schrodinger package

This is the top level package for all Schrodinger modules.

The main modules of interest are schrodinger.structure and the ones in the schrodinger.structutils package.

The Python Module Overview included with the Schrodinger distribution gives an expository introduction to the Schrodinger Python API. It is available from the Help -> Python Module Overview… link in Maestro, or from the $SCHRODINGER/docs/python_api/overview.html file.

If you have questions about the API, please contact us at help@schrodinger.com.

Subpackages

• schrodinger.Qt package
  • Subpackages
    • schrodinger.Qt.PyQt5 package
      • Submodules
        • schrodinger.Qt.PyQt5.QtCore module
        • schrodinger.Qt.PyQt5.QtGui module
        • schrodinger.Qt.PyQt5.QtNetwork module
        • schrodinger.Qt.PyQt5.QtOpenGL module
        • schrodinger.Qt.PyQt5.QtPrintSupport module
        • schrodinger.Qt.PyQt5.QtSvg module
        • schrodinger.Qt.PyQt5.QtTest module
        • schrodinger.Qt.PyQt5.QtWebKit module
        • schrodinger.Qt.PyQt5.QtWebKitWidgets module
        • schrodinger.Qt.PyQt5.QtWidgets module
• schrodinger.analysis package
  • Subpackages
    • schrodinger.analysis.visanalysis package
      • Introduction
        • Handling Three-Dimensional Data
          • Array Coordinates
          • World Coordinates
        • Converting Between Coordinate-Frames
      • Code Examples
        • Format Conversion
          • Loading a .vis File for Access in Python
          • Conversion to CCP4 Format
          • Accessing Basic VolumeData Properties
          • Create a vdW-Mask Around a Molecule
          • Analysing a Conformational-Ensemble
          • Manipulating SiteMap Volumes
      • Submodules
        • schrodinger.analysis.visanalysis.vdaxis module
        • schrodinger.analysis.visanalysis.vdcoordinateframe module
        • schrodinger.analysis.visanalysis.vdexception module
        • schrodinger.analysis.visanalysis.volumedata module
        • schrodinger.analysis.visanalysis.volumedataio module
        • schrodinger.analysis.visanalysis.volumedatastructureutils module
        • schrodinger.analysis.visanalysis.volumedatautils module
  • Submodules
    • schrodinger.analysis.cluster module
    • schrodinger.analysis.enrichment module
    • schrodinger.analysis.reaction module
    • schrodinger.analysis.transformations module
• schrodinger.application package
  • Subpackages
    • schrodinger.application.aacg package
      • Submodules
        • schrodinger.application.aacg.utils 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.antibody package
          • Submodules
            • schrodinger.application.bioluminate.antibody.management module
            • schrodinger.application.bioluminate.antibody.search_results_table module
            • schrodinger.application.bioluminate.antibody.utils module
        • schrodinger.application.bioluminate.patch_utils package
          • Submodules
            • 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.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.desmond package
      • Subpackages
        • schrodinger.application.desmond.antlr3 package
          • Submodules
            • schrodinger.application.desmond.antlr3.compat module
            • schrodinger.application.desmond.antlr3.constants module
            • schrodinger.application.desmond.antlr3.debug module
            • schrodinger.application.desmond.antlr3.dfa module
            • schrodinger.application.desmond.antlr3.dottreegen module
            • schrodinger.application.desmond.antlr3.exceptions module
            • schrodinger.application.desmond.antlr3.extras module
            • schrodinger.application.desmond.antlr3.main module
            • schrodinger.application.desmond.antlr3.recognizers module
            • schrodinger.application.desmond.antlr3.streams module
            • schrodinger.application.desmond.antlr3.tokens module
            • schrodinger.application.desmond.antlr3.tree module
            • schrodinger.application.desmond.antlr3.treewizard module
        • schrodinger.application.desmond.enhanced_sampling package
          • Submodules
            • schrodinger.application.desmond.enhanced_sampling.FcnTypes module
            • schrodinger.application.desmond.enhanced_sampling.mexpLexer module
            • schrodinger.application.desmond.enhanced_sampling.mexpParser module
        • schrodinger.application.desmond.event_analysis package
          • Submodules
            • schrodinger.application.desmond.event_analysis.pl_image_tools module
        • schrodinger.application.desmond.mdpose package
          • Submodules
            • schrodinger.application.desmond.mdpose.mdpose_analysis module
