Check out input PDB files prior parameterizing

[martimunicoy]

Description

For instance, offpele would fail if the input PDB that contains the ligand to parameterize has atoms with unconsistent residue names. The exception raised in this case is totally misleading.

Solution

Implement a safety check for PDB files in order to properly handle exceptions related with its format prior running the parameterization.

[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.