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src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/autoanalyzeCommands.py   Pymol-script-repo(Download)
from AutoDockTools.EpdbParser import EpdbParser
from AutoDockTools.histogram import HistogramRI
from AutoDockTools.cluster import Clusterer
from AutoDockTools import interactiveHistogramGraph
from AutoDockTools.InteractionDetector import InteractionDetector
        if not hasattr(d, 'clusterer'):
            if hasattr(d, 'version') and d.version>=4.0:
                d.clusterer = Clusterer(d.ch.conformations, sort='energy')
            else:
                d.clusterer = Clusterer(d.ch.conformations, sort='docking')
        mol.stop = 0
        if not hasattr(docking, 'clusterer'):
            docking.clusterer = Clusterer(docking.ch.conformations, sort='energy')
        clist = []
        for i in docking.clusterer.argsort:
            if clustFile:
                if not docking_has_clusterer:
                    docking.clusterer = Clusterer(docking.ch.conformations, 
                                            sort=sort)
                    docking.clusterer.usesSubset = 0

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Docking.py   Pymol-script-repo(Download)
from AutoDockTools.Conformation import Conformation, ConformationHandler
from AutoDockTools.Conformation import PopulationHandler
from AutoDockTools.cluster import Clusterer
from AutoDockTools.interactiveHistogramGraph import InteractiveHistogramGraph
from mglutil.math.rmsd import RMSDCalculator
        if self.version<4.0:
            cluster_type = "docking"
        self.clusterer = Clusterer(self.ch.conformations, sort=cluster_type)
        self.clusterer_dict[cluster_type] = self.clusterer
 
            cluster_type = "binding"
 
        dlo.clusterer = Clusterer(dlo.conformations, sort=cluster_type)
        #dlo.clusterer = Clusterer(dlo.conformations, sort='docking')
        if dlo.parser.clusterRecord:
        else:
            #each time you add some conformations, need a new clusterer
            clusterer = Clusterer(self.ch.conformations, sort=cluster_type)
            #clusterer = Clusterer(self.ch.conformations, sort='docking')
        self.clusterer = clusterer

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/summarize_wcg_docking.py   Pymol-script-repo(Download)
from AutoDockTools.XMLParser import XMLParser
from AutoDockTools.Docking import Docking
from AutoDockTools.cluster import Clusterer
from mglutil.math.rmsd import RMSDCalculator
from PyAutoDock.MolecularSystem import MolecularSystem
    tors_penalty = torsion_ct * 0.2744
 
    cl = Clusterer(d.ch.conformations)
    d.clusterer = cl
    cl.make_clustering(rms_tolerance)

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Conformation.py   Pymol-script-repo(Download)
from mglutil.math.statetocoords import StateToCoords
from mglutil.math.transformation import Transformation
from AutoDockTools.cluster import Clusterer
from AutoDockTools.ResultParser import ResultParser