Python Network.addNodeの例

コード例 #1

ファイル: VS_net.py プロジェクト: 8848/Pymol-script-repo

masterNet.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")

from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
    addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False)
except:
    pass
try:
    addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
    pass
try:
    ## saving node iterate ##
    from Vision.StandardNodes import Iterate
    iterate_0 = Iterate(constrkw={}, name='iterate', library=stdlib)
    masterNet.addNode(iterate_0,16,228)
    iterate_0.inputPortByName['stopOnFailure'].widget.set(0, run=False)
    apply(iterate_0.configure, (), {'paramPanelImmediate': 1})
except:
    print "WARNING: failed to restore Iterate named iterate in network masterNet"
    print_exc()
    iterate_0=None

try:
    ## saving node VirtualScreening ##
    from Adt.Macro.VirtualScreening import VirtualScreening
    VirtualScreening_1 = VirtualScreening(constrkw={}, name='VirtualScreening', library=Adt)
    masterNet.addNode(VirtualScreening_1,216,497)
    apply(VirtualScreening_1.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
    PrepareReceptor_4 = VirtualScreening_1.macroNetwork.nodes[2]
    Pdb2pqrWS_7 = PrepareReceptor_4.macroNetwork.nodes[2]

コード例 #2

ファイル: AutoGrid_0.1_net.py プロジェクト: lisarosalina/App

from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
    addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False)
except:
    pass
try:
    addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
    pass
try:
    ## saving node ComputeGrids ##
    from Adt.Macro.ComputeGrids import ComputeGrids
    ComputeGrids_0 = ComputeGrids(constrkw={},
                                  name='ComputeGrids',
                                  library=Adt)
    masterNet.addNode(ComputeGrids_0, 391, 290)
    apply(ComputeGrids_0.configure, (), {
        'paramPanelImmediate': 1,
        'expanded': False
    })
    prepareGPF_kryptonite_nbcr_net_4 = ComputeGrids_0.macroNetwork.nodes[3]
    prepareGPF_kryptonite_nbcr_net_4.inputPortByName['singlelib'].widget.set(
        r"", run=False)
    prepareGPF_kryptonite_nbcr_net_4.inputPortByName['r_url'].widget.set(
        r"", run=False)
    prepareGPF_kryptonite_nbcr_net_4.inputPortByName['zpoints'].widget.set(
        r"", run=False)
    prepareGPF_kryptonite_nbcr_net_4.inputPortByName[
        'filter_file_url'].widget.set(r"", run=False)
    apply(
        prepareGPF_kryptonite_nbcr_net_4.inputPortByName['lib'].widget.

コード例 #3

                                         "stdlib")

from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
    addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False)
except:
    pass
try:
    addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
    pass
try:
    ## saving node iterate ##
    from Vision.StandardNodes import Iterate
    iterate_0 = Iterate(constrkw={}, name='iterate', library=stdlib)
    masterNet.addNode(iterate_0, 16, 228)
    iterate_0.inputPortByName['stopOnFailure'].widget.set(0, run=False)
    apply(iterate_0.configure, (), {'paramPanelImmediate': 1})
except:
    print "WARNING: failed to restore Iterate named iterate in network masterNet"
    print_exc()
    iterate_0 = None

try:
    ## saving node VirtualScreening ##
    from Adt.Macro.VirtualScreening import VirtualScreening
    VirtualScreening_1 = VirtualScreening(constrkw={},
                                          name='VirtualScreening',
                                          library=Adt)
    masterNet.addNode(VirtualScreening_1, 216, 497)
    apply(VirtualScreening_1.configure, (), {

コード例 #4

ファイル: GROMOSClustering_0.1_net.py プロジェクト: lisarosalina/App

masterNet.getEditor().addLibraryInstance(Adt,"AutoDockTools.VisionInterface.Adt", "Adt")

masterNet.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")

masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")

from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
    addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
    pass
try:
    ## saving node GromosCluster ##
    from Adt.Macro.GromosCluster import GromosCluster
    GromosCluster_0 = GromosCluster(constrkw={}, name='GromosCluster', library=Adt)
    masterNet.addNode(GromosCluster_0,396,213)
    apply(GromosCluster_0.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
    GROMOS_ClusterFiles_kryptonite_nbcr_net_3 = GromosCluster_0.macroNetwork.nodes[2]
    GROMOS_ClusterFiles_kryptonite_nbcr_net_3.inputPortByName['expert_options'].widget.set(r"", run=False)
    GROMOS_ClusterFiles_kryptonite_nbcr_net_3.inputPortByName['prefix'].widget.set(r"", run=False)
    GROMOS_ClusterFiles_kryptonite_nbcr_net_3.inputPortByName['default_options'].widget.set(r"-o -g -dist -ev -sz -tr -ntr -clid -cl", run=False)
    GROMOS_ClusterFiles_kryptonite_nbcr_net_3.inputPortByName['localRun'].widget.set(0, run=False)
    apply(GROMOS_ClusterFiles_kryptonite_nbcr_net_3.inputPortByName['method'].widget.configure, (), {'choices': ('gromos', 'linkage', 'jarvis-patrick', 'monte-carlo', 'diagonalization')})
    GROMOS_ClusterFiles_kryptonite_nbcr_net_3.inputPortByName['method'].widget.set(r"gromos", run=False)
    GROMOS_ClusterFiles_kryptonite_nbcr_net_3.inputPortByName['execPath'].widget.set(r"", run=False)
    Entry_6 = GromosCluster_0.macroNetwork.nodes[5]
    Entry_6.inputPortByName['entry'].widget.set(r"3", run=False)

