Index

_

_chain_options (PdbReaderProject attribute) _chain_types (PdbReaderProject attribute)

_model_by_chain (PdbReaderProject attribute) _model_options (PdbReaderProject attribute) _option_by_chain (PdbReaderProject attribute)

A

A_SERIES (GLIP_SUBGROUP attribute) ABSOLUTE_BINDING (Application attribute) ACINETOBACTER_BAUMANNII (LPS attribute) ACYLATED_PHOSPHATIDYLINOSITOL_DIMANNOSIDES_ACPIM2 (LPS attribute) add_boresh_restraint() (FreeEnergyProject method) add_child() (Node method) add_core_indices() (FreeEnergyProject method) add_ligand_group() (FreeEnergyProject method) add_ligand_to_group() (FreeEnergyProject method) add_missing_residues() (PdbReaderProject method) add_morph_set() (FreeEnergyProject method) add_mutation() (PdbReaderProject method) add_phosphorylation() (PdbReaderProject method) add_protonation() (PdbReaderProject method) add_ptm() (PdbReaderProject method) add_ssbond() (PdbReaderProject method) add_staple() (PdbReaderProject method) add_sugar() (Glycosylation method) AG (AMBERFF_ION attribute) Ag (AMBERFF_ION attribute) AG1P (CHARMMFF_ION attribute) AG2P (CHARMMFF_ION attribute) AL (AMBERFF_ION attribute) AL3P (CHARMMFF_ION attribute) ALA (MutationResidueName attribute) align_membrane_protein() (MembraneBuilderProject method) alignmentOption (AlignOptionsRequest attribute), [1] (HandleRequestStep2Request attribute), [1] alignOptions (HandleRequestStep2Request attribute), [1] AlignOptionsRequest (class in molcube.models) (class in molcube.typed_dicts) ALPHA (GLYP_NODE_TYPE attribute) AMBER (ForceField attribute) amber (ForceFieldFilesRequest attribute), [1] (MDRequest attribute), [1] AMBER (Program attribute) AMBER_AMINO_ACIDS (in module molcube.free_energy.conf) amberff (AvailableIons attribute) AMBERFF (ForceFieldType attribute) AMBERFF_ION (class in molcube.pdbreader.enums) (in module molcube.pdbreader.literals)

AmberOptionRequest (class in molcube.models) (class in molcube.typed_dicts) amberOptions (CreateProjectRequest attribute), [1] (HandleRequestStep1Request attribute), [1] AmberOptionsRequest (class in molcube.models) (class in molcube.typed_dicts) angle (DihedralRequest attribute), [1] anion (CustomIonRequest attribute), [1] AnyChainIdx (in module molcube.pdbreader.pdbreader) API (class in molcube.api) APIClient (class in molcube.api) Application (class in molcube.free_energy.enum) apply_force_constant() (FreeEnergyProject method) apply_predefined_glycan() (Glycosylation method) applyPh (ForceFieldGenerationRequest attribute), [1] ApplyPHtoLigandRequest (class in molcube.models) (class in molcube.typed_dicts) approximate_atoms() (in module molcube.cubie.utils) approximate_size_atoms() (Cubie method) area (LipidsRequest attribute), [1] ARG (MutationResidueName attribute) ASN (MutationResidueName attribute) ASP (MutationResidueName attribute) AU1P (CHARMMFF_ION attribute) AU3P (CHARMMFF_ION attribute) authenticate() (API method) AuthScheme (in module molcube.api) AvailableGlycan (class in molcube.pdbreader.conf) AvailableGlycansResponse (class in molcube.pdbreader.conf) AvailableGlycolipids (class in molcube.pdbreader.conf) AvailableGlycoProtRequest (class in molcube.models) (class in molcube.typed_dicts) availableInfo (AvailableGlycansResponse attribute) AvailableInfo (class in molcube.pdbreader.conf) AvailableIons (class in molcube.pdbreader.conf) availableResidues (DihedralInfoParsed attribute) (DihedralInfoResponse attribute) (DihedralInfoResponseModel attribute) availIons (Step3RenderResponse attribute) availLinker (Step3RenderResponse attribute) availPayload (Step3RenderResponse attribute)

B

B_SERIES (GLIP_SUBGROUP attribute) BA (AMBERFF_ION attribute) BAR (CHARMMFF_ION attribute) BaseProject (class in molcube.base) Be (AMBERFF_ION attribute) BE2P (CHARMMFF_ION attribute) BETA (GLYP_NODE_TYPE attribute) BI3P (CHARMMFF_ION attribute) BILAYER (MembraneType attribute) BLADE (Program attribute)

boltzProjectId (CreateProjectRequest attribute), [1] boxMargin (HandleRequestStep3Request attribute), [1] BoxMarginRequest (class in molcube.models) (class in molcube.typed_dicts) boxShape (HandleRequestStep1Request attribute), [1] (SolutionBuilderTaskRequest attribute), [1] boxSize (SolutionBuilderTaskRequest attribute), [1] BR (AMBERFF_ION attribute) (DRUDEFF_ION attribute) BSC1 (DNA attribute) BURKHOLDERIA_CEPACIA (LPS attribute)

C

C_SERIES (GLIP_SUBGROUP attribute) CA (AMBERFF_ION attribute) CAL (CHARMMFF_ION attribute) calcPka (CreateProjectRequest attribute), [1] CAMPYLOBACTER_JEJUNI (LPS attribute) cancellationDate (CancellationSupportRequest attribute), [1] CancellationSupportRequest (class in molcube.models) (class in molcube.typed_dicts) capping (CappingInfoRequest attribute), [1] CappingInfoRequest (class in molcube.models) (class in molcube.typed_dicts) cappings (ApplyPHtoLigandRequest attribute), [1] (SaveModifiedResidueRequest attribute), [1] cation (CustomIonRequest attribute), [1] CD (AMBERFF_ION attribute) (CHARMMFF_ION attribute) CE (AMBERFF_ION attribute) Ce (AMBERFF_ION attribute) CE3P (CHARMMFF_ION attribute) CER160 (GLIP_TAIL attribute) CER180 (GLIP_TAIL attribute) CER181 (GLIP_TAIL attribute) CER200 (GLIP_TAIL attribute) CER220 (GLIP_TAIL attribute) CER240 (GLIP_TAIL attribute) CER241 (GLIP_TAIL attribute) CER3E (GLIP_TAIL attribute) CES (CHARMMFF_ION attribute) (DRUDEFF_ION attribute) chain (AvailableGlycoProtRequest attribute), [1] (ModelingRequest attribute), [1] (ResiduesRequest attribute), [1] (SelectChainModificationRequest attribute), [1] chain_id (NonStandardSDFResult attribute) CHAIN_TYPE (class in molcube.pdbreader.enums) (in module molcube.pdbreader.literals) chainIndex (ChainIndexRequest attribute), [1] (ConnProteinRequest attribute), [1] (CovalentLigandRequest attribute), [1] (DihedralRequest attribute), [1] (GlycanChainIndexRequest attribute), [1] (GlycosylationRequest attribute), [1] (HemeChainIndexRequest attribute), [1] (HemeRequest attribute), [1] (IonChainIndexRequest attribute), [1] (NonstandardRequest attribute), [1] (NucleicChainIndexRequest attribute), [1] (ResidueRequest attribute) (SaveModifiedResidueRequest attribute), [1] (StandaloneChainIndexRequest attribute), [1] (TargetLigandRequest attribute), [1] (WaterChainIndexRequest attribute) ChainIndexRequest (class in molcube.models) (class in molcube.typed_dicts) ChainInfo (in module molcube.pdbreader.pdbreader) ChainRequest (class in molcube.models) (class in molcube.typed_dicts) change_dihedral() (LigandModelerProject method) charge (AvailableGlycan attribute) (CSMLResult attribute) (CustomIonRequest attribute), [1] CHARMM (ForceField attribute) charmm (ForceFieldFilesRequest attribute), [1] CHARMM_AMINO_ACIDS (in module molcube.free_energy.conf) CharmmAmberFileRequest (class in molcube.models) (class in molcube.typed_dicts) charmmff (AvailableIons attribute) CHARMMFF (ForceFieldType attribute) CHARMMFF_ION (class in molcube.pdbreader.enums) (in module molcube.pdbreader.literals) check_atom_index() (LigandModelerProject method) check_ligand_2d_structure() (FreeEnergyProject method) check_reference_ligands() (FreeEnergyProject method) CHLAMYDIA_TRACHOMATIS (LPS attribute) Cl (AMBERFF_ION attribute) CLA (CHARMMFF_ION attribute) (DRUDEFF_ION attribute) CLOSED (GenerateMorphsetType attribute) CNW11 (MSP attribute) CNW9 (MSP attribute) CO (AMBERFF_ION attribute) CO3P (CHARMMFF_ION attribute) color (GlycanSymbol attribute) COMBI (LIPID_TYPE attribute) companyName (EnterpriseInquiryRequest attribute), [1] completeRingMatch (ConnectionsRequest attribute), [1] compositionOption (HandleRequestStep3Request attribute), [1] (HandleRequestStep4Request attribute), [1] conc (CustomIonRequest attribute), [1] (CustomSolventRequest attribute), [1]

