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src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/prepare_ligand4.py   Pymol-script-repo(Download)
from MolKit import Read
 
from AutoDockTools.MoleculePreparation import AD4LigandPreparation
 
 
        print "and check_for_fragments=", check_for_fragments
        print "and bonds_to_inactivate=", bonds_to_inactivate
    LPO = AD4LigandPreparation(mol, mode, repairs, charges_to_add, 
                            cleanup, allowed_bonds, root, 
                            outputfilename=outputfilename,

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/repair_ligand4.py   Pymol-script-repo(Download)
from MolKit.molecule import AtomSet
 
from AutoDockTools.MoleculePreparation import AD4LigandPreparation
 
 
    if verbose: print 'read ', pdbqt_filename
    mol.buildBondsByDistance()
    mol.LPO = AD4LigandPreparation(mol, mode='interactive', repairs='', charges_to_add=None,
                root=0, outputfilename=outputfilename, cleanup='')
    #rebuild torTree