Maintain wanted heterogens

[ghost]

Hello! Is it possible to select heterogens to keep with the Python API? Or is it only possible to keep all, to keep just waters and to remove all? Thank you!

[jchodera]

Currently, it isn't possible to specify which heterogens to keep, but this sounds like a good feature request!

How would you want to specify them? By residue name, residue/chain, or some other way?

[peastman]

It's actually pretty easy. removeHeterogens() is just a very simple wrapper around a call to Modeller.delete(). Here is the complete implementation of it:

        keep = set(proteinResidues).union(dnaResidues).union(rnaResidues)
        keep.add('N')
        keep.add('UNK')
        if keepWater:
            keep.add('HOH')
        toDelete = []
        for residue in self.topology.residues():
            if residue.name not in keep:
                toDelete.append(residue)
        modeller = app.Modeller(self.topology, self.positions)
        modeller.delete(toDelete)
        self.topology = modeller.topology
        self.positions = modeller.positions

If you want to delete a different set of residues, you can write similar code with your own logic for selecting them.

[ghost]

Thank you!

Then I just did the small change below to remove based on the heterogen PDB code

def removeHeterogens(self, keepWater=True, keepHet=[]):

        keep = set(proteinResidues).union(dnaResidues).union(rnaResidues)
        keep.add('N')
        keep.add('UNK')
        if keepWater:
            keep.add('HOH')
        for Het in keepHet:
            keep.add(Het)
        toDelete = []
        for residue in self.topology.residues():
            if residue.name not in keep:
                toDelete.append(residue)
        modeller = app.Modeller(self.topology, self.positions)
        modeller.delete(toDelete)
        self.topology = modeller.topology
        self.positions = modeller.positions

[ghost]

@jchodera if you do add the feature, for my user case scenarios I think it would be useful to have different ways to specify the heterogens you want to maintain: by residue name, by residue plus chain and by residue number.