confirm_chains() (PdbReaderProject method) CONJUGATED (ResidueType attribute) conjugatedLigand (ModelingRequest attribute), [1] (SelectChainModificationRequest attribute), [1] connections (MorphPairRequest attribute), [1] ConnectionsRequest (class in molcube.models) (class in molcube.typed_dicts) connProtein (HemeChainIndexRequest attribute), [1] (HemeRequest attribute), [1] ConnProteinRequest (class in molcube.models) (class in molcube.typed_dicts) contact_email (SupportInquiry attribute), [1] contact_name (SupportInquiry attribute), [1] contact_phone (SupportInquiry attribute), [1] contactEmail (CancellationSupportRequest attribute), [1] (EnterpriseInquiryRequest attribute), [1] (PaymentSupportRequest attribute), [1] contactName (CancellationSupportRequest attribute), [1] (EnterpriseInquiryRequest attribute), [1] content (CubeBuilderInquiryRequest attribute), [1] (MarketingInquiryRequest attribute), [1] core (LipidsRequest attribute), [1] CORE_1 (PREDEFINED_GLYCAN attribute) CORE_2 (PREDEFINED_GLYCAN attribute) CORE_3 (PREDEFINED_GLYCAN attribute) CORE_4 (PREDEFINED_GLYCAN attribute) CORE_5 (PREDEFINED_GLYCAN attribute) CORE_6 (PREDEFINED_GLYCAN attribute) CORE_7 (PREDEFINED_GLYCAN attribute) CORE_8 (PREDEFINED_GLYCAN attribute) coreIons (HandleRequestStep5Request attribute), [1] (HandleRequestStep6Request attribute), [1] corrTop (CreateProjectRequest attribute), [1] count (PaginatedProjectList attribute), [1] counts (CustomSolventRequest attribute), [1] COVALENT (ResidueType attribute) covalentLigand (ChainIndexRequest attribute), [1] (ModelingRequest attribute), [1] (SelectChainModificationRequest attribute), [1] CovalentLigandRequest (class in molcube.models) (class in molcube.typed_dicts) CR (AMBERFF_ION attribute) Cr (AMBERFF_ION attribute) CR2P (CHARMMFF_ION attribute) CR3P (CHARMMFF_ION attribute) create_afes_project() (API method) create_ligand_modeler_project() (API method) create_membrane_builder_project() (API method) create_pdb_reader_project() (API method) create_project() (FreeEnergyProject method) (LigandModelerProject method) (MembraneBuilderProject method) (PdbReaderProject method) (SolutionBuilderProject method) create_solution_builder_project() (API method) created_at (Project attribute), [1] (SupportInquiry attribute), [1] CreateProjectRequest (class in molcube.models) (class in molcube.typed_dicts) CS (AMBERFF_ION attribute) CSMLResult (class in molcube.pdbreader.conf) cter (DiscntTerminalsRequest attribute), [1] (TerminalRequest attribute), [1] CU (AMBERFF_ION attribute) CU1 (AMBERFF_ION attribute) CU1P (CHARMMFF_ION attribute) CU2P (CHARMMFF_ION attribute) CubeBuilderInquiryRequest (class in molcube.models) (class in molcube.typed_dicts) Cubie (class in molcube.cubie.cubie) CUSTOM (GenerateMorphsetType attribute) (PDBSource attribute) (StandaloneSDFSource attribute) customAnion (CustomIonRequest attribute), [1] customCation (CustomIonRequest attribute), [1] CustomIonRequest (class in molcube.models) (class in molcube.typed_dicts) customIons (HandleRequestStep6Request attribute), [1] customPdb (CreateProjectRequest attribute), [1] customSolvent (HandleRequestStep6Request attribute), [1] CustomSolventRequest (class in molcube.models) (class in molcube.typed_dicts) cyclization (ChainIndexRequest attribute), [1] CYS (MutationResidueName attribute) CYSF (LIPID_TAIL attribute) CYSG (LIPID_TAIL attribute) CYSL (LIPID_TAIL attribute) CYSP (LIPID_TAIL attribute) cysteinBridge (ModelingRequest attribute), [1] (SelectChainModificationRequest attribute), [1]

D

DAG (PEG_HEAD attribute) DAG_DA (GLIP_TAIL attribute) DAG_DE (GLIP_TAIL attribute) DAG_DG (GLIP_TAIL attribute) DAG_DI (GLIP_TAIL attribute) DAG_DL (GLIP_TAIL attribute) DAG_DM (GLIP_TAIL attribute) DAG_DN (GLIP_TAIL attribute) DAG_DO (GLIP_TAIL attribute) DAG_DP (GLIP_TAIL attribute) DAG_DS (GLIP_TAIL attribute) DAG_DT (GLIP_TAIL attribute) DAG_DY (GLIP_TAIL attribute) DAG_LL (GLIP_TAIL attribute) DAG_PA (GLIP_TAIL attribute) DAG_PL (GLIP_TAIL attribute) DAG_PLE (GLIP_TAIL attribute) DAG_PO (GLIP_TAIL attribute) DAG_PS (GLIP_TAIL attribute) DAG_SA (GLIP_TAIL attribute) DAG_SD (GLIP_TAIL attribute) DAG_SL (GLIP_TAIL attribute) DAG_SO (GLIP_TAIL attribute) DAG_TI (GLIP_TAIL attribute) DAG_YO (GLIP_TAIL attribute) data (SuccessResponse attribute), [1] DecimalLike (in module molcube.typed_dicts) delete() (APIClient method) delete_boresh_restraint() (FreeEnergyProject method) delete_core_indices() (FreeEnergyProject method) delete_ligand_from_group() (FreeEnergyProject method) delete_ligand_group() (FreeEnergyProject method) delete_morph_set() (FreeEnergyProject method) delete_mutation() (FreeEnergyProject method) delete_project() (API method) delete_projects() (API method)

density (CustomSolventRequest attribute), [1] desmond (MDRequest attribute), [1] DihedralInfo (in module molcube.pdbreader.responses) DihedralInfoParsed (class in molcube.pdbreader.responses) DihedralInfoResponse (class in molcube.pdbreader.responses) DihedralInfoResponseModel (class in molcube.pdbreader.responses) DihedralRequest (class in molcube.models) (class in molcube.typed_dicts) dihedrals (DihedralInfoParsed attribute) (DihedralInfoResponse attribute) (DihedralInfoResponseModel attribute) (SideChainOrientationRequest attribute), [1] discntTerminals (MissingRequest attribute), [1] DiscntTerminalsRequest (class in molcube.models) (class in molcube.typed_dicts) dna (AmberOptionsRequest attribute), [1] DNA (class in molcube.pdbreader.enums) (in module molcube.pdbreader.literals) DOUBLE_BILAYER (MembraneType attribute) download_dummy() (MembraneBuilderProject method) download_packing() (MembraneBuilderProject method) download_pdb() (PdbReaderProject method) download_pdb_from_rcsb() (in module molcube.cubie.utils) download_project() (FreeEnergyProject method) (LigandModelerProject method) (MembraneBuilderProject method) (PdbReaderProject method) (SolutionBuilderProject method) download_system() (MembraneBuilderProject method) (SolutionBuilderProject method) drudeff (AvailableIons attribute) DRUDEFF (ForceFieldType attribute) DRUDEFF_ION (class in molcube.pdbreader.enums) (in module molcube.pdbreader.literals) Dy (AMBERFF_ION attribute) DY3P (CHARMMFF_ION attribute)

