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feat: Descriptor related additions #83

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merged 4 commits into from
Mar 23, 2023
Merged

feat: Descriptor related additions #83

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d850fde
feat: add CDK descriptors for COCONUT #78
Kohulan Mar 23, 2023
0e28187
feat: add All descriptor module for CDK and RDKit #79
Kohulan Mar 23, 2023
a6db174
feat: add function to COCONUT descriptors based on toolkit #80
Kohulan Mar 23, 2023
7e2e063
feat: Add table preview & JSON,HTML toggle #76,#77
Kohulan Mar 23, 2023
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187 changes: 187 additions & 0 deletions app/modules/alldescriptors.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,187 @@
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"
97 changes: 95 additions & 2 deletions app/modules/cdkmodules.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,7 @@
jar_path = pystow.ensure("STOUT-V2", url=sru_path)

startJVM("-ea", classpath=[cdkjar_path, srujar_path])
cdk_base = "org.openscience.cdk"


def getCDKSDG(smiles: str):
Expand All @@ -40,7 +41,6 @@ def getCDKSDG(smiles: str):
Returns:
mol object : mol object with CDK SDG.
"""
cdk_base = "org.openscience.cdk"
SCOB = JClass(cdk_base + ".silent.SilentChemObjectBuilder")
SmilesParser = JClass(cdk_base + ".smiles.SmilesParser")(SCOB.getInstance())
molecule = SmilesParser.parseSmiles(smiles)
Expand All @@ -59,7 +59,6 @@ def getSugarInfo(smiles: str):
Returns:
(boolean): True or false values whtehr or not molecule has sugar.
"""
cdk_base = "org.openscience.cdk"
SCOB = JClass(cdk_base + ".silent.SilentChemObjectBuilder")
SmilesParser = JClass(cdk_base + ".smiles.SmilesParser")(SCOB.getInstance())
molecule = SmilesParser.parseSmiles(smiles)
Expand Down Expand Up @@ -111,3 +110,97 @@ def getCDKSDGMol(smiles: str):
SDFW.flush()
mol_str = str(StringW.toString())
return mol_str


def getCDKDescriptors(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()
)
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.HBondAcceptorCountDescriptor"
)()
.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),
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,
)
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