bio-forge-wasm 0.3.1 → 0.4.1

package/README.md

@@ -21,7 +21,7 @@ Load → Clean → Repair → Hydrogenate → Solvate → Topology → Write
 1. **Load** – `io::read_pdb_structure` or `io::read_mmcif_structure` parses coordinates with `IoContext` alias resolution.
 2. **Clean** – `ops::clean_structure` removes waters, ions, hetero residues, or arbitrary residue names via `CleanConfig`.
 3. **Repair** – `ops::repair_structure` realigns residues to templates and rebuilds missing heavy atoms (OXT on C-termini, OP3 on 5'-phosphorylated nucleic acids).
-4. **Hydrogenate** – `ops::add_hydrogens` infers protonation states (configurable pH and histidine strategy) and reconstructs hydrogens from template anchors.
+4. **Hydrogenate** – `ops::add_hydrogens` infers protonation states (configurable pH, histidine strategy, and salt bridge detection) and reconstructs hydrogens from template anchors.
 5. **Solvate** – `ops::solvate_structure` creates a periodic box, packs water on a configurable lattice, and swaps molecules for ions to satisfy a target charge.
 6. **Topology** – `ops::TopologyBuilder` emits bond connectivity with peptide-link detection, nucleic backbone connectivity, and disulfide heuristics.
 7. **Write** – `io::write_pdb_structure` / `io::write_mmcif_structure` serialize the processed structure; `write_*_topology` helpers emit CONECT or `struct_conn` records.
@@ -50,7 +50,7 @@ BioForge is also available as a library crate. Add it to your `Cargo.toml` depen
 
 ```toml
 [dependencies]
-bio-forge = "0.3.1"
+bio-forge = "0.4.1"
 ```
 
 #### Example: Preparing a PDB Structure

package/bio_forge_wasm.d.ts

@@ -1,5 +1,95 @@
 /* tslint:disable */
 /* eslint-disable */
+/**
+ * Comprehensive structure information.
+ */
+export interface StructureInfo {
+    /**
+     * Number of chains.
+     */
+    chainCount: number;
+    /**
+     * Total number of residues.
+     */
+    residueCount: number;
+    /**
+     * Total number of atoms.
+     */
+    atomCount: number;
+    /**
+     * Box dimensions `[a, b, c]` in Å, if present.
+     */
+    boxLengths: [number, number, number] | undefined;
+    /**
+     * Box angles `[α, β, γ]` in degrees, if present.
+     */
+    boxAngles: [number, number, number] | undefined;
+    /**
+     * Per-chain information.
+     */
+    chains: ChainInfo[];
+}
+
+/**
+ * Configuration for hydrogen addition.
+ */
+export interface HydroConfig {
+    /**
+     * Target pH for protonation state decisions. Default: `undefined` (neutral)
+     */
+    targetPh?: number | undefined;
+    /**
+     * Remove existing hydrogens before adding new ones. Default: `true`
+     */
+    removeExistingH?: boolean;
+    /**
+     * Histidine tautomer strategy: `\"hid\"`, `\"hie\"`, `\"random\"`, `\"network\"`. Default: `\"network\"`
+     */
+    hisStrategy?: "hid" | "hie" | "random" | "network";
+    /**
+     * Detect salt bridges for HIS → HIP conversion near carboxylate groups. Default: `true`
+     */
+    hisSaltBridgeProtonation?: boolean;
+}
+
+/**
+ * Configuration for solvation.
+ */
+export interface SolvateConfig {
+    /**
+     * Margin around solute (Å). Default: `10.0`
+     */
+    margin?: number;
+    /**
+     * Water grid spacing (Å). Default: `3.1`
+     */
+    waterSpacing?: number;
+    /**
+     * Minimum solvent-solute distance (Å). Default: `2.4`
+     */
+    vdwCutoff?: number;
+    /**
+     * Remove existing solvent before solvating. Default: `true`
+     */
+    removeExisting?: boolean;
+    /**
+     * Cation species: `\"Na\"`, `\"K\"`, `\"Mg\"`, `\"Ca\"`, `\"Li\"`, `\"Zn\"`. Default: `[\"Na\"]`
+     */
+    cations?: Array<"Na" | "K" | "Mg" | "Ca" | "Li" | "Zn">;
+    /**
+     * Anion species: `\"Cl\"`, `\"Br\"`, `\"I\"`, `\"F\"`. Default: `[\"Cl\"]`
+     */
+    anions?: Array<"Cl" | "Br" | "I" | "F">;
+    /**
+     * Target net charge after solvation. Default: `0`
+     */
+    targetCharge?: number;
+    /**
+     * Random seed for reproducible placement.
+     */
+    rngSeed?: number | undefined;
+}
+
 /**
  * Configuration for structure cleaning operations.
  */
@@ -40,24 +130,6 @@ export interface TopologyConfig {
     disulfideCutoff?: number;
 }
 
