Index

A

A_CC (in module vibesketch.chem.nanostructures) abbreviation_labels() (in module vibesketch.document.abbreviations) AbbreviationRefused abbreviations (vibesketch.chem.report.SpeciesReport attribute) (vibesketch.document.ket.KetFragment attribute) abbreviations_of() (in module vibesketch.document.abbreviations) ABSENT (in module vibesketch.document.io) acceptable() (vibesketch.chem.depiction.DepictionField method) across (vibesketch.document.model.NanoSite attribute) actor (vibesketch.document.Edit attribute) (vibesketch.document.model.Edit attribute) add() (vibesketch.server.store.Store method) advance() (in module vibesketch.render.fonts) aliases (vibesketch.document.reaction_library.ReactionEntry attribute) (vibesketch.document.template_library.TemplateEntry attribute) aligned_frame() (in module vibesketch.document.renders) along (vibesketch.document.model.NanoSite attribute) ALPHABETS (in module vibesketch.document.sequences) alternatives (vibesketch.chem.mapping.AtomMapping attribute) ambiguous (vibesketch.chem.mapping.AtomMapping property) amounts (vibesketch.document.model.Reaction attribute) (vibesketch.document.Reaction attribute) Analysis (class in vibesketch.chem.analysis) analysis (vibesketch.chem.report.SpeciesReport attribute) analytic_hessian (vibesketch.inputs.orca_keywords.Method attribute) anchor_points() (in module vibesketch.render.surfaces) ANCHOR_REACH (in module vibesketch.render.nanostructures) anchors (vibesketch.document.model.Surface attribute) (vibesketch.document.Surface attribute) (vibesketch.render.nanostructures.Picture attribute) angles (vibesketch.chem.depiction.DepictionField attribute) app (vibesketch.document.model.Provenance attribute) (vibesketch.document.Provenance attribute) APPARATUS (in module vibesketch.document.apparatus) APPARATUS_TEXT (in module vibesketch.document.apparatus) ApparatusRefused approximation (vibesketch.document.JobSpec attribute) (vibesketch.document.model.JobSpec attribute) (vibesketch.inputs.neb.NebSpec attribute)

approximation_keyword() (in module vibesketch.inputs.orca_keywords) APPROXIMATIONS (in module vibesketch.inputs.orca_keywords) around (vibesketch.document.model.NanoSite attribute) Arrow (in module vibesketch.document.model) arrow (vibesketch.document.coordinates.Step attribute) (vibesketch.document.ket.SceneStep attribute) (vibesketch.document.model.Reaction attribute) (vibesketch.document.Reaction attribute) arrow_kind() (in module vibesketch.document.derive) ARROW_MODES (in module vibesketch.document.ket) arrows (vibesketch.document.ket.KetScene attribute) at (vibesketch.document.Edit attribute) (vibesketch.document.model.Edit attribute) at_launch (vibesketch.inputs.recipe.ResolvedStage attribute) ATOMIC_NUMBER (in module vibesketch.elements) atomic_number() (in module vibesketch.elements) AtomMapping (class in vibesketch.chem.mapping) AtomModel (class in vibesketch.chem.nanostructures) atoms (vibesketch.chem.cip.StereoLabels attribute) (vibesketch.chem.relax.ConstraintCheck attribute) (vibesketch.document.Constraint attribute) (vibesketch.document.ket.KetAbbreviation attribute) (vibesketch.document.ket.KetFragment attribute) (vibesketch.document.model.Constraint attribute) attach_to_picture() (in module vibesketch.document.nanostructures) attach_to_surface() (in module vibesketch.document.surfaces) attachment_labels() (in module vibesketch.document.generics) attachment_points (vibesketch.document.template_library.TemplateEntry attribute) aux_basis (vibesketch.document.JobSpec attribute) (vibesketch.document.model.JobSpec attribute) (vibesketch.inputs.neb.NebSpec attribute) aux_basis_kind() (in module vibesketch.inputs.orca_keywords) average_mass (vibesketch.chem.report.SpeciesReport attribute) (vibesketch.chem.species.Properties attribute) axis (vibesketch.document.model.PeriodicCell attribute) (vibesketch.document.spectra.SpectrumExport attribute)

B

balance() (in module vibesketch.document.electrochem) balance_problems() (in module vibesketch.chem.mapping) BalanceReport (class in vibesketch.document.electrochem) baseline_recipe() (in module vibesketch.document.recipe) basis (vibesketch.document.JobSpec attribute) (vibesketch.document.model.JobSpec attribute) (vibesketch.inputs.neb.NebSpec attribute) basis_family() (in module vibesketch.inputs.orca_keywords) Batch (class in vibesketch.inputs) (class in vibesketch.inputs.registry) bold (vibesketch.render.styles.Preset attribute) bond (vibesketch.render.styles.Preset attribute) BOND_LENGTH (in module vibesketch.document.ket)

bonds (vibesketch.chem.cip.StereoLabels attribute) (vibesketch.chem.depiction.DepictionField attribute) (vibesketch.chem.nanostructures.AtomModel attribute) (vibesketch.document.model.Nanostructure attribute) bounds (vibesketch.document.ket.KetFragment attribute) bounds() (vibesketch.render.nanostructures.Picture method) bridges (vibesketch.document.sequences.Printed attribute) brk (vibesketch.render.nanostructures.Depiction attribute) broadened_spectrum() (in module vibesketch.document.spectra) build() (in module vibesketch.chem.nanostructures) (vibesketch.chem.depiction.DepictionField class method) build_endpoints() (in module vibesketch.chem.endpoints) bundles (vibesketch.inputs.Batch attribute) (vibesketch.inputs.registry.Batch attribute)

C

calculation_fields() (vibesketch.document.JobSpec static method) (vibesketch.document.model.JobSpec static method) call() (vibesketch.agent.client.RestClient method) campaign (vibesketch.document.campaign_results.CampaignSelection attribute) campaign_energies() (in module vibesketch.document.campaign_results) campaign_energy_export() (in module vibesketch.document.campaign_results) campaign_report() (in module vibesketch.document.campaign) CampaignRefused CampaignSelection (class in vibesketch.document.campaign_results) CampaignUnavailable cancel() (in module vibesketch.queue) cancel_group() (in module vibesketch.queue) canonical() (vibesketch.chem.formula.Formula method) Canvas (class in vibesketch.document) (class in vibesketch.document.model) canvas (vibesketch.document.Document attribute) (vibesketch.document.model.Document attribute) (vibesketch.inputs.neb.ReactionPath attribute) canvas_image() (in module vibesketch.render.nanostructures) (in module vibesketch.render.surfaces) CANVAS_SHAPES (in module vibesketch.render.scene) cap (vibesketch.document.model.Capping attribute) (vibesketch.render.vector.Paint attribute) cap_labelled() (in module vibesketch.document.generics) capped (vibesketch.document.model.Species attribute) (vibesketch.document.Species attribute) Capping (class in vibesketch.document.model) CapRefused CAPS (in module vibesketch.document.monomers) caption (vibesketch.document.ket.KetFragment attribute) caption_room() (in module vibesketch.render.nanostructures) carbons_per_period (vibesketch.document.model.PeriodicCell attribute) category (vibesketch.document.template_library.TemplateEntry attribute) cdx_to_cdxml() (in module vibesketch.document.cdx) cdxml_source() (in module vibesketch.document.cdxml) CdxmlRefused CdxmlUnreadable CdxUnreadable centre (vibesketch.document.ket.KetFragment attribute) (vibesketch.document.ket.KetText attribute) centre() (vibesketch.chem.mapping.AtomMapping method) chains (vibesketch.document.sequences.Printed attribute) change (vibesketch.document.monomers.Modification attribute) changes() (vibesketch.chem.mapping.AtomMapping method) charge (vibesketch.chem.report.SpeciesReport attribute) (vibesketch.chem.species.Identity attribute) (vibesketch.document.coordinates.Structure attribute) (vibesketch.document.model.Species attribute) (vibesketch.document.Species attribute) (vibesketch.inputs.neb.ReactionPath attribute) check_output() (in module vibesketch.document) (in module vibesketch.document.io) check_text() (in module vibesketch.render.fonts) checks (vibesketch.inputs.recipe.ResolvedStage attribute) chemfig_drawing() (in module vibesketch.render.chemfig) chemfig_molecule() (in module vibesketch.render.chemfig) chemfig_source() (in module vibesketch.render.chemfig) ChemfigRefused chiral_angle_deg() (in module vibesketch.chem.nanostructures) Chirality (class in vibesketch.document.model) clean() (in module vibesketch.document.clean) clean_2d() (in module vibesketch.chem.clean) clean_ket() (in module vibesketch.document.clean) Cleaned (class in vibesketch.chem.clean) cleaned (vibesketch.document.clean.CleanReport attribute) (vibesketch.document.scheme.SchemeReport attribute)

