Get missing heavy atoms#

Identifying missing non-hydrogen heavy atoms in a molecular system.

Structures solved by experimental methods such as X-ray crystallography often contain missing heavy atoms due to resolution limits or local disorder. The function molsysmt.build.get_missing_heavy_atoms() compares residues with exact chemical templates to identify missing non-hydrogen atoms. MSE, SEP, TPO, and MLY have exact component templates; other modified residues without one are absent from the returned missing-atom mapping. Detection does not guarantee that a missing atom can be placed safely. An empty mapping alone does not certify that every residue is complete.

Added in version 1.0.0.

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects of this function: molsysmt.build.get_missing_heavy_atoms().

Basic usage#

Let’s show how this function works using a protein structure loaded from PDB ID 1BRS:

import molsysmt as msm

molsys = msm.convert('1BRS', selection='molecule_type=="protein"')

msm.info(molsys, element='molecule')
index name type n atoms n groups n components chain index entity index entity name
0 BARNASE protein 864 108 1 0 0 BARNASE
1 BARNASE protein 878 110 1 1 0 BARNASE
2 BARNASE protein 839 108 1 2 0 BARNASE
3 BARSTAR protein 693 87 2 3 1 BARSTAR
4 BARSTAR protein 665 86 2 4 1 BARSTAR
5 BARSTAR protein 699 89 1 5 1 BARSTAR

We now use molsysmt.build.get_missing_heavy_atoms() to detect missing non-hydrogen atoms across all residues:

missing_heavy_atoms = msm.build.get_missing_heavy_atoms(molsys)

missing_heavy_atoms

{234: ['CD', 'CE', 'CG', 'NZ'],
 237: ['CG', 'OD1', 'OD2'],
 244: ['CD', 'OE1', 'OE2'],
 246: ['CD', 'CG', 'NE2', 'OE1'],
 254: ['CD', 'CE', 'NZ'],
 260: ['CG1', 'CG2'],
 264: ['CD', 'CE', 'CG', 'NZ'],
 282: ['OG'],
 325: ['O'],
 383: ['NE2', 'OE1'],
 385: ['NZ'],
 386: ['CD', 'CG', 'NE2', 'OE1'],
 422: ['CZ', 'NE', 'NH1', 'NH2'],
 429: ['CD', 'CG', 'NE2', 'OE1'],
 465: ['CZ', 'NE', 'NH1', 'NH2'],
 469: ['CD', 'CG', 'NE2', 'OE1'],
 471: ['CD', 'CE', 'CG', 'NZ'],
 472: ['CD', 'CG', 'NE2', 'OE1'],
 473: ['CD1', 'CD2', 'CG'],
 520: ['CD', 'CE', 'NZ'],
 526: ['CD', 'CG', 'OE1', 'OE2'],
 544: ['CD', 'CG', 'OE1', 'OE2'],
 562: ['CD', 'CG', 'OE1', 'OE2'],
 563: ['CG', 'ND2', 'OD1'],
 587: ['O']}

We can identify which molecules contain these missing heavy atoms:

residue_indices = list(missing_heavy_atoms.keys())
molecule_indices = msm.get(molsys, element='molecule', selection='group_index in @residue_indices', molecule_index=True)

msm.info(molsys, element='molecule', selection='molecule_index in @molecule_indices')
index name type n atoms n groups n components chain index entity index entity name
2 BARNASE protein 839 108 1 2 0 BARNASE
3 BARSTAR protein 693 87 2 3 1 BARSTAR
4 BARSTAR protein 665 86 2 4 1 BARSTAR
5 BARSTAR protein 699 89 1 5 1 BARSTAR

Finally, let’s check if the system has hydrogen atoms using molsysmt.build.has_hydrogens():

msm.build.has_hydrogens(molsys)

False

See also

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