E

elasticNetwork (ModelingRequest attribute), [1] (SelectChainModificationRequest attribute), [1] email (CubeBuilderInquiryRequest attribute), [1] (MarketingInquiryRequest attribute), [1] end (ConnectionsRequest attribute), [1] EnterpriseInquiryRequest (class in molcube.models) (class in molcube.typed_dicts) Er (AMBERFF_ION attribute) ER3P (CHARMMFF_ION attribute) ErrorResponse (class in molcube.models) (class in molcube.typed_dicts)

ESCHERICHIA_COLI (LPS attribute) EU (AMBERFF_ION attribute) EU2P (CHARMMFF_ION attribute) EU3 (AMBERFF_ION attribute) EU3P (CHARMMFF_ION attribute) EXISTING (ForceFieldMethod attribute) existingMethod (ForceFieldGenerationRequest attribute), [1] EXTENDED_CORE_1 (PREDEFINED_GLYCAN attribute) EXTENDED_CORE_2 (PREDEFINED_GLYCAN attribute) EXTENDED_CORE_3 (PREDEFINED_GLYCAN attribute) EXTENDED_CORE_4 (PREDEFINED_GLYCAN attribute)

F

F (AMBERFF_ION attribute) (DRUDEFF_ION attribute) FA2BG2S2 (PREDEFINED_GLYCAN attribute) FA2G2S2 (PREDEFINED_GLYCAN attribute) FA3G3S3 (PREDEFINED_GLYCAN attribute) FA4G4S4 (PREDEFINED_GLYCAN attribute) FAT (PEG_HEAD attribute) FE (AMBERFF_ION attribute) FE2 (AMBERFF_ION attribute) FE2P (CHARMMFF_ION attribute) FE3P (CHARMMFF_ION attribute) feedback (CancellationSupportRequest attribute), [1] FEP (Method attribute) FF14SB (Protein attribute), [1] FF14SBonlysc (Protein attribute), [1] FF19SB (Protein attribute), [1] ffGeneration (ModelingRequest attribute), [1] (SelectChainModificationRequest attribute), [1] fileFormatsByForceFieldType (Step3RenderResponse attribute) files (ForceFieldGenerationRequest attribute), [1] fillSpace (HandleRequestStep3Request attribute), [1] (HandleRequestStep4Request attribute), [1]

flip_kv() (in module molcube.utils) flip_kv_unique() (in module molcube.utils) flipZ (OrientationOptionRequest attribute), [1] ForceField (class in molcube.free_energy.enum) forceField (ForceFieldRequest attribute), [1] forcefield_type (PdbReaderProject attribute) ForceFieldFileFormats (class in molcube.pdbreader.conf) ForceFieldFilesRequest (class in molcube.models) (class in molcube.typed_dicts) ForceFieldGenerationRequest (class in molcube.models) (class in molcube.typed_dicts) ForceFieldMethod (class in molcube.pdbreader.enums) forceFieldMethod (ForceFieldGenerationRequest attribute), [1] ForceFieldMethod (in module molcube.pdbreader.literals) forceFieldMethods (Step3RenderResponse attribute) ForceFieldRequest (class in molcube.models) (class in molcube.typed_dicts) ForceFieldType (class in molcube.pdbreader.enums) forceFieldType (ForceFieldGenerationRequest attribute), [1] ForceFieldType (in module molcube.pdbreader.literals) format1 (ForceFieldFileFormats attribute) format2 (ForceFieldFileFormats attribute) FreeEnergyProject (class in molcube.free_energy)

G

GA3P (CHARMMFF_ION attribute) GAFF (LigandForceField attribute), [1], [2] gaff (LigandForceFieldRequest attribute), [1] (MorphPairByForceFieldTypeRequest attribute), [1] (SelectedLigandsRequest attribute), [1] GAFF_FAST (LigandForceField attribute), [1], [2] gaffFast (LigandForceFieldRequest attribute), [1] (MorphPairByForceFieldTypeRequest attribute), [1] (SelectedLigandsRequest attribute), [1] GaffFastItem (class in molcube.models) GaffItem (class in molcube.models) GALACTOCEREBROSIDES (GLIP_GROUP attribute) GANGLIO_SERIES (GLIP_GROUP attribute) GD3 (AMBERFF_ION attribute) GD3P (CHARMMFF_ION attribute) gen_ligand_ff() (LigandModelerProject method) GENERATE (ForceFieldMethod attribute) generate (GenForcefieldTypes attribute) generate_api_key() (API method) generate_ligand_group() (FreeEnergyProject method) generate_lipid_packing() (MembraneBuilderProject method) generate_morph_set() (FreeEnergyProject method) generate_system() (FreeEnergyProject method) (MembraneBuilderProject method) (SolutionBuilderProject method) generate_token() (APIClient method) GenerateMorphsetType (class in molcube.free_energy.enum) genesis (MDRequest attribute), [1] GenForcefieldTypes (class in molcube.pdbreader.conf) genForceFieldTypes (Step3RenderResponse attribute) get() (APIClient method) get_available_dihedrals() (PdbReaderProject method) get_chains() (PdbReaderProject method) get_closest_atoms() (FreeEnergyProject method) get_core_indices() (FreeEnergyProject method) get_defaults() (PdbReaderProject method) get_distance() (FreeEnergyProject method) get_glycosylation_state() (PdbReaderProject method) get_ligand_groups() (FreeEnergyProject method) get_missing_residues() (PdbReaderProject method) get_msp_types() (MembraneBuilderProject method) get_native_ligands() (LigandModelerProject method) get_nonstandard_sdf() (PdbReaderProject method) get_packing_data_form() (MembraneBuilderProject method) get_pdb_info() (PdbReaderProject method) get_post_response() (BaseProject method) get_similarity_score() (FreeEnergyProject method) get_standalone_sdf() (PdbReaderProject method) get_terminal_residues() (PdbReaderProject method)

get_valid_missing_terminals() (PdbReaderProject method) get_valid_ssbond_residues() (PdbReaderProject method) get_valid_staples() (PdbReaderProject method) get_xyz_box_from_mol() (in module molcube.cubie.utils) get_xyz_box_from_rcsb_pdb() (in module molcube.cubie.utils) GetGlyInfoRequest (class in molcube.models) (class in molcube.typed_dicts) GLIP_GROUP (class in molcube.membrane_builder.enum) GLIP_SUBGROUP (class in molcube.membrane_builder.enum) GLIP_TAIL (class in molcube.membrane_builder.enum) GLN (MutationResidueName attribute) GLOBO_SERIES (GLIP_GROUP attribute) GLU (MutationResidueName attribute) GLUCOCEREBROSIDES (GLIP_GROUP attribute) GLY (MutationResidueName attribute) glyc_chain_indices (PdbReaderProject attribute) GLYCAM06J (Glycan attribute) glycan (AmberOptionsRequest attribute), [1] GLYCAN (CHAIN_TYPE attribute) glycan (ChainRequest attribute), [1] Glycan (class in molcube.pdbreader.enums) GLYCAN (in module molcube.pdbreader.literals) glycanAvailable (AvailableInfo attribute) GlycanChainIndexRequest (class in molcube.models) (class in molcube.typed_dicts) glycans (AvailableGlycansResponse attribute) GlycanSymbol (class in molcube.pdbreader.conf) glycInfo (GlycosylationRequest attribute), [1] (GlycRequest attribute), [1] GLYCOGLYCEROLIPIDS (GLIP_GROUP attribute) GlycoInfoRequest (class in molcube.models) (class in molcube.typed_dicts) GLYCOLIPID (LIPID_TYPE attribute) glycolipidsAvailable (AvailableInfo attribute) GLYCOPHOSPHATIDYLINOSITOLS (GLIP_GROUP attribute) glycoProtein (GlycosylationRequest attribute), [1] Glycosylation (class in molcube.pdbreader.glycosylation) glycosylation (ModelingRequest attribute), [1] (SelectChainModificationRequest attribute), [1] GlycosylationRequest (class in molcube.models) (class in molcube.typed_dicts) glycosylations (PdbReaderProject attribute) GlycRequest (class in molcube.models) (class in molcube.typed_dicts) GLYM (LIPID_TAIL attribute) GLYP_NODE_TYPE (class in molcube.pdbreader.enums) (in module molcube.pdbreader.literals) gromacs (MDRequest attribute), [1] GROMACS (Program attribute)

