Check out input PDB files prior parameterizing

[martimunicoy]

Check out input PDB files prior parameterizing

[martimunicoy]

Support

List of features to check in the input PDB:

• All atom names need to be unique. Otherwise raise Exception('Ligand in input PDB has no unique atom names')
• All residue ids must match. Otherwise raise Exception('A single ligand with immutable residue ids is expected')
• All residue names must match. Otherwise raise Exception('A single ligand with immutable residue names is expected')
• Check for at least one CONECT line. Otherwise output a warning: 'Input PDB has no information about the connectivity and this could result in an unexpected bond assignment')

[laumalo]

Implementation

The function _PDB_chekup(path) has been included in the class Molecule.
And it runs prior running the parametrization, here.

#Validate PDB
self._PDB_checkup(path)

Tests

PDBs that test the three posible errors and one warning: pdb_errors.zip

• For the following PDB file in which the atom name C1 is repeated:

HETATM    1  C1  UNK     1       0.634  -0.083   0.007  1.00  0.00           C  
HETATM    2  C1  UNK     1      -0.671   0.098  -0.007  1.00  0.00           C  
HETATM    3  H1  UNK     1       1.354   0.739   0.049  1.00  0.00           H  
HETATM    4  H2  UNK     1       1.082  -1.071  -0.022  1.00  0.00           H  
HETATM    5  H3  UNK     1      -1.096   1.088   0.022  1.00  0.00           H  
HETATM    6  H4  UNK     1      -1.302  -0.770  -0.049  1.00  0.00           H  
CONECT    1    2    2    3    4
CONECT    2    5    6
END

It raises the exception:

Exception: Ligand in input PDB has no unique atom names

• For the following PDB file in which the residue id for the atom H3 does not match:

HETATM    1  C1  UNK     1       0.634  -0.083   0.007  1.00  0.00           C  
HETATM    2  C2  UNK     1      -0.671   0.098  -0.007  1.00  0.00           C  
HETATM    3  H1  UNK     1       1.354   0.739   0.049  1.00  0.00           H  
HETATM    4  H2  UNK     1       1.082  -1.071  -0.022  1.00  0.00           H  
HETATM    5  H3  UNK     2      -1.096   1.088   0.022  1.00  0.00           H  
HETATM    6  H4  UNK     1      -1.302  -0.770  -0.049  1.00  0.00           H  
CONECT    1    2    2    3    4
CONECT    2    5    6
END

It raises the exception:

Exception: A single ligand with immutable residue ids is expected

• For the following PDB file in which the residue name for the atom H1 does not match:

HETATM    1  C1  UNK     1       0.634  -0.083   0.007  1.00  0.00           C  
HETATM    2  C2  UNK     1      -0.671   0.098  -0.007  1.00  0.00           C  
HETATM    3  H1  UNN     1       1.354   0.739   0.049  1.00  0.00           H  
HETATM    4  H2  UNK     1       1.082  -1.071  -0.022  1.00  0.00           H  
HETATM    5  H3  UNK     1      -1.096   1.088   0.022  1.00  0.00           H  
HETATM    6  H4  UNK     1      -1.302  -0.770  -0.049  1.00  0.00           H  
CONECT    1    2    2    3    4
CONECT    2    5    6
END

It raises the exception:

Exception: A single ligand with immutable residue names is expected

Unit tests here.