    ## saving connections for network GromosCluster ##
    GromosCluster_0.macroNetwork.freeze()
    GromosCluster_0.macroNetwork.unfreeze()

コード例 #5

ファイル: ImageFigure_net.py プロジェクト: MolecularFlipbook/FlipbookApp

    masterNet
except (NameError, AttributeError): # we run the network outside Vision
    from NetworkEditor.net import Network
    masterNet = Network()

masterNet.getEditor().addLibraryInstance(matplotliblib,"Vision.matplotlibNodes", "matplotliblib")

masterNet.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")

masterNet.getEditor().addLibraryInstance(vizlib,"DejaVu.VisionInterface.DejaVuNodes", "vizlib")

try:
    ## saving node Histogram ##
    from Vision.matplotlibNodes import HistogramNE
    Histogram_0 = HistogramNE(constrkw={}, name='Histogram', library=matplotliblib)
    masterNet.addNode(Histogram_0,108,243)
    Histogram_0.inputPortByName['bins'].widget.set(50, run=False)
    Histogram_0.inputPortByName['normed'].widget.set(1, run=False)
    Histogram_0.inputPortByName['patch_antialiased'].widget.set(1, run=False)
    Histogram_0.inputPortByName['patch_linewidth'].widget.set(1, run=False)
    Histogram_0.inputPortByName['patch_edgecolor'].widget.set(r"black", run=False)
    Histogram_0.inputPortByName['patch_facecolor'].widget.set(r"green", run=False)
    apply(Histogram_0.configure, (), {'paramPanelImmediate': 1})
except:
    print "WARNING: failed to restore HistogramNE named Histogram in network masterNet"
    print_exc()
    Histogram_0=None

try:
    ## saving node Draw Area ##
    from Vision.matplotlibNodes import MPLDrawAreaNE

コード例 #6

ファイル: AutoDockVSlocal_0.1_net.py プロジェクト: MolecularFlipbook/FlipbookApp

masterNet.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")

from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
    addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False)
except:
    pass
try:
    addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
    pass
try:
    ## saving node iterate ##
    from Vision.StandardNodes import Iterate
    iterate_0 = Iterate(constrkw={}, name='iterate', library=stdlib)
    masterNet.addNode(iterate_0,16,228)
    iterate_0.inputPortByName['stopOnFailure'].widget.set(0, run=False)
    apply(iterate_0.configure, (), {'paramPanelImmediate': 1})
except:
    print "WARNING: failed to restore Iterate named iterate in network masterNet"
    print_exc()
    iterate_0=None

try:
    ## saving node VirtualScreening ##
    from Adt.Macro.VirtualScreening import VirtualScreening
    VirtualScreening_1 = VirtualScreening(constrkw={}, name='VirtualScreening', library=Adt)
    masterNet.addNode(VirtualScreening_1,216,497)
    apply(VirtualScreening_1.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
    PrepareReceptor_4 = VirtualScreening_1.macroNetwork.nodes[2]
    Pdb2pqrWS_7 = PrepareReceptor_4.macroNetwork.nodes[2]

コード例 #7

         'namedArgs': {
             'i': False,
             'k': False,
             'l': '',
             'o': False,
             'pdbq': '',
             'p': '',
             't': False,
             'url': '',
             'localRun': False,
             'execPath': ''
         }
     },
     name='AutodockOpalService_kryptonite_nbcr_net',
     library=wslib)
 masterNet.addNode(AutodockOpalService_kryptonite_nbcr_net_0, 173, 245)
 apply(
     AutodockOpalService_kryptonite_nbcr_net_0.inputPortByName['l'].
     configure, (), {'defaultValue': None})
 apply(
     AutodockOpalService_kryptonite_nbcr_net_0.inputPortByName['pdbq'].
     configure, (), {'defaultValue': None})
 apply(
     AutodockOpalService_kryptonite_nbcr_net_0.inputPortByName['p'].
     configure, (), {'defaultValue': None})
 apply(
     AutodockOpalService_kryptonite_nbcr_net_0.inputPortByName['url'].
     configure, (), {'defaultValue': None})
 AutodockOpalService_kryptonite_nbcr_net_0.inputPortByName['i'].widget.set(
     0, run=False)
 AutodockOpalService_kryptonite_nbcr_net_0.inputPortByName['k'].widget.set(

