@cosmol-studio/cosmolkit-core 0.5.1-rc.2 → 0.5.1-rc.4

package/package.json

@@ -1,8 +1,8 @@
 {
   "name": "@cosmol-studio/cosmolkit-core",
-  "version": "0.5.1-rc.2",
+  "version": "0.5.1-rc.4",
   "cosmolkitPreset": "core",
-  "cosmolkitVersion": "0.5.1-rc.2",
+  "cosmolkitVersion": "0.5.1-rc.4",
   "publishConfig": {
     "access": "public",
     "tag": "rc"

package/snippets/wasm-wasm-8d351253ad5d1fc8/inline36.js

@@ -0,0 +1 @@
+export function visitPdbWriteParams(v,f){try{f(v);}catch(cause){throw new TypeError('invalid PdbWriteParams',{cause});}}

package/snippets/wasm-wasm-8d351253ad5d1fc8/inline37.js

@@ -0,0 +1 @@
+export function visit_PdbWriteParamsOptions_configuration(value, visit) { visit(value); }

package/wasm_wasm.d.ts

@@ -121,6 +121,13 @@ export interface MolBlockWriteParamsOptions {
 }
 
 
+export interface PdbWriteParamsOptions {
+    coordinateSelection?: MolCoordinateSelection | null;
+    allConformers?: boolean;
+    flavor?: number;
+}
+
+
 export interface PotentialStereoParamsOptions {
     clean?: boolean;
     flagPossible?: boolean;
@@ -653,8 +660,8 @@ export class CxSmilesFields {
     bits(): number;
     contains(other: CxSmilesFields): boolean;
     or(other: CxSmilesFields): CxSmilesFields;
-    static readonly ALL_BUT_COORDS: CxSmilesFields;
     static readonly ALL: CxSmilesFields;
+    static readonly ALL_BUT_COORDS: CxSmilesFields;
     static readonly ATOM_LABELS: CxSmilesFields;
     static readonly ATOM_PROPS: CxSmilesFields;
     static readonly BOND_ATROPISOMER: CxSmilesFields;
@@ -1080,10 +1087,10 @@ export class Molecule {
     static readXyz(text: string): Molecule;
     removeHydrogensWithParams_(params: RemoveHsParams): void;
     removeHydrogens_(params?: RemoveHsParams | RemoveHsParamsOptions): void;
-    sanitizeWithParams_(params: SanitizeParams): void;
     sanitizeWithParams(params: SanitizeParams): Molecule;
-    sanitize_(params?: SanitizeParams | SanitizeParamsOptions): void;
+    sanitizeWithParams_(params: SanitizeParams): void;
     sanitize(params?: SanitizeParams | SanitizeParamsOptions): Molecule;
+    sanitize_(params?: SanitizeParams | SanitizeParamsOptions): void;
     /**
      * Returns SDF data-field names in their source order, including duplicates.
      */
@@ -1114,6 +1121,12 @@ export class Molecule {
     toFragmentSmiles(atoms: number[], params?: FragmentSmilesWriteParams | FragmentSmilesWriteParamsOptions): string;
     toMolWithParams(params: MolBlockWriteParams): string;
     toMol(params?: MolBlockWriteParams | MolBlockWriteParamsOptions): string;
+    toPdbWithParams(params: PdbWriteParams): string;
+    /**
+     * Return PDB text, never mutate the molecule. Multiple coordinate sets
+     * require dimension/ID selection or explicit allConformers.
+     */
+    toPdb(params?: PdbWriteParams | PdbWriteParamsOptions): string;
     toRandomSmilesWithParams(count: number, seed: number, params: RandomSmilesWriteParams): string[];
     toRandomSmiles(count: number, seed: number, params?: RandomSmilesWriteParams | RandomSmilesWriteParamsOptions): string[];
     toSdf2dWithParams(params: MolBlockWriteParams): string;
@@ -1326,6 +1339,47 @@ export enum ParityPolicy {
     RequiredNow = 2,
 }
 
