molstar 4.0.1 → 4.2.0

package/lib/cli/chem-comp-dict/util.d.ts

@@ -9,138 +9,138 @@ export declare function ensureDataAvailable(options: DataOptions): Promise<void>
 export declare function readFileAsCollection<S extends Database.Schema>(path: string, schema: S): Promise<import("../../mol-data/db").DatabaseCollection<S>>;
 export declare function readCCD(): Promise<import("../../mol-data/db").DatabaseCollection<{
     chem_comp: {
-        formula: import("../../mol-data/db/column").Column.Schema.Str;
-        formula_weight: import("../../mol-data/db/column").Column.Schema.Float;
-        id: import("../../mol-data/db/column").Column.Schema.Str;
-        mon_nstd_parent_comp_id: import("../../mol-data/db/column").Column.Schema.List<string>;
-        name: import("../../mol-data/db/column").Column.Schema.Str;
-        one_letter_code: import("../../mol-data/db/column").Column.Schema.Str;
-        three_letter_code: import("../../mol-data/db/column").Column.Schema.Str;
-        type: import("../../mol-data/db/column").Column.Schema.Aliased<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking">;
-        pdbx_synonyms: import("../../mol-data/db/column").Column.Schema.List<string>;
-        pdbx_type: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_ambiguous_flag: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_replaced_by: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_replaces: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_formal_charge: import("../../mol-data/db/column").Column.Schema.Int;
-        pdbx_model_coordinates_details: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_model_coordinates_db_code: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_ideal_coordinates_details: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_ideal_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
-        pdbx_model_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
-        pdbx_initial_date: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_modified_date: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_release_status: import("../../mol-data/db/column").Column.Schema.Aliased<"REL" | "HOLD" | "HPUB" | "OBS" | "DEL" | "REF_ONLY">;
-        pdbx_processing_site: import("../../mol-data/db/column").Column.Schema.Aliased<"RCSB" | "PDBE" | "PDBJ" | "PDBC" | "EBI">;
+        formula: import("../../mol-data/db").Column.Schema.Str;
+        formula_weight: import("../../mol-data/db").Column.Schema.Float;
+        id: import("../../mol-data/db").Column.Schema.Str;
+        mon_nstd_parent_comp_id: import("../../mol-data/db").Column.Schema.List<string>;
+        name: import("../../mol-data/db").Column.Schema.Str;
+        one_letter_code: import("../../mol-data/db").Column.Schema.Str;
+        three_letter_code: import("../../mol-data/db").Column.Schema.Str;
+        type: import("../../mol-data/db").Column.Schema.Aliased<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking">;
+        pdbx_synonyms: import("../../mol-data/db").Column.Schema.List<string>;
+        pdbx_type: import("../../mol-data/db").Column.Schema.Str;
+        pdbx_ambiguous_flag: import("../../mol-data/db").Column.Schema.Str;
+        pdbx_replaced_by: import("../../mol-data/db").Column.Schema.Str;
+        pdbx_replaces: import("../../mol-data/db").Column.Schema.Str;
+        pdbx_formal_charge: import("../../mol-data/db").Column.Schema.Int;
+        pdbx_model_coordinates_details: import("../../mol-data/db").Column.Schema.Str;
+        pdbx_model_coordinates_db_code: import("../../mol-data/db").Column.Schema.Str;
+        pdbx_ideal_coordinates_details: import("../../mol-data/db").Column.Schema.Str;
+        pdbx_ideal_coordinates_missing_flag: import("../../mol-data/db").Column.Schema.Aliased<"y" | "n">;
+        pdbx_model_coordinates_missing_flag: import("../../mol-data/db").Column.Schema.Aliased<"y" | "n">;
+        pdbx_initial_date: import("../../mol-data/db").Column.Schema.Str;
+        pdbx_modified_date: import("../../mol-data/db").Column.Schema.Str;
+        pdbx_release_status: import("../../mol-data/db").Column.Schema.Aliased<"REL" | "HOLD" | "HPUB" | "OBS" | "DEL" | "REF_ONLY">;