コード例 #8

ファイル: AutoDockML_0.1_net.py プロジェクト: lisarosalina/App

masterNet.getEditor().addLibraryInstance(Adt,"AutoDockTools.VisionInterface.Adt", "Adt")

masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")

masterNet.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")

from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
    addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
    pass
try:
    ## saving node AutodockVS ##
    from Adt.Macro.AutodockVS import AutodockVS
    AutodockVS_0 = AutodockVS(constrkw={}, name='AutodockVS', library=Adt)
    masterNet.addNode(AutodockVS_0,357,292)
    apply(AutodockVS_0.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
    autodock_kryptonite_nbcr_net_4 = AutodockVS_0.macroNetwork.nodes[3]
    autodock_kryptonite_nbcr_net_4.inputPortByName['ga_run'].widget.set(r"", run=False)
    apply(autodock_kryptonite_nbcr_net_4.inputPortByName['lib'].widget.configure, (), {'choices': ('sample', 'NCIDS_SC', 'NCI_DS1', 'NCI_DS2', 'human_metabolome', 'chembridge_building_blocks', 'drugbank_nutraceutics', 'drugbank_smallmol', 'fda_approved')})
    autodock_kryptonite_nbcr_net_4.inputPortByName['lib'].widget.set(r"", run=False)
    autodock_kryptonite_nbcr_net_4.inputPortByName['filter_file_url'].widget.set(r"", run=False)
    autodock_kryptonite_nbcr_net_4.inputPortByName['ga_num_evals'].widget.set(r"", run=False)
    apply(autodock_kryptonite_nbcr_net_4.inputPortByName['sched'].widget.configure, (), {'choices': ('SGE', 'CSF')})
    autodock_kryptonite_nbcr_net_4.inputPortByName['sched'].widget.set(r"SGE", run=False)
    autodock_kryptonite_nbcr_net_4.inputPortByName['ga_num_generations'].widget.set(r"", run=False)
    autodock_kryptonite_nbcr_net_4.inputPortByName['userlib'].widget.set(r"", run=False)
    autodock_kryptonite_nbcr_net_4.inputPortByName['ga_pop_size'].widget.set(r"", run=False)
    autodock_kryptonite_nbcr_net_4.inputPortByName['localRun'].widget.set(0, run=False)
    autodock_kryptonite_nbcr_net_4.inputPortByName['email'].widget.set(r"", run=False)
    autodock_kryptonite_nbcr_net_4.inputPortByName['execPath'].widget.set(r"", run=False)

コード例 #9

ファイル: PrepareReceptor_0.1_net.py プロジェクト: lisarosalina/App

masterNet.getEditor().addLibraryInstance(stdlib, "Vision.StandardNodes",
                                         "stdlib")

from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
    addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False)
except:
    pass
try:
    ## saving node PrepareReceptor2 ##
    from Adt.Macro.PrepareReceptor import PrepareReceptor
    PrepareReceptor2_0 = PrepareReceptor(constrkw={},
                                         name='PrepareReceptor2',
                                         library=Adt)
    masterNet.addNode(PrepareReceptor2_0, 301, 206)
    apply(PrepareReceptor2_0.configure, (), {
        'paramPanelImmediate': 1,
        'expanded': False
    })
    Pdb2pqrWS_3 = PrepareReceptor2_0.macroNetwork.nodes[2]
    Pdb2pqrOpalService_ws_nbcr_net_7 = Pdb2pqrWS_3.macroNetwork.nodes[3]
    Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['noopt'].widget.set(
        0, run=False)
    Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['phi'].widget.set(
        0, run=False)
    Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['psi'].widget.set(
        0, run=False)
    Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['verbose'].widget.set(
        1, run=False)
    Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['chain'].widget.set(

コード例 #10

ファイル: VSResults_0.1_pmvnet.py プロジェクト: MolecularFlipbook/FlipbookApp

from Vision.StandardNodes import stdlib
try:
    masterNet
except (NameError, AttributeError): # we run the network outside Vision
    from NetworkEditor.net import Network
    masterNet = Network()

masterNet.getEditor().addLibraryInstance(pmvlib,"Pmv.VisionInterface.PmvNodes", "pmvlib")

masterNet.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")

try:
    ## saving node GetReceptors ##
    from Vision.StandardNodes import Generic
    GetReceptors_0 = Generic(constrkw={}, name='GetReceptors', library=stdlib)
    masterNet.addNode(GetReceptors_0,12,104)
    apply(GetReceptors_0.addInputPort, (), {'singleConnection': True, 'name': 'directory', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'})
    apply(GetReceptors_0.addOutputPort, (), {'name': 'filelist', 'datatype': 'list', 'height': 12, 'width': 12, 'shape': 'oval', 'color': 'cyan'})
    apply(GetReceptors_0.addOutputPort, (), {'name': 'filelist_paths', 'datatype': 'list', 'height': 12, 'width': 12, 'shape': 'oval', 'color': 'cyan'})
    code = """def doit(self, directory):
    import glob, os
    match_str = "*"
    if directory is not None:
        cwd = os.getcwd()
        os.chdir(directory)
    try:
        pdirs = glob.glob(match_str)
        values = []

        for i in pdirs:
            if os.path.exists(i + os.sep + '''summarize_results.txt'''):

