MASSA-Algorithm 0.9.5__py3-none-any.whl → 0.9.6__py3-none-any.whl

MASSA_Algorithm/MASSAlogos.py

@@ -20,7 +20,7 @@ def initial_print():
        ██░░░▓▓▓▓░░░░░░░▓▓▓▓░░░░░░░▓▓▓▓░░░░█
      ██░░░░▓▓▓▓▓▓░░░░░▓▓▓▓▓▓░░░░░▓▓▓▓▓▓░░░░█                                 MASSA Algorithm:
    ████░░░░░▓▓▓▓░░░░░░░▓▓▓▓░░░░░░░▓▓▓▓░░░░░█████          Molecular data set sampling  —  Training-Test Separation
-  █▓▓▓███░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░███▓▓▓█                            Version: v. 0.9.5
+  █▓▓▓███░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░███▓▓▓█                            Version: v. 0.9.6
  █▒▓▓▒▒▒████░░░░░░░░░░░░░░░░░░░░░░░░░░░░████▒▒▓▓▒█
  ██▓▒▒▒▓▓▓▓██████████████████████████████▓▓▓▒▒▒▒▓█                Developed by: Gabriel Corrêa Veríssimo
  ██▒▒▒▓▓▒▒▒▒▓▓▒▒▒▒▓▓▒▒▒▒▒▒▒▒▒▒▒▒▓▓▒▒▒▒▓▓▒▒▒▓▓▒▒██                           LICENSE: AGPL-3.0

MASSA_Algorithm/MASSAopen_files.py

@@ -135,7 +135,7 @@ def read_EXCEL_smiles(file, WriteLog):
 
 def read_CSV_smiles(file, WriteLog):
     df_supplier = pd.read_csv(file, sep=",")
-    mols_sanitized = read_df_smiles(df_supplier)
+    mols_sanitized = read_df_smiles(df_supplier, WriteLog)
     return mols_sanitized
 
 

