molstar 3.4.0 → 3.6.1

package/lib/mol-io/reader/cif/schema/mmcif.d.ts

@@ -1,7 +1,7 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.356, IHM 1.17, MA 1.3.5.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.357, IHM 1.17, MA 1.3.6.
  *
  * @author molstar/ciftools package
  */
@@ -511,7 +511,7 @@ export declare const mmCIF_Schema: {
          * linking monomers, monomers with some type of N-terminal (or 5')
          * cap and monomers with some type of C-terminal (or 3') cap.
          */
-        type: 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">;
+        type: 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">;
         /**
          * Synonym list for the component.
          */
@@ -556,11 +556,11 @@ export declare const mmCIF_Schema: {
         /**
          * Stereochemical configuration across a double bond.
          */
-        pdbx_stereo_config: Schema.Aliased<"N" | "E" | "Z">;
+        pdbx_stereo_config: Schema.Aliased<"z" | "n" | "e">;
         /**
          * A flag indicating an aromatic bond.
          */
-        pdbx_aromatic_flag: Schema.Aliased<"N" | "Y">;
+        pdbx_aromatic_flag: Schema.Aliased<"y" | "n">;
     };
     /**
      * Data items in the CITATION category record details about the
@@ -692,7 +692,7 @@ export declare const mmCIF_Schema: {
         /**
          * An abbreviation that identifies the database.
          */
-        database_id: Schema.Aliased<"AlphaFoldDB" | "CAS" | "CSD" | "EMDB" | "ICSD" | "ModelArchive" | "MDF" | "MODBASE" | "NDB" | "NBS" | "PDB" | "PDF" | "RCSB" | "SWISS-MODEL_REPOSITORY" | "EBI" | "PDBE" | "BMRB" | "WWPDB" | "PDB_ACC">;
+        database_id: Schema.Aliased<"alphafolddb" | "cas" | "csd" | "emdb" | "icsd" | "modelarchive" | "mdf" | "modbase" | "ndb" | "nbs" | "pdb" | "pdf" | "rcsb" | "swiss-model_repository" | "ebi" | "pdbe" | "bmrb" | "wwpdb" | "pdb_acc">;
         /**
          * The code assigned by the database identified in
          * _database_2.database_id.
@@ -882,6 +882,10 @@ export declare const mmCIF_Schema: {
          * parent is not specified. Deoxynucleotides are
          * represented by their canonical one-letter codes of A,
          * C, G, or T.
+         *
+         * For modifications with several parent amino acids,
+         * all corresponding parent amino acid codes will be listed
+         * (ex. chromophores).
          */
         pdbx_seq_one_letter_code_can: Schema.Str;
         /**
@@ -1107,7 +1111,7 @@ export declare const mmCIF_Schema: {
          * This data item is a pointer to _struct_conf_type.id in the
          * STRUCT_CONF_TYPE category.
