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

pymol:

Module that contains functions for running PyMOL

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.bb_database namespace
  • Submodules
    • schrodinger.application.bb_database.bb_arg_utils module
    • schrodinger.application.bb_database.bb_job_utils module
    • schrodinger.application.bb_database.bb_task_utils module
• schrodinger.application.bindingsite package
  • Submodules
    • schrodinger.application.bindingsite.atomtyping module
    • schrodinger.application.bindingsite.cavutils module
    • schrodinger.application.bindingsite.common module
    • schrodinger.application.bindingsite.intfield module
    • schrodinger.application.bindingsite.schema module
• schrodinger.application.bioluminate package
  • Subpackages
    • schrodinger.application.bioluminate.actions package
      • Submodules
        • schrodinger.application.bioluminate.actions.configs module
        • schrodinger.application.bioluminate.actions.factory module
        • schrodinger.application.bioluminate.actions.icons module
        • schrodinger.application.bioluminate.actions.icons_rc module
    • schrodinger.application.bioluminate.anarci namespace
      • Submodules
        • schrodinger.application.bioluminate.anarci.anarci_adapter module
        • schrodinger.application.bioluminate.anarci.annotate module
        • schrodinger.application.bioluminate.anarci.loop_ranges module
    • schrodinger.application.bioluminate.antibody package
      • Subpackages
        • schrodinger.application.bioluminate.antibody.io namespace
          • Submodules
            • schrodinger.application.bioluminate.antibody.io.csv_reader module
      • Submodules
        • schrodinger.application.bioluminate.antibody.annotate module
        • schrodinger.application.bioluminate.antibody.annotation_constants module
        • schrodinger.application.bioluminate.antibody.antibody_homology_report_writer module
        • schrodinger.application.bioluminate.antibody.antibody_modeling_yaml module
        • schrodinger.application.bioluminate.antibody.assembly module
        • schrodinger.application.bioluminate.antibody.assembly_yaml module
        • schrodinger.application.bioluminate.antibody.grafting module
        • schrodinger.application.bioluminate.antibody.management module
        • schrodinger.application.bioluminate.antibody.models module
        • schrodinger.application.bioluminate.antibody.scaffold_search module
        • schrodinger.application.bioluminate.antibody.search_results_table module
        • schrodinger.application.bioluminate.antibody.sequence_indexer module
        • schrodinger.application.bioluminate.antibody.test_immunebuilder_adapter module
        • schrodinger.application.bioluminate.antibody.utils module
    • schrodinger.application.bioluminate.drivers package
      • Submodules
        • schrodinger.application.bioluminate.drivers.io module
    • schrodinger.application.bioluminate.epitope namespace
      • Subpackages
        • schrodinger.application.bioluminate.epitope.utils namespace
          • Submodules
            • schrodinger.application.bioluminate.epitope.utils.esc_utils module
            • schrodinger.application.bioluminate.epitope.utils.faux-epitope module
      • Submodules
        • schrodinger.application.bioluminate.epitope.driver module
        • schrodinger.application.bioluminate.epitope.psc_workflow module
    • schrodinger.application.bioluminate.immunebuilder namespace
      • Submodules
        • schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter module
    • schrodinger.application.bioluminate.met_oxidation package
      • Submodules
        • schrodinger.application.bioluminate.met_oxidation.hmc_sim_runner module
        • schrodinger.application.bioluminate.met_oxidation.md_sim_runner module
    • schrodinger.application.bioluminate.mhc namespace
      • Submodules
        • schrodinger.application.bioluminate.mhc.docking_angles module
    • schrodinger.application.bioluminate.nucleic package
      • Submodules
        • schrodinger.application.bioluminate.nucleic.constants module
        • schrodinger.application.bioluminate.nucleic.mutator module
    • schrodinger.application.bioluminate.patch_utils package
      • Submodules
        • schrodinger.application.bioluminate.patch_utils.msurfext module
        • schrodinger.application.bioluminate.patch_utils.patch_finder module
        • schrodinger.application.bioluminate.patch_utils.pre_analyze module
        • schrodinger.application.bioluminate.patch_utils.settings module
    • schrodinger.application.bioluminate.peptide_sar namespace
      • Submodules
        • schrodinger.application.bioluminate.peptide_sar.encode module
        • schrodinger.application.bioluminate.peptide_sar.io module
        • schrodinger.application.bioluminate.peptide_sar.label module
        • schrodinger.application.bioluminate.peptide_sar.sar module
        • schrodinger.application.bioluminate.peptide_sar.statistics module
    • schrodinger.application.bioluminate.pose_filtering package
      • Submodules
        • schrodinger.application.bioluminate.pose_filtering.csv_filter module
        • schrodinger.application.bioluminate.pose_filtering.hdx_analysis module
        • schrodinger.application.bioluminate.pose_filtering.hdx_calc module
        • schrodinger.application.bioluminate.pose_filtering.hdx_io module
        • schrodinger.application.bioluminate.pose_filtering.operators module
        • schrodinger.application.bioluminate.pose_filtering.residue_filter module
        • schrodinger.application.bioluminate.pose_filtering.test module
    • schrodinger.application.bioluminate.protein package
      • Submodules
        • schrodinger.application.bioluminate.protein.mutator module