CleanReport (class in vibesketch.document.clean) clearance (vibesketch.chem.depiction.DepictionField attribute) client (vibesketch.document.Edit attribute) (vibesketch.document.model.Edit attribute) codename_for_current() (in module vibesketch.codenames) codename_for_version() (in module vibesketch.codenames) Coefficient (class in vibesketch.document.model) coefficient() (vibesketch.document.model.Reaction method) (vibesketch.document.Reaction method) coefficients (vibesketch.document.campaign_results.CampaignSelection attribute) (vibesketch.document.model.Reaction attribute) (vibesketch.document.Reaction attribute) (vibesketch.document.results.Selection attribute) collapse_multiple_groups() (in module vibesketch.document.multiple_groups) compile_campaign() (in module vibesketch.document.campaign) compile_energy_recipe() (in module vibesketch.document.electrochemical_recipes) Compiled (class in vibesketch.document.campaign) composition (vibesketch.chem.formula.Formula property) (vibesketch.document.model.SolidFormula attribute) compute_2d() (in module vibesketch.chem.layout) concentric_walls() (in module vibesketch.chem.nanostructures) condensed() (in module vibesketch.document.abbreviations) conditions (vibesketch.document.coordinates.Step attribute) (vibesketch.document.formats.Imported attribute) (vibesketch.document.ket.SceneStep attribute) (vibesketch.document.model.Reaction attribute) (vibesketch.document.Reaction attribute) confidence (vibesketch.document.model.Name attribute) (vibesketch.document.Name attribute) (vibesketch.naming.NameResult attribute) configure() (vibesketch.render.styles.Preset method) Conflict Conformer (class in vibesketch.document) (class in vibesketch.document.model) conformer (vibesketch.chem.relax.Relaxed attribute) conformers (vibesketch.chem.embed.Embedded attribute) (vibesketch.document.model.Species attribute) (vibesketch.document.Species attribute) constants() (in module vibesketch.document.electrochemical_recipes) Constraint (class in vibesketch.document) (class in vibesketch.document.model) ConstraintCheck (class in vibesketch.chem.relax) constraints (vibesketch.chem.relax.Relaxed attribute) (vibesketch.document.JobSpec attribute) (vibesketch.document.model.JobSpec attribute) container (vibesketch.document.model.Run attribute) (vibesketch.document.Run attribute) container_spec() (vibesketch.inputs.vibeqc.VibeqcWriter method) content (vibesketch.document.formats.Payload attribute) (vibesketch.inputs.base.InputFile attribute) (vibesketch.inputs.InputFile attribute) Contour (in module vibesketch.render.fonts) converged (vibesketch.chem.fire.FireResult attribute) (vibesketch.chem.relax.Relaxed attribute) convert() (in module vibesketch.render.publication) cost (vibesketch.chem.mapping.AtomMapping attribute) count (vibesketch.document.model.Electrons attribute) (vibesketch.document.model.Surface attribute) (vibesketch.document.Surface attribute) counts() (vibesketch.chem.formula.Formula method) create_app() (in module vibesketch.server) created (vibesketch.document.model.Provenance attribute) (vibesketch.document.Provenance attribute) curated_peptide() (in module vibesketch.document.monomers) cxsmiles (vibesketch.document.model.Capping attribute) (vibesketch.document.model.Generic attribute) cxsmiles() (in module vibesketch.document.generics)

D

data (vibesketch.document.Canvas attribute) (vibesketch.document.model.Canvas attribute) DEFAULT_FWHM (in module vibesketch.document.spectra) default_id (vibesketch.server.store.Store attribute) Defect (class in vibesketch.document.model) defects (vibesketch.document.model.Graphene attribute) (vibesketch.document.model.Nanoribbon attribute) (vibesketch.document.model.Nanotube attribute) Definition (class in vibesketch.document.rgfile) Depiction (class in vibesketch.render.nanostructures) depiction_of() (in module vibesketch.render.nanostructures) DepictionField (class in vibesketch.chem.depiction) DepictionRefused Derivation (class in vibesketch.document.derive) derive() (in module vibesketch.document.derive) derive_generics() (in module vibesketch.document.generics) describe() (in module vibesketch.document.electrochem) described() (in module vibesketch.document.stereo) description (vibesketch.agent.mcp.Tool attribute) (vibesketch.chem.nanostructures.AtomModel attribute) (vibesketch.document.model.Nanostructure attribute) (vibesketch.inputs.base.InputWriter attribute) (vibesketch.inputs.InputWriter attribute) (vibesketch.inputs.orca.OrcaWriter attribute) (vibesketch.inputs.qcschema.QcschemaInputWriter attribute) (vibesketch.inputs.qcschema.QcschemaMoleculeWriter attribute) (vibesketch.inputs.vibeqc.VibeqcWriter attribute) (vibesketch.inputs.xyz.XyzWriter attribute) Descriptors (class in vibesketch.chem.analysis) descriptors (vibesketch.chem.report.SpeciesReport attribute) descriptors() (in module vibesketch.chem.analysis)

deviation (vibesketch.chem.clean.Cleaned attribute) (vibesketch.chem.relax.ConstraintCheck property) diameter_nm (vibesketch.document.model.Surface attribute) (vibesketch.document.Surface attribute) diameter_nm() (in module vibesketch.chem.nanostructures) digest (vibesketch.server.store.Entry attribute) digest_of() (in module vibesketch.document.io) dimensions() (in module vibesketch.render.publication) directory (vibesketch.document.model.Run attribute) (vibesketch.document.renders.StageRenders attribute) (vibesketch.document.Run attribute) dirty (vibesketch.server.store.Entry property) dispersion (vibesketch.document.JobSpec attribute) (vibesketch.document.model.JobSpec attribute) (vibesketch.inputs.neb.NebSpec attribute) dispersion_keyword() (in module vibesketch.inputs.orca_keywords) Document (class in vibesketch.document) (class in vibesketch.document.model) document (vibesketch.document.campaign.Compiled attribute) (vibesketch.document.derive.Derivation attribute) (vibesketch.queue.Submission attribute) (vibesketch.server.store.Entry attribute) document_json_schema() (in module vibesketch.document) (in module vibesketch.document.schema) DocumentError, [1] DRAWN_RADICAL (in module vibesketch.chem.species) dumps() (in module vibesketch.document) (in module vibesketch.document.io) dx (vibesketch.document.model.SurfaceAnchor attribute) (vibesketch.document.SurfaceAnchor attribute) dy (vibesketch.document.model.SurfaceAnchor attribute) (vibesketch.document.SurfaceAnchor attribute)

E

edge (vibesketch.document.model.Nanoribbon attribute) edges (vibesketch.document.model.Graphene attribute) (vibesketch.document.model.Nanoribbon attribute) Edit (class in vibesketch.document) (class in vibesketch.document.model) edits (vibesketch.document.model.Provenance attribute) (vibesketch.document.Provenance attribute) electron_count() (vibesketch.document.Conformer method) (vibesketch.document.model.Conformer method) electron_text() (in module vibesketch.document.electrochem) Electrons (class in vibesketch.document.model) electrons (vibesketch.chem.species.Identity attribute) (vibesketch.document.model.Reaction attribute) (vibesketch.document.Reaction attribute) elemental_analysis() (in module vibesketch.chem.analysis) embed() (in module vibesketch.document.embed) embed_3d() (in module vibesketch.chem.embed) embed_font() (in module vibesketch.render.fonts) Embedded (class in vibesketch.chem.embed) embedded (vibesketch.document.embed.EmbedReport attribute) EmbedFailed EmbedReport (class in vibesketch.document.embed) emf() (in module vibesketch.render.vector) Endpoints (class in vibesketch.chem.endpoints)

endpoints (vibesketch.inputs.neb.ReactionPath attribute) EndpointsFailed ends (vibesketch.document.model.Nanotube attribute) energies (vibesketch.chem.embed.Embedded attribute) energy (vibesketch.chem.fire.FireResult attribute) (vibesketch.chem.relax.Relaxed attribute) energy_before (vibesketch.chem.relax.Relaxed attribute) energy_recipe_figure() (in module vibesketch.document.electrochemical_recipes) energy_recipe_result() (in module vibesketch.document.electrochemical_recipes) entries() (vibesketch.server.store.Store method) Entry (class in vibesketch.server.store) enumerate_rgroups() (in module vibesketch.document.enumeration) EnumerationRefused eps() (in module vibesketch.render.vector) evaluations (vibesketch.chem.fire.FireResult attribute) evenodd (vibesketch.render.vector.Paint attribute) example_smiles (vibesketch.document.reaction_library.ReactionEntry attribute) expand_multiple_groups() (in module vibesketch.document.multiple_groups) export() (in module vibesketch.document.formats) EXPORT_FORMATS (in module vibesketch.document.formats) export_spectrum() (in module vibesketch.document.spectra) ExportRefused extension (vibesketch.document.formats.Payload attribute) external_chain_export() (in module vibesketch.document.external_results) external_chain_report() (in module vibesketch.document.external_results)