+        pdbx_processing_site: import("../../mol-data/db").Column.Schema.Aliased<"RCSB" | "PDBE" | "PDBJ" | "PDBC" | "EBI">;
     };
     chem_comp_atom: {
-        alt_atom_id: import("../../mol-data/db/column").Column.Schema.Str;
-        atom_id: import("../../mol-data/db/column").Column.Schema.Str;
-        charge: import("../../mol-data/db/column").Column.Schema.Int;
-        model_Cartn_x: import("../../mol-data/db/column").Column.Schema.Coordinate;
-        model_Cartn_y: import("../../mol-data/db/column").Column.Schema.Coordinate;
-        model_Cartn_z: import("../../mol-data/db/column").Column.Schema.Coordinate;
-        comp_id: import("../../mol-data/db/column").Column.Schema.Str;
-        type_symbol: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_align: import("../../mol-data/db/column").Column.Schema.Int;
-        pdbx_ordinal: import("../../mol-data/db/column").Column.Schema.Int;
-        pdbx_model_Cartn_x_ideal: import("../../mol-data/db/column").Column.Schema.Coordinate;
-        pdbx_model_Cartn_y_ideal: import("../../mol-data/db/column").Column.Schema.Coordinate;
-        pdbx_model_Cartn_z_ideal: import("../../mol-data/db/column").Column.Schema.Coordinate;
-        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"s" | "r" | "n">;
-        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
-        pdbx_leaving_atom_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
+        alt_atom_id: import("../../mol-data/db").Column.Schema.Str;
+        atom_id: import("../../mol-data/db").Column.Schema.Str;
+        charge: import("../../mol-data/db").Column.Schema.Int;
+        model_Cartn_x: import("../../mol-data/db").Column.Schema.Coordinate;
+        model_Cartn_y: import("../../mol-data/db").Column.Schema.Coordinate;
+        model_Cartn_z: import("../../mol-data/db").Column.Schema.Coordinate;
+        comp_id: import("../../mol-data/db").Column.Schema.Str;
+        type_symbol: import("../../mol-data/db").Column.Schema.Str;
+        pdbx_align: import("../../mol-data/db").Column.Schema.Int;
+        pdbx_ordinal: import("../../mol-data/db").Column.Schema.Int;
+        pdbx_model_Cartn_x_ideal: import("../../mol-data/db").Column.Schema.Coordinate;
+        pdbx_model_Cartn_y_ideal: import("../../mol-data/db").Column.Schema.Coordinate;
+        pdbx_model_Cartn_z_ideal: import("../../mol-data/db").Column.Schema.Coordinate;
+        pdbx_stereo_config: import("../../mol-data/db").Column.Schema.Aliased<"s" | "r" | "n">;
+        pdbx_aromatic_flag: import("../../mol-data/db").Column.Schema.Aliased<"y" | "n">;
+        pdbx_leaving_atom_flag: import("../../mol-data/db").Column.Schema.Aliased<"y" | "n">;
     };
     chem_comp_bond: {
-        atom_id_1: import("../../mol-data/db/column").Column.Schema.Str;
-        atom_id_2: import("../../mol-data/db/column").Column.Schema.Str;
-        comp_id: import("../../mol-data/db/column").Column.Schema.Str;
-        value_order: import("../../mol-data/db/column").Column.Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
-        pdbx_ordinal: import("../../mol-data/db/column").Column.Schema.Int;
-        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"z" | "n" | "e">;
-        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
+        atom_id_1: import("../../mol-data/db").Column.Schema.Str;
+        atom_id_2: import("../../mol-data/db").Column.Schema.Str;
+        comp_id: import("../../mol-data/db").Column.Schema.Str;
+        value_order: import("../../mol-data/db").Column.Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
+        pdbx_ordinal: import("../../mol-data/db").Column.Schema.Int;
+        pdbx_stereo_config: import("../../mol-data/db").Column.Schema.Aliased<"z" | "n" | "e">;
+        pdbx_aromatic_flag: import("../../mol-data/db").Column.Schema.Aliased<"y" | "n">;
     };
     pdbx_chem_comp_descriptor: {
-        comp_id: import("../../mol-data/db/column").Column.Schema.Str;
-        descriptor: import("../../mol-data/db/column").Column.Schema.Str;
-        type: import("../../mol-data/db/column").Column.Schema.Aliased<"smiles_cannonical" | "smiles_canonical" | "smiles" | "inchi" | "inchi_main" | "inchi_main_formula" | "inchi_main_connect" | "inchi_main_hatom" | "inchi_charge" | "inchi_stereo" | "inchi_isotope" | "inchi_fixedh" | "inchi_reconnect" | "inchikey">;
