MASSA-Algorithm 0.9.3__py3-none-any.whl → 0.9.5__py3-none-any.whl

MASSA_Algorithm/MASSAdescriptors.py

@@ -1,7 +1,8 @@
 import pandas as pd
 from rdkit.Chem import Descriptors
-from rdkit.Chem import rdMolDescriptors
-from rdkit.DataStructs import cDataStructs
+from rdkit.Chem import AllChem
+# from rdkit.Chem import rdMolDescriptors
+# from rdkit.DataStructs import cDataStructs
 
 def physicochemical_descriptors(file):
 	NumHAcceptors = {}
@@ -33,9 +34,25 @@ def physicochemical_descriptors(file):
 def atompairs_fingerprint(file):
 	FP_dict = {}
 	for i in file['molecules']:
-		FPasBitVect = rdMolDescriptors.GetHashedAtomPairFingerprintAsBitVect(i, nBits=1024) # Determine the fingerprint of the molecule using AtomPairs Fingerprint.
-		FPasBinary = cDataStructs.BitVectToText(FPasBitVect) # Convert fingerprint to text.
-		BinaryAsList = list(FPasBinary) # Each bit of fingerprint will be a string item of a list.
+		# Updated AtomPair Fingerprint (without count).
+		# To use AtomPairCount use the function (fpgen.GetCountFingerprintAsNumPy).
+		# 1) Determine the fingerprint generator using AtomPairs Fingerprint.
+		# 2) Generate the numpy array fingerprint using the generator.
+		# 3) Transform the np.array in list.
+		fpgen = AllChem.GetAtomPairGenerator(fpSize=1024)  # 1
+		FPasBinary = fpgen.GetFingerprintAsNumPy(i)  # 2
+		BinaryAsList = list(FPasBinary)  # 3
+
+		# DEPRECATED (by RDKit):
+		# 1) Determine the fingerprint of the molecule using AtomPairs Fingerprint.
+		# 2) Convert fingerprint to text.
+		# 3) Each bit of fingerprint will be a string item of a list.
+		# FPasBitVect = rdMolDescriptors.GetHashedAtomPairFingerprintAsBitVect(
+		# i, nBits=1024
+		# ) # 1
+		# FPasBinary = cDataStructs.BitVectToText(FPasBitVect) # 2
+		# BinaryAsList = list(FPasBinary) # 3
+
 		BinaryAsNewList = []
 		for a in BinaryAsList:
 			b = int(a) # Each bit of fingerprint will be a int item of a list.

MASSA_Algorithm/MASSAlogos.py

@@ -20,7 +20,7 @@ def initial_print():
        ██░░░▓▓▓▓░░░░░░░▓▓▓▓░░░░░░░▓▓▓▓░░░░█
      ██░░░░▓▓▓▓▓▓░░░░░▓▓▓▓▓▓░░░░░▓▓▓▓▓▓░░░░█                                 MASSA Algorithm:
    ████░░░░░▓▓▓▓░░░░░░░▓▓▓▓░░░░░░░▓▓▓▓░░░░░█████          Molecular data set sampling  —  Training-Test Separation
-  █▓▓▓███░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░███▓▓▓█                            Version: v. 0.9.3
+  █▓▓▓███░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░███▓▓▓█                            Version: v. 0.9.5
  █▒▓▓▒▒▒████░░░░░░░░░░░░░░░░░░░░░░░░░░░░████▒▒▓▓▒█
  ██▓▒▒▒▓▓▓▓██████████████████████████████▓▓▓▒▒▒▒▓█                Developed by: Gabriel Corrêa Veríssimo
  ██▒▒▒▓▓▒▒▒▒▓▓▒▒▒▒▓▓▒▒▒▒▒▒▒▒▒▒▒▒▓▓▒▒▒▒▓▓▒▒▒▓▓▒▒██                           LICENSE: AGPL-3.0