F

facet (vibesketch.document.model.Surface attribute) (vibesketch.document.Surface attribute) failed (vibesketch.document.embed.EmbedReport attribute) (vibesketch.document.relax.RelaxReport attribute) fallbacks (vibesketch.queue.Submission attribute) FARADAY (in module vibesketch.document.electrochem) FIELDS (in module vibesketch.document.properties) fields (vibesketch.inputs.base.InputWriter attribute) (vibesketch.inputs.InputWriter attribute) (vibesketch.inputs.orca.OrcaWriter attribute) (vibesketch.inputs.qcschema.QcschemaInputWriter attribute) (vibesketch.inputs.vibeqc.VibeqcWriter attribute) figure (vibesketch.document.ket.KetFragment attribute) file_name() (vibesketch.inputs.orca.OrcaWriter method) file_stem() (vibesketch.inputs.vibeqc.VibeqcWriter method) files (vibesketch.document.renders.StageRenders attribute) (vibesketch.inputs.base.InputBundle attribute) (vibesketch.inputs.InputBundle attribute) fill (vibesketch.render.vector.Paint attribute) find_server() (in module vibesketch.agent.client) finish_svg() (in module vibesketch.render.styles) FireResult (class in vibesketch.chem.fire) fmax (vibesketch.chem.fire.FireResult attribute) (vibesketch.chem.relax.Relaxed attribute)

font (vibesketch.render.styles.Preset attribute) force_field (vibesketch.chem.relax.Relaxed attribute) FORCE_FIELDS (in module vibesketch.chem.relax) format (vibesketch.document.Canvas attribute) (vibesketch.document.model.Canvas attribute) (vibesketch.document.spectra.SpectrumExport attribute) format_for_path() (in module vibesketch.document.formats) Formula (class in vibesketch.chem.formula) formula (vibesketch.chem.analysis.Analysis attribute) (vibesketch.chem.nanostructures.AtomModel property) (vibesketch.chem.report.SpeciesReport attribute) (vibesketch.chem.species.Properties attribute) (vibesketch.document.model.Nanostructure attribute) (vibesketch.document.model.SolidFormula attribute) (vibesketch.document.template_library.TemplateEntry attribute) FormulaError fragments (vibesketch.document.ket.KetScene attribute) from_data() (in module vibesketch.document) from_qvf() (in module vibesketch.document.qvf) from_structures() (in module vibesketch.document.coordinates) Fullerene (class in vibesketch.document.model) fwhm (vibesketch.document.spectra.SpectrumExport attribute) fwhm_unit (vibesketch.document.spectra.SpectrumExport attribute)

G

Generic (class in vibesketch.document.model) generic (vibesketch.document.model.Capping attribute) generics (vibesketch.document.Document attribute) (vibesketch.document.model.Document attribute) (vibesketch.document.model.SurfaceAnchor attribute) (vibesketch.document.SurfaceAnchor attribute) generics_report() (in module vibesketch.document.generics) get() (vibesketch.server.store.Store method) get_reaction() (in module vibesketch.document.reaction_library) get_template() (in module vibesketch.document.template_library) get_writer() (in module vibesketch.inputs) (in module vibesketch.inputs.registry)

glyph_of() (in module vibesketch.render.fonts) gradient (vibesketch.chem.fire.FireResult attribute) Graphene (class in vibesketch.document.model) group (vibesketch.document.model.Run attribute) (vibesketch.document.model.SidewallGroup attribute) (vibesketch.document.results.Selection attribute) (vibesketch.document.Run attribute) (vibesketch.queue.Submission attribute) group_states() (in module vibesketch.queue) groups (vibesketch.chem.cip.StereoLabels attribute) Guard (class in vibesketch.server.guard)

H

half_reaction_canvas() (in module vibesketch.document.electrochem) HalfReactionRefused handle() (in module vibesketch.agent.mcp) has_dispersion (vibesketch.inputs.orca_keywords.Method attribute) has_stereo (vibesketch.chem.species.Identity attribute) has_transition_metal (vibesketch.chem.species.Identity attribute) hash_spacing (vibesketch.render.styles.Preset attribute) hbond_acceptors (vibesketch.chem.analysis.Descriptors attribute) hbond_donors (vibesketch.chem.analysis.Descriptors attribute) head (vibesketch.document.ket.KetArrow attribute) (vibesketch.document.ket.SceneStep attribute) heavy_atoms (vibesketch.chem.analysis.Descriptors attribute) height (vibesketch.document.ket.KetArrow attribute) helm (vibesketch.document.model.Sequence attribute)

helm_molecules() (in module vibesketch.document.sequences) helm_of() (in module vibesketch.document.sequences) hessian_structures() (in module vibesketch.document.orca) hexagons_per_period() (in module vibesketch.chem.nanostructures) highlight_options() (in module vibesketch.render.scene) highlight_points() (in module vibesketch.document.highlights) HighlightRefused highlights (vibesketch.chem.report.SpeciesReport attribute) (vibesketch.document.Document attribute) (vibesketch.document.model.Document attribute) hill_formula() (in module vibesketch.chem.nanostructures) host (vibesketch.document.model.Run attribute) (vibesketch.document.Run attribute) how (vibesketch.chem.perceive.Perceived attribute)

I

id (vibesketch.chem.report.SpeciesReport attribute) (vibesketch.document.coordinates.Step attribute) (vibesketch.document.coordinates.Structure attribute) (vibesketch.document.Job attribute) (vibesketch.document.model.Generic attribute) (vibesketch.document.model.Job attribute) (vibesketch.document.model.Reaction attribute) (vibesketch.document.model.Run attribute) (vibesketch.document.model.Species attribute) (vibesketch.document.model.Surface attribute) (vibesketch.document.Reaction attribute) (vibesketch.document.reaction_library.ReactionEntry attribute) (vibesketch.document.Run attribute) (vibesketch.document.Species attribute) (vibesketch.document.Surface attribute) (vibesketch.document.template_library.TemplateEntry attribute) (vibesketch.server.store.Entry attribute) Identity (class in vibesketch.chem.species) identity (vibesketch.document.model.Nanostructure attribute) identity() (in module vibesketch.chem.species) identity_of() (in module vibesketch.chem.nanostructures) if_then (vibesketch.document.model.RGroup attribute) (vibesketch.document.rgfile.Definition attribute) images (vibesketch.inputs.neb.NebSpec attribute) import_into() (in module vibesketch.document.formats) import_result() (in module vibesketch.document.results)

Imported (class in vibesketch.document.formats) ImportFailed inchi (vibesketch.chem.report.SpeciesReport attribute) (vibesketch.chem.species.Properties attribute) inchikey (vibesketch.chem.report.SpeciesReport attribute) (vibesketch.chem.species.Identity attribute) (vibesketch.document.model.Sequence attribute) (vibesketch.document.model.Species attribute) (vibesketch.document.Species attribute) inert_pair_radicals() (in module vibesketch.chem.species) InputBundle (class in vibesketch.inputs) (class in vibesketch.inputs.base) InputFile (class in vibesketch.inputs) (class in vibesketch.inputs.base) InputWriter (class in vibesketch.inputs) (class in vibesketch.inputs.base) insert_reaction() (in module vibesketch.document.reaction_library) insert_template() (in module vibesketch.document.template_library) install_hint() (in module vibesketch.naming) (in module vibesketch.naming.opsin) INTERLAYER_NM (in module vibesketch.chem.nanostructures) is_loopback() (in module vibesketch.server.guard) is_metallic() (in module vibesketch.chem.nanostructures) is_reaction_arrow() (in module vibesketch.document.derive) is_rgfile() (in module vibesketch.document.rgfile) is_solid_text() (in module vibesketch.chem.formula) items (vibesketch.render.nanostructures.Picture attribute)

J

Job (class in vibesketch.document) (class in vibesketch.document.model) job() (vibesketch.inputs.neb.NebSpec method) job_by_id() (vibesketch.document.Document method) (vibesketch.document.model.Document method)

job_container() (in module vibesketch.document.qvf) jobs (vibesketch.document.Document attribute) (vibesketch.document.model.Document attribute) JobSpec (class in vibesketch.document) (class in vibesketch.document.model) join (vibesketch.render.vector.Paint attribute)