          */
-        conf_type_id: Schema.Aliased<"BEND" | "HELX_P" | "HELX_OT_P" | "HELX_RH_P" | "HELX_RH_OT_P" | "HELX_RH_AL_P" | "HELX_RH_GA_P" | "HELX_RH_OM_P" | "HELX_RH_PI_P" | "HELX_RH_27_P" | "HELX_RH_3T_P" | "HELX_RH_PP_P" | "HELX_LH_P" | "HELX_LH_OT_P" | "HELX_LH_AL_P" | "HELX_LH_GA_P" | "HELX_LH_OM_P" | "HELX_LH_PI_P" | "HELX_LH_27_P" | "HELX_LH_3T_P" | "HELX_LH_PP_P" | "HELX_N" | "HELX_OT_N" | "HELX_RH_N" | "HELX_RH_OT_N" | "HELX_RH_A_N" | "HELX_RH_B_N" | "HELX_RH_Z_N" | "HELX_LH_N" | "HELX_LH_OT_N" | "HELX_LH_A_N" | "HELX_LH_B_N" | "HELX_LH_Z_N" | "TURN_P" | "TURN_OT_P" | "TURN_TY1_P" | "TURN_TY1P_P" | "TURN_TY2_P" | "TURN_TY2P_P" | "TURN_TY3_P" | "TURN_TY3P_P" | "STRN" | "OTHER">;
+        conf_type_id: Schema.Aliased<"other" | "bend" | "helx_p" | "helx_ot_p" | "helx_rh_p" | "helx_rh_ot_p" | "helx_rh_al_p" | "helx_rh_ga_p" | "helx_rh_om_p" | "helx_rh_pi_p" | "helx_rh_27_p" | "helx_rh_3t_p" | "helx_rh_pp_p" | "helx_lh_p" | "helx_lh_ot_p" | "helx_lh_al_p" | "helx_lh_ga_p" | "helx_lh_om_p" | "helx_lh_pi_p" | "helx_lh_27_p" | "helx_lh_3t_p" | "helx_lh_pp_p" | "helx_n" | "helx_ot_n" | "helx_rh_n" | "helx_rh_ot_n" | "helx_rh_a_n" | "helx_rh_b_n" | "helx_rh_z_n" | "helx_lh_n" | "helx_lh_ot_n" | "helx_lh_a_n" | "helx_lh_b_n" | "helx_lh_z_n" | "turn_p" | "turn_ot_p" | "turn_ty1_p" | "turn_ty1p_p" | "turn_ty2_p" | "turn_ty2p_p" | "turn_ty3_p" | "turn_ty3p_p" | "strn">;
         /**
          * A description of special aspects of the conformation assignment.
          */
@@ -1856,11 +1860,11 @@ export declare const mmCIF_Schema: {
          * This code indicates whether the entry belongs to
          * Structural Genomics Project.
          */
-        SG_entry: Schema.Aliased<"N" | "Y">;
+        SG_entry: Schema.Aliased<"y" | "n">;
         /**
          * The site where the file was deposited.
          */
-        deposit_site: Schema.Aliased<"NDB" | "RCSB" | "PDBE" | "BMRB" | "PDBJ" | "BNL" | "PDBC">;
+        deposit_site: Schema.Aliased<"NDB" | "RCSB" | "PDBE" | "PDBJ" | "BMRB" | "BNL" | "PDBC">;
         /**
          * The site where the file was deposited.
          */
@@ -1880,7 +1884,7 @@ export declare const mmCIF_Schema: {
          * A value of 'N' indicates that the no PDB format data file is
          * corresponding to this entry is available in the PDB archive.
          */
-        pdb_format_compatible: Schema.Aliased<"N" | "Y">;
+        pdb_format_compatible: Schema.Aliased<"y" | "n">;
     };
     /**
      * The PDBX_NONPOLY_SCHEME category provides residue level nomenclature
@@ -1985,7 +1989,7 @@ export declare const mmCIF_Schema: {
         /**
          * The provenance of this synonym.
          */
-        provenance: Schema.Aliased<"PDB" | "AUTHOR" | "DRUGBANK" | "CHEBI" | "CHEMBL" | "PUBCHEM">;
+        provenance: Schema.Aliased<"AUTHOR" | "DRUGBANK" | "CHEBI" | "CHEMBL" | "PDB" | "PUBCHEM">;
     };
     /**
      * Data items in the CHEM_COMP_IDENTIFIER category provide
@@ -2033,7 +2037,7 @@ export declare const mmCIF_Schema: {
          * The value of polymer flag indicates whether the unobserved or
          * zero occupancy residue is part of a polymer chain or not
          */
-        polymer_flag: Schema.Aliased<"N" | "Y">;
+        polymer_flag: Schema.Aliased<"y" | "n">;
         /**
          * The value of occupancy flag indicates whether the residue
          * is unobserved (= 1) or the coordinates have an occupancy of zero (=0)
@@ -2502,11 +2506,11 @@ export declare const mmCIF_Schema: {
         /**
          * Broadly defines the function of the molecule.
