feat: add All descriptor module for CDK and RDKit #79

app/modules/alldescriptors.py

@@ -0,0 +1,182 @@
+from rdkit.Chem import Descriptors, QED, Lipinski, rdMolDescriptors, rdmolops
+from app.modules.rdkitmodules import checkRo5Violations, checkSMILES
+from app.modules.cdkmodules import getCDKSDG, JClass, cdk_base
+
+
+def getAllRDKitDescriptors(smiles: str):
+    """Take an input SMILES and generate a selected set of molecular
+    descriptors generated using RDKit as a list.
+    Args (str): SMILES string
+    Returns (list): a list of calculated descriptors
+    """
+    mol = checkSMILES(smiles)
+    if mol:
+        AtomC = rdMolDescriptors.CalcNumAtoms(mol)
+        BondC = mol.GetNumBonds()
+        HeavyAtomsC = rdMolDescriptors.CalcNumHeavyAtoms(mol)
+        MolWt = "%.2f" % Descriptors.MolWt(mol)
+        ExactMolWt = "%.2f" % Descriptors.ExactMolWt(mol)
+        ALogP = "%.2f" % QED.properties(mol).ALOGP
+        NumRotatableBonds = rdMolDescriptors.CalcNumRotatableBonds(mol)
+        PSA = "%.2f" % rdMolDescriptors.CalcTPSA(mol)
+        HBA = Descriptors.NumHAcceptors(mol)
+        HBD = Descriptors.NumHDonors(mol)
+        Lipinski_HBA = Lipinski.NumHAcceptors(mol)
+        Lipinski_HBD = Lipinski.NumHDonors(mol)
+        Ro5Violations = checkRo5Violations(mol)
+        AromaticRings = rdMolDescriptors.CalcNumAromaticRings(mol)
+        QEDWeighted = "%.2f" % QED.qed(mol)
+        FormalCharge = "%.2f" % rdmolops.GetFormalCharge(mol)
+        fsp3 = "%.3f" % rdMolDescriptors.CalcFractionCSP3(mol)
+        NumRings = rdMolDescriptors.CalcNumRings(mol)
+        return (
+            AtomC,
+            BondC,
+            HeavyAtomsC,
+            MolWt,
+            ExactMolWt,
+            ALogP,
+            NumRotatableBonds,
+            PSA,
+            HBA,
+            HBD,
+            Lipinski_HBA,
+            Lipinski_HBD,
+            Ro5Violations,
+            AromaticRings,
+            QEDWeighted,
+            FormalCharge,
+            fsp3,
+            NumRings,
+        )
+    else:
+        return "Error reading SMILES string, check again."
+
+
+def getAllCDKDescriptors(smiles: str):
+    """Take an input SMILES and generate a selected set of molecular
+    descriptors generated using CDK as a list.