K

kcl_mol_l (vibesketch.document.model.Quantity attribute) kept (vibesketch.document.embed.EmbedReport attribute) ket (vibesketch.document.formats.Imported attribute) KetAbbreviation (class in vibesketch.document.ket) KetArrow (class in vibesketch.document.ket) KetFragment (class in vibesketch.document.ket) KetScene (class in vibesketch.document.ket) KetText (class in vibesketch.document.ket) key (vibesketch.chem.species.Identity property) (vibesketch.document.model.Nanostructure attribute) (vibesketch.document.model.SolidFormula attribute) (vibesketch.render.nanostructures.Depiction attribute) key() (vibesketch.chem.formula.Formula method) keyword (vibesketch.inputs.orca_keywords.Method attribute) keyword_line() (vibesketch.inputs.orca.OrcaWriter method) keywords (vibesketch.inputs.recipe.ResolvedStage attribute) kind (vibesketch.chem.relax.ConstraintCheck attribute) (vibesketch.document.Constraint attribute) (vibesketch.document.model.Constraint attribute) (vibesketch.document.model.Defect attribute) (vibesketch.document.model.Fullerene attribute) (vibesketch.document.model.Generic attribute) (vibesketch.document.model.Graphene attribute) (vibesketch.document.model.Nanoribbon attribute) (vibesketch.document.model.Nanotube attribute) (vibesketch.document.model.Quantity attribute) (vibesketch.document.model.Surface attribute) (vibesketch.document.reaction_library.ReactionEntry attribute) (vibesketch.document.Surface attribute) (vibesketch.document.template_library.TemplateEntry attribute) (vibesketch.inputs.neb.NebSpec attribute) (vibesketch.inputs.orca_keywords.Method attribute) (vibesketch.inputs.recipe.ResolvedStage attribute)

known_methods() (in module vibesketch.inputs.orca_keywords)

L

label (vibesketch.chem.report.SpeciesReport attribute) (vibesketch.document.coordinates.Structure attribute) (vibesketch.document.ket.KetAbbreviation attribute) (vibesketch.document.model.Generic attribute) (vibesketch.document.model.Species attribute) (vibesketch.document.Species attribute) (vibesketch.document.tlc.Lane attribute) (vibesketch.render.nanostructures.Depiction attribute) label() (vibesketch.chem.mapping.Side method) labelled() (in module vibesketch.chem.cip) labels (vibesketch.document.model.Capping attribute) (vibesketch.document.model.Generic attribute) Lane (class in vibesketch.document.tlc) language (vibesketch.document.reaction_library.ReactionSource attribute) layers (vibesketch.document.model.Surface attribute) (vibesketch.document.Surface attribute) layout (vibesketch.chem.clean.Cleaned attribute) left (vibesketch.document.clean.CleanReport attribute) (vibesketch.document.scheme.SchemeReport attribute)

legacy_clean_2d() (in module vibesketch.chem.clean) length_nm (vibesketch.document.model.Graphene attribute) (vibesketch.document.model.Nanotube attribute) lengths (vibesketch.chem.depiction.DepictionField attribute) ligand_shell (vibesketch.document.model.Surface attribute) (vibesketch.document.Surface attribute) line (vibesketch.chem.analysis.Analysis attribute) (vibesketch.render.styles.Preset attribute) lineshape (vibesketch.document.spectra.SpectrumExport attribute) links (vibesketch.document.sequences.Printed attribute) list_reactions() (in module vibesketch.document.reaction_library) list_templates() (in module vibesketch.document.template_library) listing() (vibesketch.agent.mcp.Tool method) load() (in module vibesketch.document) (in module vibesketch.document.io) loads() (in module vibesketch.document) (in module vibesketch.document.io) logp (vibesketch.chem.analysis.Descriptors attribute) LOOPBACK (in module vibesketch.server.guard)

M

m (vibesketch.document.model.Chirality attribute) make_router() (in module vibesketch.server.documents) make_tools() (in module vibesketch.agent.mcp) map_reaction() (in module vibesketch.chem.mapping) mapping (vibesketch.inputs.neb.ReactionPath attribute) mapping_text() (in module vibesketch.inputs.neb) MappingFailed margin (vibesketch.render.styles.Preset attribute) Marks (in module vibesketch.render.scene) marks_for() (in module vibesketch.document.highlights) mass_percent (vibesketch.chem.analysis.Analysis attribute) masses() (in module vibesketch.document.nanostructures) material (vibesketch.document.model.Surface attribute) (vibesketch.document.Surface attribute) MAX_CLEAN_ATOMS (in module vibesketch.chem.clean) MAX_HELM (in module vibesketch.document.model) MAX_POINTS (in module vibesketch.document.spectra) MAX_POLYLINE (in module vibesketch.render.scene) MAX_RESIDUES (in module vibesketch.document.sequences) maxcore_mb (vibesketch.document.model.Resources attribute) (vibesketch.document.Resources attribute) MEDIA_TYPE (in module vibesketch.document.qvf) media_type (vibesketch.document.formats.Payload attribute) (vibesketch.inputs.base.InputFile attribute) (vibesketch.inputs.InputFile attribute) MEDIA_TYPES (in module vibesketch.document.spectra) members (vibesketch.document.rgfile.Definition attribute) message (vibesketch.chem.fire.FireResult attribute) metadata() (vibesketch.render.nanostructures.Depiction method) Method (class in vibesketch.inputs.orca_keywords) method (vibesketch.chem.endpoints.Endpoints attribute) (vibesketch.document.Conformer attribute) (vibesketch.document.coordinates.Structure attribute) (vibesketch.document.JobSpec attribute) (vibesketch.document.model.Conformer attribute) (vibesketch.document.model.JobSpec attribute) (vibesketch.inputs.neb.NebSpec attribute) method_for() (in module vibesketch.inputs.orca_keywords) method_names() (in module vibesketch.inputs.vibeqc) metrics() (vibesketch.chem.depiction.DepictionField method) minimize() (in module vibesketch.chem.fire) mode (vibesketch.document.ket.KetArrow attribute) mode() (in module vibesketch.viewer) model (vibesketch.document.model.Solvent attribute) (vibesketch.document.Solvent attribute) model_config (vibesketch.document.campaign_results.CampaignSelection attribute) (vibesketch.document.Canvas attribute) (vibesketch.document.Conformer attribute) (vibesketch.document.Constraint attribute) (vibesketch.document.Document attribute) (vibesketch.document.Edit attribute) (vibesketch.document.Job attribute) (vibesketch.document.JobSpec attribute) (vibesketch.document.model.Canvas attribute) (vibesketch.document.model.Capping attribute) (vibesketch.document.model.Chirality attribute) (vibesketch.document.model.Coefficient attribute) (vibesketch.document.model.Conformer attribute) (vibesketch.document.model.Constraint attribute) (vibesketch.document.model.Defect attribute) (vibesketch.document.model.Document attribute) (vibesketch.document.model.Edit attribute) (vibesketch.document.model.Electrons attribute) (vibesketch.document.model.Fullerene attribute) (vibesketch.document.model.Generic attribute) (vibesketch.document.model.Graphene attribute) (vibesketch.document.model.Job attribute) (vibesketch.document.model.JobSpec attribute) (vibesketch.document.model.Name attribute) (vibesketch.document.model.Nanoribbon attribute) (vibesketch.document.model.NanoSite attribute) (vibesketch.document.model.Nanostructure attribute) (vibesketch.document.model.Nanotube attribute) (vibesketch.document.model.PeriodicCell attribute) (vibesketch.document.model.Provenance attribute) (vibesketch.document.model.Quantity attribute) (vibesketch.document.model.Reaction attribute) (vibesketch.document.model.Resources attribute) (vibesketch.document.model.RGroup attribute) (vibesketch.document.model.Run attribute) (vibesketch.document.model.Sequence attribute) (vibesketch.document.model.SidewallGroup attribute) (vibesketch.document.model.SolidFormula attribute) (vibesketch.document.model.Solvent attribute) (vibesketch.document.model.Species attribute) (vibesketch.document.model.StateLabel attribute) (vibesketch.document.model.Style attribute) (vibesketch.document.model.Surface attribute) (vibesketch.document.model.SurfaceAnchor attribute) (vibesketch.document.Name attribute) (vibesketch.document.Provenance attribute) (vibesketch.document.Reaction attribute) (vibesketch.document.reaction_library.ReactionEntry attribute) (vibesketch.document.reaction_library.ReactionSource attribute) (vibesketch.document.Resources attribute) (vibesketch.document.results.Selection attribute) (vibesketch.document.Run attribute) (vibesketch.document.Solvent attribute) (vibesketch.document.Species attribute) (vibesketch.document.spectra.SpectrumExport attribute) (vibesketch.document.Style attribute) (vibesketch.document.Surface attribute) (vibesketch.document.SurfaceAnchor attribute) (vibesketch.document.template_library.TemplateEntry attribute) (vibesketch.document.tlc.Lane attribute) (vibesketch.inputs.neb.NebSpec attribute) Modification (class in vibesketch.document.monomers) MODIFIED (in module vibesketch.document.monomers) module vibesketch.agent vibesketch.agent.client vibesketch.agent.mcp vibesketch.chem vibesketch.chem.analysis vibesketch.chem.cip vibesketch.chem.clean vibesketch.chem.depiction vibesketch.chem.embed vibesketch.chem.endpoints vibesketch.chem.fire vibesketch.chem.formula vibesketch.chem.layout vibesketch.chem.mapping vibesketch.chem.nanostructures vibesketch.chem.perceive vibesketch.chem.relax vibesketch.chem.report vibesketch.chem.species vibesketch.codenames vibesketch.document vibesketch.document.abbreviations vibesketch.document.apparatus vibesketch.document.campaign vibesketch.document.campaign_results vibesketch.document.cdx vibesketch.document.cdxml vibesketch.document.clean vibesketch.document.coordinates vibesketch.document.derive vibesketch.document.electrochem vibesketch.document.electrochemical_recipes vibesketch.document.embed vibesketch.document.enumeration vibesketch.document.external_results vibesketch.document.formats vibesketch.document.generics vibesketch.document.geometry_return vibesketch.document.highlights vibesketch.document.io vibesketch.document.ket vibesketch.document.model vibesketch.document.monomers vibesketch.document.multiple_groups vibesketch.document.nanostructures vibesketch.document.nmr vibesketch.document.orca vibesketch.document.properties vibesketch.document.qvf vibesketch.document.reaction_library vibesketch.document.recipe vibesketch.document.relax vibesketch.document.renders vibesketch.document.results vibesketch.document.review vibesketch.document.rgfile vibesketch.document.schema vibesketch.document.scheme vibesketch.document.sequences vibesketch.document.solids vibesketch.document.spectra vibesketch.document.stereo vibesketch.document.stoichiometry vibesketch.document.surfaces vibesketch.document.tables vibesketch.document.template_library vibesketch.document.tlc vibesketch.elements vibesketch.inputs vibesketch.inputs.base vibesketch.inputs.neb vibesketch.inputs.orca vibesketch.inputs.orca_keywords vibesketch.inputs.qcschema vibesketch.inputs.recipe vibesketch.inputs.registry vibesketch.inputs.vibeqc vibesketch.inputs.xyz vibesketch.naming vibesketch.naming.opsin vibesketch.queue vibesketch.render vibesketch.render.chemfig vibesketch.render.fonts vibesketch.render.nanostructures vibesketch.render.publication vibesketch.render.scene vibesketch.render.styles vibesketch.render.surfaces vibesketch.render.vector vibesketch.server vibesketch.server.documents vibesketch.server.guard vibesketch.server.store vibesketch.units vibesketch.viewer