コード例 #11

ファイル: ImageFigure_net.py プロジェクト: tongjuhua/FlipbookApp

                                         "matplotliblib")

masterNet.getEditor().addLibraryInstance(stdlib, "Vision.StandardNodes",
                                         "stdlib")

masterNet.getEditor().addLibraryInstance(vizlib,
                                         "DejaVu.VisionInterface.DejaVuNodes",
                                         "vizlib")

try:
    ## saving node Histogram ##
    from Vision.matplotlibNodes import HistogramNE
    Histogram_0 = HistogramNE(constrkw={},
                              name='Histogram',
                              library=matplotliblib)
    masterNet.addNode(Histogram_0, 108, 243)
    Histogram_0.inputPortByName['bins'].widget.set(50, run=False)
    Histogram_0.inputPortByName['normed'].widget.set(1, run=False)
    Histogram_0.inputPortByName['patch_antialiased'].widget.set(1, run=False)
    Histogram_0.inputPortByName['patch_linewidth'].widget.set(1, run=False)
    Histogram_0.inputPortByName['patch_edgecolor'].widget.set(r"black",
                                                              run=False)
    Histogram_0.inputPortByName['patch_facecolor'].widget.set(r"green",
                                                              run=False)
    apply(Histogram_0.configure, (), {'paramPanelImmediate': 1})
except:
    print "WARNING: failed to restore HistogramNE named Histogram in network masterNet"
    print_exc()
    Histogram_0 = None

try:

コード例 #12

ファイル: PrepareReceptor_0.1_net.py プロジェクト: MolecularFlipbook/FlipbookApp

masterNet.getEditor().addLibraryInstance(Adt,"AutoDockTools.VisionInterface.Adt", "Adt")

masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")

masterNet.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")

from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
    addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False)
except:
    pass
try:
    ## saving node PrepareReceptor2 ##
    from Adt.Macro.PrepareReceptor import PrepareReceptor
    PrepareReceptor2_0 = PrepareReceptor(constrkw={}, name='PrepareReceptor2', library=Adt)
    masterNet.addNode(PrepareReceptor2_0,301,206)
    apply(PrepareReceptor2_0.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
    Pdb2pqrWS_3 = PrepareReceptor2_0.macroNetwork.nodes[2]
    Pdb2pqrOpalService_ws_nbcr_net_7 = Pdb2pqrWS_3.macroNetwork.nodes[3]
    Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['noopt'].widget.set(0, run=False)
    Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['phi'].widget.set(0, run=False)
    Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['psi'].widget.set(0, run=False)
    Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['verbose'].widget.set(1, run=False)
    Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['chain'].widget.set(0, run=False)
    Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['nodebump'].widget.set(0, run=False)
    Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['chi'].widget.set(0, run=False)
    Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['ligand'].widget.set(r"", run=False)
    Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['hbond'].widget.set(0, run=False)
    Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['with_ph'].widget.set(r"", run=False)
    apply(Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['forcefield'].widget.configure, (), {'choices': ('AMBER', 'CHARMM', 'PARSE', 'TYL06')})
    Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['forcefield'].widget.set(r"AMBER", run=False)

コード例 #13

ファイル: VinaVSlocal_0.1_net.py プロジェクト: lisarosalina/App

from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
    addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False)
except:
    pass
try:
    addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
    pass
try:
    ## saving node StructureBrowser ##
    from Adt.Input.StructureBrowser import StructureBrowser
    StructureBrowser_0 = StructureBrowser(constrkw={},
                                          name='StructureBrowser',
                                          library=Adt)
    masterNet.addNode(StructureBrowser_0, 32, 37)
    StructureBrowser_0.inputPortByName['receptor_file'].widget.set(
        r"VinaVSlocal_0.1_input/2HTY_A-2HTY_A.pdb", run=False)
    apply(StructureBrowser_0.configure, (), {'paramPanelImmediate': 1})
except:
    print "WARNING: failed to restore StructureBrowser named StructureBrowser in network masterNet"
    print_exc()
    StructureBrowser_0 = None

try:
    ## saving node Vina Config File Browser ##
    from Vision.StandardNodes import FileBrowserNE
    Vina_Config_File_Browser_1 = FileBrowserNE(constrkw={},
                                               name='Vina Config File Browser',
                                               library=stdlib)
    masterNet.addNode(Vina_Config_File_Browser_1, 849, 41)

