schrodinger.application package

A package for application specific modules.

desmond:

A package containing modules for the Desmond project

epik:

A package exposing the Epik functionality.

glide:

A package for creating Glide grid generation and docking jobs

inputconfig:

Module for writing and reading simplified input files

jaguar:

A package for creating Jaguar QM related tasks

ligprep:

A package containing LigPrep-related modules.

macromodel:

A package for creating and running MacroModel and Cluster jobs.

mcpro:

A package containing modules for the MCPRO+ product

phase:

A package containing Phase-related modules.

prepwizard:

Module that is used by PrepWizard

report2d:

Module that is used by 2D Viewer and generate_2d_report to produce PDF and HTML files with 2D structure images.

ska:

Module for running SKA backend (protein structure alignment)

vsw:

A package containing the VSW modules and stages

watermap:

Module with WaterMap-related functions.

Subpackages

• schrodinger.application.aacg package
  • Submodules
    • schrodinger.application.aacg.utils module
• schrodinger.application.bioluminate package
  • Subpackages
    • schrodinger.application.bioluminate.ssv package
      • Submodules
        • schrodinger.application.bioluminate.ssv.toolbars module
        • schrodinger.application.bioluminate.ssv.viewer module
  • Submodules
    • schrodinger.application.bioluminate.bwidgets module
    • schrodinger.application.bioluminate.escomp module
    • schrodinger.application.bioluminate.interaction_calculator module
    • schrodinger.application.bioluminate.pml_menus module
    • schrodinger.application.bioluminate.propfilter module
    • schrodinger.application.bioluminate.propfilter_ui module
    • schrodinger.application.bioluminate.propka_parse module
    • schrodinger.application.bioluminate.protein module
    • schrodinger.application.bioluminate.protein_protein_docking_shared module
    • schrodinger.application.bioluminate.protein_report_widget module
    • schrodinger.application.bioluminate.protein_structure_quality module
    • schrodinger.application.bioluminate.protein_structure_quality_ui module
    • schrodinger.application.bioluminate.reactive_residues module
    • schrodinger.application.bioluminate.run_propka module
    • schrodinger.application.bioluminate.sliderchart module
    • schrodinger.application.bioluminate.surfcomp module
    • schrodinger.application.bioluminate.validate_imported_modules module
    • schrodinger.application.bioluminate.workspacelabeler module
• schrodinger.application.canvas package
  • Submodules
    • schrodinger.application.canvas.base module
    • schrodinger.application.canvas.cluster module
    • schrodinger.application.canvas.clustergui module
    • schrodinger.application.canvas.driverutils module
    • schrodinger.application.canvas.fingerprint module
    • schrodinger.application.canvas.fingerprintgui module
    • schrodinger.application.canvas.r_group module
    • schrodinger.application.canvas.r_group_dee module
    • schrodinger.application.canvas.similarity module
    • schrodinger.application.canvas.similaritygui module
    • schrodinger.application.canvas.topo_descriptors module
    • schrodinger.application.canvas.utils module
• schrodinger.application.combiglide package
  • Subpackages
    • schrodinger.application.combiglide.combenumdock_dir package
      • Submodules
        • schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_cfc_ui module
        • schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_collection_viewer_ui module
        • schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_constraints_ui module
        • schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_ui module
    • schrodinger.application.combiglide.packages package
  • Submodules
    • schrodinger.application.combiglide.combenumdock module
    • schrodinger.application.combiglide.connection_storage module
    • schrodinger.application.combiglide.corehop module
    • schrodinger.application.combiglide.utils module
• schrodinger.application.epik package
• schrodinger.application.ffbuilder package
  • Submodules
    • schrodinger.application.ffbuilder.utils module
• schrodinger.application.glide package
  • Subpackages
    • schrodinger.application.glide.packages package
  • Submodules
    • schrodinger.application.glide.ensemble_selection module
    • schrodinger.application.glide.glide module
    • schrodinger.application.glide.glideanalysis module
    • schrodinger.application.glide.gui module
    • schrodinger.application.glide.http_client module
    • schrodinger.application.glide.http_server module
    • schrodinger.application.glide.poseviewconvert module
    • schrodinger.application.glide.utils module
    • schrodinger.application.glide.xpdes module
• schrodinger.application.jaguar package
  • Submodules
    • schrodinger.application.jaguar.autots_bonding module
    • schrodinger.application.jaguar.autots_constants module
    • schrodinger.application.jaguar.autots_exceptions module
    • schrodinger.application.jaguar.autots_rmsd module
    • schrodinger.application.jaguar.basis module
    • schrodinger.application.jaguar.check_headers module
    • schrodinger.application.jaguar.chirality module
    • schrodinger.application.jaguar.constants module
    • schrodinger.application.jaguar.exceptions module