        • schrodinger.application.bioluminate.protein.protein module
        • schrodinger.application.bioluminate.protein.utils module
    • schrodinger.application.bioluminate.protein_interaction package
      • Submodules
        • schrodinger.application.bioluminate.protein_interaction.calculate module
        • schrodinger.application.bioluminate.protein_interaction.tasks module
        • schrodinger.application.bioluminate.protein_interaction.utils module
    • schrodinger.application.bioluminate.residue_scanning package
      • Submodules
        • schrodinger.application.bioluminate.residue_scanning.properties module
    • schrodinger.application.bioluminate.ssv package
      • Submodules
        • schrodinger.application.bioluminate.ssv.toolbars module
        • schrodinger.application.bioluminate.ssv.viewer module
    • schrodinger.application.bioluminate.tcr namespace
      • Submodules
        • schrodinger.application.bioluminate.tcr.annotate module
    • schrodinger.application.bioluminate.update_germline_db namespace
      • Submodules
        • schrodinger.application.bioluminate.update_germline_db.translate_db module
  • Submodules
    • schrodinger.application.bioluminate.bwidgets module
    • schrodinger.application.bioluminate.classify module
    • schrodinger.application.bioluminate.escomp module
    • schrodinger.application.bioluminate.interaction_calculator module
    • schrodinger.application.bioluminate.methionine_oxidation module
    • schrodinger.application.bioluminate.mutation 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_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.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.packages package
  • Submodules
    • schrodinger.application.combiglide.connection_storage module
    • schrodinger.application.combiglide.corehop module
    • schrodinger.application.combiglide.utils module
• schrodinger.application.combinatorial_diversity package
  • Submodules
    • schrodinger.application.combinatorial_diversity.diversity_fingerprinter module
    • schrodinger.application.combinatorial_diversity.diversity_selector module
    • schrodinger.application.combinatorial_diversity.diversity_splitter module
      • Overview and Motivation
      • Splitting Chemical Sapce
    • schrodinger.application.combinatorial_diversity.driver_utils module
    • schrodinger.application.combinatorial_diversity.splitter_utils module
• schrodinger.application.combinatorial_explorer package
  • Submodules
    • schrodinger.application.combinatorial_explorer.driver_utils module
    • schrodinger.application.combinatorial_explorer.route_screener module
• schrodinger.application.combinatorial_screen package
  • Submodules
    • schrodinger.application.combinatorial_screen.combinatorial_screener module
      • Basic Algorithm
    • schrodinger.application.combinatorial_screen.driver_utils module
    • schrodinger.application.combinatorial_screen.fingerprint_utils module
• schrodinger.application.dendrogram namespace
  • Submodules
    • schrodinger.application.dendrogram.chemicalDendrogram module
    • schrodinger.application.dendrogram.core_class module
    • schrodinger.application.dendrogram.dendroMain module
    • schrodinger.application.dendrogram.gradientSelector module
    • schrodinger.application.dendrogram.proteinDendrogram module
    • schrodinger.application.dendrogram.randTestSet module
• schrodinger.application.desmond namespace
  • Subpackages
    • schrodinger.application.desmond.packages namespace
      • Submodules
        • schrodinger.application.desmond.packages.analysis module
        • schrodinger.application.desmond.packages.destro module
        • schrodinger.application.desmond.packages.staf module
        • schrodinger.application.desmond.packages.topo module
        • schrodinger.application.desmond.packages.traj module
  • Submodules
    • schrodinger.application.desmond.arkdb module
    • schrodinger.application.desmond.bennett module
    • schrodinger.application.desmond.cms module
    • schrodinger.application.desmond.cms_utils module
    • schrodinger.application.desmond.cns_io module
    • schrodinger.application.desmond.measurement module
    • schrodinger.application.desmond.remd module
    • schrodinger.application.desmond.struc module
    • schrodinger.application.desmond.system_builder_util module
    • schrodinger.application.desmond.torsion_related module
    • schrodinger.application.desmond.util module
• schrodinger.application.epik package
• schrodinger.application.fragment_virtual_screening namespace
  • Submodules
    • schrodinger.application.fragment_virtual_screening.bq_query_task module
    • schrodinger.application.fragment_virtual_screening.frag_vs_stages module
    • schrodinger.application.fragment_virtual_screening.frag_vs_utils module
• schrodinger.application.glide package
  • Subpackages
    • schrodinger.application.glide.packages package
  • Submodules
    • schrodinger.application.glide.client_module module
    • 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.ligand_designer module
    • schrodinger.application.glide.phase_subset module
    • schrodinger.application.glide.poseviewconvert module
    • schrodinger.application.glide.property_names module
    • schrodinger.application.glide.sort_parser_common module
    • schrodinger.application.glide.sort_utils module
    • schrodinger.application.glide.utils module
    • schrodinger.application.glide.xpdes module
• schrodinger.application.jaguar package
  • Subpackages
    • schrodinger.application.jaguar.distributed_frequencies package
      • Submodules
        • schrodinger.application.jaguar.distributed_frequencies.input module
        • schrodinger.application.jaguar.distributed_frequencies.keywords module
        • schrodinger.application.jaguar.distributed_frequencies.validation module