MASSA_Algorithm/MASSAopen_files.py

@@ -1,45 +1,294 @@
+import pandas as pd
 from rdkit.Chem import AllChem
 
+
+def find_smiles_column(columns):
+    """
+    Find the name of the "SMILES" column.
+
+    Args:
+        columns (list): receives a list with the name of pandas columns.
+
+    Raises:
+        ValueError: if there is no column named "SMILES" raises an error.
+
+    Returns:
+        column_name (str): returns the name of the "SMILES" column.
+    """
+    smiles_columns = []
+    smile_column = ""
+
+    for column in columns:
+        if "smiles" == column.lower():
+            smiles_columns.append(column)
+    if len(smiles_columns) > 1:
+        """
+        Warning: If there are more than one "SMILES" (case insensitive) column
+        the first one will be chosen.
+        """
+
+        print("Warning: There is more than one"
+              " column named 'smiles' (case insensitive)."
+              " The first one was chosen.")
+        smile_column = smiles_columns[0]
+        return smile_column
+    elif len(smiles_columns) == 1:
+        smile_column = smiles_columns[0]
+        return smile_column
+    else:
+        error = "Error: There is no column named 'SMILES'"
+        raise ValueError(error)
+
+
+def find_name_column(columns):
+    """
+    Find the name of the molecule name column.
+
+    Args:
+        columns (list): receives a list with the name of pandas columns.
+
+    Returns:
+        column_name (str): returns the name of the molecule name column.
+    """
+
+    for column in columns:
+        if "molecule name" == column.lower():
+            print((f"Found '{column}' column."
+                   " Using it to name the molecules."))
+            name_column = column
+            return name_column
+        elif "name" == column.lower():
+            print((f"Found '{column}' column."
+                   " Using it to name the molecules."))
+            name_column = column
+            return name_column
+        elif "molecule chembl id" == column.lower():
+            print((f"Found '{column}' column."
+                   " Using it to name the molecules."))
+            name_column = column
+            return name_column
+        elif "id" == column.lower():
+            print((f"Found '{column}' column."
+                   " Using it to name the molecules."))
+            name_column = column
+            return name_column
+        else:
+            print(("Unable to find a column with molecule names."
+                   " Using the index to name the molecules."))
+            name_column = "index"
+            return name_column
+
+
+def read_df_smiles(df, WriteLog):
+    """Reads an dataframe and returns a sanitized molecule supplier.
+
+    Args:
+        df_supplier (pd.DataFrame): pd.DataFrame object with SMILES.
+        WriteLog (file object): Log file object to write error messages.
+
+    Returns:
+        AllChem.SDMolSupplier like: Sanitized molecule supplier.
+    """
+    columns = list(df.columns)
+
+    smi_name_column = find_smiles_column(columns)
+    name_name_column = find_name_column(columns)
+
+    # name_name_column = "index"
+    columns.remove(smi_name_column)
+    columns.remove(name_name_column)
+
+    mols = []
+    for index, row in df.iterrows():
+        try:
+            mol = AllChem.MolFromSmiles(row[smi_name_column])
+            AllChem.rdmolops.SanitizeMol(mol)
+            if name_name_column == "index":
+                mol.SetProp("_Name", str(index))
+            else:
+                mol.SetProp("_Name", str(row[name_name_column]))
+            for c in columns:
+                mol.SetProp(c, str(row[c]))
+            mols.append(mol)
+        except Exception as e:
+            mols.append(None)
+            mol_of_error = str(mol.GetProp('_Name'))
+            error = str(e)
+            precomposed = (f"[Error while reading molecule: {error}. "
+                           f"Molecule name: {mol_of_error}].")
+            composed = precomposed+'\n'
+            print(precomposed)
+            WriteLog.write(composed)
+    if None in mols:
+        print("ERROR: Error while reading molecules. "
+              "Check the log.txt file for more information."
+              "\nERROR: Closing...")
+        exit()
+    return mols
+
+
+def read_EXCEL_smiles(file, WriteLog):
+    df_supplier = pd.read_excel(file)
+    mols_sanitized = read_df_smiles(df_supplier, WriteLog)
+    return mols_sanitized
+
+
+def read_CSV_smiles(file, WriteLog):
+    df_supplier = pd.read_csv(file, sep=",")
+    mols_sanitized = read_df_smiles(df_supplier)
+    return mols_sanitized
+
+
+def read_SDF(file, WriteLog):
+    """Reads an SDF file and returns a sanitized molecule supplier.
+
+    Args:
+        file (str): Path to the SDF file.
+        WriteLog (file object): Log file object to write error messages.
+
+    Returns:
+        AllChem.SDMolSupplier: Sanitized molecule supplier.
+    """
+    # Open the input file.
+    mols_supplier = AllChem.SDMolSupplier(file, sanitize=False)
+    mols = []
+    for mol in mols_supplier:
+        try:
