Ignoring valences read from sdf file

[zarkoivkovicc]

Is it possible to completely ignore the data related to valences when loading molecules from sd files? I.e.

 18 19  0  0  0  0  0  0  0  0999 V2000
   -6.4010    0.5490    0.0000 C   0  0  0  0  0  2  0  0  0  0  0  0
   -6.4010   -0.9510    0.0000 C   0  0  0  0  0  2  0  0  0  0  0  0
   -5.1019   -1.7010    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8029   -0.9510    0.0000 C   0  0  0  0  0  3  0  0  0  0  0  0
   -3.8029    0.5490    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1019    1.2990    0.0000 C   0  0  0  0  0  2  0  0  0  0  0  0
   -2.5039   -1.7010    0.0000 C   0  0  0  0  0  2  0  0  0  0  0  0
   -1.2048   -0.9510    0.0000 C   0  0  0  0  0  3  0  0  0  0  0  0
   -1.2048    0.5490    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5039    1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8029    2.0490    0.0000 C   0  0  0  0  0  1  0  0  0  0  0  0
   -1.5397    2.4481    0.0000 C   0  0  0  0  0  3  0  0  0  0  0  0
   -6.0661   -2.8500    0.0000 C   0  0  0  0  0  1  0  0  0  0  0  0
   -3.4680    2.4481    0.0000 O   0  0  0  0  0  1  0  0  0  0  0  0
   -4.1378   -2.8500    0.0000 C   0  0  0  0  0  1  0  0  0  0  0  0
    0.0942    1.2990    0.0000 C   0  0  0  0  0  3  0  0  0  0  0  0
   -2.0527    3.8576    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3932    0.5490    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0

Is it possible to ignore everything after the elements and treat the file as they are all 0, without changing the file itself?
I want to do this because with files like this it's impossible to correctly assign hydrogens for each atom. I would like each atom to have a standard number of hydrogens, or equivalently, to have a standard valence (4 for C, 2 for O, etc.)

It seems that this is known issue for nmrshiftdb2, but no one found a solution yet (or no one published the solution yet).

[greglandrum]

@zarkoivkovicc The mol file parser interprets the valence flag and sets a couple of values on the atoms. You can manually change those and then run a normal sanitization and it should clear things up.
This function seems to work for at least simple cases:

def parse_mol_and_ignore_valence_tags(mb):
    mol = Chem.MolFromMolBlock(mb,sanitize=False,removeHs=False)
    for atom in mol.GetAtoms():
        atom.SetNoImplicit(False)
        atom.SetNumExplicitHs(0)
    Chem.SanitizeMol(mol)
    Chem.AssignStereochemistry(mol,cleanIt=True)
    return mol

Here's a simple demonstration to show it working:

In [24]: mb2 = '''
    ...:   Mrv2211 02022415472D          
    ...: 
    ...:   2  1  0  0  0  0            999 V2000
    ...:     0.1562   -1.3170    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    ...:     0.8707   -0.9045    0.0000 C   0  0  0  0  0  2  0  0  0  0  0  0
    ...:   1  2  1  0  0  0  0
    ...: M  END
    ...: '''

In [25]: Chem.MolToSmiles(Chem.MolFromMolBlock(mb2))
Out[25]: '[CH]C'

In [27]: Chem.MolToSmiles(parse_mol_and_ignore_valence_tags(mb2))
Out[27]: 'CC'

[zarkoivkovicc]

Thank you so much for the fast answer. This solves my issue.