            • schrodinger.application.desmond.mdpose.mdpose_average_structure module
            • schrodinger.application.desmond.mdpose.mdpose_glide module
            • schrodinger.application.desmond.mdpose.mdpose_neutralize module
            • schrodinger.application.desmond.mdpose.mdpose_strain_energy module
            • schrodinger.application.desmond.mdpose.mdposejob module
        • schrodinger.application.desmond.packages package
          • Subpackages
            • schrodinger.application.desmond.packages.enhanced_sampling package
              • Submodules
                • schrodinger.application.desmond.packages.enhanced_sampling.FcnTypes module
                • schrodinger.application.desmond.packages.enhanced_sampling.mexpLexer module
                • schrodinger.application.desmond.packages.enhanced_sampling.mexpParser module
            • schrodinger.application.desmond.packages.msys package
              • Subpackages
                • schrodinger.application.desmond.packages.msys.molfile package
              • Submodules
                • schrodinger.application.desmond.packages.msys.atomsel module
                • schrodinger.application.desmond.packages.msys.grease module
                • schrodinger.application.desmond.packages.msys.groups module
                • schrodinger.application.desmond.packages.msys.knot module
                • schrodinger.application.desmond.packages.msys.posre module
                • schrodinger.application.desmond.packages.msys.reorder module
                • schrodinger.application.desmond.packages.msys.sequence module
                • schrodinger.application.desmond.packages.msys.thermalize module
                • schrodinger.application.desmond.packages.msys.update module
                • schrodinger.application.desmond.packages.msys.validate module
                • schrodinger.application.desmond.packages.msys.vdw module
                • schrodinger.application.desmond.packages.msys.wrap module
            • schrodinger.application.desmond.packages.viparr1 package
              • Subpackages
                • schrodinger.application.desmond.packages.viparr1.plugins package
                  • Submodules
                    • schrodinger.application.desmond.packages.viparr1.plugins.angles module
                    • schrodinger.application.desmond.packages.viparr1.plugins.atoms module
                    • schrodinger.application.desmond.packages.viparr1.plugins.bondfields module
                    • schrodinger.application.desmond.packages.viparr1.plugins.bonds module
                    • schrodinger.application.desmond.packages.viparr1.plugins.charges module
                    • schrodinger.application.desmond.packages.viparr1.plugins.cmap module
                    • schrodinger.application.desmond.packages.viparr1.plugins.dihedrals6atom module
                    • schrodinger.application.desmond.packages.viparr1.plugins.exclusions module
                    • schrodinger.application.desmond.packages.viparr1.plugins.impropers module
                    • schrodinger.application.desmond.packages.viparr1.plugins.inplanewags module
                    • schrodinger.application.desmond.packages.viparr1.plugins.mass module
                    • schrodinger.application.desmond.packages.viparr1.plugins.pairs_es module
                    • schrodinger.application.desmond.packages.viparr1.plugins.pairs_es_balanced module
                    • schrodinger.application.desmond.packages.viparr1.plugins.pairs_lj module
                    • schrodinger.application.desmond.packages.viparr1.plugins.polarizable module
                    • schrodinger.application.desmond.packages.viparr1.plugins.propers module
                    • schrodinger.application.desmond.packages.viparr1.plugins.screening module
                    • schrodinger.application.desmond.packages.viparr1.plugins.sparsify_exclusions_and_pairs module
                    • schrodinger.application.desmond.packages.viparr1.plugins.torsion_torsion module
                    • schrodinger.application.desmond.packages.viparr1.plugins.ureybradley module
                    • schrodinger.application.desmond.packages.viparr1.plugins.vdw1 module
                    • schrodinger.application.desmond.packages.viparr1.plugins.vdw1_14 module
                    • schrodinger.application.desmond.packages.viparr1.plugins.virtuals module
                • schrodinger.application.desmond.packages.viparr1.systest package
                  • Submodules
                    • schrodinger.application.desmond.packages.viparr1.systest.systest module
                • schrodinger.application.desmond.packages.viparr1.viparr package
                  • Submodules