          */
-        class: Schema.Aliased<"Antagonist" | "Antibiotic" | "Anticancer" | "Anticoagulant" | "Antifungal" | "Antigen" | "Antiinflammatory" | "Antimicrobial" | "Antineoplastic" | "Antiparasitic" | "Antiretroviral" | "Anthelmintic" | "Antithrombotic" | "Antitumor" | "Antiviral" | "CASPASE inhibitor" | "Chaperone binding" | "Enzyme inhibitor" | "Drug delivery" | "Glycan component" | "Growth factor" | "Immunosuppressant" | "Inducer" | "Inhibitor" | "Lantibiotic" | "Metabolism" | "Metal transport" | "Nutrient" | "Oxidation-reduction" | "Protein binding" | "Receptor" | "Substrate analog" | "Synthetic opioid" | "Thrombin inhibitor" | "Transition state mimetic" | "Transport activator" | "Trypsin inhibitor" | "Toxin" | "Unknown" | "Water retention" | "Anticoagulant, Antithrombotic" | "Antibiotic, Antimicrobial" | "Antibiotic, Anthelmintic" | "Antibiotic, Antineoplastic" | "Antimicrobial, Antiretroviral" | "Antimicrobial, Antitumor" | "Antimicrobial, Antiparasitic, Antibiotic" | "Thrombin inhibitor, Trypsin inhibitor">;
+        class: Schema.Aliased<"unknown" | "antagonist" | "antibiotic" | "anticancer" | "anticoagulant" | "antifungal" | "antigen" | "antiinflammatory" | "antimicrobial" | "antineoplastic" | "antiparasitic" | "antiretroviral" | "anthelmintic" | "antithrombotic" | "antitumor" | "antiviral" | "caspase inhibitor" | "chaperone binding" | "enzyme inhibitor" | "drug delivery" | "glycan component" | "growth factor" | "immunosuppressant" | "inducer" | "inhibitor" | "lantibiotic" | "metabolism" | "metal transport" | "nutrient" | "oxidation-reduction" | "protein binding" | "receptor" | "substrate analog" | "synthetic opioid" | "thrombin inhibitor" | "transition state mimetic" | "transport activator" | "trypsin inhibitor" | "toxin" | "water retention" | "anticoagulant, antithrombotic" | "antibiotic, antimicrobial" | "antibiotic, anthelmintic" | "antibiotic, antineoplastic" | "antimicrobial, antiretroviral" | "antimicrobial, antitumor" | "antimicrobial, antiparasitic, antibiotic" | "thrombin inhibitor, trypsin inhibitor">;
         /**
          * Defines the structural classification of the molecule.
          */
-        type: Schema.Aliased<"Unknown" | "Amino acid" | "Aminoglycoside" | "Anthracycline" | "Anthraquinone" | "Ansamycin" | "Chalkophore" | "Chromophore" | "Glycopeptide" | "Cyclic depsipeptide" | "Cyclic lipopeptide" | "Cyclic peptide" | "Heterocyclic" | "Imino sugar" | "Keto acid" | "Lipoglycopeptide" | "Lipopeptide" | "Macrolide" | "Non-polymer" | "Nucleoside" | "Oligopeptide" | "Oligosaccharide" | "Peptaibol" | "Peptide-like" | "Polycyclic" | "Polypeptide" | "Polysaccharide" | "Quinolone" | "Thiolactone" | "Thiopeptide" | "Siderophore" | "Chalkophore, Polypeptide">;
+        type: Schema.Aliased<"unknown" | "non-polymer" | "peptide-like" | "macrolide" | "amino acid" | "aminoglycoside" | "anthracycline" | "anthraquinone" | "ansamycin" | "chalkophore" | "chromophore" | "glycopeptide" | "cyclic depsipeptide" | "cyclic lipopeptide" | "cyclic peptide" | "heterocyclic" | "imino sugar" | "keto acid" | "lipoglycopeptide" | "lipopeptide" | "nucleoside" | "oligopeptide" | "oligosaccharide" | "peptaibol" | "polycyclic" | "polypeptide" | "polysaccharide" | "quinolone" | "thiolactone" | "thiopeptide" | "siderophore" | "chalkophore, polypeptide">;
         /**
          * A name of the molecule.
