molsysmt.physchem.get_peptide_chemical_template#

molsysmt.physchem.get_peptide_chemical_template(residue_names, n_terminal_state, c_terminal_state, skip_digestion=False, *, disulfide_group_pairs=None)[source]#

Constructing a heavy-atom peptide template with explicit chemical states.

Parameters:

  • residue_names (list, tuple or numpy.ndarray) – Ordered residue-state names, one per zero-based template group index. Names are exact and case-sensitive. HIS requires HID, HIE or HIP; ASP/ASH, GLU/GLH, LYS/LYN and CYS/CYM/CYX distinguish declared protonation or links. No aliases, pH rules or states are inferred from coordinates.

  • n_terminal_state ({'ammonium', 'amine'}) – Explicit charged or neutral amino terminus. Proline uses the corresponding secondary amine inventory. No terminal state is chosen by default.

  • c_terminal_state ({'carboxylate', 'carboxylic_acid'}) – Explicit charged or protonated carboxyl terminus, including an OXT atom.

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

  • disulfide_group_pairs (list, tuple, numpy.ndarray or None, default=None) – Keyword-only integer array of shape (n_disulfides, 2), containing template group indices. Every CYX must occur in exactly one pair; other states cannot participate. None declares no disulfides. These are chemical bonds, not geometric candidates inferred from sulfur proximity.

Returns:

Coordinate-free native MolSys under template, its detached template_provenance, and a molsysmt.peptide_template@1 report. The selected fragments, terminal states, declared links, source snapshot/digests, curation and original executed software are retained. An independent copy of the report, including template_provenance, is attached to the template’s chemical-state history. Formal charge uses elementary charge units. H counts are stored; no indexed H atoms exist.

Return type:

dict

Raises:

  • ArgumentError – If states are unsupported, indices invalid, or disulfide ports unpaired.

  • StructuralInconsistencyError – If the bundled fragment schema or declared formal-charge unit is invalid.

Notes

Experimental template factory for one linear peptide, optionally with declared disulfides. This is not an operation on an existing molecular system. Apply its result to any supported source form with apply_chemical_template and an exhaustive caller-declared atom map. Missing heavy atoms, capped/cyclic or modified backbones and arbitrary inter-group links remain outside this factory. Terminal OXT is part of the template; an absent source OXT needs separate repair.

Bundled fragments are curated from a pinned Meeko data snapshot. Meeko and RDKit are not runtime dependencies. No conformer, atom matching, protonation prediction or force-field parameters are generated. Stereochemistry remains unspecified, including peptide cis/trans and residue enantiomers; this is not a declaration of L stereochemistry. Existing conflicting source chemistry is never overwritten by template application. H5MSM and ChemicalStatesDict preserve the template’s construction report, original producer version and provenance. Its indices remain in the original synthetic template domain after extraction or edits; history does not certify current chemistry. Application uses the caller’s template_provenance, including its producer version, but does not import the reference template’s history into the source. Archive selected reference records explicitly with append_preparation_history if the destination should retain their original operation domains.

Successful construction contributes portable MolSysMT software and source-data attribution to an optional Ackredit scope; it does not credit Meeko/RDKit as executed runtime engines. Attribution absence/failure preserves the result.

See also

assess_chemical_template

Check chemistry and the explicit atom map.

apply_chemical_template

Transfer compatible chemistry while preserving pose.

molsysmt.build.add_missing_hydrogens

Generate H geometry in a separate step.

Examples

>>> import molsysmt as msm
>>> result = msm.physchem.get_peptide_chemical_template(
...     ['GLY', 'GLY'], n_terminal_state='ammonium',
...     c_terminal_state='carboxylate')
>>> result['template'].get_n_atoms()
9
>>> result['report']['n_stored_hydrogens']
8
>>> result['template'].chemical_states.get_preparation_history()[0]['report']['status']
'constructed'

Tutorial

See the chemical-template tutorial in the User Guide.

Added in version 1.0.0.