                    • schrodinger.application.desmond.packages.viparr1.viparr.alchemical_map module
                    • schrodinger.application.desmond.packages.viparr1.viparr.elements module
                    • schrodinger.application.desmond.packages.viparr1.viparr.fep module
                    • schrodinger.application.desmond.packages.viparr1.viparr.isomorph module
                    • schrodinger.application.desmond.packages.viparr1.viparr.iviparr module
                    • schrodinger.application.desmond.packages.viparr1.viparr.maeview module
                    • schrodinger.application.desmond.packages.viparr1.viparr.version module
                    • schrodinger.application.desmond.packages.viparr1.viparr.viparr module
                    • schrodinger.application.desmond.packages.viparr1.viparr.viparr_merge module
                    • schrodinger.application.desmond.packages.viparr1.viparr.viparr_plugins_util module
                    • schrodinger.application.desmond.packages.viparr1.viparr.viparr_residue module
                    • schrodinger.application.desmond.packages.viparr1.viparr.viparr_util module
          • Submodules
            • schrodinger.application.desmond.packages.analysis module
            • schrodinger.application.desmond.packages.cui module
            • schrodinger.application.desmond.packages.energygroup module
            • schrodinger.application.desmond.packages.gdesmond_utils module
            • schrodinger.application.desmond.packages.timer module
            • schrodinger.application.desmond.packages.topo module
            • schrodinger.application.desmond.packages.torsion_related module
            • schrodinger.application.desmond.packages.traj module
            • schrodinger.application.desmond.packages.traj_util module
            • schrodinger.application.desmond.packages.viparr module
        • schrodinger.application.desmond.starter package
          • Subpackages
            • schrodinger.application.desmond.starter.generator package
              • Submodules
                • schrodinger.application.desmond.starter.generator.fep_plus module
            • schrodinger.application.desmond.starter.ui package
              • Submodules
                • schrodinger.application.desmond.starter.ui.cmdline module
                • schrodinger.application.desmond.starter.ui.fep_plus module
                • schrodinger.application.desmond.starter.ui.multisim module
          • Submodules
            • schrodinger.application.desmond.starter.starter module
      • Submodules
        • schrodinger.application.desmond.ana module
        • schrodinger.application.desmond.autopartition module
        • schrodinger.application.desmond.bennett module
        • schrodinger.application.desmond.cms module
        • schrodinger.application.desmond.cns_io module
        • schrodinger.application.desmond.config module
        • schrodinger.application.desmond.correlation_tau module
        • schrodinger.application.desmond.cwidget module
        • schrodinger.application.desmond.deltaE module
        • schrodinger.application.desmond.desmond_advanced_tab_ui module
        • schrodinger.application.desmond.energygroup module
        • schrodinger.application.desmond.enhsamp module
        • schrodinger.application.desmond.envir module
        • schrodinger.application.desmond.fep_constants module
        • schrodinger.application.desmond.fep_edge_data module
        • schrodinger.application.desmond.fep_edge_report_maker module
        • schrodinger.application.desmond.fep_gui module
        • schrodinger.application.desmond.fep_mapping module
        • schrodinger.application.desmond.fep_net_charge module
        • schrodinger.application.desmond.fep_reporter module
        • schrodinger.application.desmond.fep_scholar_msj_generator module
        • schrodinger.application.desmond.fep_scholar_rules module
        • schrodinger.application.desmond.fep_scholar_util module
        • schrodinger.application.desmond.fep_struc module
        • schrodinger.application.desmond.fep_util module
        • schrodinger.application.desmond.fepana module
        • schrodinger.application.desmond.fepdiff module
        • schrodinger.application.desmond.feputils module
        • schrodinger.application.desmond.ffiostructure module
        • schrodinger.application.desmond.frag_snap module
        • schrodinger.application.desmond.gaussian_filter module
        • schrodinger.application.desmond.gchart module
        • schrodinger.application.desmond.gconfig module
        • schrodinger.application.desmond.gui module
        • schrodinger.application.desmond.guide module
        • schrodinger.application.desmond.icon module
        • schrodinger.application.desmond.input_group_ui module
