molstar 2.3.9 → 3.0.0-dev.2

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.350, IHM 1.17, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
  *
  * @author molstar/ciftools package
  */
@@ -479,7 +479,7 @@ export declare const BIRD_Schema: {
         /**
          * An identifier for the wwPDB site creating or modifying the molecule.
          */
-        processing_site: Schema.Aliased<"PDBe" | "RCSB" | "BMRB" | "PDBJ" | "PDBC">;
+        processing_site: Schema.Aliased<"RCSB" | "PDBE" | "BMRB" | "PDBJ" | "PDBC">;
         /**
          * The action associated with this audit record.
          */

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

@@ -2,7 +2,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.350, IHM 1.17, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
  *
  * @author molstar/ciftools package
  */

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.350, IHM 1.17, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
  *
  * @author molstar/ciftools package
  */
@@ -93,7 +93,7 @@ export declare const CCD_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<"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" | "other">;
+        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.
          */
@@ -318,7 +318,7 @@ export declare const CCD_Schema: {
         /**
          * Stereochemical configuration across a double bond.
          */
-        pdbx_stereo_config: Schema.Aliased<"E" | "Z" | "N">;
+        pdbx_stereo_config: Schema.Aliased<"N" | "E" | "Z">;
         /**
          * A flag indicating an aromatic bond.
          */

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

@@ -2,7 +2,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.350, IHM 1.17, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
  *
  * @author molstar/ciftools package
  */

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

@@ -106,7 +106,7 @@ export declare const CifCore_Schema: {
      * Abstracts. This ordering is used in _chemical_formula.moiety
      * and _chemical_formula.sum.
      *
-     * _chemical_formula.iupac      '[Mo (C O)4 (C18 H33 P)2]'
+     * _chemical_formula.IUPAC      '[Mo (C O)4 (C18 H33 P)2]'
      * _chemical_formula.moiety     'C40 H66 Mo O4 P2'
      * _chemical_formula.structural '((C O)4 (P (C6 H11)3)2)Mo'
      * _chemical_formula.sum         'C40 H66 Mo O4 P2'
@@ -138,7 +138,7 @@ export declare const CifCore_Schema: {
         sum: Schema.Str;
         /**
          * Mass corresponding to the formulae _chemical_formula.structural,
-         * *_iupac, *_moiety or *_sum and, together with the Z value and cell
+         * *_IUPAC, *_moiety or *_sum and, together with the Z value and cell
          * parameters yield the density given as _exptl_crystal.density_diffrn.
          */
         weight: Schema.Float;
@@ -470,7 +470,7 @@ export declare const CifCore_Schema: {
          * A concatenated series of single-letter codes which indicate the
          * refinement restraints or constraints applied to this site. This
          * item should not be used. It has been replaced by
-         * _atom_site.refinement_flags_posn, _adp and _occupancy. It is
+         * _atom_site.refinement_flags_posn, _ADP and _occupancy. It is
          * retained in this dictionary only to provide compatibility with
          * legacy CIFs.
          */
@@ -497,9 +497,9 @@ export declare const CifCore_Schema: {
          * atomic  displacement parameter, U(equiv), in angstroms squared,
          * calculated from anisotropic atomic displacement  parameters.
          *
-         * U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ a~i~ a~j~)]
+         * U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ a~i~.a~j~)]
          *
-         * a  = the real-space cell lengths
+         * a  = the real-space cell vectors
          * a* = the reciprocal-space cell lengths
          * Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776.
          */
@@ -659,8 +659,11 @@ export declare const CifCore_Aliases: {
     'geom_bond.atom_site_label_1': string[];
     'geom_bond.atom_site_label_2': string[];
     'geom_bond.distance': string[];
+    'audit.block_doi': string[];
     'database_code.cod': string[];
     'database_code.csd': string[];
+    'database_code.depnum_ccdc_archive': string[];
+    'database_code.depnum_ccdc_fiz': string[];
     'database_code.icsd': string[];
     'database_code.mdf': string[];
     'database_code.nbs': string[];