H

handle_response() (BaseProject method) HandleRequestStep1Request (class in molcube.models) (class in molcube.typed_dicts) HandleRequestStep2Request (class in molcube.models) (class in molcube.typed_dicts) HandleRequestStep3Request (class in molcube.models) (class in molcube.typed_dicts) HandleRequestStep4Request (class in molcube.models) (class in molcube.typed_dicts) HandleRequestStep5Request (class in molcube.models) (class in molcube.typed_dicts) HandleRequestStep6Request (class in molcube.models) (class in molcube.typed_dicts) HandleStepRequest (class in molcube.models) (class in molcube.typed_dicts) hasParam (ForceFieldGenerationRequest attribute), [1] HE01 (CHARMMFF_ION attribute) head (LipidsRequest attribute), [1] headGroup (LipidsRequest attribute), [1] HeadGroupItem (class in molcube.models) headType (LipidsRequest attribute), [1] height (HandleRequestStep3Request attribute), [1]

HELICOBACTER_PYLORI (LPS attribute) HEME (CHAIN_TYPE attribute) heme (ChainRequest attribute), [1] (ModelingRequest attribute), [1] (SelectChainModificationRequest attribute), [1] HemeChainIndexRequest (class in molcube.models) (class in molcube.typed_dicts) HemeRequest (class in molcube.models) (class in molcube.typed_dicts) HEXPHASE (MembraneType attribute) Hf (AMBERFF_ION attribute) HG (AMBERFF_ION attribute) HG2P (CHARMMFF_ION attribute) HID (MutationResidueName attribute) HIE (MutationResidueName attribute) HIP (MutationResidueName attribute) HIS (MutationResidueName attribute) HO3P (CHARMMFF_ION attribute) HSD (MutationResidueName attribute) HSE (MutationResidueName attribute) HSP (MutationResidueName attribute) HYBRID (PREDEFINED_GLYCAN attribute) hydrationNumber (HandleRequestStep5Request attribute), [1]

I

I (DRUDEFF_ION attribute) id (Project attribute), [1] (SupportInquiry attribute), [1] ILE (MutationResidueName attribute) IN (AMBERFF_ION attribute) IN3P (CHARMMFF_ION attribute) initSdf (SaveModifiedResidueRequest attribute), [1] innerHydrationNumber (HandleRequestStep3Request attribute), [1] innerIonConc (HandleRequestStep5Request attribute), [1] innerIons (HandleRequestStep5Request attribute), [1] innerNeutralize (HandleRequestStep5Request attribute), [1] innerNumber (LipidsRequest attribute), [1] innerRatio (LipidsRequest attribute), [1] innerWaterMargin (HandleRequestStep2Request attribute), [1] (HandleRequestStep3Request attribute), [1] inquiry_data (SupportInquiry attribute), [1] inquiry_type (SupportInquiry attribute), [1] inquiry_type_display (SupportInquiry attribute), [1] InquiryTypeEnum (class in molcube.models) (in module molcube.typed_dicts)

IOD (AMBERFF_ION attribute) ION (CHAIN_TYPE attribute) ion (ChainRequest attribute), [1] IonChainIndexRequest (class in molcube.models) (class in molcube.typed_dicts) ionConc (HandleRequestStep5Request attribute), [1] (HandleRequestStep6Request attribute), [1] (SolutionBuilderTaskRequest attribute), [1] ionElement (IonChainIndexRequest attribute), [1] ions (HandleRequestStep5Request attribute), [1] (HandleRequestStep6Request attribute), [1] (SolutionBuilderTaskRequest attribute), [1] isCustom (LipidsRequest attribute), [1] (ValidateStandaloneSdfRequest attribute), [1] isMembrane (ModelingRequest attribute), [1] ISO_GLOBO_SERIES (GLIP_GROUP attribute) issueDescription (PaymentSupportRequest attribute), [1] itervar_to_list() (in module molcube.utils)

K

K (AMBERFF_ION attribute) keepCoords (ForceFieldGenerationRequest attribute), [1]

ketcherInitSdf (SaveModifiedResidueRequest attribute), [1] (SearchIsomorphicResiduesRequest attribute), [1] KLEBSIELLA_PNEUMONIA (LPS attribute)

L

LA (AMBERFF_ION attribute) LA3P (CHARMMFF_ION attribute) LACTO_SERIES (GLIP_GROUP attribute) LEU (MutationResidueName attribute) LI (AMBERFF_ION attribute) ligandChainIndex1 (ProteinLigandRequest attribute), [1] ligandChainIndex2 (ProteinLigandRequest attribute), [1] LigandForceField (class in molcube.free_energy.enum) (class in molcube.ligand_modeler.enum) (class in molcube.pdbreader.enums) (in module molcube.pdbreader.literals) LigandForceFieldRequest (class in molcube.models) (class in molcube.typed_dicts) ligandForceFields (SetLigandForceFieldsRequest attribute), [1] LigandModelerProject (class in molcube.ligand_modeler) Link (class in molcube.pdbreader.glycosylation) LINKAGE (ResidueType attribute) linkages (GetGlyInfoRequest attribute), [1] (GlycoInfoRequest attribute) (PredefinedGlyInfoRequest attribute) LinkagesRequest (class in molcube.models) (class in molcube.typed_dicts) lipaIons (HandleRequestStep5Request attribute), [1] (HandleRequestStep6Request attribute), [1] lipid (AmberOptionRequest attribute), [1] (AmberOptionsRequest attribute), [1] Lipid (class in molcube.pdbreader.enums) LIPID (GLYP_NODE_TYPE attribute) (in module molcube.pdbreader.literals)

lipid (LipidsRequest attribute), [1] LIPID17 (Lipid attribute) LIPID21 (Lipid attribute) LIPID_TAIL (class in molcube.pdbreader.enums) (in module molcube.pdbreader.literals) LIPID_TYPE (class in molcube.membrane_builder.enum) lipidation (ChainIndexRequest attribute), [1] LipidationRequest (class in molcube.models) (class in molcube.typed_dicts) lipids (AvailableGlycolipids attribute) (HandleRequestStep3Request attribute), [1] (HandleRequestStep4Request attribute), [1] LipidsRequest (class in molcube.models) (class in molcube.typed_dicts) lipidTails (Step3RenderResponse attribute) LIT (CHARMMFF_ION attribute) (DRUDEFF_ION attribute) LOMAP (GenerateMorphsetType attribute) lowerInnerNumber (LipidsRequest attribute), [1] lowerInnerRatio (LipidsRequest attribute), [1] lowerOuterNumber (LipidsRequest attribute), [1] lowerOuterRatio (LipidsRequest attribute), [1] lowNumber (LipidsRequest attribute), [1] lowRatio (LipidsRequest attribute), [1] LPS (class in molcube.membrane_builder.enum) (LIPID_TYPE attribute) LU (AMBERFF_ION attribute) LU3P (CHARMMFF_ION attribute) LYS (MutationResidueName attribute) LYSM (LIPID_TAIL attribute)