        • schrodinger.application.desmond.maestro module
        • schrodinger.application.desmond.mapper_msj_generator module
        • schrodinger.application.desmond.mdkey module
        • schrodinger.application.desmond.measurement module
        • schrodinger.application.desmond.memory_estimate module
        • schrodinger.application.desmond.meta module
        • schrodinger.application.desmond.move_alchem_ions module
        • schrodinger.application.desmond.mplchart module
        • schrodinger.application.desmond.picklejar module
        • schrodinger.application.desmond.platforms module
        • schrodinger.application.desmond.predict_remd_temp module
        • schrodinger.application.desmond.process_fep_traj module
        • schrodinger.application.desmond.r_group_asl module
        • schrodinger.application.desmond.remd module
        • schrodinger.application.desmond.reorder_atom module
        • schrodinger.application.desmond.repair_cms module
        • schrodinger.application.desmond.replica_dE module
        • schrodinger.application.desmond.replica_exchange_review module
        • schrodinger.application.desmond.replica_sid_generator module
        • schrodinger.application.desmond.report_helper module
        • schrodinger.application.desmond.rest_inp module
        • schrodinger.application.desmond.rest_tab_ui module
        • schrodinger.application.desmond.simulation_block_data module
        • schrodinger.application.desmond.simulation_block_test module
        • schrodinger.application.desmond.smarts module
        • schrodinger.application.desmond.struc module
        • schrodinger.application.desmond.system_builder_inp module
        • schrodinger.application.desmond.system_builder_util module
        • schrodinger.application.desmond.systype module
        • schrodinger.application.desmond.title_to_hex module
        • schrodinger.application.desmond.util module
        • schrodinger.application.desmond.xvfbwrapper module
    • schrodinger.application.epik package
    • schrodinger.application.ffbuilder package
    • 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
      • Subpackages
        • 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.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.coordinate_dialog_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_pka_bottom_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.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.solvation_gas_phase_ui module
                • schrodinger.application.jaguar.gui.ui.solvation_pka_ui module
                • schrodinger.application.jaguar.gui.ui.solvation_solvent_model_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.theory_tab_widgets module
            • schrodinger.application.jaguar.gui.utils module
      • 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.textparser module
        • schrodinger.application.jaguar.user_config 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.livedesign package
      • Submodules
        • schrodinger.application.livedesign.login module
        • schrodinger.application.livedesign.login_ui module
        • schrodinger.application.livedesign.upload_utils 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
      • 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.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.utils package
                  • Submodules
                    • schrodinger.application.matsci.qexsd.qespresso.utils.logger module
                    • schrodinger.application.matsci.qexsd.qespresso.utils.mapping module
                    • schrodinger.application.matsci.qexsd.qespresso.utils.xml2nebinput module
                    • schrodinger.application.matsci.qexsd.qespresso.utils.xml2qeinput module
                • 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
        • schrodinger.application.matsci.siteselector package
          • Submodules
            • schrodinger.application.matsci.siteselector.siteselector 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.enumeration module
        • schrodinger.application.matsci.equilibrium_md module
        • schrodinger.application.matsci.freevolume module
        • schrodinger.application.matsci.guibase 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.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.textlogger module
        • schrodinger.application.matsci.zmutils module
    • schrodinger.application.mcpro package
      • Submodules
        • schrodinger.application.mcpro.ddg module
        • schrodinger.application.mcpro.fep module
        • schrodinger.application.mcpro.guide module
        • schrodinger.application.mcpro.lrm module
        • schrodinger.application.mcpro.mc module