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

@@ -113,7 +113,7 @@ exports.CifCore_Schema = {
      * Abstracts. This ordering is used in _chemical_formula.moiety
      * and _chemical_formula.sum.
      *
-     * _chemical_formula.iupac      '[Mo (C O)4 (C18 H33 P)2]'
+     * _chemical_formula.IUPAC      '[Mo (C O)4 (C18 H33 P)2]'
      * _chemical_formula.moiety     'C40 H66 Mo O4 P2'
      * _chemical_formula.structural '((C O)4 (P (C6 H11)3)2)Mo'
      * _chemical_formula.sum         'C40 H66 Mo O4 P2'
@@ -145,7 +145,7 @@ exports.CifCore_Schema = {
         sum: str,
         /**
          * Mass corresponding to the formulae _chemical_formula.structural,
-         * *_iupac, *_moiety or *_sum and, together with the Z value and cell
+         * *_IUPAC, *_moiety or *_sum and, together with the Z value and cell
          * parameters yield the density given as _exptl_crystal.density_diffrn.
          */
         weight: float,
@@ -477,7 +477,7 @@ exports.CifCore_Schema = {
          * A concatenated series of single-letter codes which indicate the
          * refinement restraints or constraints applied to this site. This
          * item should not be used. It has been replaced by
-         * _atom_site.refinement_flags_posn, _adp and _occupancy. It is
+         * _atom_site.refinement_flags_posn, _ADP and _occupancy. It is
          * retained in this dictionary only to provide compatibility with
          * legacy CIFs.
          */
@@ -504,9 +504,9 @@ exports.CifCore_Schema = {
          * atomic  displacement parameter, U(equiv), in angstroms squared,
          * calculated from anisotropic atomic displacement  parameters.
          *
-         * U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ a~i~ a~j~)]
+         * U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ a~i~.a~j~)]
          *
-         * a  = the real-space cell lengths
+         * a  = the real-space cell vectors
          * a* = the reciprocal-space cell lengths
          * Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776.
          */
@@ -681,12 +681,21 @@ exports.CifCore_Aliases = {
     'geom_bond.distance': [
         'geom_bond_dist',
     ],
+    'audit.block_doi': [
+        'audit_block_DOI',
+    ],
     'database_code.cod': [
         'database_code_COD',
     ],
     'database_code.csd': [
         'database_code_CSD',
     ],
+    'database_code.depnum_ccdc_archive': [
+        'database_code_depnum_CCDC_archive',
+    ],
+    'database_code.depnum_ccdc_fiz': [
+        'database_code_depnum_CCDC_fiz',
+    ],
     'database_code.icsd': [
         'database_code_ICSD',
     ],
@@ -697,6 +706,7 @@ exports.CifCore_Aliases = {
         'database_code_NBS',
     ],
     'atom_site.adp_type': [
+        'atom_site_ADP_type',
         'atom_site_thermal_displace_type',
     ],
     'atom_site.label': [

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

@@ -10,12 +10,12 @@ export declare const DensityServer_Header_Schema: {
         server_version: Schema.Str;
         datetime_utc: Schema.Str;
         guid: Schema.Str;
-        is_empty: Schema.Aliased<"y" | "no" | "n" | "yes">;
-        has_error: Schema.Aliased<"y" | "no" | "n" | "yes">;
+        is_empty: Schema.Aliased<"y" | "yes" | "no" | "n">;
+        has_error: Schema.Aliased<"y" | "yes" | "no" | "n">;
         error: Schema.Str;
         query_source_id: Schema.Str;
         query_type: Schema.Aliased<"cell" | "box">;
-        query_box_type: Schema.Aliased<"fractional" | "cartesian">;
+        query_box_type: Schema.Aliased<"cartesian" | "fractional">;
         query_box_a: Schema.Tensor;
         query_box_b: Schema.Tensor;
     };

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

@@ -23,16 +23,16 @@ export declare const mmCIF_chemCompBond_schema: {
     comp_id: Column.Schema.Str;
     value_order: Column.Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
     pdbx_ordinal: Column.Schema.Int;
-    pdbx_stereo_config: Column.Schema.Aliased<"E" | "Z" | "N">;
+    pdbx_stereo_config: Column.Schema.Aliased<"N" | "E" | "Z">;
     pdbx_aromatic_flag: Column.Schema.Aliased<"N" | "Y">;
 };
 /** Has `type` extended with 'Ion' and 'Lipid' */
 export declare const mmCIF_chemComp_schema: {
-    type: Column.Schema.Aliased<"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" | "other" | "Ion" | "Lipid">;
+    type: 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" | "Ion" | "Lipid">;
     formula: Column.Schema.Str;
     formula_weight: Column.Schema.Float;
     id: Column.Schema.Str;
-    mon_nstd_flag: Column.Schema.Aliased<"y" | "no" | "n" | "yes">;
+    mon_nstd_flag: Column.Schema.Aliased<"y" | "yes" | "no" | "n">;
     name: Column.Schema.Str;
     pdbx_synonyms: Column.Schema.List<string>;
 };

