Examples with Mutation ffx.potential.parsers.PDBFilter.Mutation used on opensource projects

Example 1 with Mutation

use of ffx.potential.parsers.PDBFilter.Mutation in project ffx by mjschnie.

the class TitrationUtils method openFullyProtonated.

public static MolecularAssembly openFullyProtonated(File structure) {
    String name = format("%s-prot", FilenameUtils.removeExtension(structure.getName()));
    MolecularAssembly mola = new MolecularAssembly(name);
    mola.setFile(structure);
    List<Mutation> mutations = new ArrayList<>();
    List<Residue> residues = mola.getResidueList();
    for (Residue res : residues) {
        char chain = res.getChainID();
        int resID = res.getResidueNumber();
        Titration titration = Titration.lookup(res);
        if (res.getAminoAcid3() != titration.protForm) {
            String protName = titration.protForm.name();
            mutations.add(new PDBFilter.Mutation(chain, resID, protName));
        }
    }
    PotentialsUtils utils = new PotentialsUtils();
    return utils.openWithMutations(structure, mutations);
}