    • schrodinger.application.jaguar.gui package
      • Subpackages
        • schrodinger.application.jaguar.gui.tabs package
          • Subpackages
            • schrodinger.application.jaguar.gui.tabs.input_sub_tabs package
              • Submodules
                • schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab module
                • schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set module
                • schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints module
            • schrodinger.application.jaguar.gui.tabs.per_atom_basis_pop_up package
              • Submodules
                • schrodinger.application.jaguar.gui.tabs.per_atom_basis_pop_up.per_atom_basis_ui module
            • schrodinger.application.jaguar.gui.tabs.sub_tab_widgets package
              • Submodules
                • schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets module
                • schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets module
                • schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets module
                • schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_selector module
          • Submodules
            • schrodinger.application.jaguar.gui.tabs.base_tab module
            • schrodinger.application.jaguar.gui.tabs.coordinates module
            • schrodinger.application.jaguar.gui.tabs.input_tab module
            • schrodinger.application.jaguar.gui.tabs.irc_tab module
            • schrodinger.application.jaguar.gui.tabs.molecule_tab module
            • schrodinger.application.jaguar.gui.tabs.multi_structure_tab module
            • schrodinger.application.jaguar.gui.tabs.optimization_tab module
            • schrodinger.application.jaguar.gui.tabs.output_tab module
            • schrodinger.application.jaguar.gui.tabs.properties_tab module
            • schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab module
            • schrodinger.application.jaguar.gui.tabs.reaction_properties_tab module
            • schrodinger.application.jaguar.gui.tabs.reaction_tab module
            • schrodinger.application.jaguar.gui.tabs.scan_tab module
            • schrodinger.application.jaguar.gui.tabs.scf_tab module
            • schrodinger.application.jaguar.gui.tabs.solvation_tab module
            • schrodinger.application.jaguar.gui.tabs.theory_tab module
            • schrodinger.application.jaguar.gui.tabs.transition_state_tab module
        • schrodinger.application.jaguar.gui.ui package
          • Subpackages
            • schrodinger.application.jaguar.gui.ui.input_sub_tabs package
              • Submodules
                • schrodinger.application.jaguar.gui.ui.input_sub_tabs.basis_set_ui module
                • schrodinger.application.jaguar.gui.ui.input_sub_tabs.charge_constraints_ui module
          • Submodules
            • schrodinger.application.jaguar.gui.ui.config_dialog_jaguar_ui module
            • schrodinger.application.jaguar.gui.ui.coordinate_dialog_ui module
            • schrodinger.application.jaguar.gui.ui.define_smarts_panel_ui module
            • schrodinger.application.jaguar.gui.ui.edit_dialog_ui module
            • schrodinger.application.jaguar.gui.ui.excited_state_widget_ui module
            • schrodinger.application.jaguar.gui.ui.input_hb_bottom_ui module
            • schrodinger.application.jaguar.gui.ui.input_hb_top_ui module
            • schrodinger.application.jaguar.gui.ui.input_pka_bottom_ui module
            • schrodinger.application.jaguar.gui.ui.input_pka_top_ui module
            • schrodinger.application.jaguar.gui.ui.input_std_bottom_ui module
            • schrodinger.application.jaguar.gui.ui.input_top_ui module
            • schrodinger.application.jaguar.gui.ui.irc_bottom_ui module
            • schrodinger.application.jaguar.gui.ui.irc_top_ui module
            • schrodinger.application.jaguar.gui.ui.molecule_pka_bottom_ui module
            • schrodinger.application.jaguar.gui.ui.molecule_std_bottom_ui module
            • schrodinger.application.jaguar.gui.ui.molecule_top_ui module
            • schrodinger.application.jaguar.gui.ui.multi_structures_ui module
            • schrodinger.application.jaguar.gui.ui.optimization_tab_ui module
            • schrodinger.application.jaguar.gui.ui.output_tab_ui module
            • schrodinger.application.jaguar.gui.ui.pka_smarts_page_ui module
            • schrodinger.application.jaguar.gui.ui.properties_tab_ui module
            • schrodinger.application.jaguar.gui.ui.reaction_molecules_tab_ui module
            • schrodinger.application.jaguar.gui.ui.reaction_properties_tab_ui module
            • schrodinger.application.jaguar.gui.ui.reaction_tab_ui module
            • schrodinger.application.jaguar.gui.ui.scan_tab_nextgeom_ui module
            • schrodinger.application.jaguar.gui.ui.scan_tab_ui module
            • schrodinger.application.jaguar.gui.ui.scf_tab_ui module
            • schrodinger.application.jaguar.gui.ui.solvent_pka_tab_ui module
            • schrodinger.application.jaguar.gui.ui.solvent_tab_ui module
            • schrodinger.application.jaguar.gui.ui.spin_treatment_widget_ui module
            • schrodinger.application.jaguar.gui.ui.theory_tab_ui module
            • schrodinger.application.jaguar.gui.ui.transition_state_bottom_ui module
            • schrodinger.application.jaguar.gui.ui.transition_state_top_ui module
      • Submodules
        • schrodinger.application.jaguar.gui.base_panel module
        • schrodinger.application.jaguar.gui.basis_selector module
        • schrodinger.application.jaguar.gui.edit_dialog module
        • schrodinger.application.jaguar.gui.filedialog module
        • schrodinger.application.jaguar.gui.input_tab_widgets module