        • schrodinger.application.mcpro.mini module
        • schrodinger.application.mcpro.modelsystemwizard module
        • schrodinger.application.mcpro.perturbations module
        • schrodinger.application.mcpro.read_output module
        • schrodinger.application.mcpro.residuetools module
        • schrodinger.application.mcpro.solvent module
        • schrodinger.application.mcpro.writeinputs module
        • schrodinger.application.mcpro.zmat 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_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.msv package
      • Subpackages
        • schrodinger.application.msv.gui package
          • Submodules
            • schrodinger.application.msv.gui.blast_results_dialog module
            • schrodinger.application.msv.gui.blast_results_dialog_ui module
            • schrodinger.application.msv.gui.blast_search_dialog module
            • schrodinger.application.msv.gui.blast_search_dialog_ui module
            • schrodinger.application.msv.gui.color module
            • schrodinger.application.msv.gui.color_editor module
            • schrodinger.application.msv.gui.color_editor_ui module
            • schrodinger.application.msv.gui.delegates module
            • schrodinger.application.msv.gui.dendrogram_viewer module
            • schrodinger.application.msv.gui.dialogs module
            • schrodinger.application.msv.gui.get_sequences_dialog module
            • schrodinger.application.msv.gui.get_sequences_dialog_ui module
            • schrodinger.application.msv.gui.history module
            • schrodinger.application.msv.gui.history_ui module
            • schrodinger.application.msv.gui.menu module
            • schrodinger.application.msv.gui.msv_gui module
            • schrodinger.application.msv.gui.msv_main_ui module
            • schrodinger.application.msv.gui.msv_main_window_ui module
            • schrodinger.application.msv.gui.msv_rc module
            • schrodinger.application.msv.gui.msv_widget module
            • schrodinger.application.msv.gui.popup_dialogs module
            • schrodinger.application.msv.gui.preferences module
            • schrodinger.application.msv.gui.rename_tab_dialog_ui module
            • schrodinger.application.msv.gui.stylesheets module
            • schrodinger.application.msv.gui.tab_widget module
            • schrodinger.application.msv.gui.undoable_alignment module
            • schrodinger.application.msv.gui.view module
            • schrodinger.application.msv.gui.viewconstants module
            • schrodinger.application.msv.gui.viewmodel module
        • schrodinger.application.msv.jobs package
          • Submodules
            • schrodinger.application.msv.jobs.blast module
            • schrodinger.application.msv.jobs.clustal module
            • schrodinger.application.msv.jobs.muscle module
            • schrodinger.application.msv.jobs.structure_alignment module
      • Submodules
        • schrodinger.application.msv.command module
        • schrodinger.application.msv.converters module
        • schrodinger.application.msv.seqio module
        • schrodinger.application.msv.structure_model module
        • schrodinger.application.msv.test_helpers module
        • schrodinger.application.msv.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.pldb package
      • Subpackages
        • schrodinger.application.pldb.packages package
    • 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.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.ligprep module
            • schrodinger.application.vsw.stages.macromodel module
            • schrodinger.application.vsw.stages.mmgbsa 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
• schrodinger.graphics3d package
  • Submodules
    • schrodinger.graphics3d.arrow module
    • schrodinger.graphics3d.box module
    • schrodinger.graphics3d.common module
    • schrodinger.graphics3d.gridbox module
    • schrodinger.graphics3d.lines module
    • schrodinger.graphics3d.polygon module
    • schrodinger.graphics3d.polyhedron module
    • schrodinger.graphics3d.quadrilateral module
    • schrodinger.graphics3d.sphere module
    • schrodinger.graphics3d.torus module
• schrodinger.infra package
  • Subpackages
    • schrodinger.infra.exception_handler_dir package
      • Submodules
        • schrodinger.infra.exception_handler_dir.exception_dialog module
        • schrodinger.infra.exception_handler_dir.exception_dialog_ui module
  • Submodules
    • schrodinger.infra.epydoc_to_sphinx module
    • schrodinger.infra.exception_handler module
    • schrodinger.infra.fast3d module
    • schrodinger.infra.licensing module
    • schrodinger.infra.mm module
    • schrodinger.infra.mmbitset module