{MASSA_Algorithm-0.9.5.dist-info → MASSA_Algorithm-0.9.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MASSA-Algorithm
-Version: 0.9.5
+Version: 0.9.6
 Summary: MASSA Algorithm is a Python package to separate data sets of molecules into training and test sets, considering the diversity of structural, physicochemical and biological characteristics of these molecules.
 Home-page: https://github.com/gcverissimo/MASSA_Algorithm
 Author: Gabriel Corrêa Veríssimo
@@ -60,7 +60,18 @@ Once installed, the program can be run directly from the command line:
 MASSA_Algorithm -i <input_file>.sdf -o <output_file>.sdf
 ```
 
-A list of optional arguments include:
+Required arguments:
+* **Input file**: ```-i``` or ```--input```.
+    * MASSA Algorithm accepts input files in the formats: .sdf, .mol, .mol2, .xlsx, .xls, and .csv. However, the .sdf format is preferred. Notes:
+        * .mol2 files have limitations in storing molecular properties and follow different saving patterns. Due to this, we only support .mol2 files that are generated by Discovery Studio Visualizer.
+        * For .xlsx, .xls, and .csv:
+            * MASSA will look for a column with smiles in the name and use it as the source of input molecules.
+            * MASSA will look for a column with one of the following names in the priority order: Molecule name, Name, Molecule ChEMBL ID, or ID. If none of these columns are found, it will use the molecule index.
+* **Output file**: ```-o``` or ```--output```.
+    * Enter the output file name or file path. Image files will be saved to a folder within the same directory as the output file.
+    * It is highly recommended to use an .sdf file to avoid errors.
+
+Optional arguments include:
 * **Percentage of molecules in training set**: ```-p``` or ```--percentage_of_training```.
     * Percentage of molecules in training set. Must be a number from 0 to 1.
     * Default = 0.8.
@@ -68,11 +79,11 @@ A list of optional arguments include:
     * Number of biological activities that will be used to separate the set into training and test.
     * Default = 1.
 * **Name of biological activities for separation**: ```-s``` or ```--the_biological_activities```.
-    * Enter a list with the names of biological activities separated by commas and no spaces.
+    * The biological activity(ies) or other y-property(ies) used for QSAR or machine learning modeling. The algorithm can handle one or more properties. Enter a list with the names of biological activities separated by commas and no spaces. These properties must be represented as either integers or floating-point numbers. If your dataset is represented in classes (e.g., active or inactive; soluble, partially soluble, or insoluble), you should represent them as integers (e.g., 0 or 1; 1, 2, or 3).
     * Example: ```MASSA_Algorithm -i <input_file>.sdf -o <output_file>.sdf -s pIC50,pMIC```.
     * Default = If not entered directly on the command line, it will be requested during algorithm execution.
 * **Number of principal components in PCA**: ```-n``` or ```--number_of_PCs```.
-    * Defines the number of principal components to reduce the dimensionality of variables related to biological, physicochemical and structural domains. If the value is a decimal between 0 and 1, the number of principal components is what justifies for (```<input number>```* 100)% of the variance. If the value is greater than 1, the number of PCs will be exactly the input integer, but PAY ATTENTION:
+    * Defines the number of principal components to reduce the dimensionality of variables related to biological, physicochemical and structural domains. If the value is a decimal between 0 and 1, the number of principal components is what explains for (```<input number>```* 100)% of the variance. If the value is greater than 1, the number of PCs will be exactly the input integer, but PAY ATTENTION:
 
         1) If the number of PCs is an integer and equal to or greater than the number of physicochemical properties (7), the PCA step will be bypassed for this domain.
         2) The same for the biological domain.

{MASSA_Algorithm-0.9.5.dist-info → MASSA_Algorithm-0.9.6.dist-info}/RECORD

@@ -3,16 +3,16 @@ MASSA_Algorithm/MASSAargs.py,sha256=MCOBlRm6sx6TUQHLwJrW-ktdSNiQltyFjyfJbS-1dVc,
 MASSA_Algorithm/MASSAcluster.py,sha256=orRK3rqEpH4j-C4LiS2rp3z4f1gM_rvsjgqiljvtlUI,11293
 MASSA_Algorithm/MASSAdescriptors.py,sha256=3wd4MXfqTJU6w-sUolEhsCKIOCS2ye1tSkXvOXwFn2c,2716
 MASSA_Algorithm/MASSAextraction.py,sha256=bADEWtpEE5P0hg9O-8piD659GrPfHUeqyyaAYCWlsAs,4976
-MASSA_Algorithm/MASSAlogos.py,sha256=CiSOgHodwBe8rNI2HbCWKkuQEr5MiwVc4tYIi-WuHO8,3528
+MASSA_Algorithm/MASSAlogos.py,sha256=xl1EI77Y4eU-QUWjAgZlRaFTHY-ufAUSaIc9oXaYyXM,3528
 MASSA_Algorithm/MASSAmoloutput.py,sha256=LsyeCvIc9SPiFjVXTOQ3GVXDzhB9sc-MYWGGvIbOcwQ,2512
 MASSA_Algorithm/MASSAod.py,sha256=y0tizbYYtw34iJEf8c_5XPfQHHxF9RSRGjbmSZ0qRWk,487
-MASSA_Algorithm/MASSAopen_files.py,sha256=wQWBYB7zfKei7XOceS9kqZMj8xGA8AbfIDlBptyBOjE,9918
+MASSA_Algorithm/MASSAopen_files.py,sha256=U6koZg-IBVRUasl1Htl6S3CjZcOmJ-lKx-Ud-LXz4ws,9928
 MASSA_Algorithm/MASSApreparation.py,sha256=I4JpddMfBX1btYomNI5vflN1gyllJKodbQgtYf9imWY,3208
 MASSA_Algorithm/MASSAsplit.py,sha256=qsZgvXAat4UleaF0Qaa4Y-CtsMQU_NaIJvK-ypOzkbw,5330
 MASSA_Algorithm/__init__.py,sha256=yY3Tbs-t4HSl4I0Ev0RcHMnHU7SwljlWRveiRJkeCB8,10
-MASSA_Algorithm-0.9.5.dist-info/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
-MASSA_Algorithm-0.9.5.dist-info/METADATA,sha256=pSx2OtrWq7RG_jLiXhFaBKoSDLuVenQtjVsLTfZUTnc,6537
-MASSA_Algorithm-0.9.5.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
-MASSA_Algorithm-0.9.5.dist-info/entry_points.txt,sha256=oMtqswy07Di-w2uIYAEvenBKl0ovsr9AYm_yxn6LGtU,63
-MASSA_Algorithm-0.9.5.dist-info/top_level.txt,sha256=IZyttJ20RSD8w9nAcaTHWAvkvxHV5FGaVGB7mDrw9Cc,16
-MASSA_Algorithm-0.9.5.dist-info/RECORD,,
+MASSA_Algorithm-0.9.6.dist-info/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
+MASSA_Algorithm-0.9.6.dist-info/METADATA,sha256=pGGMRnNlvEcZg3JzCoz027iZ7PBOwqEQsKAymKsErho,7967
+MASSA_Algorithm-0.9.6.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+MASSA_Algorithm-0.9.6.dist-info/entry_points.txt,sha256=oMtqswy07Di-w2uIYAEvenBKl0ovsr9AYm_yxn6LGtU,63
+MASSA_Algorithm-0.9.6.dist-info/top_level.txt,sha256=IZyttJ20RSD8w9nAcaTHWAvkvxHV5FGaVGB7mDrw9Cc,16
+MASSA_Algorithm-0.9.6.dist-info/RECORD,,

{MASSA_Algorithm-0.9.5.dist-info → MASSA_Algorithm-0.9.6.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.3.0)
+Generator: setuptools (75.6.0)
 Root-Is-Purelib: true
 Tag: py3-none-any