mol (vibesketch.chem.mapping.Side attribute) (vibesketch.chem.perceive.Perceived attribute) (vibesketch.document.ket.KetFragment attribute) mol_from_smiles() (in module vibesketch.chem.species) molar_mass() (vibesketch.chem.formula.Formula method) molar_mass_g_mol (vibesketch.document.model.SolidFormula attribute) molar_refractivity (vibesketch.chem.analysis.Descriptors attribute) molecule() (vibesketch.inputs.qcschema.QcschemaMoleculeWriter method) molecule_reason() (in module vibesketch.document.ket) molecules (vibesketch.document.formats.Imported attribute) molfile() (in module vibesketch.document.ket) monoisotopic_mass (vibesketch.chem.report.SpeciesReport attribute) (vibesketch.chem.species.Properties attribute) monoisotopic_mass() (vibesketch.chem.formula.Formula method) MonomerRefused MultipleGroupRefused multiplicity (vibesketch.chem.report.SpeciesReport attribute) (vibesketch.chem.species.Identity attribute) (vibesketch.document.coordinates.Structure attribute) (vibesketch.document.model.Species attribute) (vibesketch.document.Species attribute) (vibesketch.inputs.neb.ReactionPath attribute)

N

n (vibesketch.document.model.Chirality attribute) Name (class in vibesketch.document) (class in vibesketch.document.model) name (vibesketch.agent.mcp.Tool attribute) (vibesketch.chem.report.SpeciesReport attribute) (vibesketch.document.coordinates.Structure attribute) (vibesketch.document.model.Solvent attribute) (vibesketch.document.model.Species attribute) (vibesketch.document.reaction_library.ReactionEntry attribute) (vibesketch.document.reaction_library.ReactionSource attribute) (vibesketch.document.Solvent attribute) (vibesketch.document.Species attribute) (vibesketch.document.template_library.TemplateEntry attribute) (vibesketch.inputs.base.InputFile attribute) (vibesketch.inputs.base.InputWriter attribute) (vibesketch.inputs.InputFile attribute) (vibesketch.inputs.InputWriter attribute) (vibesketch.inputs.orca.OrcaWriter attribute) (vibesketch.inputs.qcschema.QcschemaInputWriter attribute) (vibesketch.inputs.qcschema.QcschemaMoleculeWriter attribute) (vibesketch.inputs.vibeqc.VibeqcWriter attribute) (vibesketch.inputs.xyz.XyzWriter attribute) (vibesketch.naming.opsin.OpsinResult attribute) (vibesketch.render.styles.Preset attribute) name_for() (in module vibesketch.naming) NameResult (class in vibesketch.naming) naming_available() (in module vibesketch.naming) NamingUnavailable NanoGroup (in module vibesketch.document.model)

Nanoribbon (class in vibesketch.document.model) NanoSite (class in vibesketch.document.model) Nanostructure (class in vibesketch.document.model) nanostructure (vibesketch.chem.report.SpeciesReport attribute) (vibesketch.document.model.Species attribute) (vibesketch.document.Species attribute) NanostructureRefused, [1] Nanotube (class in vibesketch.document.model) nanotube (vibesketch.document.model.Surface attribute) (vibesketch.document.Surface attribute) neb_inputs() (in module vibesketch.inputs.neb) NEB_PROGRAMS (in module vibesketch.inputs.neb) NebSpec (class in vibesketch.inputs.neb) new_document() (in module vibesketch.document) (in module vibesketch.document.io) nmr_shifts() (in module vibesketch.document.nmr) nmr_table() (in module vibesketch.document.nmr) NmrRefused node (vibesketch.document.ket.KetFragment attribute) note (vibesketch.document.reaction_library.ReactionEntry attribute) (vibesketch.document.template_library.TemplateEntry attribute) (vibesketch.naming.NameResult attribute) NotFound NothingDrawn nprocs (vibesketch.document.model.Resources attribute) (vibesketch.document.Resources attribute) number (vibesketch.document.model.RGroup attribute) (vibesketch.document.rgfile.Definition attribute) numeric (vibesketch.chem.formula.Formula property)

O

objective() (vibesketch.chem.depiction.DepictionField method) occurrence (vibesketch.document.model.RGroup attribute) (vibesketch.document.rgfile.Definition attribute) open_stereo (vibesketch.chem.embed.Embedded attribute) ops (vibesketch.render.vector.Paint attribute) opsin_available() (in module vibesketch.naming.opsin) OpsinResult (class in vibesketch.naming.opsin) OpsinUnavailable

orca_shieldings() (in module vibesketch.document.nmr) OrcaUnreadable OrcaWriter (class in vibesketch.inputs.orca) origin() (in module vibesketch.document.geometry_return) outline() (in module vibesketch.render.fonts) output_structures() (in module vibesketch.document.orca) overwrite_refusal() (in module vibesketch.document.qvf) owners (vibesketch.chem.mapping.Side attribute)

P

Paint (class in vibesketch.render.vector) paints() (in module vibesketch.render.vector) pairs (vibesketch.chem.depiction.DepictionField attribute) (vibesketch.chem.endpoints.Endpoints attribute) (vibesketch.chem.mapping.AtomMapping attribute) PALETTE (in module vibesketch.document.highlights) parameters (vibesketch.document.model.Nanostructure attribute) (vibesketch.document.template_library.TemplateEntry attribute) parse_formula() (in module vibesketch.chem.formula) parse_pin() (in module vibesketch.inputs.neb) path (vibesketch.server.store.Entry attribute) Payload (class in vibesketch.document.formats) perceive() (in module vibesketch.chem.perceive) Perceived (class in vibesketch.chem.perceive) periodic (vibesketch.chem.nanostructures.AtomModel attribute) (vibesketch.document.model.Nanostructure attribute) PeriodicCell (class in vibesketch.document.model) periods (vibesketch.document.model.Nanoribbon attribute) (vibesketch.document.model.Nanotube attribute) phases (vibesketch.chem.formula.Formula attribute) Picture (class in vibesketch.render.nanostructures) picture() (in module vibesketch.render.nanostructures) picture_svg() (in module vibesketch.render.nanostructures) picture_tikz() (in module vibesketch.render.nanostructures) pictures() (in module vibesketch.document.nanostructures) pinned (vibesketch.chem.mapping.AtomMapping attribute) placed_molecule() (in module vibesketch.document.ket) plain_sequence() (in module vibesketch.document.sequences) pluses (vibesketch.document.ket.KetScene attribute) polymorph (vibesketch.chem.formula.Formula attribute) (vibesketch.document.model.SolidFormula attribute)

