tools-only RDKit Molecular Descriptors Reference
Complete reference for molecular descriptors available in RDKit's Descriptors module.
Usage
from rdkit import Chem
from rdkit.Chem import Descriptors
mol = Chem.MolFromSmiles('CCO')
# Calculate individual descriptor
mw = Descriptors.MolWt(mol)
# Calculate all descriptors at once
all_desc = Descriptors.CalcMolDescriptors(mol)
Molecular Weight and Mass
MolWt
Average molecular weight of the molecule.
Descriptors.MolWt(mol)
ExactMolWt
Exact molecular weight using isotopic composition.
Descriptors.ExactMolWt(mol)
HeavyAtomMolWt
Average molecular weight ignoring hydrogens.
Descriptors.HeavyAtomMolWt(mol)
Lipophilicity
MolLogP
Wildman-Crippen LogP (octanol-water partition coefficient).
Descriptors.MolLogP(mol)
MolMR
Wildman-Crippen molar refractivity.
Descriptors.MolMR(mol)
Polar Surface Area
TPSA
Topological polar surface area (TPSA) based on fragment contributions.
Descriptors.TPSA(mol)
LabuteASA
Labute's Approximate Surface Area (ASA).
Descriptors.LabuteASA(mol)
Hydrogen Bonding
NumHDonors
Number of hydrogen bond donors (N-H and O-H).
Descriptors.NumHDonors(mol)
NumHAcceptors
Number of hydrogen bond acceptors (N and O).
Descriptors.NumHAcceptors(mol)
NOCount
Number of N and O atoms.
Descriptors.NOCount(mol)
NHOHCount
Number of N-H and O-H bonds.
Descriptors.NHOHCount(mol)
Atom Counts
HeavyAtomCount
Number of heavy atoms (non-hydrogen).
Descriptors.HeavyAtomCount(mol)
NumHeteroatoms
Number of heteroatoms (non-C and non-H).
Descriptors.NumHeteroatoms(mol)
NumValenceElectrons
Total number of valence electrons.
Descriptors.NumValenceElectrons(mol)
NumRadicalElectrons
Number of radical electrons.
Descriptors.NumRadicalElectrons(mol)
Ring Descriptors
RingCount
Number of rings.
Descriptors.RingCount(mol)
NumAromaticRings
Number of aromatic rings.
Descriptors.NumAromaticRings(mol)
NumSaturatedRings
Number of saturated rings.
Descriptors.NumSaturatedRings(mol)
NumAliphaticRings
Number of aliphatic (non-aromatic) rings.
Descriptors.NumAliphaticRings(mol)
NumAromaticCarbocycles
Number of aromatic carbocycles (rings with only carbons).
Descriptors.NumAromaticCarbocycles(mol)
NumAromaticHeterocycles
Number of aromatic heterocycles (rings with heteroatoms).
Descriptors.NumAromaticHeterocycles(mol)
NumSaturatedCarbocycles
Number of saturated carbocycles.
Descriptors.NumSaturatedCarbocycles(mol)
NumSaturatedHeterocycles
Number of saturated heterocycles.
Descriptors.NumSaturatedHeterocycles(mol)
NumAliphaticCarbocycles
Number of aliphatic carbocycles.
Descriptors.NumAliphaticCarbocycles(mol)
NumAliphaticHeterocycles
Number of aliphatic heterocycles.
Descriptors.NumAliphaticHeterocycles(mol)
Rotatable Bonds
NumRotatableBonds
Number of rotatable bonds (flexibility).
Descriptors.NumRotatableBonds(mol)
Aromatic Atoms
NumAromaticAtoms
Number of aromatic atoms.
Descriptors.NumAromaticAtoms(mol)
Fraction Descriptors
FractionCsp3
Fraction of carbons that are sp3 hybridized.
Descriptors.FractionCsp3(mol)
Complexity Descriptors
BertzCT
Bertz complexity index.
Descriptors.BertzCT(mol)
Ipc
Information content (complexity measure).
Descriptors.Ipc(mol)
Kappa Shape Indices
Molecular shape descriptors based on graph invariants.
Kappa1
First kappa shape index.
Descriptors.Kappa1(mol)
Kappa2
Second kappa shape index.
Descriptors.Kappa2(mol)
Kappa3
Third kappa shape index.
Descriptors.Kappa3(mol)
Chi Connectivity Indices
Molecular connectivity indices.