+            mols.append(AllChem.rdmolops.SanitizeMol(mol))
+        except Exception as e:
+            mols.append(None)
+            mol_of_error = str(mol.GetProp('_Name'))
+            error = str(e)
+            precomposed = (f"[Error while reading molecule: {error}. "
+                           f"Molecule name: {mol_of_error}].")
+            composed = precomposed+'\n'
+            print(precomposed)
+            WriteLog.write(composed)
+    if None in mols:
+        print("ERROR: Error while reading molecules. "
+              "Check the log.txt file for more information."
+              "\nERROR: Closing...")
+        exit()
+    mols_sanitized = AllChem.SDMolSupplier(file, sanitize=True)
+    return mols_sanitized
+
+
+def remove_comment_line(data):
+    # Remove lines starting with '#'
+    return '\n'.join(
+        line for line in data.splitlines() if not line.strip().startswith('#')
+        )
+
+
+def mol2_properties(data):
+    data_split = data.split("@")
+    properties = {}
+    for d in data_split:
+        if "MOL_PROPERTY" in d:
+            list_values = d.split("\n")
+            p_name = list_values[1]
+            p_value = list_values[3]
+            properties[p_name] = p_value
+    return properties
+
+
+def read_MOL2(file, WriteLog):
+    """Reads an MOL2 file from Discovery Studio
+       and returns a sanitized molecule supplier.
+
+    Args:
+        file (str): Path to the MOL2 file.
+        WriteLog (file object): Log file object to write error messages.
+
+    Returns:
+        AllChem.SDMolSupplier like: Sanitized molecule supplier.
+    """
+    with open(file, 'r') as f:
+        mol_data = f.read()
+    # Split the file contents on the delimiter
+    # Remove comment lines
+    mol_data = remove_comment_line(mol_data)
+
+    # Alert of MOL2 limitations.
+    print("""
+ATTENTION: .mol2 file detected.
+MOL2 files have limited support for storing molecular properties.
+Therefore, the biological properties in this file may not be \
+detected or even stored.
+We do not recommend using a .mol2 file.
+However, we provide support for .mol2 files generated by \
+Discovery Studio Visualizer.
+The biological properties in these files follow the format below:
+
+@<SCITEGIC>MOL_PROPERTY
+Name_of_property (e.g., pIC50 value)
+Type_of_property (e.g., SciTegic.value.DoubleValue)
+Value_of_the_property (e.g., 8.100000)
+          """)
+
+    # Split the file contents based on a delimiter for each molecule.
+    mol_blocks = mol_data.split("@<TRIPOS>MOLECULE")
+
+    # List to store molecules.
+    mols = []
+
+    # Iterate over each block and reassemble the molecule data
+    for mol_block in mol_blocks:
+        if mol_block.strip():  # To avoid empty blocks
+            mol_block = "@<TRIPOS>MOLECULE" + mol_block
+            properties = mol2_properties(mol_block)
+            mol = AllChem.MolFromMol2Block(mol_block)
+            try:
+                AllChem.rdmolops.SanitizeMol(mol)
+                for p, p_value in properties.items():
+                    mol.SetProp(p, str(p_value))
+                mols.append(mol)
+            except Exception as e:
+                mols.append(None)
+                mol_of_error = str(mol.GetProp('_Name'))
+                error = str(e)
+                precomposed = (f"[Error while reading molecule: {error}. "
+                               f"Molecule name: {mol_of_error}].")
+                composed = precomposed+'\n'
+                print(precomposed)
+                WriteLog.write(composed)
+    if None in mols:
+        print("ERROR: Error while reading molecules. "
+              "Check the log.txt file for more information."
+              "\nERROR: Closing...")
+        exit()
+    return mols
+
+
 def read_molecules(file, WriteLog):
-	mols_supplier = AllChem.SDMolSupplier(file, sanitize=False) # Open the input file.
-	mols = []
-	for mol in mols_supplier:
-		try:
-			mols.append(AllChem.rdmolops.SanitizeMol(mol))
-		except Exception as e:
-			mols.append(None)
-			mol_of_error = str(mol.GetProp('_Name'))
-			error = str(e)
-			precomposed = '[Error while reading molecule: \"' + error +  '\". Molecule name: \"' +  mol_of_error + '\".]'
-			composed = precomposed+'\n'
-			print(precomposed)
-			WriteLog.write(composed)
-	if None in mols:
-		print('ERROR: Error while reading molecules. Check the log.txt file for more information. \nERROR: Closing...') # Print an error.
-		exit()
-	mols_supplier_sanitized = AllChem.SDMolSupplier(file, sanitize=True)
-	return mols_supplier_sanitized
-
-def error_check(file):
-	for i in file:
-		if i == None: # If any molecule is not able to be read: 
-			print('ERROR: Unable to read a molecule') # Print an error.
-			exit()
-		else:
-			pass
+    if file.endswith(".mol2"):
+        molecules = read_MOL2(file, WriteLog)
+    elif file.endswith(".sdf") or file.endswith(".mol"):
+        molecules = read_SDF(file, WriteLog)
+    elif file.endswith(".xlsx") or file.endswith(".xls"):
+        molecules = read_EXCEL_smiles(file, WriteLog)
+    elif file.endswith(".csv"):
+        molecules = read_CSV_smiles(file, WriteLog)
+    return molecules
+
 