M

M3 (PREDEFINED_GLYCAN attribute) M5 (PREDEFINED_GLYCAN attribute) M9 (PREDEFINED_GLYCAN attribute) margin (BoxMarginRequest attribute), [1] (HandleRequestStep4Request attribute), [1] (SolutionBuilderTaskRequest attribute), [1] MarketingInquiryRequest (class in molcube.models) (class in molcube.typed_dicts) martini (ForceFieldFilesRequest attribute), [1] MARTINI_AMINO_ACIDS (in module molcube.free_energy.conf) martiniff (AvailableIons attribute) MARTINIFF (ForceFieldType attribute) MartiniFileRequest (class in molcube.models) (class in molcube.typed_dicts) mdEngines (HandleRequestStep5Request attribute), [1] (HandleRequestStep6Request attribute), [1] (SolutionBuilderTaskRequest attribute), [1] MDRequest (class in molcube.models) (class in molcube.typed_dicts) MEMBRANE_BUILDER (Module attribute) MembraneBuilderProject (class in molcube.membrane_builder) membraneOnly (HandleRequestStep1Request attribute), [1] MembraneType (class in molcube.membrane_builder.enum) membraneType (HandleRequestStep1Request attribute), [1] message (ErrorResponse attribute), [1] MET (MutationResidueName attribute) Method (class in molcube.free_energy.enum) MG (AMBERFF_ION attribute) (CHARMMFF_ION attribute) MICELLE (MembraneType attribute) missing (ChainIndexRequest attribute), [1] (NucleicChainIndexRequest attribute), [1] MissingRequest (class in molcube.models) (class in molcube.typed_dicts) mminimization (SolutionBuilderTaskRequest attribute), [1] MN (AMBERFF_ION attribute) MN2P (CHARMMFF_ION attribute) MN3P (CHARMMFF_ION attribute) model (ModelingRequest attribute), [1] (SelectChainModificationRequest attribute), [1] model_pdb() (PdbReaderProject method) ModelingRequest (class in molcube.models) (class in molcube.typed_dicts) modificationAvailable (AvailableInfo attribute) modifications (AvailableGlycan attribute) (PredefinedGlyInfoResidue attribute) (ResiduesRequest attribute), [1] module molcube.api molcube.base molcube.cubie molcube.cubie.cubie molcube.cubie.enum molcube.cubie.utils molcube.free_energy.conf molcube.free_energy.enum molcube.ligand_modeler.enum molcube.membrane_builder.conf molcube.membrane_builder.enum molcube.models molcube.pdbreader.conf molcube.pdbreader.enums molcube.pdbreader.glycosylation molcube.pdbreader.literals molcube.pdbreader.responses molcube.typed_dicts molcube.utils

Module (class in molcube.cubie.enum) mol_from_pdb_block() (in module molcube.cubie.utils) molcube.api module molcube.base module molcube.cubie module molcube.cubie.cubie module molcube.cubie.enum module molcube.cubie.utils module molcube.free_energy.conf module molcube.free_energy.enum module molcube.ligand_modeler.enum module molcube.membrane_builder.conf module molcube.membrane_builder.enum module molcube.models module molcube.pdbreader.conf module molcube.pdbreader.enums module molcube.pdbreader.glycosylation module molcube.pdbreader.literals module molcube.pdbreader.responses module molcube.typed_dicts module molcube.utils module MORAXELLA_CATARRHALIS (LPS attribute) MorphPairByForceFieldTypeRequest (class in molcube.models) (class in molcube.typed_dicts) MorphPairRequest (class in molcube.models) (class in molcube.typed_dicts) MSLD (Method attribute) MSP (class in molcube.membrane_builder.enum) MSP1 (MSP attribute) MSP1D1 (MSP attribute) MSP1D122 (MSP attribute) MSP1D133 (MSP attribute) MSP1D144 (MSP attribute) MSP1D1Dh5 (MSP attribute) MSP1E1D1 (MSP attribute) MSP1E2D1 (MSP attribute) MSP1E3D1 (MSP attribute) MSP2N2 (MSP attribute) MST (GenerateMorphsetType attribute) mutation (ChainIndexRequest attribute), [1] (NucleicChainIndexRequest attribute), [1] MUTATION_FE (Application attribute) MutationRequest (class in molcube.models) (class in molcube.typed_dicts) MutationResidueName (class in molcube.free_energy.enum)

N

Na (AMBERFF_ION attribute) namd (MDRequest attribute), [1] name (AvailableGlycan attribute) (AvailableGlycolipids attribute) (CubeBuilderInquiryRequest attribute), [1] (CustomSolventRequest attribute), [1] (MarketingInquiryRequest attribute), [1] (PredefinedGlyInfoResidue attribute) (ResiduesRequest attribute), [1] nanodisc (HandleRequestStep3Request attribute), [1] NANODISC (MembraneType attribute) Ncarbon (AvailableGlycan attribute) Nd (AMBERFF_ION attribute) ND3P (CHARMMFF_ION attribute) NE01 (CHARMMFF_ION attribute) NEISSERIA_GONORRHOEAE (LPS attribute) NEISSERIA_MENINGITIDIS (LPS attribute) NEO_LACTO_SERIES (GLIP_GROUP attribute) neutralize (CustomIonRequest attribute), [1] (HandleRequestStep5Request attribute), [1] (HandleRequestStep6Request attribute), [1] (SolutionBuilderTaskRequest attribute), [1] newCovalentLigand (ModelingRequest attribute), [1] (SelectChainModificationRequest attribute), [1]

NewLinkageRequest (class in molcube.models) (class in molcube.typed_dicts) next (PaginatedProjectList attribute), [1] NI (AMBERFF_ION attribute) NI2P (CHARMMFF_ION attribute) Node (class in molcube.pdbreader.glycosylation) NON_EQ_TI (Method attribute) nonStandard (ChainIndexRequest attribute), [1] (NucleicChainIndexRequest attribute), [1] NONSTANDARD (ResidueType attribute) NonstandardRequest (class in molcube.models) (class in molcube.typed_dicts) NonStandardSDFResult (class in molcube.pdbreader.conf) notes (SupportInquiry attribute), [1] nter (DiscntTerminalsRequest attribute), [1] (TerminalRequest attribute), [1] NUCLEIC_ACID (CHAIN_TYPE attribute) nucleicAcid (ChainRequest attribute), [1] NucleicChainIndexRequest (class in molcube.models) (class in molcube.typed_dicts) number (LipidsRequest attribute), [1] nUnit (LipidsRequest attribute), [1]

O

oAnti (LipidsRequest attribute), [1] OL15 (DNA attribute) OL3 (RNA attribute) OPC (Water attribute), [1] OPENFF (LigandForceField attribute), [1], [2] openff (LigandForceFieldRequest attribute), [1] (MorphPairByForceFieldTypeRequest attribute), [1] (SelectedLigandsRequest attribute), [1] OPENFF_FAST (LigandForceField attribute), [1], [2] openffFast (LigandForceFieldRequest attribute), [1] (MorphPairByForceFieldTypeRequest attribute), [1] (SelectedLigandsRequest attribute), [1] OpenffFastItem (class in molcube.models) OpenffItem (class in molcube.models)

openmm (MDRequest attribute), [1] OPENMM (Program attribute) optimize (ForceFieldGenerationRequest attribute), [1] organization (MarketingInquiryRequest attribute), [1] orient_side_chains() (PdbReaderProject method) orientationOption (AlignOptionsRequest attribute), [1] (HandleRequestStep2Request attribute), [1] OrientationOptionRequest (class in molcube.models) (class in molcube.typed_dicts) ORIGINAL (StandaloneSDFSource attribute) OTHERS (GLIP_SUBGROUP attribute) oUnit (LipidsRequest attribute), [1] outerNumber (LipidsRequest attribute), [1] outerRatio (LipidsRequest attribute), [1]