-        program: import("../../mol-data/db/column").Column.Schema.Str;
-        program_version: import("../../mol-data/db/column").Column.Schema.Str;
+        comp_id: import("../../mol-data/db").Column.Schema.Str;
+        descriptor: import("../../mol-data/db").Column.Schema.Str;
+        type: import("../../mol-data/db").Column.Schema.Aliased<"smiles_cannonical" | "smiles_canonical" | "smiles" | "inchi" | "inchi_main" | "inchi_main_formula" | "inchi_main_connect" | "inchi_main_hatom" | "inchi_charge" | "inchi_stereo" | "inchi_isotope" | "inchi_fixedh" | "inchi_reconnect" | "inchikey">;
+        program: import("../../mol-data/db").Column.Schema.Str;
+        program_version: import("../../mol-data/db").Column.Schema.Str;
     };
     pdbx_chem_comp_identifier: {
-        comp_id: import("../../mol-data/db/column").Column.Schema.Str;
-        identifier: import("../../mol-data/db/column").Column.Schema.Str;
-        type: import("../../mol-data/db/column").Column.Schema.Aliased<"COMMON NAME" | "SYSTEMATIC NAME" | "CAS REGISTRY NUMBER" | "PUBCHEM Identifier" | "MDL Identifier" | "SYNONYM" | "CONDENSED IUPAC CARB SYMBOL" | "IUPAC CARB SYMBOL" | "SNFG CARB SYMBOL" | "CONDENSED IUPAC CARBOHYDRATE SYMBOL" | "IUPAC CARBOHYDRATE SYMBOL" | "SNFG CARBOHYDRATE SYMBOL">;
-        program: import("../../mol-data/db/column").Column.Schema.Str;
-        program_version: import("../../mol-data/db/column").Column.Schema.Str;
+        comp_id: import("../../mol-data/db").Column.Schema.Str;
+        identifier: import("../../mol-data/db").Column.Schema.Str;
+        type: import("../../mol-data/db").Column.Schema.Aliased<"COMMON NAME" | "SYSTEMATIC NAME" | "CAS REGISTRY NUMBER" | "PUBCHEM Identifier" | "MDL Identifier" | "SYNONYM" | "CONDENSED IUPAC CARB SYMBOL" | "IUPAC CARB SYMBOL" | "SNFG CARB SYMBOL" | "CONDENSED IUPAC CARBOHYDRATE SYMBOL" | "IUPAC CARBOHYDRATE SYMBOL" | "SNFG CARBOHYDRATE SYMBOL">;
+        program: import("../../mol-data/db").Column.Schema.Str;
+        program_version: import("../../mol-data/db").Column.Schema.Str;
     };
 }>>;
 export declare function readPVCD(): Promise<import("../../mol-data/db").DatabaseCollection<{
     chem_comp: {
-        formula: import("../../mol-data/db/column").Column.Schema.Str;
-        formula_weight: import("../../mol-data/db/column").Column.Schema.Float;
-        id: import("../../mol-data/db/column").Column.Schema.Str;
-        mon_nstd_parent_comp_id: import("../../mol-data/db/column").Column.Schema.List<string>;
-        name: import("../../mol-data/db/column").Column.Schema.Str;
-        one_letter_code: import("../../mol-data/db/column").Column.Schema.Str;
-        three_letter_code: import("../../mol-data/db/column").Column.Schema.Str;
-        type: import("../../mol-data/db/column").Column.Schema.Aliased<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking">;
-        pdbx_synonyms: import("../../mol-data/db/column").Column.Schema.List<string>;
-        pdbx_type: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_ambiguous_flag: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_replaced_by: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_replaces: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_formal_charge: import("../../mol-data/db/column").Column.Schema.Int;
-        pdbx_model_coordinates_details: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_model_coordinates_db_code: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_ideal_coordinates_details: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_ideal_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
-        pdbx_model_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
-        pdbx_initial_date: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_modified_date: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_release_status: import("../../mol-data/db/column").Column.Schema.Aliased<"REL" | "HOLD" | "HPUB" | "OBS" | "DEL" | "REF_ONLY">;
-        pdbx_processing_site: import("../../mol-data/db/column").Column.Schema.Aliased<"RCSB" | "PDBE" | "PDBJ" | "PDBC" | "EBI">;
