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src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/MoleculePreparation.py   Pymol-script-repo(Download)
 
from AutoDockTools.atomTypeTools import NonpolarHydrogenMerger
from AutoDockTools.atomTypeTools import LonepairMerger
from AutoDockTools.atomTypeTools import SolvationParameterizer
from AutoDockTools.atomTypeTools import AromaticCarbonManager
        merge_lonepairs = 'lps' in self.cleanup_type_list
        if merge_lonepairs:
            LPM = self.LPM = LonepairMerger()
            #lps = filter(lambda x: x.element=='Xx' and \
                  #(x.name[0]=='L' or x.name[1]=='L'), mol.allAtoms)
        merge_lonepairs = 'lps' in cleanup_list
        if merge_lonepairs:
            LPM = self.LPM = LonepairMerger()
            #lps = filter(lambda x: x.element=='Xx' and \
                  #(x.name[0]=='L' or x.name[1]=='L'), mol.allAtoms)

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/VisionInterface/AdtNodes.py   Pymol-script-repo(Download)
from MolKit.protein import Residue, ResidueSet, Chain, ChainSet
from AutoDockTools.atomTypeTools import AutoDock4_AtomTyper
from AutoDockTools.atomTypeTools import NonpolarHydrogenMerger, LonepairMerger
from AutoDockTools.atomTypeTools import AromaticCarbonManager, SolvationParameterizer
from AutoDockTools.MoleculePreparation import RotatableBondManager