Chi0, Chi1, Chi2, Chi3, Chi4
Simple chi connectivity indices.
Descriptors.Chi0(mol)
Descriptors.Chi1(mol)
Descriptors.Chi2(mol)
Descriptors.Chi3(mol)
Descriptors.Chi4(mol)
Chi0n, Chi1n, Chi2n, Chi3n, Chi4n
Valence-modified chi connectivity indices.
Descriptors.Chi0n(mol)
Descriptors.Chi1n(mol)
Descriptors.Chi2n(mol)
Descriptors.Chi3n(mol)
Descriptors.Chi4n(mol)
Chi0v, Chi1v, Chi2v, Chi3v, Chi4v
Valence chi connectivity indices.
Descriptors.Chi0v(mol)
Descriptors.Chi1v(mol)
Descriptors.Chi2v(mol)
Descriptors.Chi3v(mol)
Descriptors.Chi4v(mol)
Hall-Kier Alpha
HallKierAlpha
Hall-Kier alpha value (molecular flexibility).
Descriptors.HallKierAlpha(mol)
Balaban's J Index
BalabanJ
Balaban's J index (branching descriptor).
Descriptors.BalabanJ(mol)
EState Indices
Electrotopological state indices.
MaxEStateIndex
Maximum E-state value.
Descriptors.MaxEStateIndex(mol)
MinEStateIndex
Minimum E-state value.
Descriptors.MinEStateIndex(mol)
MaxAbsEStateIndex
Maximum absolute E-state value.
Descriptors.MaxAbsEStateIndex(mol)
MinAbsEStateIndex
Minimum absolute E-state value.
Descriptors.MinAbsEStateIndex(mol)
Partial Charges
MaxPartialCharge
Maximum partial charge.
Descriptors.MaxPartialCharge(mol)
MinPartialCharge
Minimum partial charge.
Descriptors.MinPartialCharge(mol)
MaxAbsPartialCharge
Maximum absolute partial charge.
Descriptors.MaxAbsPartialCharge(mol)
MinAbsPartialCharge
Minimum absolute partial charge.
Descriptors.MinAbsPartialCharge(mol)
Fingerprint Density
Measures the density of molecular fingerprints.
FpDensityMorgan1
Morgan fingerprint density at radius 1.
Descriptors.FpDensityMorgan1(mol)
FpDensityMorgan2
Morgan fingerprint density at radius 2.
Descriptors.FpDensityMorgan2(mol)
FpDensityMorgan3
Morgan fingerprint density at radius 3.
Descriptors.FpDensityMorgan3(mol)
PEOE VSA Descriptors
Partial Equalization of Orbital Electronegativities (PEOE) VSA descriptors.
PEOE_VSA1 through PEOE_VSA14
MOE-type descriptors using partial charges and surface area contributions.
Descriptors.PEOE_VSA1(mol)
# ... through PEOE_VSA14
SMR VSA Descriptors
Molecular refractivity VSA descriptors.
SMR_VSA1 through SMR_VSA10
MOE-type descriptors using MR contributions and surface area.
Descriptors.SMR_VSA1(mol)
# ... through SMR_VSA10
SLogP VSA Descriptors
LogP VSA descriptors.
SLogP_VSA1 through SLogP_VSA12
MOE-type descriptors using LogP contributions and surface area.
Descriptors.SLogP_VSA1(mol)
# ... through SLogP_VSA12
EState VSA Descriptors
EState_VSA1 through EState_VSA11
MOE-type descriptors using E-state indices and surface area.
Descriptors.EState_VSA1(mol)
# ... through EState_VSA11
VSA Descriptors
van der Waals surface area descriptors.
VSA_EState1 through VSA_EState10
EState VSA descriptors.
Descriptors.VSA_EState1(mol)
# ... through VSA_EState10
BCUT Descriptors
Burden-CAS-University of Texas eigenvalue descriptors.
BCUT2D_MWHI
Highest eigenvalue of Burden matrix weighted by molecular weight.
Descriptors.BCUT2D_MWHI(mol)
BCUT2D_MWLOW
Lowest eigenvalue of Burden matrix weighted by molecular weight.
Descriptors.BCUT2D_MWLOW(mol)
BCUT2D_CHGHI
Highest eigenvalue weighted by partial charges.
Descriptors.BCUT2D_CHGHI(mol)
BCUT2D_CHGLO
Lowest eigenvalue weighted by partial charges.