        • schrodinger.application.jaguar.gui.input_tab_widgets_hb module
        • schrodinger.application.jaguar.gui.input_tab_widgets_pka module
        • schrodinger.application.jaguar.gui.solvent_selector module
        • schrodinger.application.jaguar.gui.theory_selector module
        • schrodinger.application.jaguar.gui.theory_tab_widgets module
        • schrodinger.application.jaguar.gui.timing module
        • schrodinger.application.jaguar.gui.utils module
    • schrodinger.application.jaguar.qrnn package
      • Submodules
        • schrodinger.application.jaguar.qrnn.constants module
        • schrodinger.application.jaguar.qrnn.input module
        • schrodinger.application.jaguar.qrnn.keywords module
        • schrodinger.application.jaguar.qrnn.temp_opt module
        • schrodinger.application.jaguar.qrnn.validation module
  • Submodules
    • schrodinger.application.jaguar.autots_bonding module
    • schrodinger.application.jaguar.autots_constants module
    • schrodinger.application.jaguar.autots_exceptions module
    • schrodinger.application.jaguar.autots_input module
    • schrodinger.application.jaguar.autots_input_constants module
    • schrodinger.application.jaguar.autots_keywords module
    • schrodinger.application.jaguar.autots_rmsd module
    • schrodinger.application.jaguar.autots_validation module
    • schrodinger.application.jaguar.basis module
    • schrodinger.application.jaguar.check_headers module
    • schrodinger.application.jaguar.constants module
    • schrodinger.application.jaguar.csrch_input_constants module
    • schrodinger.application.jaguar.discretized_1d_function module
    • schrodinger.application.jaguar.esol_constants module
    • schrodinger.application.jaguar.esol_input module
    • schrodinger.application.jaguar.esol_keywords module
    • schrodinger.application.jaguar.esol_validation module
    • schrodinger.application.jaguar.exceptions module
    • schrodinger.application.jaguar.file_logger module
    • schrodinger.application.jaguar.global_macros module
    • schrodinger.application.jaguar.hess_guess module
    • schrodinger.application.jaguar.hydrokinetic_constants module
    • schrodinger.application.jaguar.hydrokinetic_input module
    • schrodinger.application.jaguar.hydrokinetic_input_constants module
    • schrodinger.application.jaguar.hydrokinetic_keywords module
    • schrodinger.application.jaguar.hydrokinetic_validation module
    • schrodinger.application.jaguar.input module
    • schrodinger.application.jaguar.jagconvert module
    • schrodinger.application.jaguar.jaguar_config_dialog module
    • schrodinger.application.jaguar.jaguar_diff module
    • schrodinger.application.jaguar.jaguar_keyword_utils module
    • schrodinger.application.jaguar.jaguar_tasks module
    • schrodinger.application.jaguar.keywordDB module
    • schrodinger.application.jaguar.kinetics module
    • schrodinger.application.jaguar.macro_pka_constants module
    • schrodinger.application.jaguar.macro_pka_input module
    • schrodinger.application.jaguar.macro_pka_keywords module
    • schrodinger.application.jaguar.macro_pka_utils module
    • schrodinger.application.jaguar.macro_pka_validation module
    • schrodinger.application.jaguar.make_headers module
    • schrodinger.application.jaguar.mmjag module
    • schrodinger.application.jaguar.neural_network_optimizer module
    • schrodinger.application.jaguar.nmr_basis module
    • schrodinger.application.jaguar.nmr_interactions module
    • schrodinger.application.jaguar.nmr_utils module
    • schrodinger.application.jaguar.output module
    • schrodinger.application.jaguar.permutation_symmetry module
    • schrodinger.application.jaguar.pk50_report module
    • schrodinger.application.jaguar.results module
    • schrodinger.application.jaguar.rotation_barriers_input module
    • schrodinger.application.jaguar.rotation_barriers_keywords module
    • schrodinger.application.jaguar.rotation_barriers_validation module
    • schrodinger.application.jaguar.scan module
    • schrodinger.application.jaguar.simple_spec module
    • schrodinger.application.jaguar.solvation_input module
    • schrodinger.application.jaguar.solvation_keywords module
    • schrodinger.application.jaguar.solvation_validation module
    • schrodinger.application.jaguar.spectroscopy_defaults module
    • schrodinger.application.jaguar.spin_simulator_v2 module
    • schrodinger.application.jaguar.textparser module
    • schrodinger.application.jaguar.update_pka_settings module
    • schrodinger.application.jaguar.update_pka_settings_ui module
    • schrodinger.application.jaguar.user_config module
    • schrodinger.application.jaguar.utils module
    • schrodinger.application.jaguar.validation module
    • schrodinger.application.jaguar.workflow_input module
    • schrodinger.application.jaguar.workflow_keywords module
    • schrodinger.application.jaguar.workflow_validation module
• schrodinger.application.job_monitor package
  • Submodules
    • schrodinger.application.job_monitor.buttons module
    • schrodinger.application.job_monitor.diagnostics_dialog_ui module
    • schrodinger.application.job_monitor.file_browser_ui module
    • schrodinger.application.job_monitor.job_info_view_ui module
    • schrodinger.application.job_monitor.job_monitor_diagnostics_dialog module
    • schrodinger.application.job_monitor.job_monitor_file_browser module
    • schrodinger.application.job_monitor.job_monitor_gui module
    • schrodinger.application.job_monitor.job_monitor_icons_rc module
    • schrodinger.application.job_monitor.job_monitor_models module
    • schrodinger.application.job_monitor.job_monitor_progress_bar module
    • schrodinger.application.job_monitor.job_monitor_stylesheets module
    • schrodinger.application.job_monitor.job_monitor_table module
