Cheminformatics Agent v1.0.0

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name: pharmaclaw-cheminformatics

description: 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.

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# Cheminformatics Agent v1.0.0

Overview

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

`scripts/conformer_gen.py`

3D 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.py`

Convert 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.py`

Pharmacophore 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.py`

RECAP (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.py`

Stereoisomer 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.py`

Standard 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:

Output 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"
}

Chaining

| 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 |

Dependencies