COSMolKit Python

COSMolKit is a Python package for molecule graph workflows, SMILES/SDF/MOL2/XYZ IO, coordinate access, native 3D conformer generation, UFF/MMFF optimization, stable atom chiral-tag assignment from selected 3D conformers, Morgan fingerprints, molecular descriptors, molecule depiction, Python pickle round-tripping, SMARTS parse metadata, protein structure access, and high-throughput batch processing.

Important API model: COSMolKit presents value-style Molecule objects. Transform methods return new Molecule objects and do not mutate the original object in place. Internally the library uses copy-on-write (COW) storage to share unchanged data efficiently. This differs from common RDKit Python workflows where code often updates an existing molecule or RWMol directly.

User Guide

• Installation
• Quick Start
  • Value-Style Molecule Values
• ConfSeq
• Molecule Values
  • Read Finalization
  • In-Place Operations
  • SMILES Output
  • Explicit Editing
  • Serialization
  • Depictions
  • Stereo
  • Atom Chiral Tags From 3D Coordinates
  • Conformer Generation And Force-Field Optimization
  • Manual Coordinate Assignment
  • Substructure And SMARTS
• Batch Workflows
  • Error Handling
  • Batch Values
  • Export Images
  • Export SDF
  • Derived Outputs
  • SMILES Options
  • Batch Chirality
  • Parallel Work
• Fingerprints
  • Single Molecules
  • Additional Output
  • Supported Parameters
  • Batch Fingerprints
• Molecular Descriptors
  • Basic Descriptors
  • Formula Options
  • Rotatable-Bond Modes
• Protein Structures
  • Chains, Residues, And Atoms
  • Residue Information
  • Protein vs Molecule PDB APIs
• File IO and Arrays
  • SDF Files
  • SDF Strings
  • MOL2 Files
  • PDB and mmCIF Blocks
  • XYZ Blocks
  • Coordinate Arrays
  • Depiction Files
• API Reference
  • Atom
  • BatchError
  • BatchErrorMode
  • BatchExportReport
  • BatchValidationError
  • Bond
  • BondDirection
  • BondOrder
  • BondStereo
  • ChiralTag
  • InchiAllocationError
  • InchiDiagnosticWarning
  • InchiError
  • InchiToInchiKey()
  • InchiUnsupportedStateError
  • Molecule
  • MoleculeBatch
  • MoleculeEdit
  • ResidueCode
  • ResidueInfo
  • ResidueInfoKind
  • SdfDataset
  • SdfReader
  • SdfRecord
  • SdfRecordMetadata
  • calc_crippen_descriptors()
  • calc_exact_mol_wt()
  • calc_fraction_csp3()
  • calc_mol_formula()
  • calc_mol_wt()
  • calc_num_aromatic_rings()
  • calc_num_hba()
  • calc_num_hbd()
  • calc_num_rotatable_bonds()
  • calc_qed()
  • calc_tpsa()
  • expand_one_letter()
  • expand_one_letter_sequence()
  • expand_protein_one_letter()
  • expand_protein_one_letter_string()
  • find_tabulated_residue()
  • find_tabulated_residue_idx()
  • get_residue_info()
  • get_substruct_match()
  • get_substruct_matches()
  • get_substruct_matches_with_params()
  • has_substruct_match()
  • mmff_has_all_molecule_params()
  • mmff_optimize_molecule()
  • mmff_optimize_molecule_confs()
  • mol_from_binary()
  • mol_to_binary()
  • parse_smarts()
  • residue_code_from_name()
  • uff_has_all_molecule_params()
  • uff_optimize_molecule()
  • uff_optimize_molecule_confs()
  • InChI API
  • Protein API