          */
@@ -2653,7 +2657,7 @@ export declare const mmCIF_Schema: {
         /**
          * This data item contains the descriptor type.
          */
-        type: Schema.Aliased<"LINUCS" | "Glycam Condensed Sequence" | "Glycam Condensed Core Sequence" | "WURCS">;
+        type: Schema.Aliased<"linucs" | "glycam condensed sequence" | "glycam condensed core sequence" | "wurcs">;
         /**
          * This data item contains the name of the program
          * or library used to compute the descriptor.
@@ -2681,7 +2685,7 @@ export declare const mmCIF_Schema: {
         /**
          * A feature type associated with entity instance.
          */
-        feature_type: Schema.Aliased<"OTHER" | "SUBJECT OF INVESTIGATION" | "NO FUNCTIONAL ROLE">;
+        feature_type: Schema.Aliased<"SUBJECT OF INVESTIGATION" | "NO FUNCTIONAL ROLE" | "OTHER">;
         /**
          * Author instance identifier (formerly PDB Chain ID)
          */
@@ -2800,7 +2804,7 @@ export declare const mmCIF_Schema: {
         /**
          * The chiral configuration of the first atom making the linkage.
          */
-        atom_stereo_config_1: Schema.Aliased<"N" | "R" | "S">;
+        atom_stereo_config_1: Schema.Aliased<"s" | "r" | "n">;
         /**
          * The atom identifier/name for the second atom making the linkage.
          */
@@ -2812,7 +2816,7 @@ export declare const mmCIF_Schema: {
         /**
          * The chiral configuration of the second atom making the linkage.
          */
-        atom_stereo_config_2: Schema.Aliased<"N" | "R" | "S">;
+        atom_stereo_config_2: Schema.Aliased<"s" | "r" | "n">;
         /**
          * The bond order target for the chemical linkage.
          */
@@ -3320,15 +3324,15 @@ export declare const mmCIF_Schema: {
         /**
          * A flag to indicate if the modeling is multi scale.
          */
-        multi_scale_flag: Schema.Aliased<"YES" | "NO">;
+        multi_scale_flag: Schema.Aliased<"yes" | "no">;
         /**
          * A flag to indicate if the modeling is multi state.
          */
-        multi_state_flag: Schema.Aliased<"YES" | "NO">;
+        multi_state_flag: Schema.Aliased<"yes" | "no">;
         /**
          * A flag to indicate if the modeling involves an ensemble ordered by time or other order.
          */
-        ordered_flag: Schema.Aliased<"YES" | "NO">;
+        ordered_flag: Schema.Aliased<"yes" | "no">;
         /**
          * The file id corresponding to the script used in the modeling protocol step.
          * This data item is a pointer to _ihm_external_files.id in the IHM_EXTERNAL_FILES category.
@@ -3617,7 +3621,7 @@ export declare const mmCIF_Schema: {
          * A flag that indicates whether the dataset is archived in
          * an IHM related database or elsewhere.
          */
-        database_hosted: Schema.Aliased<"YES" | "NO">;
+        database_hosted: Schema.Aliased<"yes" | "no">;
     };
     /**
      * Category to define groups or collections of input datasets.
@@ -3694,7 +3698,7 @@ export declare const mmCIF_Schema: {
         /**
          * The name of the database containing the dataset entry.
          */
-        db_name: Schema.Aliased<"EMDB" | "PDB" | "BMRB" | "Other" | "PDB-Dev" | "EMPIAR" | "SASBDB" | "PRIDE" | "MODEL ARCHIVE" | "MASSIVE" | "BioGRID" | "ProXL">;
+        db_name: Schema.Aliased<"BMRB" | "PDB" | "Other" | "PDB-Dev" | "EMDB" | "EMPIAR" | "SASBDB" | "PRIDE" | "MODEL ARCHIVE" | "MASSIVE" | "BioGRID" | "ProXL">;
         /**
          * The accession code for the database entry.