-/**
- * Configuration for hydrogen addition.
- */
-export interface HydroConfig {
-    /**
-     * Target pH for protonation state decisions. Default: `undefined` (neutral)
-     */
-    targetPh?: number | undefined;
-    /**
-     * Remove existing hydrogens before adding new ones. Default: `true`
-     */
-    removeExistingH?: boolean;
-    /**
-     * Histidine tautomer strategy: `\"hid\"`, `\"hie\"`, `\"random\"`, `\"network\"`. Default: `\"network\"`
-     */
-    hisStrategy?: "hid" | "hie" | "random" | "network";
-}
-
 /**
  * Per-chain information.
  */
@@ -82,231 +154,172 @@ export interface ChainInfo {
     polymerTypes: Array<"protein" | "nucleic" | "solvent" | "hetero">;
 }
 
+
 /**
- * Configuration for solvation.
+ * A molecular structure for manipulation and export.
  */
-export interface SolvateConfig {
+export class Structure {
+    private constructor();
+    free(): void;
+    [Symbol.dispose](): void;
     /**
-     * Margin around solute (Å). Default: `10.0`
+     * Adds hydrogen atoms.
      */
-    margin?: number;
+    addHydrogens(config?: HydroConfig | null): void;
     /**
-     * Water grid spacing (Å). Default: `3.1`
+     * Centers the geometric centroid at the origin.
      */
-    waterSpacing?: number;
+    centerGeometry(): void;
     /**
-     * Minimum solvent-solute distance (Å). Default: `2.4`
+     * Centers the center of mass at the origin.
      */
-    vdwCutoff?: number;
+    centerMass(): void;
     /**
-     * Remove existing solvent before solvating. Default: `true`
+     * Removes unwanted components (water, ions, hydrogens, hetero residues).
      */
-    removeExisting?: boolean;
+    clean(config?: CleanConfig | null): void;
     /**
-     * Cation species: `\"Na\"`, `\"K\"`, `\"Mg\"`, `\"Ca\"`, `\"Li\"`, `\"Zn\"`. Default: `[\"Na\"]`
+     * Creates a deep copy of the structure.
      */
-    cations?: Array<"Na" | "K" | "Mg" | "Ca" | "Li" | "Zn">;
+    clone(): Structure;
     /**
-     * Anion species: `\"Cl\"`, `\"Br\"`, `\"I\"`, `\"F\"`. Default: `[\"Cl\"]`
+     * Parses an mmCIF string into a Structure.
      */
-    anions?: Array<"Cl" | "Br" | "I" | "F">;
+    static fromMmcif(content: string): Structure;
     /**
-     * Target net charge after solvation. Default: `0`
+     * Parses an mmCIF byte array into a Structure.
      */
-    targetCharge?: number;
+    static fromMmcifBytes(content: Uint8Array): Structure;
     /**
-     * Random seed for reproducible placement.
+     * Parses a PDB string into a Structure.
      */
-    rngSeed?: number | undefined;
-}
-
-/**
- * Comprehensive structure information.
- */
-export interface StructureInfo {
+    static fromPdb(content: string): Structure;
     /**
-     * Number of chains.
+     * Parses a PDB byte array into a Structure.
      */
-    chainCount: number;
+    static fromPdbBytes(content: Uint8Array): Structure;
     /**
-     * Total number of residues.
+     * Returns comprehensive structure statistics.
      */
