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src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/write_models_from_states.py   Pymol-script-repo(Download)
from MolKit import Read
from mglutil.math.statetocoords import StateToCoords
from AutoDockTools.Conformation import Conformation
 
from AutoDockTools.Docking import Docking
            if ntors>0:
                torsion_angles = fl[7:]
                newConf = Conformation(lig,origin,translation, quaternion, torsion_angles)
                newCrds = newConf.getCoords()
                if interim_state:
            if ntors>0:
                torsion_angles = fl[7:]
                newConf = Conformation(lig,origin,translation, quaternion, torsion_angles)
                newCrds = newConf.getCoords()
                #write some MODEL stuff then newCrds

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/write_random_state_ligand.py   Pymol-script-repo(Download)
from MolKit.molecule import BondSet
from mglutil.math.statetocoords import StateToCoords
from AutoDockTools.Conformation import Conformation
#from MolKit.pdbWriter import PdbqWriter, PdbqtWriter
 
            dihe.append(dscale * random.uniform(-1,1))
        if verbose: print 'dihe=', dihe
        conf = Conformation(m, origin, TRANS, rot, dihe)
        new_coords = conf.getCoords()
        #verify that no new bonds would be formed for this conformation

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Docking.py   Pymol-script-repo(Download)
from AutoDockTools.DockingParameters import DockingParameters
from AutoDockTools.DlgParser import DlgParser
from AutoDockTools.Conformation import Conformation, ConformationHandler
from AutoDockTools.Conformation import PopulationHandler
from AutoDockTools.cluster import Clusterer