          */
@@ -4224,7 +4228,7 @@ export declare const mmCIF_Schema: {
          * whether the whole image is used or only a portion of it is used (by masking
          * or by other means) as restraint in the modeling.
          */
-        image_segment_flag: Schema.Aliased<"YES" | "NO">;
+        image_segment_flag: Schema.Aliased<"yes" | "no">;
         /**
          * Number of 2D projections of the model used in the fitting.
          */
@@ -4377,7 +4381,7 @@ export declare const mmCIF_Schema: {
          * whether the whole SAS profile is used or only a portion of it is used
          * (by masking or by other means) as restraint in the modeling.
          */
-        profile_segment_flag: Schema.Aliased<"YES" | "NO">;
+        profile_segment_flag: Schema.Aliased<"yes" | "no">;
         /**
          * The type of atoms in the model fit to the SAS data.
          */
@@ -4971,7 +4975,7 @@ export declare const mmCIF_Schema: {
         /**
          * The type of QA metric.
          */
-        type: Schema.Aliased<"other" | "zscore" | "energy" | "distance" | "normalized score" | "pLDDT" | "PAE" | "contact probability">;
+        type: Schema.Aliased<"other" | "zscore" | "energy" | "distance" | "normalized score" | "pLDDT" | "pLDDT in [0,1]" | "pLDDT all-atom" | "pLDDT all-atom in [0,1]" | "PAE" | "pTM" | "ipTM" | "contact probability">;
         /**
          * The mode of calculation of the QA metric.
          */

package/lib/mol-io/reader/cif/schema/mmcif.js

@@ -1,7 +1,7 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.356, IHM 1.17, MA 1.3.5.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.357, IHM 1.17, MA 1.3.6.
  *
  * @author molstar/ciftools package
  */
@@ -14,6 +14,7 @@ var coord = Schema.coord;
 var Aliased = Schema.Aliased;
 var Matrix = Schema.Matrix;
 var Vector = Schema.Vector;
+var lstr = Schema.lstr;
 var List = Schema.List;
 export var mmCIF_Schema = {
     /**
@@ -508,7 +509,7 @@ export var mmCIF_Schema = {
          * _chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class and
          * _chem_comp.mon_nstd_details data items.
          */
-        mon_nstd_flag: Aliased(str),
+        mon_nstd_flag: Aliased(lstr),
         /**
          * The full name of the component.
          */
@@ -519,7 +520,7 @@ export var mmCIF_Schema = {
          * linking monomers, monomers with some type of N-terminal (or 5')
          * cap and monomers with some type of C-terminal (or 3') cap.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * Synonym list for the component.
          */
@@ -556,7 +557,7 @@ export var mmCIF_Schema = {
          * bond associated with the specified atoms, expressed as a bond
          * order.
          */
-        value_order: Aliased(str),
+        value_order: Aliased(lstr),
         /**
          * Ordinal index for the component bond list.
          */
@@ -564,11 +565,11 @@ export var mmCIF_Schema = {
         /**
          * Stereochemical configuration across a double bond.
          */
-        pdbx_stereo_config: Aliased(str),
+        pdbx_stereo_config: Aliased(lstr),
         /**
          * A flag indicating an aromatic bond.
          */
-        pdbx_aromatic_flag: Aliased(str),
+        pdbx_aromatic_flag: Aliased(lstr),
     },
     /**
      * Data items in the CITATION category record details about the
@@ -700,7 +701,7 @@ export var mmCIF_Schema = {
         /**
          * An abbreviation that identifies the database.
          */
-        database_id: Aliased(str),
+        database_id: Aliased(lstr),
         /**
          * The code assigned by the database identified in
          * _database_2.database_id.
@@ -763,7 +764,7 @@ export var mmCIF_Schema = {
          * manipulated sources are expected to have further information in
          * the ENTITY_SRC_GEN category.