package/lib/commonjs/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.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.350, IHM 1.17, CARB draft.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
  *
  * @author molstar/ciftools package
  */
@@ -478,7 +478,7 @@ export declare const mmCIF_Schema: {
          * _chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class and
          * _chem_comp.mon_nstd_details data items.
          */
-        mon_nstd_flag: Schema.Aliased<"y" | "no" | "n" | "yes">;
+        mon_nstd_flag: Schema.Aliased<"y" | "yes" | "no" | "n">;
         /**
          * The full name of the component.
          */
@@ -489,7 +489,7 @@ 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<"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" | "other">;
+        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.
          */
@@ -534,7 +534,7 @@ export declare const mmCIF_Schema: {
         /**
          * Stereochemical configuration across a double bond.
          */
-        pdbx_stereo_config: Schema.Aliased<"E" | "Z" | "N">;
+        pdbx_stereo_config: Schema.Aliased<"N" | "E" | "Z">;
         /**
          * A flag indicating an aromatic bond.
          */
@@ -786,12 +786,12 @@ export declare const mmCIF_Schema: {
          * one monomer-to-monomer link different from that implied by
          * _entity_poly.type.
          */
-        nstd_linkage: Schema.Aliased<"y" | "no" | "n" | "yes">;
+        nstd_linkage: Schema.Aliased<"y" | "yes" | "no" | "n">;
         /**
          * A flag to indicate whether the polymer contains at least
          * one monomer that is not considered standard.
          */
-        nstd_monomer: Schema.Aliased<"y" | "no" | "n" | "yes">;
+        nstd_monomer: Schema.Aliased<"y" | "yes" | "no" | "n">;
         /**
          * The type of the polymer.
          */
@@ -885,7 +885,7 @@ export declare const mmCIF_Schema: {
          * A flag to indicate whether this monomer in the polymer is
          * heterogeneous in sequence.
          */
-        hetero: Schema.Aliased<"y" | "no" | "n" | "yes">;
+        hetero: Schema.Aliased<"y" | "yes" | "no" | "n">;
         /**
          * This data item is a pointer to _chem_comp.id in the CHEM_COMP
          * category.
@@ -1420,7 +1420,7 @@ export declare const mmCIF_Schema: {
          * those that are given in the data block (in which case the value
          * of code is 'generate').
          */
-        code: Schema.Aliased<"generate" | "given">;
+        code: Schema.Aliased<"given" | "generate">;
         /**
          * A description of special aspects of the noncrystallographic
          * symmetry operator.
@@ -1974,7 +1974,7 @@ export declare const mmCIF_Schema: {
          * The value of occupancy flag indicates whether the residue
          * is unobserved (= 1) or the coordinates have an occupancy of zero (=0)
          */
-        occupancy_flag: Schema.Aliased<"0" | "1">;
+        occupancy_flag: Schema.Aliased<"1" | "0">;
         /**
          * Part of the identifier for the unobserved or zero occupancy residue.
          *
@@ -2660,7 +2660,7 @@ export declare const mmCIF_Schema: {
          * A flag to indicate whether this monomer in the entity is
          * heterogeneous in sequence.
          */
-        hetero: Schema.Aliased<"y" | "no" | "n" | "yes">;
+        hetero: Schema.Aliased<"y" | "yes" | "no" | "n">;
         /**
          * This data item is a pointer to _chem_comp.id in the CHEM_COMP
          * category.
@@ -2779,7 +2779,7 @@ export declare const mmCIF_Schema: {
          * A flag to indicate whether this monomer in the entity is
          * heterogeneous in sequence.
          */
-        hetero: Schema.Aliased<"y" | "no" | "n" | "yes">;
+        hetero: Schema.Aliased<"y" | "yes" | "no" | "n">;
         /**
          * Pointer to _atom_site.label_asym_id.
          */
@@ -3083,7 +3083,7 @@ export declare const mmCIF_Schema: {
         /**
          * The primitive object used to model this segment.
          */
-        model_object_primitive: Schema.Aliased<"sphere" | "other" | "atomistic" | "gaussian">;
+        model_object_primitive: Schema.Aliased<"other" | "sphere" | "atomistic" | "gaussian">;
         /**
          * The identifier for the starting structural model.
          * This data item is a pointer to _ihm_starting_model_details.starting_model_id
@@ -3343,7 +3343,7 @@ export declare const mmCIF_Schema: {
         /**
          * The type of post modeling analysis being carried out.
          */
-        type: Schema.Aliased<"filter" | "none" | "other" | "cluster" | "rescore" | "validation">;
+        type: Schema.Aliased<"none" | "filter" | "other" | "cluster" | "rescore" | "validation">;
         /**
          * The parameter/feature used in the post modeling analysis.
          */
@@ -3566,7 +3566,7 @@ export declare const mmCIF_Schema: {
         /**
          * The application / utilization of the dataset group in modeling.
          */
-        application: Schema.Aliased<"filter" | "representation" | "other" | "validation" | "restraint" | "sampling">;
+        application: Schema.Aliased<"filter" | "other" | "validation" | "restraint" | "representation" | "sampling">;
         /**
          * Additional details regarding the dataset group.
          */
@@ -4595,7 +4595,7 @@ export declare const mmCIF_Schema: {
         /**
          * The type of entity.
          */
-        entity_type: Schema.Aliased<"non-polymer" | "other" | "polymer" | "water">;
+        entity_type: Schema.Aliased<"other" | "non-polymer" | "polymer" | "water">;
     };
     /**
      * Data items in the IHM_POLY_RESIDUE_FEATURE category provides the defintions