+/**
+ * Structured PDB writer failure. The thrown Error exposes this value as detail.
+ */
+export class PdbWriteError {
+    private constructor();
+    free(): void;
+    [Symbol.dispose](): void;
+    readonly cause: Error | null;
+    readonly coordinateId: number | null;
+    readonly dimension: CoordinateDimension | null;
+    readonly domain: string;
+    readonly feature: string | null;
+    readonly kind: string;
+    readonly message: string;
+    readonly threeD: number | null;
+    readonly twoD: number | null;
+}
+
+/**
+ * PDB writer options. No coordinates are generated or written back.
+ */
+export class PdbWriteParams {
+    free(): void;
+    [Symbol.dispose](): void;
+    constructor(coordinate_selection?: MolCoordinateSelection | null, all_conformers?: boolean, flavor?: number);
+    /**
+     * Write all stored sets: 2D then 3D, each in storage order. Mutually
+     * exclusive with explicit single-set selection. PDB loses CK IDs/dimensions.
+     */
+    allConformers: boolean;
+    /**
+     * Unique-or-error automatic resolution or an explicit dimension and stored ID.
+     */
+    get coordinateSelection(): MolCoordinateSelection;
+    set coordinateSelection(value: MolCoordinateSelection | null);
+    /**
+     * RDKit PDB writer flavor bit mask.
+     */
+    flavor: number;
+}
+
 export class PotentialStereoCenter {
     private constructor();
     free(): void;
@@ -1562,10 +1616,10 @@ export class SanitizeOperations {
     or(other: SanitizeOperations): SanitizeOperations;
     static readonly ADJUST_HS: SanitizeOperations;
     static readonly ALL: SanitizeOperations;
+    static readonly CLEANUP: SanitizeOperations;
     static readonly CLEANUP_ATROPISOMERS: SanitizeOperations;
     static readonly CLEANUP_CHIRALITY: SanitizeOperations;
     static readonly CLEANUP_ORGANOMETALLICS: SanitizeOperations;
-    static readonly CLEANUP: SanitizeOperations;
     static readonly FIND_RADICALS: SanitizeOperations;
     static readonly KEKULIZE: SanitizeOperations;
     static readonly NONE: SanitizeOperations;
@@ -2157,6 +2211,8 @@ export interface InitOutput {
     readonly __wbg_operationerror_free: (a: number, b: number) => void;
     readonly __wbg_operationinvariantentry_free: (a: number, b: number) => void;
     readonly __wbg_paritymatrixentry_free: (a: number, b: number) => void;
+    readonly __wbg_pdbwriteerror_free: (a: number, b: number) => void;
+    readonly __wbg_pdbwriteparams_free: (a: number, b: number) => void;
     readonly __wbg_potentialstereocenter_free: (a: number, b: number) => void;
     readonly __wbg_potentialstereoerror_free: (a: number, b: number) => void;
     readonly __wbg_potentialstereoinfo_free: (a: number, b: number) => void;
@@ -2668,6 +2724,8 @@ export interface InitOutput {
     readonly molecule_toFragmentSmilesWithParams: (a: number, b: number) => [number, number, number, number];
     readonly molecule_toMol: (a: number, b: any) => [number, number, number, number];
     readonly molecule_toMolWithParams: (a: number, b: any) => [number, number, number, number];
+    readonly molecule_toPdb: (a: number, b: any) => [number, number, number, number];
+    readonly molecule_toPdbWithParams: (a: number, b: any) => [number, number, number, number];
     readonly molecule_toRandomSmiles: (a: number, b: any, c: any, d: any) => [number, number, number];
     readonly molecule_toRandomSmilesWithParams: (a: number, b: any, c: any, d: number) => [number, number, number];
     readonly molecule_toSdf: (a: number, b: any) => [number, number, number, number];
@@ -2836,6 +2894,22 @@ export interface InitOutput {
     readonly paritymatrixentry_operation: (a: number) => number;
     readonly paritymatrixentry_profile: (a: number) => [number, number];
     readonly paritymatrixentry_rdkitVersion: (a: number) => any;
+    readonly pdbwriteerror_cause: (a: number) => any;
+    readonly pdbwriteerror_coordinateId: (a: number) => any;
+    readonly pdbwriteerror_dimension: (a: number) => any;
+    readonly pdbwriteerror_domain: (a: number) => [number, number];
+    readonly pdbwriteerror_feature: (a: number) => any;
+    readonly pdbwriteerror_kind: (a: number) => [number, number];
+    readonly pdbwriteerror_message: (a: number) => [number, number];
+    readonly pdbwriteerror_threeD: (a: number) => any;
+    readonly pdbwriteerror_twoD: (a: number) => any;
+    readonly pdbwriteparams_allConformers: (a: number) => number;
+    readonly pdbwriteparams_coordinateSelection: (a: number) => number;
+    readonly pdbwriteparams_flavor: (a: number) => number;
+    readonly pdbwriteparams_new: (a: any, b: any, c: any) => [number, number, number];
+    readonly pdbwriteparams_set_allConformers: (a: number, b: any) => [number, number];
+    readonly pdbwriteparams_set_coordinateSelection: (a: number, b: any) => [number, number];
+    readonly pdbwriteparams_set_flavor: (a: number, b: any) => [number, number];
     readonly potentialstereocenter_index: (a: number) => number;
     readonly potentialstereocenter_kind: (a: number) => [number, number];
     readonly potentialstereoerror_cause: (a: number) => [number, number, number];
@@ -3223,54 +3297,56 @@ export interface InitOutput {
     readonly xyzwriteparams_precision: (a: number) => number;
     readonly xyzwriteparams_set_conformerId: (a: number, b: any) => [number, number];
     readonly xyzwriteparams_set_precision: (a: number, b: any) => [number, number];
-    readonly wasm_bindgen__convert__closures________invoke__h041ac5624941c820: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h17356b03f701c7ed: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h199149965a7b00d0: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h2030185edeab4119: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h2030185edeab4119_439: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h2030185edeab4119_528: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h2030185edeab4119_857: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h2030185edeab4119_859: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h2030185edeab4119_917: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h2034f5d62c3af59c: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h2034f5d62c3af59c_944: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h2034f5d62c3af59c_945: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h25f77cfde9741188: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h27b399cb0907d6e0: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h29974995fc07e855: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h29974995fc07e855_441: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h29974995fc07e855_529: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h29974995fc07e855_686: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h29974995fc07e855_860: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h29974995fc07e855_887: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h2bfae6cc6287f397: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h2fe9ddaffd8f73a2: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h2fe9ddaffd8f73a2_438: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h2fe9ddaffd8f73a2_440: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h2fe9ddaffd8f73a2_762: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h2fe9ddaffd8f73a2_775: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h316a017402b7e37f: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h31f5d0a2e632d21a: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h4f4e8413ff407936: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h62a6c444a28a1722: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h62a6c444a28a1722_897: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h62a6c444a28a1722_898: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h6301bd1056d2a1b2: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h643cba485b8edde4: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h747a03697a341357: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h747a03697a341357_275: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h747a03697a341357_895: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h747a03697a341357_896: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h747a03697a341357_943: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h747a03697a341357_946: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__h9176c75e5fea8006: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__ha5b58acb51da3f82: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__hd149408b1d7c8589: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__hd83dd081a1fa2068: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__hee2db61edd29c007: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__hf22a78f32c9b010a: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__hff0aa86e7f633133: (a: number, b: number, c: number) => void;
-    readonly wasm_bindgen__convert__closures________invoke__hff8d8f3dfc48215c: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h02073c1f86bb7c3c: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h02073c1f86bb7c3c_915: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h02073c1f86bb7c3c_916: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h0a5d6543acca7d81: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h0a5d6543acca7d81_439: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h0a5d6543acca7d81_440: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h0a5d6543acca7d81_762: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h0a5d6543acca7d81_775: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h0abc97a6508bc891: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h11791d68cec3ecbe: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h11791d68cec3ecbe_438: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h11791d68cec3ecbe_528: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h11791d68cec3ecbe_686: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h11791d68cec3ecbe_856: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h11791d68cec3ecbe_907: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h181ae9d1e42bc4cc: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h1bd2b11a1ece5ccd: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h1bd2b11a1ece5ccd_441: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h1bd2b11a1ece5ccd_527: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h1bd2b11a1ece5ccd_858: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h1bd2b11a1ece5ccd_860: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h1bd2b11a1ece5ccd_937: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h22c585b121119d5c: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h253c00d64f7becc1: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h2a6db85594714140: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h2c97957f6bfbcac0: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h30bf1425f64a85b7: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h34cee221250355f5: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h34cee221250355f5_275: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h34cee221250355f5_917: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h34cee221250355f5_918: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h34cee221250355f5_964: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h34cee221250355f5_966: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h38bb4f21582aad1c: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h38fb6834bb992f81: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h39a86d9d168b3703: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h39a86d9d168b3703_963: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h39a86d9d168b3703_965: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h40a8fbd20c150268: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h47d8809ebeeeb64a: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h5bf9ff1c0894ba8b: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h5bf9ff1c0894ba8b_889: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h5bf9ff1c0894ba8b_890: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h63aafa3d123897bf: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__h9beea76e39932e84: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__habf46f649e99e2c5: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__hb7ac9c65f2135e41: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__hc68f8496e1001214: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__hdb815258ce778109: (a: number, b: number, c: number) => void;
+    readonly wasm_bindgen__convert__closures________invoke__he0e529d311a53b72: (a: number, b: number, c: number) => void;
     readonly __wbindgen_malloc: (a: number, b: number) => number;
     readonly __wbindgen_realloc: (a: number, b: number, c: number, d: number) => number;
     readonly __wbindgen_exn_store: (a: number) => void;