          */
-        src_method: Aliased(str),
+        src_method: Aliased(lstr),
         /**
          * Defines the type of the entity.
          *
@@ -776,7 +777,7 @@ export var mmCIF_Schema = {
          * Water entities are not expected to have corresponding
          * entries in the ENTITY category.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * A description of the entity.
          *
@@ -816,12 +817,12 @@ export var mmCIF_Schema = {
          * one monomer-to-monomer link different from that implied by
          * _entity_poly.type.
          */
-        nstd_linkage: Aliased(str),
+        nstd_linkage: Aliased(lstr),
         /**
          * A flag to indicate whether the polymer contains at least
          * one monomer that is not considered standard.
          */
-        nstd_monomer: Aliased(str),
+        nstd_monomer: Aliased(lstr),
         /**
          * The type of the polymer.
          */
@@ -890,6 +891,10 @@ export var mmCIF_Schema = {
          * parent is not specified. Deoxynucleotides are
          * represented by their canonical one-letter codes of A,
          * C, G, or T.
+         *
+         * For modifications with several parent amino acids,
+         * all corresponding parent amino acid codes will be listed
+         * (ex. chromophores).
          */
         pdbx_seq_one_letter_code_can: str,
         /**
@@ -915,7 +920,7 @@ export var mmCIF_Schema = {
          * A flag to indicate whether this monomer in the polymer is
          * heterogeneous in sequence.
          */
-        hetero: Aliased(str),
+        hetero: Aliased(lstr),
         /**
          * This data item is a pointer to _chem_comp.id in the CHEM_COMP
          * category.
@@ -992,7 +997,7 @@ export var mmCIF_Schema = {
          * The classification of the software according to the most
          * common types.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * The version of the software.
          */
@@ -1115,7 +1120,7 @@ export var mmCIF_Schema = {
          * This data item is a pointer to _struct_conf_type.id in the
          * STRUCT_CONF_TYPE category.
          */
-        conf_type_id: Aliased(str),
+        conf_type_id: Aliased(lstr),
         /**
          * A description of special aspects of the conformation assignment.
          */
@@ -1215,7 +1220,7 @@ export var mmCIF_Schema = {
          * This data item is a pointer to _struct_conn_type.id in the
          * STRUCT_CONN_TYPE category.
          */
-        conn_type_id: Aliased(str),
+        conn_type_id: Aliased(lstr),
         /**
          * A description of special aspects of the connection.
          */
@@ -1435,7 +1440,7 @@ export var mmCIF_Schema = {
          * The chemical bond order associated with the specified atoms in
          * this contact.
          */
-        pdbx_value_order: Aliased(str),
+        pdbx_value_order: Aliased(lstr),
     },
     /**
      * Data items in the STRUCT_CONN_TYPE category record details
@@ -1450,7 +1455,7 @@ export var mmCIF_Schema = {
         /**
          * The chemical or structural type of the interaction.
          */
-        id: Aliased(str),
+        id: Aliased(lstr),
         /**
          * A reference that specifies the criteria used to define the
          * interaction.
@@ -1804,7 +1809,7 @@ export var mmCIF_Schema = {
         /**
          * The cell settings for this space-group symmetry.
          */
-        cell_setting: Aliased(str),
+        cell_setting: Aliased(lstr),
         /**
          * Space-group number from International Tables for Crystallography
          * Vol. A (2002).
@@ -1864,7 +1869,7 @@ export var mmCIF_Schema = {
          * This code indicates whether the entry belongs to
          * Structural Genomics Project.
          */
-        SG_entry: Aliased(str),
+        SG_entry: Aliased(lstr),
         /**
          * The site where the file was deposited.
          */
@@ -1888,7 +1893,7 @@ export var mmCIF_Schema = {
          * A value of 'N' indicates that the no PDB format data file is
          * corresponding to this entry is available in the PDB archive.
