_argument('-v', '--version', action='version', version=f'%(prog)s {__version__}',
                         help='Show the version of the HSR package and exit.')
 

build/lib/hsr/similarity.py

@@ -141,7 +141,7 @@ def compute_similarity_from_ndarray(mol1_nd: np.array, mol2_nd: np.array, scalin
         The computed similarity score between the two molecules.
     """
     distance_score = compute_distance_from_ndarray(mol1_nd, mol2_nd, scaling=scaling, chirality=chirality)
-    similarity_score = calculate_similarity_from_distance(distance_score, mol1_nd.shape[1])
+    similarity_score = calculate_similarity_from_distance(distance_score, (mol1_nd.shape[1]+1)*3)
     return similarity_score
 
 def compute_distance(mol1, mol2, features=DEFAULT_FEATURES, scaling='matrix', removeHs=False, chirality=False):

build/lib/hsr/version.py

@@ -4,4 +4,4 @@
 # See the LICENSE file for more details.
 
 # HSR version
-__version__ = "0.1.11"
+__version__ = "0.1.13"

hsr/version.py

@@ -4,4 +4,4 @@
 # See the LICENSE file for more details.
 
 # HSR version
-__version__ = "0.1.11"
+__version__ = "0.1.13"

setup.py

@@ -20,6 +20,7 @@ def read_version():
     version=__version__,
     author="Marcello Costamagna", 
     license="AGPL-3.0",
+    description="Hypershape recognition (HSR): a general framework for moment-based similarity measures",
     long_description=long_description,
     long_description_content_type='text/markdown',
     packages=find_packages(exclude=["tests", "tests.*"]),