+        formula: import("../../mol-data/db").Column.Schema.Str;
+        formula_weight: import("../../mol-data/db").Column.Schema.Float;
+        id: import("../../mol-data/db").Column.Schema.Str;
+        mon_nstd_parent_comp_id: import("../../mol-data/db").Column.Schema.List<string>;
+        name: import("../../mol-data/db").Column.Schema.Str;
+        one_letter_code: import("../../mol-data/db").Column.Schema.Str;
+        three_letter_code: import("../../mol-data/db").Column.Schema.Str;
+        type: import("../../mol-data/db").Column.Schema.Aliased<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking">;
+        pdbx_synonyms: import("../../mol-data/db").Column.Schema.List<string>;
+        pdbx_type: import("../../mol-data/db").Column.Schema.Str;
+        pdbx_ambiguous_flag: import("../../mol-data/db").Column.Schema.Str;
+        pdbx_replaced_by: import("../../mol-data/db").Column.Schema.Str;
+        pdbx_replaces: import("../../mol-data/db").Column.Schema.Str;
+        pdbx_formal_charge: import("../../mol-data/db").Column.Schema.Int;
+        pdbx_model_coordinates_details: import("../../mol-data/db").Column.Schema.Str;
+        pdbx_model_coordinates_db_code: import("../../mol-data/db").Column.Schema.Str;
+        pdbx_ideal_coordinates_details: import("../../mol-data/db").Column.Schema.Str;
+        pdbx_ideal_coordinates_missing_flag: import("../../mol-data/db").Column.Schema.Aliased<"y" | "n">;
+        pdbx_model_coordinates_missing_flag: import("../../mol-data/db").Column.Schema.Aliased<"y" | "n">;
+        pdbx_initial_date: import("../../mol-data/db").Column.Schema.Str;
+        pdbx_modified_date: import("../../mol-data/db").Column.Schema.Str;
+        pdbx_release_status: import("../../mol-data/db").Column.Schema.Aliased<"REL" | "HOLD" | "HPUB" | "OBS" | "DEL" | "REF_ONLY">;
+        pdbx_processing_site: import("../../mol-data/db").Column.Schema.Aliased<"RCSB" | "PDBE" | "PDBJ" | "PDBC" | "EBI">;
     };
     chem_comp_atom: {
-        alt_atom_id: import("../../mol-data/db/column").Column.Schema.Str;
-        atom_id: import("../../mol-data/db/column").Column.Schema.Str;
-        charge: import("../../mol-data/db/column").Column.Schema.Int;
-        model_Cartn_x: import("../../mol-data/db/column").Column.Schema.Coordinate;
-        model_Cartn_y: import("../../mol-data/db/column").Column.Schema.Coordinate;
-        model_Cartn_z: import("../../mol-data/db/column").Column.Schema.Coordinate;
-        comp_id: import("../../mol-data/db/column").Column.Schema.Str;
-        type_symbol: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_align: import("../../mol-data/db/column").Column.Schema.Int;
-        pdbx_ordinal: import("../../mol-data/db/column").Column.Schema.Int;
-        pdbx_model_Cartn_x_ideal: import("../../mol-data/db/column").Column.Schema.Coordinate;
-        pdbx_model_Cartn_y_ideal: import("../../mol-data/db/column").Column.Schema.Coordinate;
-        pdbx_model_Cartn_z_ideal: import("../../mol-data/db/column").Column.Schema.Coordinate;
-        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"s" | "r" | "n">;
-        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
-        pdbx_leaving_atom_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
+        alt_atom_id: import("../../mol-data/db").Column.Schema.Str;
+        atom_id: import("../../mol-data/db").Column.Schema.Str;
+        charge: import("../../mol-data/db").Column.Schema.Int;
+        model_Cartn_x: import("../../mol-data/db").Column.Schema.Coordinate;
+        model_Cartn_y: import("../../mol-data/db").Column.Schema.Coordinate;
+        model_Cartn_z: import("../../mol-data/db").Column.Schema.Coordinate;
+        comp_id: import("../../mol-data/db").Column.Schema.Str;
+        type_symbol: import("../../mol-data/db").Column.Schema.Str;
+        pdbx_align: import("../../mol-data/db").Column.Schema.Int;
+        pdbx_ordinal: import("../../mol-data/db").Column.Schema.Int;
+        pdbx_model_Cartn_x_ideal: import("../../mol-data/db").Column.Schema.Coordinate;
+        pdbx_model_Cartn_y_ideal: import("../../mol-data/db").Column.Schema.Coordinate;