    • schrodinger.application.jaguar.file_logger module
    • schrodinger.application.jaguar.global_macros module
    • schrodinger.application.jaguar.input module
    • schrodinger.application.jaguar.jaguar_diff module
    • schrodinger.application.jaguar.jaguar_keyword_utils module
    • schrodinger.application.jaguar.keywordDB module
    • schrodinger.application.jaguar.make_headers module
    • schrodinger.application.jaguar.mmjag module
    • schrodinger.application.jaguar.output module
    • schrodinger.application.jaguar.reactiq_input module
    • schrodinger.application.jaguar.reactiq_input_constants module
    • schrodinger.application.jaguar.reactiq_keywords module
    • schrodinger.application.jaguar.reactiq_validation module
    • schrodinger.application.jaguar.results module
    • schrodinger.application.jaguar.rmsd module
    • schrodinger.application.jaguar.scan module
    • schrodinger.application.jaguar.structure_isomorphism module
    • schrodinger.application.jaguar.textparser module
    • schrodinger.application.jaguar.user_config module
    • schrodinger.application.jaguar.utils.bak module
    • schrodinger.application.jaguar.utils module
    • schrodinger.application.jaguar.validation module
• schrodinger.application.licensing package
  • Submodules
    • schrodinger.application.licensing.flexlm module
    • schrodinger.application.licensing.licadmin module
    • schrodinger.application.licensing.licerror module
    • schrodinger.application.licensing.lmgrd_log_parser module
    • schrodinger.application.licensing.netsuiteapi module
• schrodinger.application.ligprep package
  • Submodules
    • schrodinger.application.ligprep.ionizer module
• schrodinger.application.macromodel package
  • Major changes between version 3.5 and 3.6
  • Major changes between version 3.0 and 3.5
  • Major changes between version 2.3 and 3.0
  • Subpackages
    • schrodinger.application.macromodel.packages package
  • Submodules
    • schrodinger.application.macromodel.apps module
    • schrodinger.application.macromodel.input module
    • schrodinger.application.macromodel.paraUtils module
    • schrodinger.application.macromodel.tools module
    • schrodinger.application.macromodel.utils module
• schrodinger.application.matsci package
  • Subpackages
    • schrodinger.application.matsci.espresso package
      • Submodules
        • schrodinger.application.matsci.espresso.ppdb module
        • schrodinger.application.matsci.espresso.qeinput module
        • schrodinger.application.matsci.espresso.qeoutput module
        • schrodinger.application.matsci.espresso.utils module
    • schrodinger.application.matsci.genetic_optimization package
      • Submodules
        • schrodinger.application.matsci.genetic_optimization.genetic_optimization module
    • schrodinger.application.matsci.mlearn package
      • Submodules
        • schrodinger.application.matsci.mlearn.base module
        • schrodinger.application.matsci.mlearn.features module
    • schrodinger.application.matsci.nano package
      • Submodules
        • schrodinger.application.matsci.nano.check module
        • schrodinger.application.matsci.nano.constants module
        • schrodinger.application.matsci.nano.interface_mod module
        • schrodinger.application.matsci.nano.particle module
        • schrodinger.application.matsci.nano.plane module
        • schrodinger.application.matsci.nano.sheet module
        • schrodinger.application.matsci.nano.slab module
        • schrodinger.application.matsci.nano.surfaces_interfaces_mod module
        • schrodinger.application.matsci.nano.tube module
        • schrodinger.application.matsci.nano.util module
        • schrodinger.application.matsci.nano.xtal module
    • schrodinger.application.matsci.qexsd package
      • Subpackages
        • schrodinger.application.matsci.qexsd.qespresso package
          • Subpackages
            • schrodinger.application.matsci.qexsd.qespresso.xsdtypes package
              • Submodules
                • schrodinger.application.matsci.qexsd.qespresso.xsdtypes.etree module
                • schrodinger.application.matsci.qexsd.qespresso.xsdtypes.exceptions module
                • schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument module
                • schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema module
                • schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes module
          • Submodules
            • schrodinger.application.matsci.qexsd.qespresso.cards module
            • schrodinger.application.matsci.qexsd.qespresso.converters module
            • schrodinger.application.matsci.qexsd.qespresso.documents module
            • schrodinger.application.matsci.qexsd.qespresso.exceptions module
            • schrodinger.application.matsci.qexsd.qespresso.options module
      • Submodules
        • schrodinger.application.matsci.qexsd.utils module
    • schrodinger.application.matsci.rxn_channel package
      • Submodules
        • schrodinger.application.matsci.rxn_channel.rxn_channel module
  • Submodules
    • schrodinger.application.matsci.amorphous module
    • schrodinger.application.matsci.atomicsymbols module
    • schrodinger.application.matsci.atomicsymbolsgui module
    • schrodinger.application.matsci.bandshape_utils module
    • schrodinger.application.matsci.basiselements module
    • schrodinger.application.matsci.buildcomplex module