    • schrodinger.application.job_monitor.job_monitor_widgets module
    • schrodinger.application.job_monitor.top_level_view_ui module
    • schrodinger.application.job_monitor.util module
• schrodinger.application.jobserver_cert_gui_dir namespace
  • Submodules
    • schrodinger.application.jobserver_cert_gui_dir.jobserver_cert_gui_icons_rc module
    • schrodinger.application.jobserver_cert_gui_dir.registration_dialogs module
    • schrodinger.application.jobserver_cert_gui_dir.registration_panel_ui module
• schrodinger.application.licensing package
  • Subpackages
    • schrodinger.application.licensing.licserver package
      • Submodules
        • schrodinger.application.licensing.licserver.client module
        • schrodinger.application.licensing.licserver.exceptions module
        • schrodinger.application.licensing.licserver.install module
        • schrodinger.application.licensing.licserver.main module
        • schrodinger.application.licensing.licserver.quick_slm_setup module
        • schrodinger.application.licensing.licserver.server module
  • 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.livedesign package
  • Submodules
    • schrodinger.application.livedesign.constants module
    • schrodinger.application.livedesign.cubes module
    • schrodinger.application.livedesign.data_classes module
    • schrodinger.application.livedesign.entry_types module
    • schrodinger.application.livedesign.export_map_manager module
    • schrodinger.application.livedesign.export_models module
    • schrodinger.application.livedesign.export_setup_ui module
    • schrodinger.application.livedesign.export_tasks module
    • schrodinger.application.livedesign.export_ui module
    • schrodinger.application.livedesign.icons_rc module
    • schrodinger.application.livedesign.import_utils module
    • schrodinger.application.livedesign.invalid_ge_id_warning_ui module
    • schrodinger.application.livedesign.io_utils module
    • schrodinger.application.livedesign.ld_base_classes module
    • schrodinger.application.livedesign.ld_connection_checker module
    • schrodinger.application.livedesign.ld_export module
    • schrodinger.application.livedesign.ld_export_gui module
    • schrodinger.application.livedesign.ld_folder_tree module
    • schrodinger.application.livedesign.ld_glide_utils module
    • schrodinger.application.livedesign.ld_import module
    • schrodinger.application.livedesign.ld_import_utils module
    • schrodinger.application.livedesign.ld_ligand_strain_utils module
    • schrodinger.application.livedesign.ld_maestro_actions module
    • schrodinger.application.livedesign.ld_maestro_actions_constants module
    • schrodinger.application.livedesign.ld_mmgbsa_utils module
    • schrodinger.application.livedesign.ld_model_input module
    • schrodinger.application.livedesign.ld_settings module
    • schrodinger.application.livedesign.ld_strain_rescore_utils module
    • schrodinger.application.livedesign.ld_tasks module
    • schrodinger.application.livedesign.ld_utils module
    • schrodinger.application.livedesign.ldclient_proxy module
    • schrodinger.application.livedesign.lid module
    • schrodinger.application.livedesign.live_report_widget module
    • schrodinger.application.livedesign.live_report_widget_ui module
    • schrodinger.application.livedesign.login module
    • schrodinger.application.livedesign.login2_ui module
    • schrodinger.application.livedesign.login_gui module
    • schrodinger.application.livedesign.login_gui2 module
    • schrodinger.application.livedesign.login_ui module
    • schrodinger.application.livedesign.maestro_ld_connection module
    • schrodinger.application.livedesign.maestro_ld_mapping_ui module
    • schrodinger.application.livedesign.maestro_sync module
    • schrodinger.application.livedesign.mapping_widgets module
    • schrodinger.application.livedesign.mappings_manager_ui module
    • schrodinger.application.livedesign.panel_components module
    • schrodinger.application.livedesign.pose_name_panel module
    • schrodinger.application.livedesign.pose_name_panel_ui module
    • schrodinger.application.livedesign.pse_helpers module
    • schrodinger.application.livedesign.save_mapping_dialog_ui module
    • schrodinger.application.livedesign.selection_pop_up_ui module
    • schrodinger.application.livedesign.summary module
    • schrodinger.application.livedesign.summary_ui module
    • schrodinger.application.livedesign.tasks module
    • schrodinger.application.livedesign.two_d_render module
    • schrodinger.application.livedesign.upload_utils module
    • schrodinger.application.livedesign.widgets module
• schrodinger.application.macromodel package
  • Major changes between version 3.5 and 3.6
    • API Changes
      • Utils Module
  • Major changes between version 3.0 and 3.5
    • API Changes
      • Utils Module
    • Deprecated Features
      • Tools Module
  • Major changes between version 2.3 and 3.0
    • API Changes
      • Tools Module
      • Utils Module
  • 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.cctbx package
      • Submodules
        • schrodinger.application.matsci.cctbx.rot_mx module
    • schrodinger.application.matsci.elasticity package
      • Submodules
        • schrodinger.application.matsci.elasticity.elastic module
        • schrodinger.application.matsci.elasticity.strain module
        • schrodinger.application.matsci.elasticity.stress module
        • schrodinger.application.matsci.elasticity.tensors module
    • 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.gsas package
      • Submodules
        • schrodinger.application.matsci.gsas.ElementTable module
          • ElementTable: Periodic Table Data
        • schrodinger.application.matsci.gsas.GSASIIElem module
          • GSASIIElem: functions for element types
        • schrodinger.application.matsci.gsas.GSASIIfiles module
          • GSASIIfiles: data (non-GUI) I/O routines
        • schrodinger.application.matsci.gsas.GSASIIlattice module
          • GSASIIlattice: Unit cells
        • schrodinger.application.matsci.gsas.GSASIImath module
          • GSASIImath: computation module
        • schrodinger.application.matsci.gsas.GSASIIpwd module
          • GSASII powder calculation module
        • schrodinger.application.matsci.gsas.GSASIIspc module
          • GSASIIspc: Space group module
        • schrodinger.application.matsci.gsas.atmdata module
          • atmdata: Table of atomic data
    • schrodinger.application.matsci.mlearn package
      • Subpackages
        • schrodinger.application.matsci.mlearn.sklearn_json package
          • Submodules
            • schrodinger.application.matsci.mlearn.sklearn_json.classification module
            • schrodinger.application.matsci.mlearn.sklearn_json.common module
            • schrodinger.application.matsci.mlearn.sklearn_json.csr module
            • schrodinger.application.matsci.mlearn.sklearn_json.decomposition module
            • schrodinger.application.matsci.mlearn.sklearn_json.regression module
      • Submodules
        • schrodinger.application.matsci.mlearn.base module
        • schrodinger.application.matsci.mlearn.descriptor 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.space_groups module
        • schrodinger.application.matsci.nano.surfaces_interfaces_mod module
        • schrodinger.application.matsci.nano.tools module
        • schrodinger.application.matsci.nano.tube module
        • schrodinger.application.matsci.nano.util module
        • schrodinger.application.matsci.nano.xtal module
    • schrodinger.application.matsci.siteselector package
      • Submodules
        • schrodinger.application.matsci.siteselector.siteselector module
  • Submodules
    • schrodinger.application.matsci.amorphous module
    • schrodinger.application.matsci.anharmonic module
    • schrodinger.application.matsci.appbase module
    • schrodinger.application.matsci.aseutils module
    • schrodinger.application.matsci.atom_group module
    • schrodinger.application.matsci.atomicsymbols module
    • schrodinger.application.matsci.atomicsymbolsgui module
    • schrodinger.application.matsci.automated_cg_mapping module
    • schrodinger.application.matsci.automated_martini_mapping_protein module
    • schrodinger.application.matsci.bandshape_utils module
    • schrodinger.application.matsci.basiselements module
    • schrodinger.application.matsci.boltzmann_avg_props module
    • schrodinger.application.matsci.buildcomplex module
    • schrodinger.application.matsci.buildcomplex2d module
    • schrodinger.application.matsci.builderwidgets module
    • schrodinger.application.matsci.cache module
    • schrodinger.application.matsci.cg_mapping 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.codeutils module
    • schrodinger.application.matsci.colorutils module
    • schrodinger.application.matsci.configdlgs module
    • schrodinger.application.matsci.controlicons_rc module
    • schrodinger.application.matsci.crest module
    • schrodinger.application.matsci.density_analysis module
    • schrodinger.application.matsci.density_analysis_widget module
    • schrodinger.application.matsci.desconfig module
    • schrodinger.application.matsci.desmondutils module
    • schrodinger.application.matsci.deswidgets module
    • schrodinger.application.matsci.elementalprops module
    • schrodinger.application.matsci.enc module
    • schrodinger.application.matsci.enumeration module
    • schrodinger.application.matsci.equilibrium_md module
    • schrodinger.application.matsci.etarotamers module
    • schrodinger.application.matsci.etatoggle module
    • schrodinger.application.matsci.fragments module
    • schrodinger.application.matsci.freevolume module
    • schrodinger.application.matsci.genetic_optimization module
    • schrodinger.application.matsci.geometry module
    • schrodinger.application.matsci.graph module
    • schrodinger.application.matsci.gutils module
    • schrodinger.application.matsci.hdfutils module
    • schrodinger.application.matsci.jaguar_multistage_workflow_utils module
    • schrodinger.application.matsci.jaguar_restart module
    • schrodinger.application.matsci.jaguarworkflows module
    • schrodinger.application.matsci.jagwidgets module
    • schrodinger.application.matsci.jobdirdlg module
    • schrodinger.application.matsci.jobutils module
    • schrodinger.application.matsci.jwsteps module
    • schrodinger.application.matsci.kmc module
    • schrodinger.application.matsci.kmcgui module
    • schrodinger.application.matsci.maestrocmds module
    • schrodinger.application.matsci.mecp_mod module
    • schrodinger.application.matsci.ml_formulations_gui_utils module
    • schrodinger.application.matsci.montecarlo module
    • schrodinger.application.matsci.msconst module
    • schrodinger.application.matsci.msminimize module
    • schrodinger.application.matsci.msprops module
    • schrodinger.application.matsci.mstest module
    • schrodinger.application.matsci.msutils module
    • schrodinger.application.matsci.mswidgets module
    • schrodinger.application.matsci.multiapp module
    • schrodinger.application.matsci.optoelectronics module
    • schrodinger.application.matsci.order_parameter_mod module
    • schrodinger.application.matsci.packmol module
    • schrodinger.application.matsci.parserutils module
    • schrodinger.application.matsci.pbcutils module
    • schrodinger.application.matsci.permittivity module
    • schrodinger.application.matsci.plotwidgets module
    • schrodinger.application.matsci.pmgutils module
    • schrodinger.application.matsci.polymer module
