Advanced cheminformatics agent for 3D molecular analysis, pharmacophore mapping, format conversion, RECAP fragmentation, and stereoisomer enumeration. The "senior cheminformatician" upgrade to Chemistry Query. Use for 3D conformer generation/ensembles (ETKDG + MMFF/UFF), pharmacophore feature extraction and fingerprints, molecular format conversion (SMILES/SDF/MOL/InChI/PDB/XYZ), RECAP retrosynthetic fragmentation for library design, stereoisomer enumeration (R/S, E/Z), and cheminformatics profiling. Chains from chemistry-query (receives SMILES) and feeds into pharmacology, catalyst-design, ip-expansion. Triggers on conformer, 3D structure, pharmacophore, SDF, MOL file, format conversion, RECAP, fragmentation, stereoisomer, chirality, enantiomer, cheminformatics, library design, building blocks, docking prep.
Advanced cheminformatics toolkit for 3D molecular analysis and drug development workflows. Extends Chemistry Query (which handles 2D lookup/properties/visualization) with predictive and structural capabilities that require 3D reasoning.
Chemistry Query = "What is this molecule?" (2D, lookup, descriptors) Cheminformatics = "What can this molecule become?" (3D, conformers, pharmacophores, fragments, stereoisomers)
scripts/conformer_gen.py3D conformer ensemble generation using ETKDG with MMFF/UFF optimization.
--smiles <SMILES> --action <generate|ensemble|best> [--num_confs N] [--optimize mmff|uff|none] [--energy_window F] [--prune_rms F] [--output file.sdf]
| Action | Description |
|---|---|
| generate |
| Generate N conformers with energies and RMSD matrix |
| ensemble | Same as generate + write SDF file |
| best | Find lowest-energy conformer with 3D coordinates |
python scripts/conformer_gen.py --smiles "CC(=O)Oc1ccccc1C(=O)O" --action generate --num_confs 20
python scripts/conformer_gen.py --smiles "CCO" --action best --output best.sdf
python scripts/conformer_gen.py --smiles "c1ccccc1" --action ensemble --num_confs 50 --output benzene_confs.sdf
Output includes: conformer energies (kcal/mol), relative energies, convergence status, RMSD matrix (top 20), SDF file.
scripts/format_converter.pyConvert between molecular file formats.
--smiles <SMILES> | --input <file> --to <format> [--output file] [--batch] [--name label]
Supported formats: smiles, sdf, mol, inchi, inchikey, pdb, xyz
python scripts/format_converter.py --smiles "CCO" --to sdf --output ethanol.sdf
python scripts/format_converter.py --smiles "CCO" --to inchi
python scripts/format_converter.py --input mols.sdf --to smiles --batch
python scripts/format_converter.py --smiles "CCO" --to pdb --output ethanol.pdb
Batch mode reads multi-molecule SDF files. All 3D formats auto-generate and optimize conformers.
scripts/pharmacophore.pyPharmacophore feature extraction, fingerprints, and comparison.
--smiles <SMILES> --action <features|fingerprint|compare|map> [--target_smiles "smi1,smi2"] [--output file.png]
| Action | Description |
|---|---|
| features | Extract 3D pharmacophoric features (HBD, HBA, aromatic, hydrophobic, ionizable) with coordinates |
| fingerprint | Generate Gobbi 2D pharmacophore fingerprint |
| compare | Pairwise pharmacophore similarity (Tanimoto) across multiple molecules |
| map | Generate color-coded pharmacophore PNG (green=donor, red=acceptor, yellow=aromatic, blue=hydrophobic) |
python scripts/pharmacophore.py --smiles "CC(=O)Oc1ccccc1C(=O)O" --action features
python scripts/pharmacophore.py --smiles "CC(=O)Oc1ccccc1C(=O)O" --action map --output pharm.png
python scripts/pharmacophore.py --target_smiles "CCO,CC(=O)O,c1ccccc1" --action compare
scripts/recap_fragment.pyRECAP (Retrosynthetic Combinatorial Analysis Procedure) fragmentation at synthetically accessible bonds (amide, ester, amine, urea, ether, olefin, sulfonamide, etc.).
--smiles <SMILES> --action <fragment|leaves|tree|common_fragments> [--target_smiles "smi1,smi2"] [--max_depth N]
| Action | Description |
|---|---|
| fragment | All RECAP fragments with metadata |
| leaves | Terminal building blocks only (for library design) |
| tree | Hierarchical decomposition tree |
| common_fragments | Shared fragments across multiple molecules (common scaffolds) |
python scripts/recap_fragment.py --smiles "CC(=O)Nc1ccc(O)cc1" --action fragment
python scripts/recap_fragment.py --smiles "CC(=O)Nc1ccc(O)cc1" --action leaves
python scripts/recap_fragment.py --target_smiles "CC(=O)Nc1ccc(O)cc1,CC(=O)Nc1ccccc1" --action common_fragments
Use case: Leaf fragments → building blocks for combinatorial library enumeration. Common fragments across a compound series → shared pharmacophoric scaffolds.
scripts/stereoisomers.pyStereoisomer enumeration and analysis (chiral centers R/S, double bond E/Z).
--smiles <SMILES> --action <enumerate|analyze|compare> [--max_isomers N] [--only_unassigned]
| Action | Description |
|---|---|
| enumerate | Generate all stereoisomers with configurations |
| analyze | Count chiral centers and stereo bonds without enumerating |
| compare | Compare properties across all stereoisomers (drug dev relevance) |
python scripts/stereoisomers.py --smiles "C(F)(Cl)Br" --action enumerate
python scripts/stereoisomers.py --smiles "CC=CC" --action analyze
python scripts/stereoisomers.py --smiles "OC(F)(Cl)Br" --action compare
Drug relevance: FDA requires characterization of each stereoisomer for chiral drug candidates. Flags meso forms and provides R/S assignments.
scripts/chain_entry.pyStandard agent chain interface. Runs all 5 modules on a SMILES input.
python scripts/chain_entry.py --input-json '{"smiles": "CC(=O)Nc1ccc(O)cc1", "context": "user"}'
python scripts/chain_entry.py --input-json '{"smiles": "CCO", "actions": ["conformers", "pharmacophore"]}'
Input JSON fields:
smiles (required): Input SMILEScontext: Chain context stringactions: Array to run subset — ["conformers", "pharmacophore", "recap", "stereoisomers", "formats"]output_dir: Directory for SDF/PNG output filesOutput schema:
{
"agent": "cheminformatics",
"version": "1.0.0",
"smiles": "<canonical>",
"status": "success|error",
"report": {
"conformers": {...},
"pharmacophore": {...},
"recap": {...},
"stereoisomers": {...},
"formats": {...}
},
"risks": [],
"warnings": [],
"viz": ["path/to/file.sdf", "path/to/pharmacophore_map.png"],
"recommend_next": ["pharmacology", "catalyst-design", "ip-expansion"],
"confidence": 0.9,
"timestamp": "ISO8601"
}
| From | To | What passes |
|---|---|---|
| Chemistry Query → | Cheminformatics | SMILES + basic properties |
| Cheminformatics → | Pharmacology | SMILES + pharmacophore profile for ADME context |
| Cheminformatics → | Catalyst Design | 3D conformer data for catalyst selection |
| Cheminformatics → | IP Expansion | Stereoisomers as patentable variants |
| Cheminformatics → | Toxicology | Fragment analysis for structural alerts |