          */
-        pdb_format_compatible: Aliased(str),
+        pdb_format_compatible: Aliased(lstr),
     },
     /**
      * The PDBX_NONPOLY_SCHEME category provides residue level nomenclature
@@ -2041,7 +2046,7 @@ export var mmCIF_Schema = {
          * The value of polymer flag indicates whether the unobserved or
          * zero occupancy residue is part of a polymer chain or not
          */
-        polymer_flag: Aliased(str),
+        polymer_flag: Aliased(lstr),
         /**
          * The value of occupancy flag indicates whether the residue
          * is unobserved (= 1) or the coordinates have an occupancy of zero (=0)
@@ -2294,7 +2299,7 @@ export var mmCIF_Schema = {
         /**
          * Defines the polymer characteristic of the entity.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * Additional details about this entity.
          */
@@ -2389,7 +2394,7 @@ export var mmCIF_Schema = {
         /**
          * The bond order target for the chemical linkage.
          */
-        value_order: Aliased(str),
+        value_order: Aliased(lstr),
         /**
          * The entity component identifier for the first of two entities containing the linkage.
          */
@@ -2475,7 +2480,7 @@ export var mmCIF_Schema = {
         /**
          * The bond order target for the non-standard linkage.
          */
-        value_order: Aliased(str),
+        value_order: Aliased(lstr),
     },
     /**
      * Data items in the PDBX_MOLECULE category identify reference molecules
@@ -2510,11 +2515,11 @@ export var mmCIF_Schema = {
         /**
          * Broadly defines the function of the molecule.
          */
-        class: Aliased(str),
+        class: Aliased(lstr),
         /**
          * Defines the structural classification of the molecule.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * A name of the molecule.
          */
@@ -2661,7 +2666,7 @@ export var mmCIF_Schema = {
         /**
          * This data item contains the descriptor type.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * This data item contains the name of the program
          * or library used to compute the descriptor.
@@ -2736,7 +2741,7 @@ export var mmCIF_Schema = {
          * A flag to indicate whether this monomer in the entity is
          * heterogeneous in sequence.
          */
-        hetero: Aliased(str),
+        hetero: Aliased(lstr),
         /**
          * This data item is a pointer to _chem_comp.id in the CHEM_COMP
          * category.
@@ -2808,7 +2813,7 @@ export var mmCIF_Schema = {
         /**
          * The chiral configuration of the first atom making the linkage.
          */
-        atom_stereo_config_1: Aliased(str),
+        atom_stereo_config_1: Aliased(lstr),
         /**
          * The atom identifier/name for the second atom making the linkage.
          */
@@ -2820,11 +2825,11 @@ export var mmCIF_Schema = {
         /**
          * The chiral configuration of the second atom making the linkage.
          */
-        atom_stereo_config_2: Aliased(str),
+        atom_stereo_config_2: Aliased(lstr),
         /**
          * The bond order target for the chemical linkage.
          */
-        value_order: Aliased(str),
+        value_order: Aliased(lstr),
     },
     /**
      * Data items in the PDBX_ENTITY_BRANCH category specify the list
@@ -2855,7 +2860,7 @@ export var mmCIF_Schema = {
          * A flag to indicate whether this monomer in the entity is
          * heterogeneous in sequence.
          */
-        hetero: Aliased(str),
+        hetero: Aliased(lstr),
         /**
          * Pointer to _atom_site.label_asym_id.
          */
@@ -3328,15 +3333,15 @@ export var mmCIF_Schema = {
         /**
          * A flag to indicate if the modeling is multi scale.
          */
-        multi_scale_flag: Aliased(str),
+        multi_scale_flag: Aliased(lstr),
         /**
          * A flag to indicate if the modeling is multi state.
          */
-        multi_state_flag: Aliased(str),
+        multi_state_flag: Aliased(lstr),
         /**
          * A flag to indicate if the modeling involves an ensemble ordered by time or other order.
          */
-        ordered_flag: Aliased(str),
+        ordered_flag: Aliased(lstr),
         /**
          * The file id corresponding to the script used in the modeling protocol step.