    • schrodinger.application.matsci.qualityslider module
    • schrodinger.application.matsci.qubec_utils module
    • schrodinger.application.matsci.rdpattern module
    • schrodinger.application.matsci.rdpattern_gui module
    • schrodinger.application.matsci.reaction_workflow_enum_utils module
    • schrodinger.application.matsci.reaction_workflow_gui_utils module
    • schrodinger.application.matsci.reaction_workflow_utils module
    • schrodinger.application.matsci.reorder module
    • schrodinger.application.matsci.reordergui module
    • schrodinger.application.matsci.reportutils module
    • schrodinger.application.matsci.rxn_channel module
    • schrodinger.application.matsci.rxn_path module
    • schrodinger.application.matsci.sculptcomplex module
    • schrodinger.application.matsci.shapes module
    • schrodinger.application.matsci.sliceplot module
    • schrodinger.application.matsci.smartsutils module
    • schrodinger.application.matsci.smartsutilsgui module
    • schrodinger.application.matsci.species module
    • schrodinger.application.matsci.speciesgui module
    • schrodinger.application.matsci.spectra module
    • schrodinger.application.matsci.stage_widgets module
    • schrodinger.application.matsci.stress_strain module
    • schrodinger.application.matsci.swap_fragments_utils module
    • schrodinger.application.matsci.textlogger module
    • schrodinger.application.matsci.typography module
    • schrodinger.application.matsci.uq_utils module
    • schrodinger.application.matsci.wfmanagement module
    • schrodinger.application.matsci.xrd module
    • schrodinger.application.matsci.yamlutils module
    • schrodinger.application.matsci.zmutils module
• schrodinger.application.medchem package
  • Submodules
    • schrodinger.application.medchem.property 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_startup module
    • schrodinger.application.mopac.mopac_surfaces module
    • schrodinger.application.mopac.results_main module
    • schrodinger.application.mopac.structure_launchers module
    • schrodinger.application.mopac.utils module
• schrodinger.application.pathfinder package
  • Submodules
    • schrodinger.application.pathfinder.aligner module
    • schrodinger.application.pathfinder.analysis module
    • schrodinger.application.pathfinder.multiroute module
    • schrodinger.application.pathfinder.reaction module
    • schrodinger.application.pathfinder.render module
    • schrodinger.application.pathfinder.route module
    • schrodinger.application.pathfinder.synthesis module
• schrodinger.application.phase package
  • Subpackages
    • schrodinger.application.phase.packages package
      • Subpackages
        • schrodinger.application.phase.packages.hypo_refine namespace
          • Submodules
            • schrodinger.application.phase.packages.hypo_refine.hypo_utils module
            • schrodinger.application.phase.packages.hypo_refine.job_utils module
            • schrodinger.application.phase.packages.hypo_refine.option_utils module
            • schrodinger.application.phase.packages.hypo_refine.project_utils module
            • schrodinger.application.phase.packages.hypo_refine.screen_utils module
      • Submodules
        • schrodinger.application.phase.packages.align_ligands_driver_options module
        • schrodinger.application.phase.packages.bedroc_screener module
        • schrodinger.application.phase.packages.cat_hypo_converter module
        • schrodinger.application.phase.packages.conformer_reader module
        • schrodinger.application.phase.packages.conformer_storage module
        • schrodinger.application.phase.packages.ligand_aligner module
        • schrodinger.application.phase.packages.mmp2d module
        • schrodinger.application.phase.packages.mmp3d_driver_utils module
        • schrodinger.application.phase.packages.mmp3dscreener module
        • schrodinger.application.phase.packages.mmp_compare_utils module
        • schrodinger.application.phase.packages.oned_app_utils module
        • schrodinger.application.phase.packages.oned_option_utils module
        • schrodinger.application.phase.packages.oned_task_utils module
        • schrodinger.application.phase.packages.phase_convert_MOE module
        • schrodinger.application.phase.packages.phase_database_arg_utils module
        • schrodinger.application.phase.packages.phase_database_job_utils module
        • schrodinger.application.phase.packages.phase_option_utils module
        • schrodinger.application.phase.packages.phase_screen_driver_utils module
        • schrodinger.application.phase.packages.phase_screen_utils module
        • schrodinger.application.phase.packages.phase_utils module
        • schrodinger.application.phase.packages.shape_binary_utils module
        • schrodinger.application.phase.packages.shape_creation_logic module
        • schrodinger.application.phase.packages.shape_diversity module
        • schrodinger.application.phase.packages.shape_generator module
        • schrodinger.application.phase.packages.shape_ligprep module
        • schrodinger.application.phase.packages.shape_screen_al_driver module
        • schrodinger.application.phase.packages.shape_screen_al_node module
        • schrodinger.application.phase.packages.shape_screen_al_utils module
        • schrodinger.application.phase.packages.shape_screen_arg_utils module
        • schrodinger.application.phase.packages.shape_screen_gpu_generate module
        • schrodinger.application.phase.packages.shape_screen_gpu_update module
        • schrodinger.application.phase.packages.shape_screen_job_utils module
        • schrodinger.application.phase.packages.shape_screen_oned_driver_utils module
        • schrodinger.application.phase.packages.test module
    • schrodinger.application.phase.shape_screen_reporter package
