molsysmt.physchem.get_hydrophobic_sites#

molsysmt.physchem.get_hydrophobic_sites(molecular_system, selection='all', structure_indices='all', chemical_state='reference', method='smarts_hydrophobic_atoms', assume_complete_connectivity=False, syntax='MolSysMT', skip_digestion=False, *, max_matches=100000)[source]#

Recognizing hydrophobic atom sites from complete declared chemical graphs.

Parameters:

  • molecular_system (molecular system) – Any supported form supplying elements, complete connectivity, covalent orders, formal charges and atom/bond aromatic flags.

  • selection (str, list, tuple, or numpy.ndarray, default='all') – Source atom selection. Recognize the full graph before filtering atoms.

  • structure_indices (int, list, tuple, or numpy.ndarray, default='all') – Structure indices (0-based) for state resolution and spatial selections. Recognition itself does not require coordinates.

  • chemical_state ({'reference', 'structure'}, int, or None, default='reference') – State supplying chemistry. Structure assignments must resolve one state.

  • method (str, default='smarts_hydrophobic_atoms') – Exact ProLIF 2.2.2 atomic Hydrophobic SMARTS, without geometry.

  • assume_complete_connectivity (bool, default=False) – Record an explicit completeness assumption without filling missing bonds or chemical assignments.

  • syntax (str, default='MolSysMT') – Selection syntax used to evaluate selection.

  • skip_digestion (bool, default=False) – Whether to skip MolSysMT’s internal argument digestion mechanism.

  • max_matches (int, default=100000) – Keyword-only maximum full-source matches before selection. Exceeded limits raise rather than silently truncating chemical sites.

Returns:

hydrophobic_atom_indices is a sorted int64 array with shape (n_sites,), including (0,) when empty. Indices refer to source atoms, not IDs. Metadata retains state, source/selected axes, SMARTS, chemical evidence, actual producer versions and detached reference bibliography.

Return type:

dict

Raises:

  • ArgumentError – If the method, selection, state or match limit is invalid.

  • StructuralInconsistencyError – If required chemistry is absent or altered by sanitization.

  • UnsupportedHeavyOperationError – If a match limit is exceeded.

  • MemoryBudgetExceededError – If chemical matching exceeds its numerical memory estimate.

Notes

This experimental definition reproduces ProLIF 2.2.2, whose patterns are adapted from RDKit chemical features. It includes neutral aromatic c/s, Br/I, sulfur with no hydrogens and valence two, and specified nonterminal aliphatic carbon environments; carbon linked to N/O/F and charged atoms are excluded. Terminal methyl carbon is not a blanket match. F and Cl themselves do not match. Indexed or annotated hydrogen counts participate in RDKit valence interpretation; no hydrogens or coordinates are invented. Missing formal-charge/aromatic assignments are not inferred silently.

Sites are not residue hydrophobicity scale values, interaction energies or evidence that an atom universally behaves hydrophobically. ProLIF is a reference, not an executed dependency. Optional Ackredit credits completed recognition; the bibliography also exists without that provider.

See also

molsysmt.physchem.get_hydrophobicity

Looking up independent residue hydrophobicity scales.

molsysmt.topology.get_substructure_matches

Matching arbitrary SMARTS on declared chemical graphs.

molsysmt.interactions.hydrophobic.get_hydrophobic_interactions

Evaluating typed atom-pair proximity observations.

Examples

>>> import molsysmt as msm
>>> from rdkit import Chem
>>> sites = msm.physchem.get_hydrophobic_sites(Chem.MolFromSmiles('CCC.CSC.CF'))
>>> sites['hydrophobic_atom_indices'].tolist()
[1, 4]

User guide

See Getting hydrophobic sites.

Added in version 1.0.0.