positions (vibesketch.chem.nanostructures.AtomModel attribute) (vibesketch.document.coordinates.Structure attribute) preopt_ends (vibesketch.inputs.neb.NebSpec attribute) prepare() (in module vibesketch.render.styles) Preset (class in vibesketch.render.styles) preset (vibesketch.document.model.Style attribute) (vibesketch.document.Style attribute) Printed (class in vibesketch.document.sequences) printed (vibesketch.document.monomers.Modification attribute) printed() (in module vibesketch.document.sequences) product (vibesketch.chem.endpoints.Endpoints attribute) products (vibesketch.chem.mapping.AtomMapping attribute) (vibesketch.document.coordinates.Step attribute) (vibesketch.document.model.Reaction attribute) (vibesketch.document.Reaction attribute) program (vibesketch.document.Job attribute) (vibesketch.document.model.Job attribute) (vibesketch.inputs.base.InputBundle attribute) (vibesketch.inputs.InputBundle attribute) (vibesketch.inputs.recipe.ResolvedStage attribute) Properties (class in vibesketch.chem.species) properties() (in module vibesketch.chem.species) PropertiesRefused property_lines() (in module vibesketch.document.properties) property_table() (in module vibesketch.document.properties) PROTOCOL_VERSIONS (in module vibesketch.agent.mcp) Provenance (class in vibesketch.document) (class in vibesketch.document.model) provenance (vibesketch.document.Document attribute) (vibesketch.document.model.Document attribute)

Q

QcschemaInputWriter (class in vibesketch.inputs.qcschema) QcschemaMoleculeWriter (class in vibesketch.inputs.qcschema) quantities (vibesketch.document.model.Reaction attribute) (vibesketch.document.Reaction attribute) quantities() (in module vibesketch.document.electrochem) Quantity (class in vibesketch.document.model)

queue (vibesketch.document.model.Run attribute) (vibesketch.document.Run attribute) queue_status() (in module vibesketch.queue) QueueUnavailable qvf_available() (in module vibesketch.document.qvf) QvfError QvfUnavailable

R

raw() (vibesketch.agent.client.RestClient method) reactant (vibesketch.chem.endpoints.Endpoints attribute) reactants (vibesketch.chem.mapping.AtomMapping attribute) (vibesketch.document.coordinates.Step attribute) (vibesketch.document.model.Reaction attribute) (vibesketch.document.Reaction attribute) Reaction (class in vibesketch.document) (class in vibesketch.document.model) reaction (vibesketch.document.formats.Imported attribute) (vibesketch.inputs.neb.ReactionPath attribute) reaction_energies() (in module vibesketch.document.results) reaction_fragment() (in module vibesketch.document.reaction_library) reaction_mapping() (in module vibesketch.inputs.neb) reaction_path() (in module vibesketch.inputs.neb) reaction_species() (in module vibesketch.queue) reaction_table() (in module vibesketch.document.tables) ReactionEntry (class in vibesketch.document.reaction_library) ReactionPath (class in vibesketch.inputs.neb) ReactionRefused reactions (vibesketch.document.campaign_results.CampaignSelection attribute) (vibesketch.document.Document attribute) (vibesketch.document.model.Document attribute) (vibesketch.document.results.Selection attribute) ReactionSource (class in vibesketch.document.reaction_library) read_cdxml() (in module vibesketch.document.cdxml) read_half_reaction() (in module vibesketch.document.electrochem) read_name() (in module vibesketch.naming.opsin) read_rgfile() (in module vibesketch.document.rgfile) read_scene() (in module vibesketch.document.ket) read_structures() (in module vibesketch.document.formats) reagents (vibesketch.document.coordinates.Step attribute) (vibesketch.document.ket.SceneStep attribute) (vibesketch.document.model.Reaction attribute) (vibesketch.document.Reaction attribute) rear (vibesketch.render.nanostructures.Depiction attribute) reason (vibesketch.document.scheme.SchemeReport attribute) (vibesketch.naming.opsin.OpsinResult attribute) recipe (vibesketch.document.campaign_results.CampaignSelection attribute) recipe_report() (in module vibesketch.document.recipe) recipes (vibesketch.document.Document attribute) (vibesketch.document.model.Document attribute) record (vibesketch.document.campaign.Compiled attribute) (vibesketch.document.renders.StageRenders attribute) record() (vibesketch.chem.nanostructures.AtomModel method) records() (in module vibesketch.document.surfaces) reduction_potential() (in module vibesketch.document.electrochemical_recipes) reference (vibesketch.document.model.Quantity attribute) ReferenceElectrode (in module vibesketch.document.model) refine() (vibesketch.chem.depiction.DepictionField method) refusals (vibesketch.inputs.neb.ReactionPath attribute) (vibesketch.inputs.recipe.ResolvedStage attribute) refusals() (vibesketch.inputs.base.InputWriter method) (vibesketch.inputs.InputWriter method) refused (vibesketch.inputs.Batch attribute) (vibesketch.inputs.recipe.ResolvedStage property) (vibesketch.inputs.registry.Batch attribute) (vibesketch.queue.Submission attribute) register() (in module vibesketch.inputs) (in module vibesketch.inputs.registry) relax() (in module vibesketch.document.relax) relax_3d() (in module vibesketch.chem.relax) Relaxed (class in vibesketch.chem.relax) relaxed (vibesketch.document.relax.RelaxReport attribute) RelaxFailed RelaxReport (class in vibesketch.document.relax)

remove() (vibesketch.server.store.Store method) remove_recipe() (in module vibesketch.document.recipe) render() (in module vibesketch.render) render_stages() (in module vibesketch.document.renders) render_svg() (in module vibesketch.render) RenderRefused RendersRefused RenderUnavailable repeat (vibesketch.document.model.SurfaceAnchor attribute) (vibesketch.document.SurfaceAnchor attribute) replace() (vibesketch.server.store.Store method) report() (in module vibesketch.chem.report) (vibesketch.inputs.neb.ReactionPath method) residue (vibesketch.document.monomers.Modification attribute) resolve() (in module vibesketch.render.styles) resolve_recipe() (in module vibesketch.inputs.recipe) resolve_stage() (in module vibesketch.inputs.recipe) ResolvedStage (class in vibesketch.inputs.recipe) Resources (class in vibesketch.document) (class in vibesketch.document.model) resources (vibesketch.document.JobSpec attribute) (vibesketch.document.model.JobSpec attribute) (vibesketch.inputs.neb.NebSpec attribute) rest_h (vibesketch.document.model.RGroup attribute) (vibesketch.document.rgfile.Definition attribute) RestClient (class in vibesketch.agent.client) result (vibesketch.document.derive.Derivation attribute) (vibesketch.document.model.Run attribute) (vibesketch.document.Run attribute) (vibesketch.server.store.Entry attribute) result_figure() (in module vibesketch.document.results) ResultRefused results (vibesketch.document.relax.RelaxReport attribute) retrieved (vibesketch.document.reaction_library.ReactionSource attribute) retry_node() (in module vibesketch.document.campaign) return_geometry() (in module vibesketch.document.geometry_return) revalidate_campaign() (in module vibesketch.document.review) review_campaign() (in module vibesketch.document.review) revision (vibesketch.document.Document attribute) (vibesketch.document.Edit attribute) (vibesketch.document.model.Document attribute) (vibesketch.document.model.Edit attribute) rgfile() (in module vibesketch.document.rgfile) RgfileUnreadable RGroup (class in vibesketch.document.model) rgroup_node() (in module vibesketch.document.ket) rgroups (vibesketch.document.Document attribute) (vibesketch.document.formats.Imported attribute) (vibesketch.document.model.Document attribute) (vibesketch.document.model.Generic attribute) ring_distances (vibesketch.chem.depiction.DepictionField attribute) ring_pairs (vibesketch.chem.depiction.DepictionField attribute) rings (vibesketch.chem.analysis.Descriptors attribute) rmsd (vibesketch.chem.endpoints.Endpoints attribute) rotatable_bonds (vibesketch.chem.analysis.Descriptors attribute) rows (vibesketch.document.scheme.SchemeReport attribute) Run (class in vibesketch.document) (class in vibesketch.document.model) run (vibesketch.agent.mcp.Tool attribute) (vibesketch.document.spectra.SpectrumExport attribute) run_arguments() (vibesketch.inputs.vibeqc.VibeqcWriter method) run_command (vibesketch.document.campaign.Compiled property) run_states() (in module vibesketch.queue) runs (vibesketch.document.Job attribute) (vibesketch.document.model.Job attribute) (vibesketch.document.results.Selection attribute)