P

PaginatedProjectList (class in molcube.models) (class in molcube.typed_dicts) param (CharmmAmberFileRequest attribute), [1] parse_avail_mutation() (FreeEnergyProject method) patch (PhosphorylationRequest attribute) (ProtonationRequest attribute) (PTMRequest attribute), [1] (StaplingRequest attribute), [1] patchDescription (Step3RenderResponse attribute) PatchedProjectRequest (class in molcube.models) (class in molcube.typed_dicts) PaymentSupportRequest (class in molcube.models) (class in molcube.typed_dicts) PB (AMBERFF_ION attribute) PB2P (CHARMMFF_ION attribute) PD (AMBERFF_ION attribute) PD2P (CHARMMFF_ION attribute) pdb (CSMLResult attribute) PDB (SDFSource attribute) PDB_READER (Module attribute) pdbId (CreateProjectRequest attribute), [1] pdbProjectPk (SolutionBuilderProjectRequest attribute), [1] pdbreaderPk (AlignOptionsRequest attribute), [1] PdbreaderPKRequest (class in molcube.models) (class in molcube.typed_dicts) PdbReaderProject (class in molcube.pdbreader) pdbreaderProject (HandleRequestStep1Request attribute), [1] pdbreaderProjects (HandleRequestStep1Request attribute), [1] PDBSource (class in molcube.pdbreader.enums) pdbSource (CreateProjectRequest attribute), [1] PDBSource (in module molcube.pdbreader.literals) PE (PEG_HEAD attribute) PEG_HEAD (class in molcube.membrane_builder.enum) PEGL (LIPID_TYPE attribute) PERSONAL (Workspace attribute) perturbationPaths (UpdatePerturbationPathsRequest attribute), [1] ph (ApplyPHtoLigandRequest attribute), [1] (ModelingRequest attribute), [1] (SelectChainModificationRequest attribute), [1] PHE (MutationResidueName attribute) phosphorylation (ChainIndexRequest attribute), [1] PhosphorylationRequest (class in molcube.models) (class in molcube.typed_dicts) PI_CER160 (GLIP_TAIL attribute) PI_CER180 (GLIP_TAIL attribute) PI_CER181 (GLIP_TAIL attribute) PI_CER200 (GLIP_TAIL attribute) PI_CER220 (GLIP_TAIL attribute) PI_CER240 (GLIP_TAIL attribute) PI_CER241 (GLIP_TAIL attribute) PI_CER3E (GLIP_TAIL attribute) PI_DAG_DA (GLIP_TAIL attribute) PI_DAG_DE (GLIP_TAIL attribute) PI_DAG_DG (GLIP_TAIL attribute) PI_DAG_DI (GLIP_TAIL attribute) PI_DAG_DL (GLIP_TAIL attribute) PI_DAG_DM (GLIP_TAIL attribute) PI_DAG_DN (GLIP_TAIL attribute) PI_DAG_DO (GLIP_TAIL attribute) PI_DAG_DP (GLIP_TAIL attribute) PI_DAG_DS (GLIP_TAIL attribute) PI_DAG_DT (GLIP_TAIL attribute) PI_DAG_DY (GLIP_TAIL attribute) PI_DAG_LL (GLIP_TAIL attribute) PI_DAG_PA (GLIP_TAIL attribute) PI_DAG_PL (GLIP_TAIL attribute) PI_DAG_PLE (GLIP_TAIL attribute) PI_DAG_PO (GLIP_TAIL attribute) PI_DAG_PS (GLIP_TAIL attribute) PI_DAG_SA (GLIP_TAIL attribute) PI_DAG_SD (GLIP_TAIL attribute) PI_DAG_SL (GLIP_TAIL attribute) PI_DAG_SO (GLIP_TAIL attribute) PI_DAG_TI (GLIP_TAIL attribute) PI_DAG_YO (GLIP_TAIL attribute) pk (CustomIonRequest attribute), [1] (CustomSolventRequest attribute), [1] PM3P (CHARMMFF_ION attribute) pollingId (PaymentSupportRequest attribute), [1] pollingType (PaymentSupportRequest attribute), [1] PollingTypeEnum (class in molcube.models) (in module molcube.typed_dicts) poreR (HandleRequestStep3Request attribute), [1] post() (APIClient method) post_files() (APIClient method) post_multipart() (APIClient method) post_raw() (APIClient method) POT (CHARMMFF_ION attribute) (DRUDEFF_ION attribute) PR (AMBERFF_ION attribute)

PR3P (CHARMMFF_ION attribute) PREDEFINED_GLYCAN (class in molcube.pdbreader.enums) (in module molcube.pdbreader.literals) PredefinedGlycanData (class in molcube.pdbreader.conf) predefinedGlycans (Step3RenderResponse attribute) PredefinedGlyInfoLinkage (class in molcube.pdbreader.conf) PredefinedGlyInfoRequest (class in molcube.pdbreader.conf) PredefinedGlyInfoResidue (class in molcube.pdbreader.conf) previous (PaginatedProjectList attribute), [1] PRO (MutationResidueName attribute) processing_ligand() (FreeEnergyProject method) Program (class in molcube.free_energy.enum) Project (class in molcube.models) (class in molcube.typed_dicts) project_type (PatchedProjectRequest attribute), [1] (Project attribute), [1] (ProjectRequest attribute), [1] projectCategory (CubeBuilderInquiryRequest attribute), [1] projectForceField (CreateProjectRequest attribute), [1] (HandleRequestStep1Request attribute), [1] (SolutionBuilderProjectRequest attribute), [1] projectId (CubeBuilderInquiryRequest attribute), [1] projectPk (AvailableGlycoProtRequest attribute), [1] (CreateProjectRequest attribute), [1] (ForceFieldFilesRequest attribute), [1] (GlycRequest attribute), [1] (HandleRequestStep2Request attribute), [1] (HandleRequestStep3Request attribute), [1] (HandleRequestStep4Request attribute), [1] (HandleRequestStep5Request attribute), [1] (HandleRequestStep6Request attribute), [1] (HandleStepRequest attribute), [1] (ModelingRequest attribute), [1] (PdbreaderPKRequest attribute), [1] (ProjectPKRequest attribute) (RenameProejctRequest attribute), [1] (SaveModifiedResidueRequest attribute), [1] (SelectChainModificationRequest attribute), [1] (SetLigandForceFieldsRequest attribute), [1] (SideChainOrientationRequest attribute), [1] (SolutionBuilderTaskRequest attribute), [1] (UpdatePerturbationPathsRequest attribute), [1] (UpdateReferenceLigandProjectRequest attribute), [1] (UpdateSelectedForceFieldsRequest attribute), [1] (UpdateSelectedLigandsRequest attribute), [1] (UpdateSimilarityScoreMatrixRequest attribute), [1] (UpdateTargetLigandRequest attribute), [1] (ValidateStandaloneSdfRequest attribute), [1] ProjectPKRequest (class in molcube.models) (class in molcube.typed_dicts) ProjectRequest (class in molcube.models) (class in molcube.typed_dicts) projectStep (HandleStepRequest attribute), [1] projectTitle (CreateProjectRequest attribute), [1] (HandleRequestStep1Request attribute), [1] (RenameProejctRequest attribute), [1] (SolutionBuilderProjectRequest attribute), [1] projectType (CubeBuilderInquiryRequest attribute), [1] ProjectTypeEnum (class in molcube.models) (in module molcube.typed_dicts) protAtoms (ApplyPHtoLigandRequest attribute), [1] (SaveModifiedResidueRequest attribute), [1] protein (AmberOptionRequest attribute), [1] (AmberOptionsRequest attribute), [1] PROTEIN (CHAIN_TYPE attribute) protein (ChainRequest attribute), [1] Protein (class in molcube.free_energy.enum) (class in molcube.pdbreader.enums) PROTEIN (GLYP_NODE_TYPE attribute) Protein (in module molcube.pdbreader.literals) ProteinChain (class in molcube.models) proteinChainIndex (ProteinLigandRequest attribute), [1] proteinChains (AlignOptionsRequest attribute), [1] (HandleRequestStep2Request attribute), [1] proteinLigand (NewLinkageRequest attribute), [1] ProteinLigandRequest (class in molcube.models) (class in molcube.typed_dicts) proteinResid (ProteinLigandRequest attribute), [1] protonation (ChainIndexRequest attribute), [1] ProtonationRequest (class in molcube.models) (class in molcube.typed_dicts) PSEUDOMONAS_AERUGINOSA (LPS attribute) PT (AMBERFF_ION attribute) PT2P (CHARMMFF_ION attribute) ptm (ChainIndexRequest attribute), [1] PTMLike (in module molcube.pdbreader.literals) PTMRequest (class in molcube.models) (class in molcube.typed_dicts) PU3P (CHARMMFF_ION attribute) put() (APIClient method)