      • Submodules
        • schrodinger.application.phase.shape_screen_reporter.option_utils module
        • schrodinger.application.phase.shape_screen_reporter.prop_utils module
        • schrodinger.application.phase.shape_screen_reporter.task_utils module
        • schrodinger.application.phase.shape_screen_reporter.tasks module
  • Submodules
    • schrodinger.application.phase.compare_utils module
    • 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.license module
    • schrodinger.application.phase.phase_markers module
    • schrodinger.application.phase.phase_widgets module
    • schrodinger.application.phase.pt_hypothesis module
    • schrodinger.application.phase.utils module
• schrodinger.application.prepwizard2 package
  • Submodules
    • schrodinger.application.prepwizard2.diagnostics module
    • schrodinger.application.prepwizard2.tasks module
• schrodinger.application.prime package
  • Subpackages
    • schrodinger.application.prime.gui package
      • Subpackages
        • schrodinger.application.prime.gui.ui package
          • Submodules
            • schrodinger.application.prime.gui.ui.analyze_energy_ui module
            • schrodinger.application.prime.gui.ui.environment_options_ui module
      • Submodules
        • schrodinger.application.prime.gui.analyze_energy module
  • Submodules
    • schrodinger.application.prime.input module
    • schrodinger.application.prime.primefix module
    • schrodinger.application.prime.residue_interaction module
    • schrodinger.application.prime.wrapper module
• schrodinger.application.pymol package
  • Subpackages
    • schrodinger.application.pymol.ui namespace
      • Submodules
        • schrodinger.application.pymol.ui.advanced_settings_wdg_ui module
        • schrodinger.application.pymol.ui.export_to_pymol_dlg_ui module
  • Submodules
    • schrodinger.application.pymol.constants module
    • schrodinger.application.pymol.export_handler module
    • schrodinger.application.pymol.export_to_pymol_gui module
    • schrodinger.application.pymol.gui_models module
    • schrodinger.application.pymol.mae_sync module
    • schrodinger.application.pymol.pymol4maestro module
    • schrodinger.application.pymol.pymol4maestro_ui module
    • schrodinger.application.pymol.utils module
• schrodinger.application.qsite package
  • Submodules
    • schrodinger.application.qsite.input module
    • schrodinger.application.qsite.output module
• schrodinger.application.scaffold_enumeration package
  • Submodules
    • schrodinger.application.scaffold_enumeration.atomlist module
    • schrodinger.application.scaffold_enumeration.common module
    • schrodinger.application.scaffold_enumeration.cxsmiles module
    • schrodinger.application.scaffold_enumeration.layered module
    • schrodinger.application.scaffold_enumeration.linknode module
    • schrodinger.application.scaffold_enumeration.markush module
    • schrodinger.application.scaffold_enumeration.mdl module
    • schrodinger.application.scaffold_enumeration.posvarbond module
    • schrodinger.application.scaffold_enumeration.rdcml module
• schrodinger.application.steps package
  • Submodules
    • schrodinger.application.steps.basesteps module
    • schrodinger.application.steps.converters module
    • schrodinger.application.steps.dataclasses module
    • schrodinger.application.steps.docking module
    • schrodinger.application.steps.enumerators module
    • schrodinger.application.steps.env_keys module
    • schrodinger.application.steps.filters module
    • schrodinger.application.steps.licensing module
    • schrodinger.application.steps.ligprep module
    • schrodinger.application.steps.scorers module
    • schrodinger.application.steps.test module
    • schrodinger.application.steps.transformers module
    • schrodinger.application.steps.utils module
• schrodinger.application.transforms package
  • Subpackages
    • schrodinger.application.transforms.enumerators module
    • schrodinger.application.transforms.template namespace
      • Submodules
        • schrodinger.application.transforms.template.starter module
        • schrodinger.application.transforms.template.workflow module
  • Submodules
    • schrodinger.application.transforms.chem module
    • schrodinger.application.transforms.chemio module
    • schrodinger.application.transforms.dock module
    • schrodinger.application.transforms.dofn_utils module
    • schrodinger.application.transforms.enumerators module
    • schrodinger.application.transforms.filters module
    • schrodinger.application.transforms.ligprep module
    • schrodinger.application.transforms.test module
    • schrodinger.application.transforms.validators module
• schrodinger.application.vss package
  • Submodules
    • schrodinger.application.vss.config module
    • schrodinger.application.vss.control module
    • schrodinger.application.vss.csvsmiles module
    • schrodinger.application.vss.database module
    • schrodinger.application.vss.dise module
    • schrodinger.application.vss.pilot module
    • schrodinger.application.vss.tasks module
• schrodinger.application.watermap package
  • Submodules
    • schrodinger.application.watermap.shapes module
    • schrodinger.application.watermap.utils module
    • schrodinger.application.watermap.watermap_inp module
    • schrodinger.application.watermap.watermap_scoring module
• schrodinger.application.xtb package
  • Submodules
    • schrodinger.application.xtb.constants module
    • schrodinger.application.xtb.input module
    • schrodinger.application.xtb.keywords module
    • schrodinger.application.xtb.output module
    • schrodinger.application.xtb.runner module
    • schrodinger.application.xtb.textparser module
    • schrodinger.application.xtb.utilities module

Submodules

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