S

save() (in module vibesketch.document) (in module vibesketch.document.io) (vibesketch.server.store.Store method) saved_revision (vibesketch.server.store.Entry attribute) SaveRefused, [1] scene_svg() (in module vibesketch.render.scene) SceneStep (class in vibesketch.document.ket) schema (vibesketch.agent.mcp.Tool attribute) SCHEMA_FILE (in module vibesketch.document.schema) SCHEMA_ID (in module vibesketch.document.model) schema_id (vibesketch.document.Document attribute) (vibesketch.document.model.Document attribute) SCHEMA_URI (in module vibesketch.document.schema) scheme_metrics() (in module vibesketch.document.scheme) SchemeReport (class in vibesketch.document.scheme) scope (vibesketch.document.reaction_library.ReactionEntry attribute) (vibesketch.document.template_library.TemplateEntry attribute) seed (vibesketch.chem.depiction.DepictionField attribute) Selection (class in vibesketch.document.results) Sequence (class in vibesketch.document.model) sequence (vibesketch.document.model.Species attribute) (vibesketch.document.Species attribute) sequence_export() (in module vibesketch.document.sequences) SEQUENCE_FORMATS (in module vibesketch.document.sequences) sequence_molecules() (in module vibesketch.document.sequences) sequenced (vibesketch.document.formats.Imported attribute) SequenceRefused serve() (in module vibesketch.agent.mcp) ServerError set_recipe() (in module vibesketch.document.recipe) SHAPES (in module vibesketch.render.scene) show() (in module vibesketch.viewer) shown (vibesketch.naming.NameResult property) Side (class in vibesketch.chem.mapping) side (vibesketch.document.model.Electrons attribute) side() (in module vibesketch.chem.mapping) sidewall (vibesketch.document.model.Graphene attribute) (vibesketch.document.model.Nanoribbon attribute) (vibesketch.document.model.Nanotube attribute) SidewallGroup (class in vibesketch.document.model) site (vibesketch.document.model.Defect attribute) (vibesketch.document.model.SidewallGroup attribute) (vibesketch.document.model.SurfaceAnchor attribute) (vibesketch.document.SurfaceAnchor attribute) size (vibesketch.document.model.Fullerene attribute) (vibesketch.render.styles.Preset attribute) smiles (vibesketch.chem.report.SpeciesReport attribute) (vibesketch.chem.species.Identity attribute) (vibesketch.document.coordinates.Structure attribute) (vibesketch.document.model.Species attribute) (vibesketch.document.Species attribute) (vibesketch.document.template_library.TemplateEntry attribute) (vibesketch.naming.opsin.OpsinResult attribute) smiles_for_name() (in module vibesketch.naming) solid (vibesketch.document.model.Species attribute) (vibesketch.document.Species attribute) solid_data() (in module vibesketch.document.solids) solid_refusal() (in module vibesketch.document.solids) solid_runs() (in module vibesketch.document.solids) SolidFormula (class in vibesketch.document.model) Solvent (class in vibesketch.document) (class in vibesketch.document.model) solvent (vibesketch.document.JobSpec attribute) (vibesketch.document.model.JobSpec attribute) (vibesketch.inputs.neb.NebSpec attribute) solvent_name() (in module vibesketch.inputs.orca_keywords) source (vibesketch.document.Conformer attribute) (vibesketch.document.model.Conformer attribute) (vibesketch.document.model.Name attribute) (vibesketch.document.Name attribute) (vibesketch.naming.NameResult attribute) source_digest() (in module vibesketch.document.campaign) sources (vibesketch.document.reaction_library.ReactionEntry attribute) (vibesketch.document.template_library.TemplateEntry attribute) spacing (vibesketch.render.styles.Preset attribute) spans (vibesketch.document.sequences.Printed attribute) spec (vibesketch.document.Job attribute) (vibesketch.document.model.Job attribute) Species (class in vibesketch.document) (class in vibesketch.document.model) species (vibesketch.chem.mapping.Side attribute) (vibesketch.document.Document attribute) (vibesketch.document.Job attribute) (vibesketch.document.model.Coefficient attribute) (vibesketch.document.model.Document attribute) (vibesketch.document.model.Job attribute) (vibesketch.document.model.StateLabel attribute) (vibesketch.inputs.base.InputBundle attribute) (vibesketch.inputs.InputBundle attribute) (vibesketch.render.nanostructures.Depiction attribute)

species_by_id() (vibesketch.document.Document method) (vibesketch.document.model.Document method) species_digest() (in module vibesketch.document.results) species_ids() (vibesketch.document.model.Reaction method) (vibesketch.document.Reaction method) species_mols() (in module vibesketch.document.formats) species_qvf() (in module vibesketch.document.qvf) SpeciesReport (class in vibesketch.chem.report) spectrum (vibesketch.document.spectra.SpectrumExport attribute) spectrum_lines() (in module vibesketch.document.spectra) SpectrumExport (class in vibesketch.document.spectra) SpectrumRefused spots (vibesketch.document.tlc.Lane attribute) stage (vibesketch.document.campaign_results.CampaignSelection attribute) (vibesketch.inputs.recipe.ResolvedStage attribute) stage_container() (in module vibesketch.document.qvf) StageRenders (class in vibesketch.document.renders) stale_labels() (in module vibesketch.document.stereo) start (vibesketch.document.spectra.SpectrumExport attribute) start_server() (in module vibesketch.agent.client) State (in module vibesketch.document.model) state (vibesketch.chem.formula.Formula attribute) (vibesketch.document.model.SolidFormula attribute) (vibesketch.document.model.StateLabel attribute) StateLabel (class in vibesketch.document.model) states (vibesketch.document.JobSpec attribute) (vibesketch.document.model.JobSpec attribute) (vibesketch.document.model.Reaction attribute) (vibesketch.document.Reaction attribute) status (vibesketch.naming.NameResult attribute) Step (class in vibesketch.document.coordinates) step (vibesketch.document.spectra.SpectrumExport attribute) steps (vibesketch.chem.fire.FireResult attribute) (vibesketch.chem.relax.Relaxed attribute) stereo (vibesketch.chem.report.SpeciesReport attribute) stereo_labels (vibesketch.render.styles.Preset attribute) stereo_labels() (in module vibesketch.chem.cip) stereo_reason() (in module vibesketch.document.ket) stereo_report() (in module vibesketch.document.stereo) StereoLabels (class in vibesketch.chem.cip) stoichiometry() (in module vibesketch.document.stoichiometry) stoichiometry_table() (in module vibesketch.document.stoichiometry) StoichiometryRefused stop (vibesketch.document.spectra.SpectrumExport attribute) Store (class in vibesketch.server.store) stroke (vibesketch.render.vector.Paint attribute) Structure (class in vibesketch.document.coordinates) Style (class in vibesketch.document) (class in vibesketch.document.model) style (vibesketch.document.Document attribute) (vibesketch.document.model.Document attribute) (vibesketch.render.nanostructures.Depiction attribute) Submission (class in vibesketch.queue) submit() (in module vibesketch.queue) submitted (vibesketch.document.model.Run attribute) (vibesketch.document.Run attribute) (vibesketch.queue.Submission attribute) substituents (vibesketch.document.model.RGroup attribute) summary (vibesketch.document.Edit attribute) (vibesketch.document.model.Edit attribute) summary() (in module vibesketch.document.nanostructures) superpose() (in module vibesketch.document.renders) Surface (class in vibesketch.document) (class in vibesketch.document.model) surface_of() (in module vibesketch.render.surfaces) surface_picture() (in module vibesketch.render.surfaces) SurfaceAnchor (class in vibesketch.document) (class in vibesketch.document.model) surfaces (vibesketch.document.Document attribute) (vibesketch.document.model.Document attribute) symbols (vibesketch.chem.endpoints.Endpoints attribute) (vibesketch.chem.nanostructures.AtomModel attribute) (vibesketch.document.Conformer attribute) (vibesketch.document.coordinates.Structure attribute) (vibesketch.document.model.Conformer attribute)