コード例 #14

ファイル: AutoGrid_0.1_net.py プロジェクト: MolecularFlipbook/FlipbookApp

masterNet.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")

from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
    addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False)
except:
    pass
try:
    addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
    pass
try:
    ## saving node ComputeGrids ##
    from Adt.Macro.ComputeGrids import ComputeGrids
    ComputeGrids_0 = ComputeGrids(constrkw={}, name='ComputeGrids', library=Adt)
    masterNet.addNode(ComputeGrids_0,391,290)
    apply(ComputeGrids_0.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
    prepareGPF_kryptonite_nbcr_net_4 = ComputeGrids_0.macroNetwork.nodes[3]
    prepareGPF_kryptonite_nbcr_net_4.inputPortByName['singlelib'].widget.set(r"", run=False)
    prepareGPF_kryptonite_nbcr_net_4.inputPortByName['r_url'].widget.set(r"", run=False)
    prepareGPF_kryptonite_nbcr_net_4.inputPortByName['zpoints'].widget.set(r"", run=False)
    prepareGPF_kryptonite_nbcr_net_4.inputPortByName['filter_file_url'].widget.set(r"", run=False)
    apply(prepareGPF_kryptonite_nbcr_net_4.inputPortByName['lib'].widget.configure, (), {'choices': ('sample', 'NCIDS_SC', 'NCI_DS1', 'NCI_DS2', 'oldNCI', 'human_metabolome', 'chembridge_building_blocks', 'drugbank_nutraceutics', 'drugbank_smallmol', 'fda_approved')})
    prepareGPF_kryptonite_nbcr_net_4.inputPortByName['lib'].widget.set(r"", run=False)
    prepareGPF_kryptonite_nbcr_net_4.inputPortByName['ypoints'].widget.set(r"", run=False)
    prepareGPF_kryptonite_nbcr_net_4.inputPortByName['xcenter'].widget.set(r"auto", run=False)
    prepareGPF_kryptonite_nbcr_net_4.inputPortByName['p'].widget.set(r"", run=False)
    prepareGPF_kryptonite_nbcr_net_4.inputPortByName['o'].widget.set(r"", run=False)
    prepareGPF_kryptonite_nbcr_net_4.inputPortByName['zcenter'].widget.set(r"auto", run=False)
    prepareGPF_kryptonite_nbcr_net_4.inputPortByName['v'].widget.set(0, run=False)
    prepareGPF_kryptonite_nbcr_net_4.inputPortByName['userlib'].widget.set(r"", run=False)

コード例 #15

ファイル: VinaVSlocal_0.1_net.py プロジェクト: MolecularFlipbook/FlipbookApp

masterNet.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")

from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
    addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False)
except:
    pass
try:
    addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
    pass
try:
    ## saving node StructureBrowser ##
    from Adt.Input.StructureBrowser import StructureBrowser
    StructureBrowser_0 = StructureBrowser(constrkw={}, name='StructureBrowser', library=Adt)
    masterNet.addNode(StructureBrowser_0,32,37)
    StructureBrowser_0.inputPortByName['receptor_file'].widget.set(r"VinaVSlocal_0.1_input/2HTY_A-2HTY_A.pdb", run=False)
    apply(StructureBrowser_0.configure, (), {'paramPanelImmediate': 1})
except:
    print "WARNING: failed to restore StructureBrowser named StructureBrowser in network masterNet"
    print_exc()
    StructureBrowser_0=None

try:
    ## saving node Vina Config File Browser ##
    from Vision.StandardNodes import FileBrowserNE
    Vina_Config_File_Browser_1 = FileBrowserNE(constrkw={}, name='Vina Config File Browser', library=stdlib)
    masterNet.addNode(Vina_Config_File_Browser_1,849,41)
    Vina_Config_File_Browser_1.inputPortByName['filename'].widget.set(r"VinaVSlocal_0.1_input/test.config", run=False)
    apply(Vina_Config_File_Browser_1.configure, (), {'paramPanelImmediate': 1})
except:

コード例 #16

ファイル: VinaVSpublic_0.1_net.py プロジェクト: lisarosalina/App

from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
    addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False)
except:
    pass
try:
    addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
    pass
try:
    ## saving node StructureBrowser ##
    from Adt.Input.StructureBrowser import StructureBrowser
    StructureBrowser_0 = StructureBrowser(constrkw={},
                                          name='StructureBrowser',
                                          library=Adt)
    masterNet.addNode(StructureBrowser_0, 32, 37)
    StructureBrowser_0.inputPortByName['receptor_file'].widget.set(
        r"VinaVSpublic_0.1_input/2HTY_A-2HTY_A.pdb", run=False)
    apply(StructureBrowser_0.configure, (), {'paramPanelImmediate': 1})
except:
    print "WARNING: failed to restore StructureBrowser named StructureBrowser in network masterNet"
    print_exc()
    StructureBrowser_0 = None

try:
    ## saving node PublicServerLigandDB ##
    from Adt.Input.PublicServerLigandDB import PublicServerLigandDB
    PublicServerLigandDB_1 = PublicServerLigandDB(constrkw={},
                                                  name='PublicServerLigandDB',
                                                  library=Adt)
    masterNet.addNode(PublicServerLigandDB_1, 419, 38)