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

@@ -2,7 +2,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.350, IHM 1.17, CARB draft.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
  *
  * @author molstar/ciftools package
  */

package/lib/commonjs/mol-io/reader/ply/schema.d.ts

@@ -24,7 +24,7 @@ export declare const PlyTypeByteLength: {
 };
 export declare type PlyType = keyof typeof PlyTypeByteLength;
 export declare const PlyTypes: Set<string>;
-export declare function PlyType(str: string): "ushort" | "float" | "int" | "float32" | "uint8" | "int32" | "uint16" | "uint32" | "char" | "double" | "int8" | "uchar" | "short" | "uint" | "int16" | "float64";
+export declare function PlyType(str: string): "double" | "float" | "char" | "int" | "uint8" | "int8" | "uint16" | "int16" | "uint32" | "int32" | "float32" | "ushort" | "uchar" | "short" | "uint" | "float64";
 export interface PlyFile {
     readonly comments: ReadonlyArray<string>;
     readonly elementNames: ReadonlyArray<string>;

package/lib/commonjs/mol-io/reader/sdf/parser-v3-util.d.ts

@@ -0,0 +1,9 @@
+import { MolFile } from '../mol/parser';
+import { Tokenizer } from '../common/text/tokenizer';
+export declare function isV3(versionLine: string): boolean;
+export declare function handleCountsV3(tokenizer: Tokenizer): {
+    atomCount: number;
+    bondCount: number;
+};
+export declare function handleAtomsV3(tokenizer: Tokenizer, atomCount: number): MolFile['atoms'];
+export declare function handleBondsV3(tokenizer: Tokenizer, bondCount: number): MolFile['bonds'];