    • schrodinger.application.matsci.builderwidgets module
    • schrodinger.application.matsci.cgforcefield module
    • schrodinger.application.matsci.cgforcefieldgui module
    • schrodinger.application.matsci.chargegui module
    • schrodinger.application.matsci.clusterstruct module
    • schrodinger.application.matsci.clusterstructgui module
    • schrodinger.application.matsci.coarsegrain module
    • schrodinger.application.matsci.controlicons_rc module
    • schrodinger.application.matsci.desmondutils module
    • schrodinger.application.matsci.elementalprops module
    • schrodinger.application.matsci.enumeration module
    • schrodinger.application.matsci.equilibrium_md module
    • schrodinger.application.matsci.freevolume module
    • schrodinger.application.matsci.guibase module
    • schrodinger.application.matsci.jaguar_multistage_workflow_utils module
    • schrodinger.application.matsci.jaguarworkflows module
    • schrodinger.application.matsci.jobdirdlg module
    • schrodinger.application.matsci.jobutils module
    • schrodinger.application.matsci.mecp_mod module
    • schrodinger.application.matsci.montecarlo module
    • schrodinger.application.matsci.msutils module
    • schrodinger.application.matsci.mswidgets module
    • schrodinger.application.matsci.optoelectronics module
    • schrodinger.application.matsci.order_parameter_mod module
    • schrodinger.application.matsci.parserutils module
    • schrodinger.application.matsci.property_names module
    • schrodinger.application.matsci.qualityslider module
    • schrodinger.application.matsci.reaction_workflow_utils module
    • schrodinger.application.matsci.reorder module
    • schrodinger.application.matsci.reordergui module
    • schrodinger.application.matsci.rxn_path module
    • schrodinger.application.matsci.shapes module
    • schrodinger.application.matsci.sliceplot module
    • schrodinger.application.matsci.smartsutils module
    • schrodinger.application.matsci.smartsutilsgui module
    • schrodinger.application.matsci.spectra module
    • schrodinger.application.matsci.swap_fragments_utils module
    • schrodinger.application.matsci.textlogger module
    • schrodinger.application.matsci.zmutils module
• schrodinger.application.mopac package
  • Submodules
    • schrodinger.application.mopac.exceptions module
    • schrodinger.application.mopac.mopac_backend module
    • schrodinger.application.mopac.mopac_launchers module
    • schrodinger.application.mopac.mopac_parser module
    • schrodinger.application.mopac.mopac_results module
    • schrodinger.application.mopac.mopac_startup module
    • schrodinger.application.mopac.results2012 module
    • schrodinger.application.mopac.results71 module
    • schrodinger.application.mopac.structure_launchers module
    • schrodinger.application.mopac.utils module
• schrodinger.application.phase package
  • Subpackages
    • schrodinger.application.phase.packages package
  • Submodules
    • schrodinger.application.phase.constants module
    • schrodinger.application.phase.create_xvol module
    • schrodinger.application.phase.featureselector module
    • schrodinger.application.phase.hypothesis module
    • schrodinger.application.phase.hypothesis_binding_modes module
    • schrodinger.application.phase.input module
    • schrodinger.application.phase.phase_markers module
    • schrodinger.application.phase.phase_widgets module
    • schrodinger.application.phase.pt_hypothesis module
• schrodinger.application.prime package
  • Submodules
    • schrodinger.application.prime.input module
    • schrodinger.application.prime.primefix module
    • schrodinger.application.prime.residue_interaction module
• schrodinger.application.qsite package
  • Submodules
    • schrodinger.application.qsite.input module
    • schrodinger.application.qsite.output module
• schrodinger.application.vsw package
  • Subpackages
    • schrodinger.application.vsw.stages package
      • Submodules
        • schrodinger.application.vsw.stages.combine module
        • schrodinger.application.vsw.stages.convert module
        • schrodinger.application.vsw.stages.filtering module
        • schrodinger.application.vsw.stages.gencodes module
        • schrodinger.application.vsw.stages.glide module
        • schrodinger.application.vsw.stages.macromodel module
        • schrodinger.application.vsw.stages.phase module
        • schrodinger.application.vsw.stages.prime module
        • schrodinger.application.vsw.stages.pull module
        • schrodinger.application.vsw.stages.qikprop module
        • schrodinger.application.vsw.stages.qsite module
        • schrodinger.application.vsw.stages.rmsd module
        • schrodinger.application.vsw.stages.semiemp module
  • Submodules
    • schrodinger.application.vsw.input module
    • schrodinger.application.vsw.pipeutils module
    • schrodinger.application.vsw.vswinput module
• schrodinger.application.watermap package
  • Submodules
    • schrodinger.application.watermap.utils module
    • schrodinger.application.watermap.watermap_inp module
    • schrodinger.application.watermap.watermap_scoring module

Submodules

• schrodinger.application.hitexpander module
• schrodinger.application.inputconfig module
• schrodinger.application.prepwizard module
• schrodinger.application.report2d module
• schrodinger.application.ska module
• schrodinger.application.utils module