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name: molecules-and-io description: "Prepare ProLIF molecules, residues, and input files from RDKit, MDAnalysis, SDF, MOL2, PDBQT, PDB, and CIF/template-backed sources." disable-model-invocation: true metadata: disco-role: operating license: Apache 2.0

ProLIF Molecules and I/O

Use this sub-skill when an agent needs to turn chemistry or trajectory inputs into ProLIF Molecule, Residue, ResidueId, or ResidueGroup objects before interaction fingerprinting.

Route Here For

• Creating prolif.Molecule objects with Molecule.from_mda, Molecule.from_rdkit, sdf_supplier, mol2_supplier, pdbqt_supplier, or split_molecule.
• Diagnosing residue labels, chain versus segid behavior, residue masks, and ResidueId string/index lookup.
• Preparing docking poses from SDF, MOL2, or PDBQT files before passing ligand pose iterables to fingerprint workflows.
• Preparing PDB/PDB-like structures, non-standard residues, CIF templates, and MoleculeStandardizer inputs.
• Running the bundled safe helper scripts/inspect_inputs.py to smoke-test installed package data or inspect user SDF/MOL2/PDBQT files.

Do Not Use This For

• Choosing interaction classes, tuning interaction parameters, or water/implicit hydrogen interaction modes; use ../interactions/SKILL.md.
• Running Fingerprint.run, run_from_iterable, generate, exports, pickles, or parallel execution; use ../fingerprints/SKILL.md.
• Plotting residues, networks, barcodes, or 3D complexes; use ../visualization/SKILL.md.
• Claiming or invoking a ProLIF CLI. ProLIF is used as a Python API; the helper in this skill is only a bundled diagnostic script.

Quick Decision Map

1. MDAnalysis Universe or AtomGroup: use Molecule.from_mda(obj, selection=None, use_segid=None, **converter_kwargs); verify the selection is non-empty and decide whether residue identity should use chain IDs or segment indices.
2. RDKit molecule: use Molecule.from_rdkit(mol, resname="UNL", resnumber=1, chain="", use_segid=False) when atoms may not already carry AtomPDBResidueInfo.
3. SDF docking poses: use sdf_supplier(path, sanitize=True, resname=..., resnumber=..., chain=...); it behaves like a reusable sequence of Molecule poses.
4. MOL2 docking poses: use mol2_supplier(path, cleanup_substructures=True, sanitize=True, ...); disable cleanup/sanitization only as a targeted troubleshooting step.
5. PDBQT docking poses: use pdbqt_supplier(paths, template, converter_kwargs=None, ...); a template with correct bond orders and charges is mandatory.
6. PDB or non-standard residues: use RDKit/MDAnalysis loading plus prolif.io.MoleculeStandardizer with CIF or RDKit-molecule templates when bond orders, residue names, or protonation-sensitive residues need correction.

References

• references/api-reference.md covers classes, constructor signatures, suppliers, standardization APIs, and residue selection.
• references/workflows.md provides input-preparation recipes for trajectories, docking, PDB, and residue splitting.
• references/data-formats.md explains SDF, MOL2, PDBQT, PDB, CIF/template, and package-data behavior.
• references/troubleshooting.md lists common conversion, labeling, hydrogen, standardization, and supplier failures.

Safe Inspection Helper

Run from any project where ProLIF is installed:

python scripts/inspect_inputs.py
python scripts/inspect_inputs.py --sdf poses.sdf
python scripts/inspect_inputs.py --mol2 poses.mol2
python scripts/inspect_inputs.py --pdbqt pose1.pdbqt --pdbqt-template-smiles 'CCO'

The helper prints JSON, performs no destructive writes, and only reads user-specified files plus installed prolif.datafiles package data in no-argument mode.