package/lib/commonjs/mol-io/reader/sdf/parser-v3-util.js

@@ -0,0 +1,91 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.handleBondsV3 = exports.handleAtomsV3 = exports.handleCountsV3 = exports.isV3 = void 0;
+var db_1 = require("../../../mol-data/db");
+var tokenizer_1 = require("../common/text/tokenizer");
+var token_1 = require("../common/text/column/token");
+function isV3(versionLine) {
+    return versionLine.trim().endsWith('V3000');
+}
+exports.isV3 = isV3;
+function handleCountsV3(tokenizer) {
+    var atomCount = tokenizer_1.TokenBuilder.create(tokenizer.data, 1);
+    var bondCount = tokenizer_1.TokenBuilder.create(tokenizer.data, 1);
+    tokenizer_1.Tokenizer.eatLine(tokenizer); // BEGIN CTAB
+    skipSingleValue(tokenizer); // M
+    skipSingleValue(tokenizer); // V30
+    skipSingleValue(tokenizer); // COUNTS
+    addSingleValue(tokenizer, atomCount);
+    addSingleValue(tokenizer, bondCount);
+    tokenizer_1.Tokenizer.eatLine(tokenizer);
+    return {
+        atomCount: (0, token_1.TokenColumnProvider)(atomCount)(db_1.Column.Schema.int).value(0),
+        bondCount: (0, token_1.TokenColumnProvider)(bondCount)(db_1.Column.Schema.int).value(0)
+    };
+}
+exports.handleCountsV3 = handleCountsV3;
+function handleAtomsV3(tokenizer, atomCount) {
+    var x = tokenizer_1.TokenBuilder.create(tokenizer.data, atomCount * 2);
+    var y = tokenizer_1.TokenBuilder.create(tokenizer.data, atomCount * 2);
+    var z = tokenizer_1.TokenBuilder.create(tokenizer.data, atomCount * 2);
+    var type_symbol = tokenizer_1.TokenBuilder.create(tokenizer.data, atomCount * 2);
+    for (var i = 0; i < atomCount; ++i) {
+        tokenizer_1.Tokenizer.markLine(tokenizer);
+        skipSingleValue(tokenizer); // M
+        skipSingleValue(tokenizer); // V30
+        skipSingleValue(tokenizer); // Index
+        var position = tokenizer.position;
+        addSingleValue(tokenizer, type_symbol);
+        addSingleValue(tokenizer, x);
+        addSingleValue(tokenizer, y);
+        addSingleValue(tokenizer, z);
+        tokenizer.position = position;
+    }
+    tokenizer_1.Tokenizer.eatLine(tokenizer); // Previous Line
+    tokenizer_1.Tokenizer.eatLine(tokenizer); // END ATOM
+    return {
+        count: atomCount,
+        x: (0, token_1.TokenColumnProvider)(x)(db_1.Column.Schema.float),
+        y: (0, token_1.TokenColumnProvider)(y)(db_1.Column.Schema.float),
+        z: (0, token_1.TokenColumnProvider)(z)(db_1.Column.Schema.float),
+        type_symbol: (0, token_1.TokenColumnProvider)(type_symbol)(db_1.Column.Schema.str),
+    };
+}
+exports.handleAtomsV3 = handleAtomsV3;
+function handleBondsV3(tokenizer, bondCount) {
+    var atomIdxA = tokenizer_1.TokenBuilder.create(tokenizer.data, bondCount * 2);
+    var atomIdxB = tokenizer_1.TokenBuilder.create(tokenizer.data, bondCount * 2);
+    var order = tokenizer_1.TokenBuilder.create(tokenizer.data, bondCount * 2);
+    for (var i = 0; i < bondCount; ++i) {
+        tokenizer_1.Tokenizer.markLine(tokenizer);
+        skipSingleValue(tokenizer); // M
+        skipSingleValue(tokenizer); // V30
+        skipSingleValue(tokenizer); // Index
+        var position = tokenizer.position;
+        addSingleValue(tokenizer, order);
+        addSingleValue(tokenizer, atomIdxA);
+        addSingleValue(tokenizer, atomIdxB);
+        tokenizer.position = position;
+    }
+    tokenizer_1.Tokenizer.eatLine(tokenizer); // Previous Line
+    tokenizer_1.Tokenizer.eatLine(tokenizer); // END BOND
+    return {
+        count: bondCount,
+        atomIdxA: (0, token_1.TokenColumnProvider)(atomIdxA)(db_1.Column.Schema.float),
+        atomIdxB: (0, token_1.TokenColumnProvider)(atomIdxB)(db_1.Column.Schema.float),
+        order: (0, token_1.TokenColumnProvider)(order)(db_1.Column.Schema.float),
+    };
+}
+exports.handleBondsV3 = handleBondsV3;
+function skipSingleValue(tokenizer) {
+    tokenizer_1.Tokenizer.skipWhitespace(tokenizer);
+    tokenizer_1.Tokenizer.eatValue(tokenizer);
+}
+function addSingleValue(tokenizer, tokens) {
+    var valueStart = tokenizer.position;
+    tokenizer_1.Tokenizer.skipWhitespace(tokenizer);
+    tokenizer_1.Tokenizer.eatValue(tokenizer);
+    tokenizer_1.Tokenizer.trim(tokenizer, valueStart, tokenizer.position);
+    tokenizer_1.TokenBuilder.addUnchecked(tokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+}
+//# sourceMappingURL=parser-v3-util.js.map

package/lib/commonjs/mol-io/reader/sdf/parser.d.ts

@@ -8,7 +8,7 @@ import { Column } from '../../../mol-data/db';
 import { MolFile } from '../mol/parser';
 import { Task } from '../../../mol-task';
 import { ReaderResult as Result } from '../result';
-/** http://c4.cabrillo.edu/404/ctfile.pdf - page 41 */
+/** http://c4.cabrillo.edu/404/ctfile.pdf - page 41 & 79 */
 export interface SdfFileCompound {
     readonly molFile: MolFile;
     readonly dataItems: {