    • schrodinger.infra.mmcheck module
    • schrodinger.infra.mmerr module
    • schrodinger.infra.mmgpgpu module
    • schrodinger.infra.mmim module
    • schrodinger.infra.mminit module
    • schrodinger.infra.mmjob module
    • schrodinger.infra.mmkv module
    • schrodinger.infra.mmlist module
    • schrodinger.infra.mmobject module
    • schrodinger.infra.mmproj module
    • schrodinger.infra.mmreflect module
    • schrodinger.infra.mmsurf module
    • schrodinger.infra.phase module
    • schrodinger.infra.propedit module
    • schrodinger.infra.structure module
    • schrodinger.infra.table module
    • schrodinger.infra.util module
• schrodinger.job package
  • Submodules
    • schrodinger.job.app module
    • schrodinger.job.host_check module
    • schrodinger.job.hunt_stub module
    • schrodinger.job.jobcontrol module
    • schrodinger.job.launchapi module
    • schrodinger.job.launcher module
    • schrodinger.job.launchparams module
    • schrodinger.job.queue module
    • schrodinger.job.remote_command module
    • schrodinger.job.util module
• schrodinger.maestro package
  • Submodules
    • schrodinger.maestro.commands module
    • schrodinger.maestro.maestro module
    • schrodinger.maestro.markers module
• schrodinger.models package
  • Submodules
    • schrodinger.models.mappers module
    • schrodinger.models.parameters module
• schrodinger.pipeline package
  • Subpackages
    • schrodinger.pipeline.stages package
      • Submodules
        • schrodinger.pipeline.stages.canvas module
        • schrodinger.pipeline.stages.combine module
        • schrodinger.pipeline.stages.convert module
        • schrodinger.pipeline.stages.example module
        • schrodinger.pipeline.stages.filtering module
        • schrodinger.pipeline.stages.gencodes module
        • schrodinger.pipeline.stages.glide module
        • schrodinger.pipeline.stages.ligprep module
        • schrodinger.pipeline.stages.macromodel module
        • schrodinger.pipeline.stages.phase module
        • schrodinger.pipeline.stages.prime module
        • schrodinger.pipeline.stages.pull module
        • schrodinger.pipeline.stages.qikprop module
        • schrodinger.pipeline.stages.qsite module
        • schrodinger.pipeline.stages.rmsd module
        • schrodinger.pipeline.stages.semiemp module
  • Submodules
    • schrodinger.pipeline.input module
    • schrodinger.pipeline.pipeio module
    • schrodinger.pipeline.pipeline module
      • Input Object Syntax
      • Stage Syntax
    • schrodinger.pipeline.pipeutils module
    • schrodinger.pipeline.stage module
• schrodinger.protein package
  • Submodules
    • schrodinger.protein.align module
    • schrodinger.protein.alignment module
    • schrodinger.protein.analysis module
    • schrodinger.protein.analysis_params module
    • schrodinger.protein.annotation module
    • schrodinger.protein.assignment module
    • schrodinger.protein.captermini module
    • schrodinger.protein.constants module
    • schrodinger.protein.findhets module
    • schrodinger.protein.getpdb module
    • schrodinger.protein.getpdb_utility module
    • schrodinger.protein.helix module
    • schrodinger.protein.membrane module
    • schrodinger.protein.pdbname module
    • schrodinger.protein.reliability module
    • schrodinger.protein.remediate module
    • schrodinger.protein.residue module
    • schrodinger.protein.rotamers module
    • schrodinger.protein.sequence module
• schrodinger.structutils package
  • Subpackages
    • schrodinger.structutils.interactions package
      • Examples
      • Submodules
        • schrodinger.structutils.interactions.hbond module
        • schrodinger.structutils.interactions.pi module
        • schrodinger.structutils.interactions.salt_bridge module
          • Examples
        • schrodinger.structutils.interactions.ssbond module
        • schrodinger.structutils.interactions.steric_clash module
  • Submodules
    • schrodinger.structutils.analyze module
    • schrodinger.structutils.assignbondorders module
    • schrodinger.structutils.build module
    • schrodinger.structutils.color module
    • schrodinger.structutils.createfragments module
    • schrodinger.structutils.filter module
    • schrodinger.structutils.interactionfp module
    • schrodinger.structutils.io module
    • schrodinger.structutils.measure module
    • schrodinger.structutils.minimize module
      • API examples
    • schrodinger.structutils.rgroup_enumerate module
    • schrodinger.structutils.ringspear module
    • schrodinger.structutils.rmsd module
    • schrodinger.structutils.shuffle module
    • schrodinger.structutils.sitealign module
    • schrodinger.structutils.smiles module
    • schrodinger.structutils.smilesfilter module
