molsysmt.build.get_disulfide_bonds#

molsysmt.build.get_disulfide_bonds(molecular_system, selection='all', structure_index=0, max_bond_length=None, group_names=None, pbc=True, syntax='MolSysMT', engine='MolSysMT', sorted=True, skip_digestion=False)[source]#

Identifying candidate disulfide bonds between sulfur atoms.

This build-oriented compatibility function returns S–S pairs inferred from group identity and distance in one structure. A candidate is not proof of a covalent bond in the topology.

Parameters:

  • molecular_system (molecular system) – Molecular system in any supported MolSysMT format.

  • selection (str, list, tuple, or numpy.ndarray, default='all') – Selection string or boolean/integer array specifying elements.

  • structure_index (object, default=0) – Argument structure_index.

  • max_bond_length (object, default=None) – Argument max_bond_length.

  • group_names (object, default=None) – Argument group_names.

  • pbc (bool, default=True) – Whether to take periodic boundary conditions into account.

  • syntax (str, default='MolSysMT') – Selection syntax used to evaluate selection (e.g., ‘MolSysMT’, ‘MDTraj’).

  • engine (object, default='MolSysMT') – Argument engine.

  • sorted (bool, default=True) – Whether to sort the returned bonded atom pairs.

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

Returns:

Candidate atom-index pairs in the selected structure.

Return type:

list of [int, int]

Raises:

  • NotSupportedFormError – If the molecular system format is not supported.

  • ArgumentError – If input values do not meet required conditions.

Notes

  • Sulfur atoms are identified based on element type and filtered by group name (e.g., ‘CYS’).

  • The default group name is CYS. Other eligible names may be supplied.

  • Distance units are internally standardized to nanometers.

  • The per-structure detector and its measured distances are available from molsysmt.interactions.disulfides.get_disulfide_candidates().

See also

molsysmt.Topology.add_bonds()

Add identified bonds directly to a native topology.

molsysmt.structure.get_neighbors()

Find neighboring atoms within a distance or bond limit.

molsysmt.build.get_missing_bonds()

Automatically infer missing covalent bonds.

Examples

>>> import molsysmt as msm
>>> from molsysmt.build.get_disulfide_bonds import get_disulfide_bonds
>>> molsys = msm.convert('5XJH')
>>> s_s_pairs = get_disulfide_bonds(molsys, max_bond_length='2.15 angstroms')
>>> len(s_s_pairs)
2

User guide

Follow this link for a tutorial on how to work with this function: User Guide > Tools > Build > Get disulfide bonds

Added in version 1.0.0.

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