+    Args (str): SMILES string
+    Returns (list): a list of calculated descriptors
+    """
+    Mol = getCDKSDG(smiles)
+    if Mol:
+        AtomCountDescriptor = (
+            JClass(cdk_base + ".qsar.descriptors.molecular.AtomCountDescriptor")()
+            .calculate(Mol)
+            .getValue()
+        )
+        BondCountDescriptor = JClass(cdk_base+".qsar.descriptors.molecular.BondCountDescriptor")().calculate(Mol).getValue()
+        HeavyAtomsC = Mol.getAtomCount()
+        WeightDescriptor = (
+            JClass(cdk_base + ".qsar.descriptors.molecular.WeightDescriptor")()
+            .calculate(Mol)
+            .getValue().toString()
+        )
+        TotalExactMass = JClass(
+            cdk_base + ".tools.manipulator.AtomContainerManipulator"
+        ).getTotalExactMass(Mol)
+        ALogP = (
+            JClass(cdk_base + ".qsar.descriptors.molecular.ALOGPDescriptor")()
+            .calculate(Mol)
+            .getValue()
+        )
+        NumRotatableBonds = (
+            JClass(
+                cdk_base + ".qsar.descriptors.molecular.RotatableBondsCountDescriptor"
+            )()
+            .calculate(Mol)
+            .getValue()
+        )
+        TPSADescriptor = (
+            JClass(cdk_base + ".qsar.descriptors.molecular.TPSADescriptor")()
+            .calculate(Mol)
+            .getValue().toString()
+        )
+        HBondAcceptorCountDescriptor = (
+            JClass(
+                cdk_base + ".qsar.descriptors.molecular.HBondAcceptorCountDescriptor"
+            )()
+            .calculate(Mol)
+            .getValue()
+        )
+        HBondDonorCountDescriptor = (
+            JClass(
+                cdk_base + ".qsar.descriptors.molecular.HBondDonorCountDescriptor"
+            )()
+            .calculate(Mol)
+            .getValue()
+        )
+        RuleOfFiveDescriptor = (
+            JClass(cdk_base + ".qsar.descriptors.molecular.RuleOfFiveDescriptor")()
+            .calculate(Mol)
+            .getValue()
+        )
+        AromaticRings = None
+        QEDWeighted = None
+        FormalCharge = JClass(
+            cdk_base + ".tools.manipulator.AtomContainerManipulator"
+        ).getTotalFormalCharge(Mol)
+        FractionalCSP3Descriptor = (
+            JClass(cdk_base + ".qsar.descriptors.molecular.FractionalCSP3Descriptor")()
+            .calculate(Mol)
+            .getValue().toString()
+        )
+        NumRings = JClass(cdk_base + ".graph.Cycles").mcb(Mol).numberOfCycles()
+
+        return (
+            str(AtomCountDescriptor),
+            str(BondCountDescriptor),
+            HeavyAtomsC,
+            "{:.2f}".format(float(str(WeightDescriptor))),
+            "{:.2f}".format(float(str(TotalExactMass))),
+            "{:.2f}".format(float(str(ALogP).split(",")[0])),
+            str(NumRotatableBonds),
+            "{:.2f}".format(float(str(TPSADescriptor))),
+            str(HBondAcceptorCountDescriptor),
+            str(HBondDonorCountDescriptor),
+            str(HBondAcceptorCountDescriptor),
+            str(HBondDonorCountDescriptor),
+            str(RuleOfFiveDescriptor),
+            str(AromaticRings),
+            str(QEDWeighted),
+            FormalCharge,
+            "{:.2f}".format(float(str(FractionalCSP3Descriptor))),
+            NumRings,
+        )
+
+
+def getCDKRDKitcombinedDescriptors(smiles: str):
+    """Take an input SMILES and generates a selected set of molecular
+    descriptors using CDK and RDKit and returns as a dictionary.
+    Args (str): SMILES string.
+    Returns (dist): a dictionary of calculated descriptors.
+    """
+    RDKitDescriptors = getAllRDKitDescriptors(smiles)
+    CDKDescriptors = getAllCDKDescriptors(smiles)
+    AllDescriptors = {
+        "Atom count",
+        "Bond count",
+        "Heavy atom count",
+        "Molecular weight",
+        "Exact molecular weight",
+        "ALogP",
+        "Rotatable bond count",
+        "Topological polar surface area",
+        "Hydrogen bond acceptors",
+        "Hydrogen bond donors",
+        "Hydrogen bond acceptors(Lipinski)",
+        "Hydrogen bond donors(Lipinski)",
+        "Lipinski's rule of five violations",
+        "Aromatic rings count",
+        "QED drug likeliness",
+        "Formal Charge",
+        "FractionCSP3",
+        "Number of Minimal Rings",
+    }
+
+    if len(AllDescriptors) == len(RDKitDescriptors) == len(CDKDescriptors):
+        combinedDict = dict(zip(AllDescriptors, zip(RDKitDescriptors, CDKDescriptors)))
+        return combinedDict
+    else:
+        return "Error dictionary lenth invalid"