molsysmt.build.add_missing_heavy_atoms#

molsysmt.build.add_missing_heavy_atoms(molecular_system, selection='all', syntax='MolSysMT', engine='PDBFixer', skip_digestion=False)[source]#

Adding missing non-hydrogen atoms to a molecular system.

This function checks for missing heavy atoms (non-hydrogens) in a molecular system and adds them when possible. The missing atoms are identified based on known residue templates and inferred topological context. The coordinates of new atoms are estimated using internal geometry rules or external reconstruction engines such as PDBFixer.

Parameters:

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

  • selection (tuple, list, numpy.ndarray or str, default 'all') – Selection of atoms that define the residues or molecules to analyze. Can be provided as indices (list, tuple, array of 0-based integers) or as a string using any of the supported selection syntaxes.

  • syntax (str, default 'MolSysMT') – Selection syntax used when selection is a string.

  • engine ({'MolSysMT', 'PDBFixer'}, default 'PDBFixer') – Engine used to rebuild the missing atoms. If ‘MolSysMT’ is chosen, internal geometry templates are used. If ‘PDBFixer’ is selected, the external PDBFixer engine is called.

Returns:

A molecular system with the missing heavy atoms added, in the same form as the input system.

Return type:

molecular system

Raises:

  • NotSupportedFormError – Raised if the input molecular system is in an unsupported format.

  • ArgumentError – Raised if one or more input arguments are invalid.

  • EngineError – Raised if the specified engine fails to rebuild the atoms.

Notes

This function adds only non-hydrogen atoms (heavy atoms) that are missing from standard residues. Hydrogen atoms can be added using other tools or methods.

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

The list of supported selection syntaxes is available at: User Guide > Introduction > Selection syntaxes

See also

molsysmt.build.get_missing_heavy_atoms()

Identify heavy atoms that are missing based on residue templates.

molsysmt.basic.remove()

Remove atoms from a molecular system.

molsysmt.basic.contains()

Check whether specific elements are present in a molecular system.

molsysmt.build.build_peptide()

Build capped peptide structures from amino acid sequences.

Examples

>>> import molsysmt as msm
>>> molsys = msm.build.build_peptide('AAA')
>>> msm.get(molsys, selection='atom_name=="CB"', n_atoms=True)
3
>>> molsys = msm.build.remove(molsys, selection='atom_name=="CB"')
>>> msm.get(molsys, selection='atom_name=="CB"', n_atoms=True)
0
>>> molsys = msm.build.add_missing_heavy_atoms(molsys)
>>> msm.get(molsys, selection='atom_name=="CB"', n_atoms=True)
3

User guide

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

Added in version 1.0.0.