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src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/prepare_dpf42.py   Pymol-script-repo(Download)
import os.path
from MolKit import Read
from AutoDockTools.DockingParameters import DockingParameters, genetic_algorithm_list4_2, \
                genetic_algorithm_local_search_list4_2, local_search_list4_2,\
                simulated_annealing_list4_2, epdb_list4_2
    def __init__(self, verbose = None):
        self.verbose = verbose
        self.dpo = DockingParameters()
 
 

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/dpf3_to_dpf4.py   Pymol-script-repo(Download)
from MolKit.pdbWriter import PdbqtWriter
from AutoDockTools.atomTypeTools import AutoDock4_AtomTyper
from AutoDockTools.DockingParameters import DockingParameters
from AutoDockTools.DockingParameters import genetic_algorithm_list4
from AutoDockTools.DockingParameters import genetic_algorithm_local_search_list4
 
    #what about nucleic acids???
    DPO4 = DockingParameters()
    print "default: ligand_types=", DPO4['ligand_types']['value']
    orig_compute_unbound_extended_flag = DPO4['compute_unbound_extended_flag']['value']
    if dpf3_filename:
        DPO4.read(dpf3_filename)
        if verbose: print 'read ', dpf3_filename
        DPO4['compute_unbound_extended_flag']['value'] = orig_compute_unbound_extended_flag

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/prepare_dpf41.py   Pymol-script-repo(Download)
import os.path
from MolKit import Read
from AutoDockTools.DockingParameters import DockingParameters, genetic_algorithm_list4_1, \
                genetic_algorithm_local_search_list4_1, local_search_list4_1,\
                simulated_annealing_list4_1
    def __init__(self, verbose = None):
        self.verbose = verbose
        self.dpo = DockingParameters()
 
 

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/prepare_dpf4.py   Pymol-script-repo(Download)
import os.path
from MolKit import Read
from AutoDockTools.DockingParameters import DockingParameters, genetic_algorithm_list4, \
                genetic_algorithm_local_search_list4, local_search_list4,\
                simulated_annealing_list4
    def __init__(self, verbose = None):
        self.verbose = verbose
        self.dpo = DockingParameters()
 
 

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/prepare_dpf.py   Pymol-script-repo(Download)
import os.path
from MolKit import Read
from AutoDockTools.DockingParameters import DockingParameters, genetic_algorithm_list, \
                genetic_algorithm_local_search_list, local_search_list,\
                simulated_annealing_list
    def __init__(self, verbose = None):
        self.verbose = verbose
        self.dpo = DockingParameters()
 
 

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/lib_parameter_file_writer.py   Pymol-script-repo(Download)
from MolKit import Read
from AutoDockTools.GridParameters import GridParameters, grid_parameter_list
from AutoDockTools.DockingParameters import DockingParameters
from AutoDockTools.DockingParameters import genetic_algorithm_list, \
                genetic_algorithm_local_search_list, local_search_list,\
    def setup(self, dpffile):
        self.dpffile = dpffile
        self.dpo = DockingParameters() 
        self.dpo.read(dpffile)
 

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/Utilities24/summarize_docking_directory.py   Pymol-script-repo(Download)
    # get filenames from the dpf and gpf
    #
    from AutoDockTools.DockingParameters import DockingParameters
    from AutoDockTools.GridParameters import GridParameters
 
    dpo = DockingParameters()

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
        self.dlo_list.append(dlo)
        # parse the dpf file
        dlo.dpo = DockingParameters()
        dlo.dpo.read(dpf)
        dlo.macroStem = dlo.dpo.receptor_stem
    def _buildDpo(self, lines):
        dpo = DockingParameters()
        dpo._parse(lines)
        return dpo
 

src/p/y/Pymol-script-repo-HEAD/modules/ADT/AutoDockTools/autoanalyzeCommands.py   Pymol-script-repo(Download)
from MolKit.pdbParser import PdbParser, PdbqParser, PdbqsParser, PdbqtParser
from MolKit.stringSelector import CompoundStringSelector
from AutoDockTools.DockingParameters import DockingParameters
from AutoDockTools.Conformation import AutodockState, ConformationHandler
from AutoDockTools.ConfPlayer import ConformationPlayer, PopulationPlayer