package/lib/commonjs/mol-io/reader/sdf/parser.js

@@ -14,6 +14,7 @@ var mol_task_1 = require("../../../mol-task");
 var result_1 = require("../result");
 var tokenizer_1 = require("../common/text/tokenizer");
 var token_1 = require("../common/text/column/token");
+var parser_v3_util_1 = require("./parser-v3-util");
 var delimiter = '$$$$';
 function handleDataItems(tokenizer) {
     var dataHeader = tokenizer_1.TokenBuilder.create(tokenizer.data, 32);
@@ -49,12 +50,19 @@ function handleDataItems(tokenizer) {
         data: (0, token_1.TokenColumnProvider)(data)(db_1.Column.Schema.str)
     };
 }
+function handleCountsV2(countsAndVersion) {
+    return {
+        atomCount: +countsAndVersion.substr(0, 3),
+        bondCount: +countsAndVersion.substr(3, 3)
+    };
+}
 function handleMolFile(tokenizer) {
     var title = tokenizer_1.Tokenizer.readLine(tokenizer).trim();
     var program = tokenizer_1.Tokenizer.readLine(tokenizer).trim();
     var comment = tokenizer_1.Tokenizer.readLine(tokenizer).trim();
-    var counts = tokenizer_1.Tokenizer.readLine(tokenizer);
-    var atomCount = +counts.substr(0, 3), bondCount = +counts.substr(3, 3);
+    var countsAndVersion = tokenizer_1.Tokenizer.readLine(tokenizer);
+    var molIsV3 = (0, parser_v3_util_1.isV3)(countsAndVersion);
+    var _a = molIsV3 ? (0, parser_v3_util_1.handleCountsV3)(tokenizer) : handleCountsV2(countsAndVersion), atomCount = _a.atomCount, bondCount = _a.bondCount;
     if (Number.isNaN(atomCount) || Number.isNaN(bondCount)) {
         // try to skip to next molecule
         while (tokenizer.position < tokenizer.length) {
@@ -64,8 +72,8 @@ function handleMolFile(tokenizer) {
         }
         return;
     }
-    var atoms = (0, parser_1.handleAtoms)(tokenizer, atomCount);
-    var bonds = (0, parser_1.handleBonds)(tokenizer, bondCount);
+    var atoms = molIsV3 ? (0, parser_v3_util_1.handleAtomsV3)(tokenizer, atomCount) : (0, parser_1.handleAtoms)(tokenizer, atomCount);
+    var bonds = molIsV3 ? (0, parser_v3_util_1.handleBondsV3)(tokenizer, bondCount) : (0, parser_1.handleBonds)(tokenizer, bondCount);
     var dataItems = handleDataItems(tokenizer);
     return {
         molFile: { title: title, program: program, comment: comment, atoms: atoms, bonds: bonds },

package/lib/commonjs/mol-math/linear-algebra/3d/vec3.d.ts

@@ -138,6 +138,12 @@ declare namespace Vec3 {
      * Computes the dihedral angles of 4 points, reports in radians.
      */
     function dihedralAngle(a: Vec3, b: Vec3, c: Vec3, d: Vec3): number;
+    /**
+     * @param inclination in radians [0, PI]
+     * @param azimuth in radians [0, 2 * PI]
+     * @param radius [0, +Inf]
+     */
+    function directionFromSpherical(out: Vec3, inclination: number, azimuth: number, radius: number): Vec3;
     /**
      * Returns whether or not the vectors have exactly the same elements in the same position (when compared with ===)
      */

package/lib/commonjs/mol-math/linear-algebra/3d/vec3.js

@@ -469,6 +469,15 @@ exports.Vec3 = Vec3;
         return dot(tmp_dh_cb, tmp_dh_cross) > 0 ? _angle : -_angle;
     }
     Vec3.dihedralAngle = dihedralAngle;
+    /**
+     * @param inclination in radians [0, PI]
+     * @param azimuth in radians [0, 2 * PI]
+     * @param radius [0, +Inf]
+     */
+    function directionFromSpherical(out, inclination, azimuth, radius) {
+        return Vec3.set(out, radius * Math.cos(azimuth) * Math.sin(inclination), radius * Math.sin(azimuth) * Math.sin(inclination), radius * Math.cos(inclination));
+    }
+    Vec3.directionFromSpherical = directionFromSpherical;
     /**
      * Returns whether or not the vectors have exactly the same elements in the same position (when compared with ===)
      */