molsysmt.build.build_peptide#

molsysmt.build.build_peptide(molecular_system, to_form='molsysmt.MolSys', engine='LEaP')[source]#

Building a peptide from a sequence.

This function constructs a capped or uncapped peptide from a sequence of amino acids. It generates the complete atomic topology, including bonds, angles, and coordinates for the resulting system. Optionally, terminal capping groups can be included in the input sequence.

Parameters:

  • molecular_system (str or list of str) – The peptide sequence provided using either three-letter or one-letter amino acid codes. The sequence can also include optional terminal caps such as ‘ACE’ or ‘NME’.

  • to_form (str, default='molsysmt.MolSys') – Output form of the resulting molecular system. Must be one of the supported forms.

  • engine ({'LEaP', 'MolSysMT'}, default 'LEaP') – Engine used to build the peptide. 'LEaP' uses AmberTools and requires tleap in the environment. 'MolSysMT' builds the peptide using bundled residue templates.

Returns:

A new molecular system representing the fully constructed peptide, including coordinates and all relevant topological information.

Return type:

molecular system

Raises:

  • NotImplementedError – Raised if the selected engine is not supported.

  • ArgumentError – Raised if the input sequence is invalid or contains unsupported codes.

  • NotSupportedFormError – Raised if the output form is not recognized or supported.

Notes

  • The sequence must contain amino acid and/or capping group codes recognized by the selected engine.

  • String inputs are interpreted as peptide sequences in this context, even when the same characters are also valid SMILES.

  • Terminal caps can be specified explicitly by using residue names such as ‘ACE’ (N-terminus) and ‘NME’ (C-terminus).

  • The resulting structure is built in vacuum and can be subsequently solvated using molsysmt.build.solvate().

See also

molsysmt.build.add_missing_terminal_cappings()

Add terminal groups to complete or neutralize peptide ends.

molsysmt.build.solvate()

Surround a molecular system with solvent molecules.

molsysmt.structure.center()

Center a molecular system in a simulation box.

molsysmt.basic.view()

Visualize the resulting molecular system in a Jupyter notebook.

Examples

>>> import molsysmt as msm
>>> molsys = msm.build.build_peptide('AceGlyGlyNme')
>>> msm.basic.get(molsys, n_groups=True)
4

User guide

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

Added in version 1.0.0.

On this page