コード例 #17

ファイル: NAMDNBCR_0.1_net.py プロジェクト: MolecularFlipbook/FlipbookApp

    masterNet = Network()

masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")

masterNet.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")

from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
    addOpalServerAsCategory("http://oolite.calit2.optiputer.net/opal2", replace=False)
except:
    pass
try:
    ## saving node FileWithCommandOrdering ##
    from Vision.StandardNodes import FileBrowserNE
    FileWithCommandOrdering_87 = FileBrowserNE(constrkw={}, name='FileWithCommandOrdering', library=stdlib)
    masterNet.addNode(FileWithCommandOrdering_87,30,10)
    FileWithCommandOrdering_87.inputPortByName['filename'].widget.set(r"NAMDNBCR_0.1_input/order.txt", run=False)
    apply(FileWithCommandOrdering_87.configure, (), {'paramPanelImmediate': 1})
except:
    print "WARNING: failed to restore FileBrowserNE named FileWithCommandOrdering in network masterNet"
    print_exc()
    FileWithCommandOrdering_87=None

try:
    ## saving node GetOrdering ##
    from Vision.StandardNodes import Generic
    GetOrdering_88 = Generic(constrkw={}, name='GetOrdering', library=stdlib)
    masterNet.addNode(GetOrdering_88,30,107)
    apply(GetOrdering_88.addInputPort, (), {'singleConnection': True, 'name': 'order_file', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'})
    apply(GetOrdering_88.addOutputPort, (), {'name': 'order_list', 'datatype': 'list', 'height': 12, 'width': 12, 'shape': 'oval', 'color': 'cyan'})
    code = """def doit(self, order_file):

コード例 #18

    masterNet = Network()

masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")

masterNet.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")

from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
    addOpalServerAsCategory("http://rocce.ucsd.edu/opal2", replace=False)
except:
    pass
try:
    ## saving node Input Directory Browser ##
    from Vision.StandardNodes import DirBrowserNE
    Input_Directory_Browser_0 = DirBrowserNE(constrkw={}, name='Input Directory Browser', library=stdlib)
    masterNet.addNode(Input_Directory_Browser_0,375,8)
    Input_Directory_Browser_0.inputPortByName['directory'].widget.set(r"AMDNBCR_0.2_input", run=False)
    apply(Input_Directory_Browser_0.configure, (), {'paramPanelImmediate': 1})
except:
    print "WARNING: failed to restore DirBrowserNE named Input Directory Browser in network masterNet"
    print_exc()
    Input_Directory_Browser_0=None

try:
    ## saving node NumProcessors ##
    from Vision.StandardNodes import EntryNE
    NumProcessors_1 = EntryNE(constrkw={}, name='NumProcessors', library=stdlib)
    masterNet.addNode(NumProcessors_1,1043,12)
    NumProcessors_1.inputPortByName['entry'].widget.set(r"4", run=False)
    code = """def doit(self, entry):
    if len(str(entry))!=0:

コード例 #19

ファイル: visualization_0.1.1_pmvnet.py プロジェクト: lisarosalina/App

from Vision.StandardNodes import stdlib
try:
    masterNet
except (NameError, AttributeError): # we run the network outside Vision
    from NetworkEditor.net import Network
    masterNet = Network()

masterNet.getEditor().addLibraryInstance(pmvlib,"Pmv.VisionInterface.PmvNodes", "pmvlib")

masterNet.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")

try:
    ## saving node AutoDock VS Result Directory ##
    from Vision.StandardNodes import DirBrowserNE
    AutoDock_VS_Result_Directory_28 = DirBrowserNE(constrkw={}, name='AutoDock VS Result Directory', library=stdlib)
    masterNet.addNode(AutoDock_VS_Result_Directory_28,47,27)
    AutoDock_VS_Result_Directory_28.inputPortByName['directory'].widget.set(r"visualization_0.1.1_input", run=False)
    apply(AutoDock_VS_Result_Directory_28.configure, (), {'paramPanelImmediate': 1})
except:
    print "WARNING: failed to restore DirBrowserNE named AutoDock VS Result Directory in network masterNet"
    print_exc()
    AutoDock_VS_Result_Directory_28=None

try:
    ## saving node GetReceptors ##
    from Vision.StandardNodes import Generic
    GetReceptors_29 = Generic(constrkw={}, name='GetReceptors', library=stdlib)
    masterNet.addNode(GetReceptors_29,47,123)
    apply(GetReceptors_29.addInputPort, (), {'singleConnection': True, 'name': 'dir', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'})
    apply(GetReceptors_29.addOutputPort, (), {'name': 'receptors', 'datatype': 'list', 'height': 12, 'width': 12, 'shape': 'oval', 'color': 'cyan'})
    apply(GetReceptors_29.addOutputPort, (), {'name': 'receptor_paths', 'datatype': 'list', 'height': 12, 'width': 12, 'shape': 'oval', 'color': 'cyan'})