T

tags (vibesketch.document.template_library.TemplateEntry attribute) tail (vibesketch.document.ket.KetArrow attribute) (vibesketch.document.ket.SceneStep attribute) target (vibesketch.chem.relax.ConstraintCheck attribute) Task (in module vibesketch.document.model) task (vibesketch.document.JobSpec attribute) (vibesketch.document.model.JobSpec attribute) tasks (vibesketch.inputs.base.InputWriter attribute) (vibesketch.inputs.InputWriter attribute) (vibesketch.inputs.orca.OrcaWriter attribute) (vibesketch.inputs.qcschema.QcschemaInputWriter attribute) (vibesketch.inputs.qcschema.QcschemaMoleculeWriter attribute) (vibesketch.inputs.vibeqc.VibeqcWriter attribute) (vibesketch.inputs.xyz.XyzWriter attribute) template_fragment() (in module vibesketch.document.template_library) TemplateEntry (class in vibesketch.document.template_library) TERMINAL (in module vibesketch.queue) text (vibesketch.chem.formula.Formula attribute) (vibesketch.document.ket.KetText attribute) (vibesketch.document.model.Quantity attribute) (vibesketch.document.model.SolidFormula attribute) (vibesketch.document.sequences.Printed attribute) TEXT_FORMATS (in module vibesketch.document.formats) text_node() (in module vibesketch.document.ket)

texts (vibesketch.document.ket.KetScene attribute) thumbnail() (in module vibesketch.render) tidied (vibesketch.document.scheme.SchemeReport attribute) tidy_ket() (in module vibesketch.document.scheme) tidy_scheme() (in module vibesketch.document.scheme) tint() (in module vibesketch.document.highlights) TlcRefused to_dict() (vibesketch.chem.analysis.Analysis method) (vibesketch.chem.analysis.Descriptors method) (vibesketch.chem.cip.StereoLabels method) (vibesketch.chem.relax.ConstraintCheck method) (vibesketch.chem.relax.Relaxed method) (vibesketch.chem.report.SpeciesReport method) (vibesketch.inputs.recipe.ResolvedStage method) to_json_data() (vibesketch.document.Document method) (vibesketch.document.model.Document method) to_qvf() (in module vibesketch.document.qvf) Tool (class in vibesketch.agent.mcp) tpsa (vibesketch.chem.analysis.Descriptors attribute) TRANSITION_METALS (in module vibesketch.chem.species) translation_angstrom (vibesketch.document.model.PeriodicCell attribute) translation_angstrom() (in module vibesketch.chem.nanostructures) triples (vibesketch.chem.depiction.DepictionField attribute) TubeEnd (in module vibesketch.document.model)

U

u (vibesketch.document.model.SurfaceAnchor attribute) (vibesketch.document.SurfaceAnchor attribute) undefined_centres (vibesketch.chem.cip.StereoLabels attribute) unit (vibesketch.document.model.Quantity attribute) units_per_em() (in module vibesketch.render.fonts) UnknownCampaign UnknownRecipe

UnknownReference, [1] UnknownSpecies UnknownWriter, [1] unpaired() (in module vibesketch.chem.species) unrolled() (in module vibesketch.chem.nanostructures) unspecified_double_bonds (vibesketch.chem.cip.StereoLabels attribute) unsupported (vibesketch.document.ket.KetFragment attribute) url (vibesketch.document.reaction_library.ReactionSource attribute)

V

v (vibesketch.document.model.SurfaceAnchor attribute) (vibesketch.document.SurfaceAnchor attribute) validation_errors() (in module vibesketch.document.io) value (vibesketch.chem.relax.ConstraintCheck attribute) (vibesketch.document.Constraint attribute) (vibesketch.document.model.Coefficient attribute) (vibesketch.document.model.Constraint attribute) (vibesketch.document.model.Name attribute) (vibesketch.document.model.Quantity attribute) (vibesketch.document.Name attribute) (vibesketch.naming.NameResult attribute) version_label() (in module vibesketch.codenames) VibeqcWriter (class in vibesketch.inputs.vibeqc) vibesketch.agent module vibesketch.agent.client module vibesketch.agent.mcp module vibesketch.chem module vibesketch.chem.analysis module vibesketch.chem.cip module vibesketch.chem.clean module vibesketch.chem.depiction module vibesketch.chem.embed module vibesketch.chem.endpoints module vibesketch.chem.fire module vibesketch.chem.formula module vibesketch.chem.layout module vibesketch.chem.mapping module vibesketch.chem.nanostructures module vibesketch.chem.perceive module vibesketch.chem.relax module vibesketch.chem.report module vibesketch.chem.species module vibesketch.codenames module vibesketch.document module vibesketch.document.abbreviations module vibesketch.document.apparatus module vibesketch.document.campaign module vibesketch.document.campaign_results module vibesketch.document.cdx module vibesketch.document.cdxml module vibesketch.document.clean module vibesketch.document.coordinates module vibesketch.document.derive module vibesketch.document.electrochem module vibesketch.document.electrochemical_recipes module vibesketch.document.embed module vibesketch.document.enumeration module vibesketch.document.external_results module vibesketch.document.formats module vibesketch.document.generics module vibesketch.document.geometry_return module vibesketch.document.highlights module vibesketch.document.io module vibesketch.document.ket module vibesketch.document.model module vibesketch.document.monomers module vibesketch.document.multiple_groups module vibesketch.document.nanostructures module

vibesketch.document.nmr module vibesketch.document.orca module vibesketch.document.properties module vibesketch.document.qvf module vibesketch.document.reaction_library module vibesketch.document.recipe module vibesketch.document.relax module vibesketch.document.renders module vibesketch.document.results module vibesketch.document.review module vibesketch.document.rgfile module vibesketch.document.schema module vibesketch.document.scheme module vibesketch.document.sequences module vibesketch.document.solids module vibesketch.document.spectra module vibesketch.document.stereo module vibesketch.document.stoichiometry module vibesketch.document.surfaces module vibesketch.document.tables module vibesketch.document.template_library module vibesketch.document.tlc module vibesketch.elements module vibesketch.inputs module vibesketch.inputs.base module vibesketch.inputs.neb module vibesketch.inputs.orca module vibesketch.inputs.orca_keywords module vibesketch.inputs.qcschema module vibesketch.inputs.recipe module vibesketch.inputs.registry module vibesketch.inputs.vibeqc module vibesketch.inputs.xyz module vibesketch.naming module vibesketch.naming.opsin module vibesketch.queue module vibesketch.render module vibesketch.render.chemfig module vibesketch.render.fonts module vibesketch.render.nanostructures module vibesketch.render.publication module vibesketch.render.scene module vibesketch.render.styles module vibesketch.render.surfaces module vibesketch.render.vector module vibesketch.server module vibesketch.server.documents module vibesketch.server.guard module vibesketch.server.store module vibesketch.units module vibesketch.viewer module ViewerUnavailable

W

wall_properties() (in module vibesketch.chem.nanostructures) walls (vibesketch.chem.nanostructures.AtomModel attribute) (vibesketch.document.model.Nanotube attribute) warnings (vibesketch.chem.embed.Embedded attribute) (vibesketch.chem.endpoints.Endpoints attribute) (vibesketch.chem.relax.Relaxed attribute) (vibesketch.chem.report.SpeciesReport attribute) (vibesketch.document.campaign.Compiled attribute) (vibesketch.document.derive.Derivation attribute) (vibesketch.document.embed.EmbedReport attribute) (vibesketch.document.formats.Imported attribute) (vibesketch.document.relax.RelaxReport attribute) (vibesketch.document.renders.StageRenders attribute) (vibesketch.server.store.Entry attribute) web_bundle() (in module vibesketch.server) widened() (in module vibesketch.document.electrochem) WIDTH (in module vibesketch.document.scheme) width (vibesketch.document.model.Nanoribbon attribute) (vibesketch.render.vector.Paint attribute) width_nm (vibesketch.document.model.Graphene attribute) with_abbreviations() (in module vibesketch.document.abbreviations) with_amounts() (in module vibesketch.document.stoichiometry) with_apparatus() (in module vibesketch.document.apparatus) with_edit() (in module vibesketch.document) (in module vibesketch.document.io) with_energy_recipe() (in module vibesketch.document.electrochemical_recipes) with_half_reaction() (in module vibesketch.document.electrochem)

with_highlight() (in module vibesketch.document.highlights) with_nanostructure() (in module vibesketch.document.nanostructures) with_nmr_labels() (in module vibesketch.document.nmr) with_picture() (in module vibesketch.document.nanostructures) with_property_text() (in module vibesketch.document.properties) with_selection_highlighted() (in module vibesketch.document.highlights) with_sequences() (in module vibesketch.document.sequences) with_solids() (in module vibesketch.document.solids) with_stereo_labels() (in module vibesketch.document.stereo) with_superatoms() (in module vibesketch.document.abbreviations) with_surface() (in module vibesketch.document.surfaces) with_tlc_plate() (in module vibesketch.document.tlc) without_abbreviations() (in module vibesketch.document.abbreviations) without_highlights() (in module vibesketch.document.highlights) write() (vibesketch.inputs.base.InputWriter method) (vibesketch.inputs.InputWriter method) write_input() (in module vibesketch.inputs) (in module vibesketch.inputs.registry) write_inputs() (in module vibesketch.inputs) (in module vibesketch.inputs.registry) write_output() (in module vibesketch.document) (in module vibesketch.document.io) write_scene() (in module vibesketch.document.ket) WriterRefusal, [1] writers() (in module vibesketch.inputs) (in module vibesketch.inputs.registry) written (vibesketch.chem.formula.Formula attribute)

X

x (vibesketch.chem.fire.FireResult attribute) xy (vibesketch.chem.clean.Cleaned attribute)

xyz_angstrom (vibesketch.document.Conformer attribute) (vibesketch.document.model.Conformer attribute) XyzWriter (class in vibesketch.inputs.xyz)

Y

yield_ (vibesketch.document.model.Reaction attribute) (vibesketch.document.Reaction attribute)

yield_text (vibesketch.document.coordinates.Step attribute)