`molprop-calc-v4`

Baseline calculator that turns a SMILES list into a wide, analysis-ready CSV with core physicochemical properties, CNS MPO, oral filters, Ro5/Ro3, med‑chem flags, toxicity alerts, metabolism soft spots, hERG/CYP heuristics, QED, SA/complexity, and developability indices.

calc-v4 calc-v5 prep analyze report sketch series picklists similarity featurize retro schema

Typical usage

Output format is inferred from the filename extension: .csv, .tsv, or .parquet.

# CSV
molprop-calc-v4 input.smi -o results.csv

# Parquet
molprop-calc-v4 input.smi -o results.parquet

# equivalent (script form)
python calculators/mpo_v4.py input.smi -o results.csv

What it outputs

A single CSV where each row is a compound and columns include both numeric descriptors (e.g., MolWt/LogP/TPSA) and interpretable flags/classes (e.g., CNS_MPO_Class, RO5_Violations, Tox_Risk, hERG_Risk, Dev_Score).

Ligand preparation (how the calculator standardizes structures)

The v4 calculator uses the same preparation chain as v5 when preparation is enabled: RDKit MolStandardize cleanup, parent-fragment selection (salt stripping), optional uncharging/reionization, optional canonical tautomer selection, then stereochemistry assignment for auditing. The standardized structure is recorded in Canonical_SMILES and the calculation structure is recorded in Calc_Canonical_SMILES. If you need an “options as sequences” view (including 3D/protomer choices), use the v5 tool page.

Common options

The most authoritative reference is molprop-calc-v4 --help. Common workflow knobs include pH/ionization, stereo handling, tautomer handling, and output filling.

# choose pH and ionization mode (heuristic or none)
molprop-calc-v4 input.smi -o results.csv --ph 7.4 --ionization heuristic
molprop-calc-v4 input.smi -o results.csv --ionization none

# stereochemistry handling
molprop-calc-v4 input.smi -o results.csv --stereo-mode keep
molprop-calc-v4 input.smi -o results.csv --stereo-mode strip
molprop-calc-v4 input.smi -o results.csv --stereo-mode enumerate --stereo-max 32

# missing values
touch results.csv
molprop-calc-v4 input.smi -o results.csv --fill-missing 0