          * This data item is a pointer to _ihm_external_files.id in the IHM_EXTERNAL_FILES category.
@@ -3625,7 +3630,7 @@ export var mmCIF_Schema = {
          * A flag that indicates whether the dataset is archived in
          * an IHM related database or elsewhere.
          */
-        database_hosted: Aliased(str),
+        database_hosted: Aliased(lstr),
     },
     /**
      * Category to define groups or collections of input datasets.
@@ -4232,7 +4237,7 @@ export var mmCIF_Schema = {
          * whether the whole image is used or only a portion of it is used (by masking
          * or by other means) as restraint in the modeling.
          */
-        image_segment_flag: Aliased(str),
+        image_segment_flag: Aliased(lstr),
         /**
          * Number of 2D projections of the model used in the fitting.
          */
@@ -4385,7 +4390,7 @@ export var mmCIF_Schema = {
          * whether the whole SAS profile is used or only a portion of it is used
          * (by masking or by other means) as restraint in the modeling.
          */
-        profile_segment_flag: Aliased(str),
+        profile_segment_flag: Aliased(lstr),
         /**
          * The type of atoms in the model fit to the SAS data.
          */

package/lib/mol-io/reader/cif/schema.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

package/lib/mol-io/reader/cif/schema.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -42,13 +42,33 @@ export function toTable(schema, category) {
 }
 function getColumnCtor(t) {
     switch (t.valueType) {
-        case 'str': return function (f, c, k) { return createColumn(t, f, f.str, f.toStringArray); };
+        case 'str': return function (f, c, k) { return createStringColumn(t, f, f.str, f.toStringArray); };
         case 'int': return function (f, c, k) { return createColumn(t, f, f.int, f.toIntArray); };
         case 'float': return function (f, c, k) { return createColumn(t, f, f.float, f.toFloatArray); };
         case 'list': throw new Error('Use createListColumn instead.');
         case 'tensor': throw new Error('Use createTensorColumn instead.');
     }
 }
+function createStringColumn(schema, field, value, toArray) {
+    return {
+        schema: schema,
+        __array: field.__array,
+        isDefined: field.isDefined,
+        rowCount: field.rowCount,
+        value: schema.transform === 'lowercase'
+            ? function (row) { return value(row).toLowerCase(); }
+            : schema.transform === 'uppercase'
+                ? function (row) { return value(row).toUpperCase(); }
+                : value,
+        valueKind: field.valueKind,
+        areValuesEqual: field.areValuesEqual,
+        toArray: schema.transform === 'lowercase'
+            ? function (p) { return Array.from(toArray(p)).map(function (x) { return x.toLowerCase(); }); }
+            : schema.transform === 'uppercase'
+                ? function (p) { return Array.from(toArray(p)).map(function (x) { return x.toUpperCase(); }); }
+                : toArray,
+    };
+}
 function createColumn(schema, field, value, toArray) {
     return {
         schema: schema,

package/lib/mol-io/writer/mol/encoder.js

@@ -48,7 +48,7 @@ var MolEncoder = /** @class */ (function (_super) {
             StringBuilder.writeSafe(ctab, '  0');
             StringBuilder.writeIntegerPadLeft(ctab, _this.mapCharge(charge), 3);
             StringBuilder.writeSafe(ctab, '  0  0  0  0  0  0  0  0  0  0\n');
-            if (stereo_config !== 'N')
+            if (stereo_config !== 'n')
                 chiral = true;
             // no data for metal ions
             if (!(bondMap === null || bondMap === void 0 ? void 0 : bondMap.map))

package/lib/mol-math/geometry/common.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -24,6 +24,7 @@ export declare type DensityData = {
     field: Tensor;
     idField: Tensor;
     resolution: number;
+    maxRadius: number;
 };
 export declare type DensityTextureData = {
     transform: Mat4;

package/lib/mol-math/geometry/common.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

package/lib/mol-math/geometry/gaussian-density/cpu.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */