This small class is functional but it is greatly superseded by Fragmenstein, which can be used for renaming and a lot more.
Given a molecule label the atoms (names/labels) according to a reference ligand from the PDB.
RDKit is not good with atom names, while macromolecular tools like Rosetta or even PyMOL rely heavily on them. This is aimed at fixing that. An atom has several properties, here I will mention:
- symbol (or element name), say C for calcium
- index (an integer specifying the order it is in which often comes from the order they appeared in a SMILES string)
- labels (or atom name), say CA for C-α
Open babel if given a sdf of an amino acid and asked to convert to a mol2 will label them as CA etc. But most other times and most programs don't.
This stems also from the fact that mol (sdf) files do not specify atom labels in the main block. Mol2 and PDB do however.
It is different from the more traditional approach using rdMolAlign.AlignMol. As demonstrated in example_of_alt_way.py.
The rdMolAlign.AlignMol is simpler, but does not keep atom names.
So this script is useful if you want to
- subtly change one molecule with another and just let the pose loading in rosetta fix it
- play around in PyMOL app and manually align or show atom labels
Both end results can be given to mol_to_params.py fine —or to my 2to3 port of mol_to_params.py which can be used as a module.
This short script given a molecule (e.g. mol = Chem.MolFromSmiles('C1=NC2=C(N1)C(=O)NC(=N2)N')) and reference PDB ligand code (e.g. ATP) will label in place the molecule (adding the property AtomLabel) and return a list of atom names (with indices matching the atomic indices obvious).
>>> from rdkit import Chem
>>> from atomic_renamer import AtomicNamer
>>> mol = Chem.MolFromSmiles('C1=NC2=C(N1)C(=O)NC(=N2)N')
>>> labels = AtomicNamer('ATP').name(mol)
>>> labels
['C8', 'N9', 'C4', 'C5', 'N7', 'C6', 'OX1', 'N6', 'C2', 'N3', 'N1']
The atom name/label is assigned to the prop AtomLabel (following https://www.rdkit.org/docs/RDKit_Book.html).
Note, that while there is a bound method called .display(mol), I have not finished it as I been able to get it to work.
These labels can be saved as mol2 in a convoluted way, becuase the mol2 writer in Rdkit is a bit tempramental. So using open babel is better and using the bound method AtomicNamer.fix to fix these.
>>> mol.UpdatePropertyCache() # I might have changed some atoms around
>>> #if you are an optimist you could try... Chem.SanitizeMol(mol)
>>> mol = Chem.AddHs(mol) #protonate explicitly
>>> Chem.GetSSSR(mol) #not communists, but resonance fixing
>>> AllChem.EmbedMolecule(mol) #initialise for 3d.
>>> AllChem.UFFOptimizeMolecule(mol, maxIters=2000)
>>> Chem.MolToMolFile(mol, 'guanine.mol')
>>> os.system(f"obabel -i mol guanine.mol -o mol2 -O guanine.mol2")
>>> AtomicNamer.fix('guanine.mol2', 'guanine.better.mol2', labels)
>>> os.system(f"obabel -i mol2 guanine2.better.mol2 -o mol2 -O guanine.conf.mol2 --conformer --nconf 30 --writeconformers")
Once this is done, the mol2 can be used. If using Rosetta and are about to parametrise it, why not check out my rdkit to params file converter?
Also, for more stuff, see my blog post about Rdkit.
The attributes .ref and .reflabels contain the RDKit Chem.rdchem.Mol object and the list of atom names. So if you want to use something that isn't a PDB ligand code you can.
The reason for using the PDB ligand code is that if you change the name of a residue (in TextEdit or PyMOL) and run the structure through Rosetta will change it. This is handy for post translation modifications —for more see my blog post about PTMs and Rosetta.