 def hydrogen_add(file):
-	molsH = []
-	for i in file:
-		molsH.append(AllChem.AddHs(i, addCoords = True)) # Add hydrogens keeping 3D coordenates.
-	return molsH
-
-def get_sdf_property_names(file): # Extracting the property names from the ".sdf" input file.
-	sdf_property_names = []
-	for i in file:
-		for a in list(i.GetPropNames()):
-			sdf_property_names.append(a)
-	sdf_property_names = list(set(sdf_property_names))
-	if 'Name' in sdf_property_names: # Drop the molecule name from the property list.
-		sdf_property_names.remove('Name')
-	return sdf_property_names
+    molsH = []
+    for i in file:
+        i = AllChem.AddHs(i, addCoords=True)
+        molsH.append(i)
+        # Add hydrogens keeping 3D coordenates.
+    return molsH
+
+
+def get_sdf_property_names(file):
+    # Extracting the property names from the ".sdf" input file.
+    sdf_property_names = []
+    for i in file:
+        for a in list(i.GetPropNames()):
+            sdf_property_names.append(a)
+    sdf_property_names = list(set(sdf_property_names))
+    if 'Name' in sdf_property_names:
+        # Drop the molecule name from the property list.
+        sdf_property_names.remove('Name')
+    return sdf_property_names