+        pdbx_model_Cartn_z_ideal: import("../../mol-data/db").Column.Schema.Coordinate;
+        pdbx_stereo_config: import("../../mol-data/db").Column.Schema.Aliased<"s" | "r" | "n">;
+        pdbx_aromatic_flag: import("../../mol-data/db").Column.Schema.Aliased<"y" | "n">;
+        pdbx_leaving_atom_flag: import("../../mol-data/db").Column.Schema.Aliased<"y" | "n">;
     };
     chem_comp_bond: {
-        atom_id_1: import("../../mol-data/db/column").Column.Schema.Str;
-        atom_id_2: import("../../mol-data/db/column").Column.Schema.Str;
-        comp_id: import("../../mol-data/db/column").Column.Schema.Str;
-        value_order: import("../../mol-data/db/column").Column.Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
-        pdbx_ordinal: import("../../mol-data/db/column").Column.Schema.Int;
-        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"z" | "n" | "e">;
-        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
+        atom_id_1: import("../../mol-data/db").Column.Schema.Str;
+        atom_id_2: import("../../mol-data/db").Column.Schema.Str;
+        comp_id: import("../../mol-data/db").Column.Schema.Str;
+        value_order: import("../../mol-data/db").Column.Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
+        pdbx_ordinal: import("../../mol-data/db").Column.Schema.Int;
+        pdbx_stereo_config: import("../../mol-data/db").Column.Schema.Aliased<"z" | "n" | "e">;
+        pdbx_aromatic_flag: import("../../mol-data/db").Column.Schema.Aliased<"y" | "n">;
     };
     pdbx_chem_comp_descriptor: {
-        comp_id: import("../../mol-data/db/column").Column.Schema.Str;
-        descriptor: import("../../mol-data/db/column").Column.Schema.Str;
-        type: import("../../mol-data/db/column").Column.Schema.Aliased<"smiles_cannonical" | "smiles_canonical" | "smiles" | "inchi" | "inchi_main" | "inchi_main_formula" | "inchi_main_connect" | "inchi_main_hatom" | "inchi_charge" | "inchi_stereo" | "inchi_isotope" | "inchi_fixedh" | "inchi_reconnect" | "inchikey">;
-        program: import("../../mol-data/db/column").Column.Schema.Str;
-        program_version: import("../../mol-data/db/column").Column.Schema.Str;
+        comp_id: import("../../mol-data/db").Column.Schema.Str;
+        descriptor: import("../../mol-data/db").Column.Schema.Str;
+        type: import("../../mol-data/db").Column.Schema.Aliased<"smiles_cannonical" | "smiles_canonical" | "smiles" | "inchi" | "inchi_main" | "inchi_main_formula" | "inchi_main_connect" | "inchi_main_hatom" | "inchi_charge" | "inchi_stereo" | "inchi_isotope" | "inchi_fixedh" | "inchi_reconnect" | "inchikey">;
+        program: import("../../mol-data/db").Column.Schema.Str;
+        program_version: import("../../mol-data/db").Column.Schema.Str;
     };
     pdbx_chem_comp_identifier: {
-        comp_id: import("../../mol-data/db/column").Column.Schema.Str;
-        identifier: import("../../mol-data/db/column").Column.Schema.Str;
-        type: import("../../mol-data/db/column").Column.Schema.Aliased<"COMMON NAME" | "SYSTEMATIC NAME" | "CAS REGISTRY NUMBER" | "PUBCHEM Identifier" | "MDL Identifier" | "SYNONYM" | "CONDENSED IUPAC CARB SYMBOL" | "IUPAC CARB SYMBOL" | "SNFG CARB SYMBOL" | "CONDENSED IUPAC CARBOHYDRATE SYMBOL" | "IUPAC CARBOHYDRATE SYMBOL" | "SNFG CARBOHYDRATE SYMBOL">;
-        program: import("../../mol-data/db/column").Column.Schema.Str;
-        program_version: import("../../mol-data/db/column").Column.Schema.Str;
+        comp_id: import("../../mol-data/db").Column.Schema.Str;
+        identifier: import("../../mol-data/db").Column.Schema.Str;
+        type: import("../../mol-data/db").Column.Schema.Aliased<"COMMON NAME" | "SYSTEMATIC NAME" | "CAS REGISTRY NUMBER" | "PUBCHEM Identifier" | "MDL Identifier" | "SYNONYM" | "CONDENSED IUPAC CARB SYMBOL" | "IUPAC CARB SYMBOL" | "SNFG CARB SYMBOL" | "CONDENSED IUPAC CARBOHYDRATE SYMBOL" | "IUPAC CARBOHYDRATE SYMBOL" | "SNFG CARBOHYDRATE SYMBOL">;
+        program: import("../../mol-data/db").Column.Schema.Str;
+        program_version: import("../../mol-data/db").Column.Schema.Str;
     };
 }>>;
 export declare function getEncodedCif(name: string, database: Database<Database.Schema>, binary?: boolean): string | Uint8Array;

