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src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/LigandMixin.py   Pymol-script-repo(Download)
    def setup(self, useProteinAromaticList=1,
                    aromaticCutOff=7.5, maxtors=32,
                    autoMergeNPHS=1):
        if self.chains[0].hasBonds==0:
            self.buildBondsByDistance()
        #what if self doesn't have bonds
        if not self.chains[0].hasBonds:
            self.buildBondsByDistance()
        hs = self.allAtoms.get(lambda x: x.element=='H')
        self.nphs = AtomSet()