{MASSA_Algorithm-0.9.3.dist-info → MASSA_Algorithm-0.9.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MASSA-Algorithm
-Version: 0.9.3
+Version: 0.9.5
 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
@@ -18,13 +18,13 @@ Classifier: Topic :: Scientific/Engineering :: Chemistry
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy <2.0
+Requires-Dist: numpy<2.0
 Requires-Dist: rdkit
 Requires-Dist: pandas
-Requires-Dist: matplotlib >=3.2
-Requires-Dist: scipy >=1.6
-Requires-Dist: scikit-learn >0.24
-Requires-Dist: kmodes >=0.10
+Requires-Dist: matplotlib>=3.2
+Requires-Dist: scipy>=1.6
+Requires-Dist: scikit-learn>0.24
+Requires-Dist: kmodes>=0.10
 
 # MASSA Algorithm
 MASSA Algorithm: A tool for separating data sets of molecules into training and test sets. Developed with the objective of preparing data sets for the generation of prediction models in cheminformatics.

{MASSA_Algorithm-0.9.3.dist-info → MASSA_Algorithm-0.9.5.dist-info}/RECORD

@@ -1,18 +1,18 @@
 MASSA_Algorithm/MASSA.py,sha256=PltTwmOsK-_q6MzmCxqY1AQMTXM-5XKB-3S6Yqe_VTo,9196
 MASSA_Algorithm/MASSAargs.py,sha256=MCOBlRm6sx6TUQHLwJrW-ktdSNiQltyFjyfJbS-1dVc,6777
 MASSA_Algorithm/MASSAcluster.py,sha256=orRK3rqEpH4j-C4LiS2rp3z4f1gM_rvsjgqiljvtlUI,11293
-MASSA_Algorithm/MASSAdescriptors.py,sha256=502A3NPxYMikXfSVsOz8u8p22hu5hgmZR5_4Am-8X5s,2141
+MASSA_Algorithm/MASSAdescriptors.py,sha256=3wd4MXfqTJU6w-sUolEhsCKIOCS2ye1tSkXvOXwFn2c,2716
 MASSA_Algorithm/MASSAextraction.py,sha256=bADEWtpEE5P0hg9O-8piD659GrPfHUeqyyaAYCWlsAs,4976
-MASSA_Algorithm/MASSAlogos.py,sha256=h12kNzcQFWNMIZM-S7Pt3KaDquwmjkuNFSv0wQ-QaIE,3528
+MASSA_Algorithm/MASSAlogos.py,sha256=CiSOgHodwBe8rNI2HbCWKkuQEr5MiwVc4tYIi-WuHO8,3528
 MASSA_Algorithm/MASSAmoloutput.py,sha256=LsyeCvIc9SPiFjVXTOQ3GVXDzhB9sc-MYWGGvIbOcwQ,2512
 MASSA_Algorithm/MASSAod.py,sha256=y0tizbYYtw34iJEf8c_5XPfQHHxF9RSRGjbmSZ0qRWk,487
-MASSA_Algorithm/MASSAopen_files.py,sha256=aPYCBNSmSPasL1wyuYvM7Nd1mTyGG9GMcyDdOAYQ3GE,1600
+MASSA_Algorithm/MASSAopen_files.py,sha256=wQWBYB7zfKei7XOceS9kqZMj8xGA8AbfIDlBptyBOjE,9918
 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-0.9.3.dist-info/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
-MASSA_Algorithm-0.9.3.dist-info/METADATA,sha256=IRbwh48vKeRgQGxbJn9iZLhovV8hPBocSzZ8anP2gO4,6542
-MASSA_Algorithm-0.9.3.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
-MASSA_Algorithm-0.9.3.dist-info/entry_points.txt,sha256=oMtqswy07Di-w2uIYAEvenBKl0ovsr9AYm_yxn6LGtU,63
-MASSA_Algorithm-0.9.3.dist-info/top_level.txt,sha256=IZyttJ20RSD8w9nAcaTHWAvkvxHV5FGaVGB7mDrw9Cc,16
-MASSA_Algorithm-0.9.3.dist-info/RECORD,,
+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-0.9.3.dist-info → MASSA_Algorithm-0.9.5.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.2)
+Generator: setuptools (75.3.0)
 Root-Is-Purelib: true
 Tag: py3-none-any