package/lib/cli/cifschema/util/cif-dic.js

@@ -37,6 +37,7 @@ export function getFieldType(type, description, values, container) {
         case 'pdbx_related_db_id':
         case 'sequence_dep':
         case 'pdb_id':
+        case 'pdb_id_u': // should be case insensitve, but can't express that
         case 'emd_id':
         // todo, consider adding specialised fields
         case 'yyyy-mm-dd':

package/lib/cli/cifschema/util/generate.js

@@ -6,21 +6,21 @@
 import { indentString } from '../../../mol-util/string';
 import { FieldPath } from '../../../mol-io/reader/cif/schema';
 function header(name, info, moldataImportPath) {
-    return `/**
- * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Code-generated '${name}' schema file. ${info}
- *
- * @author molstar/ciftools package
- */
-
-import { Database, Column } from '${moldataImportPath}/db';
-
+    return `/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated '${name}' schema file. ${info}
+ *
+ * @author molstar/ciftools package
+ */
+
+import { Database, Column } from '${moldataImportPath}/db';
+
 import Schema = Column.Schema;`;
 }
 function footer(name) {
-    return `
-export type ${name}_Schema = typeof ${name}_Schema;
+    return `
+export type ${name}_Schema = typeof ${name}_Schema;
 export interface ${name}_Database extends Database<${name}_Schema> {};`;
 }
 function getTypeShorthands(schema, fields) {

package/lib/cli/lipid-params/index.js

@@ -41,15 +41,15 @@ async function run(out) {
     }
     const lipidNames = JSON.stringify(lipids.array);
     if (out) {
-        const output = `/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Code-generated lipid params file. Names extracted from Martini FF lipids itp.
- *
- * @author molstar/lipid-params cli
- */
-
-export const LipidNames = new Set(${lipidNames.replace(/"/g, "'").replace(/,/g, ', ')});
+        const output = `/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated lipid params file. Names extracted from Martini FF lipids itp.
+ *
+ * @author molstar/lipid-params cli
+ */
+
+export const LipidNames = new Set(${lipidNames.replace(/"/g, "'").replace(/,/g, ', ')});
 `;
         fs.writeFileSync(out, output);
     }

package/lib/cli/mvs/mvs-print-schema.d.ts

@@ -1,3 +1,4 @@
+#!/usr/bin/env node
 /**
  * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *

package/lib/cli/mvs/mvs-print-schema.js

@@ -1,3 +1,4 @@
+#!/usr/bin/env node
 /**
  * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *

package/lib/cli/mvs/mvs-render.d.ts

@@ -1,3 +1,4 @@
+#!/usr/bin/env node
 /**
  * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *

package/lib/cli/mvs/mvs-render.js

@@ -1,3 +1,4 @@
+#!/usr/bin/env node
 /**
  * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *

package/lib/cli/mvs/mvs-validate.d.ts

@@ -1,3 +1,4 @@
+#!/usr/bin/env node
 /**
  * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *

package/lib/cli/mvs/mvs-validate.js

@@ -1,3 +1,4 @@
+#!/usr/bin/env node
 /**
  * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *

package/lib/commonjs/apps/docking-viewer/viewport.d.ts

@@ -24,12 +24,12 @@ export declare const StructurePreset: StructureRepresentationPresetProvider<{
     representations?: undefined;
 } | {
     components: {
-        ligand: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
-        polymer: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+        ligand: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../mol-state").StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>> | undefined;
+        polymer: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../mol-state").StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>> | undefined;
     };
     representations: {
-        ligand: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
-        polymer: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
+        ligand: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../mol-state").StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>>;
+        polymer: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../mol-state").StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>>;
     };
 }>;
 export declare const IllustrativePreset: StructureRepresentationPresetProvider<{
@@ -50,12 +50,12 @@ export declare const IllustrativePreset: StructureRepresentationPresetProvider<{
     representations?: undefined;
 } | {
     components: {
-        ligand: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
-        polymer: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+        ligand: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../mol-state").StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>> | undefined;
+        polymer: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../mol-state").StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>> | undefined;
     };
     representations: {
-        ligand: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
-        polymer: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
+        ligand: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../mol-state").StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>>;
+        polymer: import("../../mol-state").StateObjectSelector<import("../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../mol-state").StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>>;
     };
 }>;
 export declare const ShowButtons: import("../../mol-plugin/config").PluginConfigItem<boolean>;

package/lib/commonjs/apps/mesoscale-explorer/behavior/camera.d.ts

@@ -6,7 +6,7 @@
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { PluginBehavior } from '../../../mol-plugin/behavior';
 import { Binding } from '../../../mol-util/binding';
-export declare const MesoFocusLoci: import("../../../mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, PD.Values<{
+export declare const MesoFocusLoci: import("../../../mol-state").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, PD.Values<{
     minRadius: PD.Numeric;
     extraRadius: PD.Numeric;
     durationMs: PD.Numeric;