    • schrodinger.structutils.sort module
    • schrodinger.structutils.structalign module
    • schrodinger.structutils.transform module
• schrodinger.tasks package
  • Submodules
    • schrodinger.tasks.jobtasks module
    • schrodinger.tasks.runners module
    • schrodinger.tasks.tasks module
• schrodinger.thirdparty package
  • Submodules
    • schrodinger.thirdparty.rdkit_adapter module
• schrodinger.trajectory package
  • Subpackages
    • schrodinger.trajectory.prody package
      • Submodules
        • schrodinger.trajectory.prody.compare module
        • schrodinger.trajectory.prody.crosscorrelation module
        • schrodinger.trajectory.prody.ensemble module
        • schrodinger.trajectory.prody.main module
        • schrodinger.trajectory.prody.main2 module
        • schrodinger.trajectory.prody.mode module
        • schrodinger.trajectory.prody.modeset module
        • schrodinger.trajectory.prody.nma module
        • schrodinger.trajectory.prody.pca module
        • schrodinger.trajectory.prody.test_arrow module
        • schrodinger.trajectory.prody.writenmd module
          • NMD Format
            • Description
            • Data fields
            • Autoload Trick
  • Submodules
    • schrodinger.trajectory.BondRotator module
    • schrodinger.trajectory.Torsion module
    • schrodinger.trajectory.analysis module
    • schrodinger.trajectory.analysistool module
    • schrodinger.trajectory.atomselection module
    • schrodinger.trajectory.automatic_analysis_generator module
    • schrodinger.trajectory.cmsstructure module
    • schrodinger.trajectory.desmondsimulation module
    • schrodinger.trajectory.ffstructure module
    • schrodinger.trajectory.hydrophobiccontactfinder module
    • schrodinger.trajectory.jcoupling module
    • schrodinger.trajectory.lipid_analysis module
    • schrodinger.trajectory.order_parameters module
    • schrodinger.trajectory.pbc_manager module
    • schrodinger.trajectory.proteininteractionsfinder module
    • schrodinger.trajectory.protliginteractionfinder module
    • schrodinger.trajectory.rmsd2d module
    • schrodinger.trajectory.saltbridgefinder module
• schrodinger.ui package
  • Subpackages
    • schrodinger.ui.picking_dir package
      • Submodules
        • schrodinger.ui.picking_dir.pick_constraint_res_no_maestro_dialog_ui module
        • schrodinger.ui.picking_dir.pick_lig_no_maestro_dialog_ui module
        • schrodinger.ui.picking_dir.pick_res_no_maestro_dialog_ui module
    • schrodinger.ui.widget package
      • Submodules
        • schrodinger.ui.widget.default module
        • schrodinger.ui.widget.pmwwidget module
        • schrodinger.ui.widget.tkinterwidget module
  • Submodules
    • schrodinger.ui.chooseligand module
    • schrodinger.ui.ligfilter module
    • schrodinger.ui.ligfilter_definition_dialog_ui module
    • schrodinger.ui.ligfilter_ui module
    • schrodinger.ui.picking module
    • schrodinger.ui.propertyselector module
    • schrodinger.ui.rama module
    • schrodinger.ui.residueselector module
• schrodinger.utils package
  • Subpackages
    • schrodinger.utils.welcome_dialog_dir package
      • Submodules
        • schrodinger.utils.welcome_dialog_dir.base_welcome module
  • Submodules
    • schrodinger.utils.cgxutils module
    • schrodinger.utils.cmdline module
      • Command Line Guidelines
        • Form of Options
          • Long Options
          • Boolean Options
        • Usage messages
          • Form
          • Examples
    • schrodinger.utils.colorscheme module
    • schrodinger.utils.config module
    • schrodinger.utils.csv_unicode module
    • schrodinger.utils.documentation module
    • schrodinger.utils.env module
    • schrodinger.utils.fileutils module
    • schrodinger.utils.imputils module
    • schrodinger.utils.installation_check module
    • schrodinger.utils.license module
    • schrodinger.utils.licutils module
    • schrodinger.utils.ligfilter module
    • schrodinger.utils.log module
    • schrodinger.utils.maestro_scripts_path module
    • schrodinger.utils.mmutil module
    • schrodinger.utils.moduleproxy module
    • schrodinger.utils.multifpfile module
    • schrodinger.utils.preferences module
    • schrodinger.utils.profiling module
    • schrodinger.utils.pymol module
    • schrodinger.utils.sea module
    • schrodinger.utils.sshconfig module
    • schrodinger.utils.subproc module
    • schrodinger.utils.subprocess module
    • schrodinger.utils.sysinfo module
    • schrodinger.utils.unicodesupport module
    • schrodinger.utils.units module
    • schrodinger.utils.urllib module
    • schrodinger.utils.welcome_dialog module

Submodules

• schrodinger.project module
• schrodinger.project_surface module
• schrodinger.structure module
• schrodinger.surface module