R

Ra (AMBERFF_ION attribute) RA2P (CHARMMFF_ION attribute) RADIAL (GenerateMorphsetType attribute) radius (HandleRequestStep3Request attribute), [1] range (MissingRequest attribute), [1] ratio (CustomSolventRequest attribute), [1] (LipidsRequest attribute), [1] RB (AMBERFF_ION attribute) RCSB (PDBSource attribute) (SDFSource attribute) (StandaloneSDFSource attribute) read_ligand_modeler_project() (FreeEnergyProject method) reason (CancellationSupportRequest attribute), [1] referenceLigandProjectId (UpdateReferenceLigandProjectRequest attribute), [1] RELATIVE_BINDING (Application attribute) remove_child() (Node method) remove_matching_list_items() (in module molcube.utils) remove_missing_residues() (PdbReaderProject method) remove_none_recursive() (in module molcube.utils) remove_ssbond() (PdbReaderProject method) remove_sugar() (Glycosylation method) renameDupl (CreateProjectRequest attribute), [1] RenameProejctRequest (class in molcube.models) (class in molcube.typed_dicts) replace_packing() (MembraneBuilderProject method) reset_glycosylations() (PdbReaderProject method) resid (AvailableGlycoProtRequest attribute), [1] (CappingInfoRequest attribute), [1] (ConnProteinRequest attribute), [1] (DihedralRequest attribute), [1] (LipidationRequest attribute), [1] (MutationRequest attribute), [1] (NonstandardRequest attribute), [1] (PhosphorylationRequest attribute) (ProtonationRequest attribute) (PTMRequest attribute), [1] (ResidueRequest attribute) (ResiduesRequest attribute), [1] residue1 (LinkagesRequest attribute), [1] (PredefinedGlyInfoLinkage attribute) (SsbondRequest attribute), [1] (StaplingRequest attribute), [1]

residue2 (LinkagesRequest attribute), [1] (PredefinedGlyInfoLinkage attribute) (SsbondRequest attribute), [1] (StaplingRequest attribute), [1] ResidueLinkType (in module molcube.pdbreader.literals) residueName (TargetLigandRequest attribute), [1] ResidueRequest (class in molcube.models) (class in molcube.typed_dicts) residues (GetGlyInfoRequest attribute), [1] (GlycoInfoRequest attribute) (PredefinedGlyInfoRequest attribute) ResiduesRequest (class in molcube.models) (class in molcube.typed_dicts) ResidueType (class in molcube.pdbreader.enums) (in module molcube.pdbreader.literals) resname (CovalentLigandRequest attribute), [1] (CSMLResult attribute) (ForceFieldGenerationRequest attribute), [1] (NewLinkageRequest attribute), [1] (NonStandardSDFResult attribute) (SaveModifiedResidueRequest attribute), [1] (SearchIsomorphicResiduesRequest attribute), [1] (StandaloneChainIndexRequest attribute), [1] (ValidateStandaloneSdfRequest attribute), [1] results (PaginatedProjectList attribute), [1] resume_project() (BaseProject method) (PdbReaderProject method) RH3P (CHARMMFF_ION attribute) rna (AmberOptionsRequest attribute), [1] RNA (class in molcube.pdbreader.enums) (in module molcube.pdbreader.literals) root (InquiryTypeEnum attribute) (OpenffItem attribute) (PollingTypeEnum attribute) (ProjectTypeEnum attribute) (ProteinChain attribute) (StatusEnum attribute) (WorkspaceEnum attribute) RUB (CHARMMFF_ION attribute) (DRUDEFF_ION attribute)

S

SALMONELLA_ENTERICA (LPS attribute) SAVED (StandaloneSDFSource attribute) SaveModifiedResidueRequest (class in molcube.models) (class in molcube.typed_dicts) SC3P (CHARMMFF_ION attribute) sdf (ApplyPHtoLigandRequest attribute), [1] (ForceFieldFilesRequest attribute), [1] (NonStandardSDFResult attribute) (SaveModifiedResidueRequest attribute), [1] (SearchIsomorphicResiduesRequest attribute), [1] (ValidateStandaloneSdfRequest attribute), [1] SDFSource (class in molcube.pdbreader.enums) (in module molcube.pdbreader.literals) search_projects() (API method) SearchIsomorphicResiduesRequest (class in molcube.models) (class in molcube.typed_dicts) SelectChainModificationRequest (class in molcube.models) (class in molcube.typed_dicts) selected (ChainIndexRequest attribute), [1] (CustomIonRequest attribute), [1] (CustomSolventRequest attribute), [1] (GlycanChainIndexRequest attribute), [1] (HemeChainIndexRequest attribute), [1] (IonChainIndexRequest attribute), [1] (MissingRequest attribute), [1] (NucleicChainIndexRequest attribute), [1] (StandaloneChainIndexRequest attribute), [1] (WaterChainIndexRequest attribute) SelectedForceField (class in molcube.models) selectedForceFields (UpdateSelectedForceFieldsRequest attribute), [1] selectedLigands (UpdateSelectedLigandsRequest attribute), [1] SelectedLigandsRequest (class in molcube.models) (class in molcube.typed_dicts) sequence (LipidsRequest attribute), [1] SER (MutationResidueName attribute) set_authorization_token() (APIClient method) set_defaults() (PdbReaderProject method) set_glycan_name_lookup() (Glycosylation method) set_ligand_group() (FreeEnergyProject method) set_modification() (Glycosylation method) set_mutation() (FreeEnergyProject method) set_target_chain() (FreeEnergyProject method) set_terminal_patch() (PdbReaderProject method) set_token() (APIClient method) SetLigandForceFieldsRequest (class in molcube.models) (class in molcube.typed_dicts) shape (GlycanSymbol attribute) SHAW (RNA attribute) SHIGELLA_FLEXNERI (LPS attribute) sideChainOrient (DihedralInfoParsed attribute) (DihedralInfoResponse attribute) (DihedralInfoResponseModel attribute) (ModelingRequest attribute), [1] SideChainOrientationRequest (class in molcube.models) (class in molcube.typed_dicts) similarityScoreMatrix (UpdateSimilarityScoreMatrixRequest attribute), [1] site1 (LinkagesRequest attribute), [1] (PredefinedGlyInfoLinkage attribute)