package/lib/commonjs/apps/mesoscale-explorer/behavior/select.d.ts

@@ -6,7 +6,7 @@
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { PluginBehavior } from '../../../mol-plugin/behavior';
 import { Binding } from '../../../mol-util/binding';
-export declare const MesoSelectLoci: import("../../../mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, PD.Values<{
+export declare const MesoSelectLoci: import("../../../mol-state").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, PD.Values<{
     bindings: PD.Value<{
         clickToggleSelect: Binding;
         hoverHighlightOnly: Binding;

package/lib/commonjs/apps/mesoscale-explorer/data/cellpack/model.d.ts

@@ -9,12 +9,12 @@ import { PluginStateObject as PSO } from '../../../../mol-plugin-state/objects';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
 export { CellpackAssembly };
 type CellpackAssembly = typeof CellpackAssembly;
-declare const CellpackAssembly: import("../../../../mol-state/transformer").StateTransformer<PSO.Molecule.Model, PSO.Molecule.Structure, PD.Normalize<{
+declare const CellpackAssembly: import("../../../../mol-state").StateTransformer<PSO.Molecule.Model, PSO.Molecule.Structure, PD.Normalize<{
     id: string;
 }>>;
 export { CellpackStructure };
 type CellpackStructure = typeof CellpackStructure;
-declare const CellpackStructure: import("../../../../mol-state/transformer").StateTransformer<PSO.Root, PSO.Molecule.Structure, PD.Normalize<{
+declare const CellpackStructure: import("../../../../mol-state").StateTransformer<PSO.Root, PSO.Molecule.Structure, PD.Normalize<{
     structureRef: string;
     entityId: string;
 }>>;

package/lib/commonjs/apps/mesoscale-explorer/data/cellpack/preset.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Ludovic Autin <ludovic.autin@gmail.com>

package/lib/commonjs/apps/mesoscale-explorer/data/cellpack/preset.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2019-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Ludovic Autin <ludovic.autin@gmail.com>
@@ -86,11 +86,11 @@ async function createCellpackHierarchy(plugin, trajectory) {
         .commit();
     const compRoot = await state.build()
         .toRoot()
-        .applyOrUpdateTagged('group:comp:', state_1.MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `comp:`, label: 'compartment', color: { type: 'custom', value: names_1.ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1 } }, { tags: 'group:comp:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
+        .applyOrUpdateTagged('group:comp:', state_1.MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `comp:`, label: 'compartment', color: { type: 'custom', value: names_1.ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'group:comp:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
         .commit();
     const funcRoot = await state.build()
         .toRoot()
-        .applyOrUpdateTagged('group:func:', state_1.MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `func:`, label: 'function', color: { type: 'custom', value: names_1.ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1 } }, { tags: 'group:func:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
+        .applyOrUpdateTagged('group:func:', state_1.MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `func:`, label: 'function', color: { type: 'custom', value: names_1.ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'group:func:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
         .commit();
     if (entities._rowCount > 1) {
         for (let i = 0; i < entities._rowCount; i++) {
@@ -140,7 +140,7 @@ async function createCellpackHierarchy(plugin, trajectory) {
                     parent.cell.state.isCollapsed = false;
                     const group = await state.build()
                         .to(parent)
-                        .applyOrUpdateTagged(`group:comp:${n}`, state_1.MesoscaleGroup, { ...groupParams, root: parent === compRoot, index: colorIdx, tag: `comp:${n}`, label, color: { type: 'generate', value: color, variability: 20, shift: 0, lightness: 0, alpha: 1 } }, { tags: `comp:${p}`, state: { isCollapsed: true, isHidden: groupParams.hidden } })
+                        .applyOrUpdateTagged(`group:comp:${n}`, state_1.MesoscaleGroup, { ...groupParams, root: parent === compRoot, index: colorIdx, tag: `comp:${n}`, label, color: { type: 'generate', value: color, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `comp:${p}`, state: { isCollapsed: true, isHidden: groupParams.hidden } })
                         .commit({ revertOnError: true });
                     compGroups.set(n, group);
                 }
@@ -151,7 +151,7 @@ async function createCellpackHierarchy(plugin, trajectory) {
                 const color = colorIdx !== undefined ? baseFuncColors[colorIdx] : names_1.ColorNames.white;
                 const group = await state.build()
                     .to(funcRoot)
-                    .applyOrUpdateTagged(`group:func:${f}`, state_1.MesoscaleGroup, { ...groupParams, index: colorIdx, tag: `func:${f}`, label: f, color: { type: 'custom', value: color, variability: 20, shift: 0, lightness: 0, alpha: 1 } }, { tags: 'func:', state: { isCollapsed: true, isHidden: groupParams.hidden } })
+                    .applyOrUpdateTagged(`group:func:${f}`, state_1.MesoscaleGroup, { ...groupParams, index: colorIdx, tag: `func:${f}`, label: f, color: { type: 'custom', value: color, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'func:', state: { isCollapsed: true, isHidden: groupParams.hidden } })
                     .commit({ revertOnError: true });
                 funcGroups.set(f, group);
             }