コード例 #20

ファイル: NAMDTeragrid_0.1_net.py プロジェクト: lisarosalina/App

masterNet.getEditor().addLibraryInstance(stdlib, "Vision.StandardNodes",
                                         "stdlib")

from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
    addOpalServerAsCategory("http://oolitevm.calit2.optiputer.net/opal2",
                            replace=False)
except:
    pass
try:
    ## saving node FileWithCommandOrdering ##
    from Vision.StandardNodes import FileBrowserNE
    FileWithCommandOrdering_0 = FileBrowserNE(constrkw={},
                                              name='FileWithCommandOrdering',
                                              library=stdlib)
    masterNet.addNode(FileWithCommandOrdering_0, 30, 10)
    FileWithCommandOrdering_0.inputPortByName['filename'].widget.set(
        r"NAMDTeragridGPU_0.1_input/order.txt", run=False)
    apply(FileWithCommandOrdering_0.configure, (), {'paramPanelImmediate': 1})
except:
    print "WARNING: failed to restore FileBrowserNE named FileWithCommandOrdering in network masterNet"
    print_exc()
    FileWithCommandOrdering_0 = None

try:
    ## saving node GetOrdering ##
    from Vision.StandardNodes import Generic
    GetOrdering_1 = Generic(constrkw={}, name='GetOrdering', library=stdlib)
    masterNet.addNode(GetOrdering_1, 30, 107)
    apply(
        GetOrdering_1.addInputPort, (), {

コード例 #21

ファイル: NAMDTeragrid_0.1_net.py プロジェクト: MolecularFlipbook/FlipbookApp

    masterNet = Network()

masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")

masterNet.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")

from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
    addOpalServerAsCategory("http://oolitevm.calit2.optiputer.net/opal2", replace=False)
except:
    pass
try:
    ## saving node FileWithCommandOrdering ##
    from Vision.StandardNodes import FileBrowserNE
    FileWithCommandOrdering_0 = FileBrowserNE(constrkw={}, name='FileWithCommandOrdering', library=stdlib)
    masterNet.addNode(FileWithCommandOrdering_0,30,10)
    FileWithCommandOrdering_0.inputPortByName['filename'].widget.set(r"NAMDTeragridGPU_0.1_input/order.txt", run=False)
    apply(FileWithCommandOrdering_0.configure, (), {'paramPanelImmediate': 1})
except:
    print "WARNING: failed to restore FileBrowserNE named FileWithCommandOrdering in network masterNet"
    print_exc()
    FileWithCommandOrdering_0=None

try:
    ## saving node GetOrdering ##
    from Vision.StandardNodes import Generic
    GetOrdering_1 = Generic(constrkw={}, name='GetOrdering', library=stdlib)
    masterNet.addNode(GetOrdering_1,30,107)
    apply(GetOrdering_1.addInputPort, (), {'singleConnection': True, 'name': 'order_file', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'})
    apply(GetOrdering_1.addOutputPort, (), {'name': 'order_list', 'datatype': 'list', 'height': 12, 'width': 12, 'shape': 'oval', 'color': 'cyan'})
    code = """def doit(self, order_file):

コード例 #22

                                         "stdlib")

from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
    addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False)
except:
    pass
try:
    addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
    pass
try:
    ## saving node iterate ##
    from Vision.StandardNodes import Iterate
    iterate_0 = Iterate(constrkw={}, name='iterate', library=stdlib)
    masterNet.addNode(iterate_0, 16, 228)
    iterate_0.inputPortByName['stopOnFailure'].widget.set(0, run=False)
    apply(iterate_0.configure, (), {'paramPanelImmediate': 1})
except:
    print "WARNING: failed to restore Iterate named iterate in network masterNet"
    print_exc()
    iterate_0 = None

try:
    ## saving node VirtualScreening ##
    from Adt.Macro.VirtualScreening import VirtualScreening
    VirtualScreening_1 = VirtualScreening(constrkw={},
                                          name='VirtualScreening',
                                          library=Adt)
    masterNet.addNode(VirtualScreening_1, 216, 497)
    apply(VirtualScreening_1.configure, (), {