site2 (LinkagesRequest attribute), [1] (PredefinedGlyInfoLinkage attribute) sites (AvailableGlycan attribute) sizeX (BoxMarginRequest attribute), [1] sizeY (BoxMarginRequest attribute), [1] sizeZ (BoxMarginRequest attribute), [1] SM (AMBERFF_ION attribute) Sm (AMBERFF_ION attribute) SM2P (CHARMMFF_ION attribute) SM3P (CHARMMFF_ION attribute) Sn (AMBERFF_ION attribute) SN2P (CHARMMFF_ION attribute) SOD (CHARMMFF_ION attribute) (DRUDEFF_ION attribute) SOLUTION_BUILDER (Module attribute) SolutionBuilderProject (class in molcube.solution_builder) SolutionBuilderProjectRequest (class in molcube.models) (class in molcube.typed_dicts) SolutionBuilderTaskRequest (class in molcube.models) (class in molcube.typed_dicts) species (LipidsRequest attribute), [1] SR (AMBERFF_ION attribute) SR2P (CHARMMFF_ION attribute) ssbond (ModelingRequest attribute), [1] (SelectChainModificationRequest attribute), [1] SsbondRequest (class in molcube.models) (class in molcube.typed_dicts) STANDALONE (ResidueType attribute) STANDALONE_LIGAND (CHAIN_TYPE attribute) StandaloneChainIndexRequest (class in molcube.models) (class in molcube.typed_dicts) standaloneLigand (ChainRequest attribute), [1] StandaloneSDFSource (class in molcube.pdbreader.enums) (in module molcube.pdbreader.literals) STANDARD (LIPID_TYPE attribute) stapling (ModelingRequest attribute), [1] (SelectChainModificationRequest attribute), [1] (StaplingRequest attribute), [1] StaplingRequest (class in molcube.models) (class in molcube.typed_dicts) start (ConnectionsRequest attribute), [1] status (ErrorResponse attribute), [1] (SuccessResponse attribute), [1] (SupportInquiry attribute), [1] status_display (SupportInquiry attribute), [1] StatusEnum (class in molcube.models) (in module molcube.typed_dicts) Step3RenderResponse (class in molcube.pdbreader.conf) stereochemistry (AvailableGlycan attribute) SUBSTITUTION (ForceFieldMethod attribute) SuccessResponse (class in molcube.models) (class in molcube.typed_dicts) SULFOGLYCOLIPIDS (GLIP_GROUP attribute) SupportInquiry (class in molcube.models) (class in molcube.typed_dicts) swap (LipidationRequest attribute), [1] symbol (AvailableGlycan attribute) systemLayer (AlignOptionsRequest attribute), [1]

T

tail1 (LipidsRequest attribute), [1] tail2 (LipidsRequest attribute), [1] tailGroup (LipidsRequest attribute), [1] TailGroupItem (class in molcube.models) tailType (LipidsRequest attribute), [1] targetLigand (UpdateTargetLigandRequest attribute), [1] TargetLigandRequest (class in molcube.models) (class in molcube.typed_dicts) TB (AMBERFF_ION attribute) TB3P (CHARMMFF_ION attribute) TEAM (Workspace attribute) teamName (CancellationSupportRequest attribute), [1] teamSize (EnterpriseInquiryRequest attribute), [1] temperature (HandleRequestStep5Request attribute), [1] (HandleRequestStep6Request attribute), [1] (SolutionBuilderTaskRequest attribute), [1] terminal (ChainIndexRequest attribute), [1] (NucleicChainIndexRequest attribute), [1] terminalCharge (ModelingRequest attribute), [1] (SelectChainModificationRequest attribute), [1] TerminalRequest (class in molcube.models) (class in molcube.typed_dicts) Th (AMBERFF_ION attribute) thickness (LipidsRequest attribute), [1] THR (MutationResidueName attribute) threshold (MorphPairRequest attribute), [1] TI (Method attribute) TI1P (CHARMMFF_ION attribute) TI3P (CHARMMFF_ION attribute) tightPacking (HandleRequestStep3Request attribute), [1] (HandleRequestStep4Request attribute), [1]

tightPackingScaling (HandleRequestStep3Request attribute), [1] (HandleRequestStep4Request attribute), [1] TIP3P (Water attribute), [1] TIP4PD (Water attribute), [1] TIP4PEW (Water attribute), [1] title (PatchedProjectRequest attribute), [1] (PdbReaderProject attribute) (Project attribute), [1] (ProjectRequest attribute), [1] TL (AMBERFF_ION attribute) Tl (AMBERFF_ION attribute) TL3P (CHARMMFF_ION attribute) Tm (AMBERFF_ION attribute) toBeResname (ForceFieldGenerationRequest attribute), [1] (MutationRequest attribute), [1] (NonstandardRequest attribute), [1] toggle_chain() (PdbReaderProject method) token (TokenVerifyRequest attribute), [1] TokenVerifyRequest (class in molcube.models) (class in molcube.typed_dicts) top (CharmmAmberFileRequest attribute), [1] (MartiniFileRequest attribute), [1] transZ (OrientationOptionRequest attribute), [1] TRP (MutationResidueName attribute) TU3P (CHARMMFF_ION attribute) type (AvailableGlycan attribute) (LipidsRequest attribute), [1] (PredefinedGlyInfoResidue attribute) (ResiduesRequest attribute), [1] typeOfResidue (SaveModifiedResidueRequest attribute), [1] TYR (MutationResidueName attribute)

U

U3P (CHARMMFF_ION attribute) update_boresh_restraint() (FreeEnergyProject method) update_ring_match() (FreeEnergyProject method) updated_at (Project attribute), [1] (SupportInquiry attribute), [1] UpdatePerturbationPathsRequest (class in molcube.models) (class in molcube.typed_dicts) UpdateReferenceLigandProjectRequest (class in molcube.models) (class in molcube.typed_dicts) UpdateSelectedForceFieldsRequest (class in molcube.models) (class in molcube.typed_dicts) UpdateSelectedLigandsRequest (class in molcube.models) (class in molcube.typed_dicts) UpdateSimilarityScoreMatrixRequest (class in molcube.models) (class in molcube.typed_dicts) UpdateTargetLigandRequest (class in molcube.models) (class in molcube.typed_dicts)

UPLOAD (ForceFieldMethod attribute) upload (GenForcefieldTypes attribute) upNumber (LipidsRequest attribute), [1] upperInnerNumber (LipidsRequest attribute), [1] upperInnerRatio (LipidsRequest attribute), [1] upperOuterNumber (LipidsRequest attribute), [1] upperOuterRatio (LipidsRequest attribute), [1] upRatio (LipidsRequest attribute), [1] useBoxSize (SolutionBuilderTaskRequest attribute), [1] useCase (EnterpriseInquiryRequest attribute), [1] useHmr (HandleRequestStep5Request attribute), [1] (HandleRequestStep6Request attribute), [1] (SolutionBuilderTaskRequest attribute), [1] useHydrationNumber (HandleRequestStep5Request attribute), [1] useInnerHydrationNumber (HandleRequestStep3Request attribute), [1] user (Project attribute), [1]

V

V2 (AMBERFF_ION attribute) V2P (CHARMMFF_ION attribute) V3P (CHARMMFF_ION attribute) VAL (MutationResidueName attribute)

ValidateStandaloneSdfRequest (class in molcube.models) (class in molcube.typed_dicts) VESICLE (MembraneType attribute) VIBRIO_CHOLERAE (LPS attribute)

W

water (AmberOptionRequest attribute), [1] (AmberOptionsRequest attribute), [1] WATER (CHAIN_TYPE attribute) water (ChainRequest attribute), [1] Water (class in molcube.free_energy.enum) (class in molcube.pdbreader.enums) (in module molcube.pdbreader.literals) WaterChainIndexRequest (class in molcube.models) (class in molcube.typed_dicts)

waterMargin (HandleRequestStep5Request attribute), [1] Workspace (class in molcube.pdbreader.enums) workspace (CreateProjectRequest attribute), [1] (HandleRequestStep1Request attribute), [1] Workspace (in module molcube.pdbreader.literals) workspace (SolutionBuilderProjectRequest attribute), [1] WorkspaceEnum (class in molcube.models) (in module molcube.typed_dicts)

X

XFF (LigandForceField attribute), [1], [2] xff (LigandForceFieldRequest attribute), [1] (MorphPairByForceFieldTypeRequest attribute), [1] (SelectedLigandsRequest attribute), [1] XFF_FAST (LigandForceField attribute), [1], [2]

xffFast (LigandForceFieldRequest attribute), [1] (MorphPairByForceFieldTypeRequest attribute), [1] (SelectedLigandsRequest attribute), [1] XffFastItem (class in molcube.models) XffItem (class in molcube.models)

Y

Y (AMBERFF_ION attribute) Y3P (CHARMMFF_ION attribute) YB2 (AMBERFF_ION attribute)

YB2P (CHARMMFF_ION attribute) YB3P (CHARMMFF_ION attribute) YERSINIA_PESTIS (LPS attribute) YIL (RNA attribute)

Z

ZERO_SERIES (GLIP_SUBGROUP attribute) ZN (AMBERFF_ION attribute) (CHARMMFF_ION attribute) (DRUDEFF_ION attribute)

Zr (AMBERFF_ION attribute)