package/lib/commonjs/apps/mesoscale-explorer/data/generic/preset.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/commonjs/apps/mesoscale-explorer/data/generic/preset.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -118,7 +118,7 @@ async function createGenericHierarchy(plugin, file) {
     async function addGroup(g, cell, parent) {
         const group = await state.build()
             .to(cell)
-            .apply(state_1.MesoscaleGroup, { ...groupParams, index: undefined, tag: `${g.root}:${g.id}`, label: g.label || g.id, color: { type: 'custom', value: names_1.ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1 } }, { tags: [`group:${g.root}:${g.id}`, g.root === parent ? `${g.root}:` : `${g.root}:${parent}`], state: { isCollapsed: true, isHidden: groupParams.hidden } })
+            .apply(state_1.MesoscaleGroup, { ...groupParams, index: undefined, tag: `${g.root}:${g.id}`, label: g.label || g.id, color: { type: 'custom', value: names_1.ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: [`group:${g.root}:${g.id}`, g.root === parent ? `${g.root}:` : `${g.root}:${parent}`], state: { isCollapsed: true, isHidden: groupParams.hidden } })
             .commit();
         if (g.children) {
             for (const c of g.children) {
@@ -129,7 +129,7 @@ async function createGenericHierarchy(plugin, file) {
     for (const r of manifest.roots) {
         const root = await state.build()
             .toRoot()
-            .apply(state_1.MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `${r.id}:`, label: r.label || r.id, color: { type: 'custom', value: names_1.ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1 } }, { tags: `group:${r.id}:`, state: { isCollapsed: false, isHidden: groupParams.hidden } })
+            .apply(state_1.MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `${r.id}:`, label: r.label || r.id, color: { type: 'custom', value: names_1.ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `group:${r.id}:`, state: { isCollapsed: false, isHidden: groupParams.hidden } })
             .commit();
         if (r.children) {
             for (const c of r.children) {

package/lib/commonjs/apps/mesoscale-explorer/data/mmcif/preset.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/commonjs/apps/mesoscale-explorer/data/mmcif/preset.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -103,7 +103,7 @@ async function createMmcifHierarchy(plugin, trajectory) {
     const clipVariant = willBeMerged ? 'pixel' : 'instance';
     const entRoot = await state.build()
         .toRoot()
-        .applyOrUpdateTagged('group:ent:', state_1.MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `ent:`, label: 'entity', color: { type: 'custom', value: names_1.ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1 } }, { tags: 'group:ent:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
+        .applyOrUpdateTagged('group:ent:', state_1.MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `ent:`, label: 'entity', color: { type: 'custom', value: names_1.ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'group:ent:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
         .commit();
     const getEntityType = (i) => {
         if (entities.type.value(i) === 'water')
@@ -133,7 +133,7 @@ async function createMmcifHierarchy(plugin, trajectory) {
             const color = colorIdx !== undefined ? baseEntColors[colorIdx] : names_1.ColorNames.white;
             const group = await state.build()
                 .to(entRoot)
-                .applyOrUpdateTagged(`group:ent:${t}`, state_1.MesoscaleGroup, { ...groupParams, index: colorIdx, tag: `ent:${t}`, label: t, color: { type: 'generate', value: color, variability: 20, shift: 0, lightness: 0, alpha: 1 } }, { tags: `ent:`, state: { isCollapsed: true, isHidden: groupParams.hidden } })
+                .applyOrUpdateTagged(`group:ent:${t}`, state_1.MesoscaleGroup, { ...groupParams, index: colorIdx, tag: `ent:${t}`, label: t, color: { type: 'generate', value: color, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `ent:`, state: { isCollapsed: true, isHidden: groupParams.hidden } })
                 .commit({ revertOnError: true });
             entGroups.set(t, group);
         }