Descriptors.BCUT2D_CHGLO(mol)
BCUT2D_LOGPHI
Highest eigenvalue weighted by LogP.
Descriptors.BCUT2D_LOGPHI(mol)
BCUT2D_LOGPLOW
Lowest eigenvalue weighted by LogP.
Descriptors.BCUT2D_LOGPLOW(mol)
BCUT2D_MRHI
Highest eigenvalue weighted by molar refractivity.
Descriptors.BCUT2D_MRHI(mol)
BCUT2D_MRLOW
Lowest eigenvalue weighted by molar refractivity.
Descriptors.BCUT2D_MRLOW(mol)
Autocorrelation Descriptors
AUTOCORR2D
2D autocorrelation descriptors (if enabled). Various autocorrelation indices measuring spatial distribution of properties.
MQN Descriptors
Molecular Quantum Numbers - 42 simple descriptors.
mqn1 through mqn42
Integer descriptors counting various molecular features.
# Access via CalcMolDescriptors
desc = Descriptors.CalcMolDescriptors(mol)
mqns = {k: v for k, v in desc.items() if k.startswith('mqn')}
QED
qed
Quantitative Estimate of Drug-likeness.
Descriptors.qed(mol)
Lipinski's Rule of Five
Check drug-likeness using Lipinski's criteria:
def lipinski_rule_of_five(mol):
mw = Descriptors.MolWt(mol) <= 500
logp = Descriptors.MolLogP(mol) <= 5
hbd = Descriptors.NumHDonors(mol) <= 5
hba = Descriptors.NumHAcceptors(mol) <= 10
return mw and logp and hbd and hba
Batch Descriptor Calculation
Calculate all descriptors at once:
from rdkit import Chem
from rdkit.Chem import Descriptors
mol = Chem.MolFromSmiles('CCO')
# Get all descriptors as dictionary
all_descriptors = Descriptors.CalcMolDescriptors(mol)
# Access specific descriptor
mw = all_descriptors['MolWt']
logp = all_descriptors['MolLogP']
# Get list of available descriptor names
from rdkit.Chem import Descriptors
descriptor_names = [desc[0] for desc in Descriptors._descList]
Descriptor Categories Summary
- Physicochemical: MolWt, MolLogP, MolMR, TPSA
- Topological: BertzCT, BalabanJ, Kappa indices
- Electronic: Partial charges, E-state indices
- Shape: Kappa indices, BCUT descriptors
- Connectivity: Chi indices
- 2D Fingerprints: FpDensity descriptors
- Atom counts: Heavy atoms, heteroatoms, rings
- Drug-likeness: QED, Lipinski parameters
- Flexibility: NumRotatableBonds, HallKierAlpha
- Surface area: VSA-based descriptors
Common Use Cases
Drug-likeness Screening
def screen_druglikeness(mol):
return {
'MW': Descriptors.MolWt(mol),
'LogP': Descriptors.MolLogP(mol),
'HBD': Descriptors.NumHDonors(mol),
'HBA': Descriptors.NumHAcceptors(mol),
'TPSA': Descriptors.TPSA(mol),
'RotBonds': Descriptors.NumRotatableBonds(mol),
'AromaticRings': Descriptors.NumAromaticRings(mol),
'QED': Descriptors.qed(mol)
}
Lead-like Filtering
def is_leadlike(mol):
mw = 250 <= Descriptors.MolWt(mol) <= 350
logp = Descriptors.MolLogP(mol) <= 3.5
rot_bonds = Descriptors.NumRotatableBonds(mol) <= 7
return mw and logp and rot_bonds
Diversity Analysis
def molecular_complexity(mol):
return {
'BertzCT': Descriptors.BertzCT(mol),
'NumRings': Descriptors.RingCount(mol),
'NumRotBonds': Descriptors.NumRotatableBonds(mol),
'FractionCsp3': Descriptors.FractionCsp3(mol),
'NumAromaticRings': Descriptors.NumAromaticRings(mol)
}
Tips
- Use batch calculation for multiple descriptors to avoid redundant computations
- Check for None - some descriptors may return None for invalid molecules
- Normalize descriptors for machine learning applications
- Select relevant descriptors - not all 200+ descriptors are useful for every task
- Consider 3D descriptors separately (require 3D coordinates)
- Validate ranges - check if descriptor values are in expected ranges