コード例 #23

ファイル: Axes_net.py プロジェクト: MolecularFlipbook/FlipbookApp

from Vision.StandardNodes import stdlib
try:
    masterNet
except (NameError, AttributeError): # we run the network outside Vision
    from NetworkEditor.net import Network
    masterNet = Network()

masterNet.getEditor().addLibraryInstance(matplotliblib,"Vision.matplotlibNodes", "matplotliblib")

masterNet.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")

try:
    ## saving node ReadTable ##
    from Vision.StandardNodes import ReadTable
    ReadTable_0 = ReadTable(constrkw={}, name='ReadTable', library=stdlib)
    masterNet.addNode(ReadTable_0,71,7)
    ReadTable_0.inputPortByName['filename'].widget.set(r"Data/axes_data.dat", run=False)
    ReadTable_0.inputPortByName['numOfTopLinesToJump'].widget.set(0, run=False)
    apply(ReadTable_0.inputPortByName['numOfBottomLinesToJump'].widget.configure, (), {'oneTurn': 10.0})
    ReadTable_0.inputPortByName['numOfBottomLinesToJump'].widget.set(2, run=False)
    ReadTable_0.inputPortByName['sep'].widget.set(r",", run=False)
    ReadTable_0.inputPortByName['datatype'].widget.set(r"float", run=False)
    apply(ReadTable_0.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
    print "WARNING: failed to restore ReadTable named ReadTable in network masterNet"
    print_exc()
    ReadTable_0=None

try:
    ## saving node Index ##
    from Vision.StandardNodes import Index

コード例 #24

ファイル: TrajQRClustering_0.1_net.py プロジェクト: lisarosalina/App

masterNet.getEditor().addLibraryInstance(Adt,"AutoDockTools.VisionInterface.Adt", "Adt")

masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")

masterNet.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")

from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
    addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
    pass
try:
    ## saving node Directory_Containing_Input_PDB_Files ##
    from Vision.StandardNodes import DirBrowserNE
    Directory_Containing_Input_PDB_Files_0 = DirBrowserNE(constrkw={}, name='Directory_Containing_Input_PDB_Files', library=stdlib)
    masterNet.addNode(Directory_Containing_Input_PDB_Files_0,45,40)
    Directory_Containing_Input_PDB_Files_0.inputPortByName['directory'].widget.set(r"TrajQRClustering_0.1_input", run=False)
    apply(Directory_Containing_Input_PDB_Files_0.configure, (), {'paramPanelImmediate': 1})
except:
    print "WARNING: failed to restore DirBrowserNE named Directory_Containing_Input_PDB_Files in network masterNet"
    print_exc()
    Directory_Containing_Input_PDB_Files_0=None

try:
    ## saving node RMSD ##
    from Vision.StandardNodes import EntryNE
    RMSD_1 = EntryNE(constrkw={}, name='RMSD', library=stdlib)
    masterNet.addNode(RMSD_1,379,44)
    RMSD_1.inputPortByName['entry'].widget.set(r"0.5", run=False)
    apply(RMSD_1.configure, (), {'paramPanelImmediate': 1})
except:

コード例 #25

ファイル: VS_net.py プロジェクト: lisarosalina/App

                                         "stdlib")

from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
    addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False)
except:
    pass
try:
    addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
    pass
try:
    ## saving node iterate ##
    from Vision.StandardNodes import Iterate
    iterate_0 = Iterate(constrkw={}, name='iterate', library=stdlib)
    masterNet.addNode(iterate_0, 16, 228)
    iterate_0.inputPortByName['stopOnFailure'].widget.set(0, run=False)
    apply(iterate_0.configure, (), {'paramPanelImmediate': 1})
except:
    print "WARNING: failed to restore Iterate named iterate in network masterNet"
    print_exc()
    iterate_0 = None

try:
    ## saving node VirtualScreening ##
    from Adt.Macro.VirtualScreening import VirtualScreening
    VirtualScreening_1 = VirtualScreening(constrkw={},
                                          name='VirtualScreening',
                                          library=Adt)
    masterNet.addNode(VirtualScreening_1, 216, 497)
    apply(VirtualScreening_1.configure, (), {

コード例 #26

masterNet.getEditor().addLibraryInstance(stdlib, "Vision.StandardNodes",
                                         "stdlib")

from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
    addOpalServerAsCategory("http://oolite.calit2.optiputer.net/opal2",
                            replace=False)
except:
    pass
try:
    ## saving node FileWithCommandOrdering ##
    from Vision.StandardNodes import FileBrowserNE
    FileWithCommandOrdering_87 = FileBrowserNE(constrkw={},
                                               name='FileWithCommandOrdering',
                                               library=stdlib)
    masterNet.addNode(FileWithCommandOrdering_87, 30, 10)
    FileWithCommandOrdering_87.inputPortByName['filename'].widget.set(
        r"NAMDNBCR_0.1_input/order.txt", run=False)
    apply(FileWithCommandOrdering_87.configure, (), {'paramPanelImmediate': 1})
except:
    print "WARNING: failed to restore FileBrowserNE named FileWithCommandOrdering in network masterNet"
    print_exc()
    FileWithCommandOrdering_87 = None

try:
    ## saving node GetOrdering ##
    from Vision.StandardNodes import Generic
    GetOrdering_88 = Generic(constrkw={}, name='GetOrdering', library=stdlib)
    masterNet.addNode(GetOrdering_88, 30, 107)
    apply(
        GetOrdering_88.addInputPort, (), {