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src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/autoanalyzeCommands.py   Pymol-script-repo(Download)
from AutoDockTools.Conformation import AutodockState, ConformationHandler
from AutoDockTools.ConfPlayer import ConformationPlayer, PopulationPlayer
from AutoDockTools.Docking import Docking, FoxResultProcessor
from AutoDockTools.DlgParser import DlgParser
from AutoDockTools.EntropiaParser import EntropiaParser
                msg = "Added %d docked conformations to %s\nUse keyboard arrow keys to view" %( len(ligand.allAtoms[0]._coords), ligand.name)
                self.vf.warningMsg(msg)
        d = self.vf.docked = Docking()
        top = None
        if  self.vf.userpref['VS_ShowClusteringHistogram']['value']=='Yes':
            p = XMLParser()
            if not addToPrevious or not self.vf.docked:
                d = self.vf.docked = Docking(parser=p)
                print isinstance(d.parser, XMLParser)
            if not isinstance(self.vf.docked.parser, XMLParser):
            #d will be a new docking instance
            if not addToPrevious or not self.vf.docked:
                d = self.vf.docked = Docking()
            #set up rmsTool for the clusterer here
            #this is used by the spw in showStates
                d = self.vf.docked
            else:
                d = Docking()
            d.readDlg(resultsFile)
        elif ext=='.res' or ext=='.results':

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/summarize_wcg_docking.py   Pymol-script-repo(Download)
from MolKit.hydrogenBondBuilder import HydrogenBondBuilder
from AutoDockTools.XMLParser import XMLParser
from AutoDockTools.Docking import Docking
from AutoDockTools.cluster import Clusterer
from mglutil.math.rmsd import RMSDCalculator
    print "xml_list =", xml_list
    p = XMLParser()
    d = Docking(parser=p)
    for xml_file in xml_list:
        print "calling readXMLResults with", xml_file

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/process_VSResults.py   Pymol-script-repo(Download)
 
from MolKit import Read
from AutoDockTools.Docking import Docking, DockingResultProcessor
from mglutil.math.rmsd import RMSDCalculator
from AutoDockTools.InteractionDetector import InteractionDetector

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/process_VinaResult.py   Pymol-script-repo(Download)
 
from MolKit import Read
from AutoDockTools.Docking import Docking, VinaResultProcessor
from mglutil.math.rmsd import RMSDCalculator
from AutoDockTools.InteractionDetector import InteractionDetector

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/compute_rms_between_methods.py   Pymol-script-repo(Download)
 
from MolKit import Read
from AutoDockTools.Docking import Docking
from mglutil.math.rmsd import RMSDCalculator
 
    #read all the docking logs in reference directory as one Docking
    ref_dlg_list = glob.glob(refdirectory + '/*.dlg')
    ref_d = Docking()
    for dlg in ref_dlg_list:
        ref_d.readDlg(dlg)
    #process docking in test directory
    dlg_list = glob.glob(directory + '/*.dlg')
    d = Docking()
    for dlg in dlg_list:
        d.readDlg(dlg)

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/write_vs_hits.py   Pymol-script-repo(Download)
import os
 
from AutoDockTools.Docking import Docking
 
if __name__ == '__main__':
        dlgFN = path_to_dockings + "/" + fn +".dlg"
        #create a docking
        d = Docking()
        d.readDlg(dlgFN)
        #set ligand to lowest energy conformation LE

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/write_lowest_energy_ligand.py   Pymol-script-repo(Download)
 
from MolKit import Read
from AutoDockTools.Docking import Docking
 
 
    #what about nucleic acids???
 
    d = Docking()
    d.readDlg(dlgfilename)
 

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/write_largest_cluster_ligand.py   Pymol-script-repo(Download)
 
from MolKit import Read
from AutoDockTools.Docking import Docking
from mglutil.math.rmsd import RMSDCalculator
 
 
    dlg_list = glob.glob('*.dlg')
    d = Docking()
    for dlg in dlg_list:
        d.readDlg(dlg)

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/write_conformations_from_dlg.py   Pymol-script-repo(Download)
import os
 
from AutoDockTools.Docking import Docking
 
 
 
 
    d = Docking()
    d.readDlg(docking_filename)
    lines = d.ligMol.parser.allLines

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/write_clustering_histogram_postscript.py   Pymol-script-repo(Download)
from MolKit import Read
 
from AutoDockTools.Docking import Docking
from AutoDockTools.interactiveHistogramGraph import InteractiveHistogramGraph
from AutoDockTools.histogram import HistogramRI
    #read all the docking logs in as one Docking
    dlg_list = glob.glob(directory + '/*.dlg')
    d = Docking()
    for dlg in dlg_list:
        d.readDlg(dlg)

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