molsysmt.build.add_missing_terminal_cappings#

molsysmt.build.add_missing_terminal_cappings(molecular_system, N_terminal=None, C_terminal=None, pH=7.4, keep_ids=False, selection='all', syntax='MolSysMT', engine='PDBFixer', skip_digestion=False)[source]#

Adding terminal cappings to peptides and proteins.

This function adds chemical groups to the N- and/or C-termini of protein or peptide chains. These terminal groups can either neutralize terminal charges or simply complete missing atoms for a standard terminal residue. The resulting cappings are consistent with typical protonation states at the specified pH.

Parameters:

  • molecular_system (molecular system) – Molecular system in any of the supported forms to which terminal cappings will be added.

  • N_terminal (str or None, default None) – Residue name to cap the N-terminus. If None, the missing atoms are added to the native terminal residue without introducing a separate cap. Use ‘ACE’ to cap with an acetyl group, or other recognized residue names.

  • C_terminal (str or None, default None) – Residue name to cap the C-terminus. If None, the missing atoms are added to the native terminal residue without introducing a separate cap. Use ‘NME’ to cap with a N-methyl amide group, or other recognized residue names.

  • pH (float, default 7.4) – Approximate pH used to determine the protonation states of terminal groups and nearby residues.

  • keep_ids (bool, default False) – If True, preserves the original atom and group ids. Otherwise, new IDs may be reassigned.

  • selection (str, list, tuple, or numpy.ndarray, default 'all') – Selection of atoms or residues to which this operation applies. Can be a list of indices or a query string following MolSysMT selection syntax.

  • syntax (str, default 'MolSysMT') – Syntax used to parse the selection argument, if it is a string.

  • engine ({'PDBFixer'}, default 'PDBFixer') – Engine used to perform capping. Determines atom placement and protonation based on templates.

Returns:

A new molecular system with modified termini, in the same form as the input system.

Return type:

molecular system

Raises:

  • NotSupportedFormError – Raised if the input molecular system is in a non-supported form.

  • ArgumentError – Raised if an input argument value is invalid.

Notes

Common capping groups:

  • ‘ACE’ for acetyl (N-terminal)

  • ‘NME’ for N-methyl amide (C-terminal)

If no capping residues are provided, the function only completes missing terminal atoms in the native residues (which are often charged).

The list of supported molecular system forms is detailed in: User Guide > Introduction > Molecular systems > Forms

See also

molsysmt.build.build_peptide()

Construct a peptide sequence with optional terminal cappings.

molsysmt.build.add_missing_heavy_atoms()

Add missing non-hydrogen atoms to standard residues.

molsysmt.basic.info()

Inspect the content and composition of a molecular system.

molsysmt.physchem.get_charge()

Calculate the total or partial charge of a system.

Examples

>>> import molsysmt as msm
>>> molsys = msm.build.build_peptide('AlaValPro')
>>> molsys = msm.build.add_missing_terminal_cappings(molsys, N_terminal='ACE', C_terminal='NME')
>>> msm.physchem.get_charge(capped_system)
0.0 elementary_charge
>>> msm.convert(molsys, to_form='string:amino_acids_3')
'AceAlaValProNme'

User guide

Follow this link for a tutorial on how to work with this function: User Guide > Tools > Build > Add missing terminal cappings

Added in version 1.0.0.