-    residueCount: number;
+    info(): StructureInfo;
     /**
-     * Total number of atoms.
+     * Reconstructs missing atoms from templates.
      */
-    atomCount: number;
+    repair(): void;
     /**
-     * Box dimensions `[a, b, c]` in Å, if present.
+     * Rotates using Euler angles (XYZ convention, all in radians).
      */
-    boxLengths: [number, number, number] | undefined;
+    rotateEuler(x: number, y: number, z: number): void;
     /**
-     * Box angles `[α, β, γ]` in degrees, if present.
+     * Rotates around the X axis (angle in radians).
      */
-    boxAngles: [number, number, number] | undefined;
+    rotateX(radians: number): void;
     /**
-     * Per-chain information.
+     * Rotates around the Y axis (angle in radians).
      */
-    chains: ChainInfo[];
-}
-
-
-export class Structure {
-  private constructor();
-  free(): void;
-  [Symbol.dispose](): void;
-  /**
-   * Parses an mmCIF string into a Structure.
-   */
-  static fromMmcif(content: string): Structure;
-  /**
-   * Centers the center of mass at the origin.
-   */
-  centerMass(): void;
-  /**
-   * Builds a Topology from this structure.
-   */
-  toTopology(config?: TopologyConfig | null, templates?: Template[] | null): Topology;
-  /**
-   * Rotates using Euler angles (XYZ convention, all in radians).
-   */
-  rotateEuler(x: number, y: number, z: number): void;
-  /**
-   * Serializes to PDB format as bytes.
-   */
-  toPdbBytes(): Uint8Array;
-  /**
-   * Adds hydrogen atoms.
-   */
-  addHydrogens(config?: HydroConfig | null): void;
-  /**
-   * Parses a PDB byte array into a Structure.
-   */
-  static fromPdbBytes(content: Uint8Array): Structure;
-  /**
-   * Serializes to mmCIF format as bytes.
-   */
-  toMmcifBytes(): Uint8Array;
-  /**
-   * Centers the geometric centroid at the origin.
-   */
-  centerGeometry(): void;
-  /**
-   * Creates a deep copy of the structure.
-   */
-  clone(): Structure;
-  /**
-   * Parses an mmCIF byte array into a Structure.
-   */
-  static fromMmcifBytes(content: Uint8Array): Structure;
-  /**
-   * Returns comprehensive structure statistics.
-   */
-  info(): StructureInfo;
-  /**
-   * Removes unwanted components (water, ions, hydrogens, hetero residues).
-   */
-  clean(config?: CleanConfig | null): void;
-  /**
-   * Reconstructs missing atoms from templates.
-   */
-  repair(): void;
-  /**
-   * Serializes to PDB format.
-   */
-  toPdb(): string;
-  /**
-   * Solvates the structure with water and ions.
-   */
-  solvate(config?: SolvateConfig | null): void;
-  /**
-   * Parses a PDB string into a Structure.
-   */
-  static fromPdb(content: string): Structure;
-  /**
-   * Rotates around the X axis (angle in radians).
-   */
-  rotateX(radians: number): void;
-  /**
-   * Rotates around the Y axis (angle in radians).
-   */
-  rotateY(radians: number): void;
-  /**
-   * Rotates around the Z axis (angle in radians).
-   */
-  rotateZ(radians: number): void;
-  /**
-   * Serializes to mmCIF format.
-   */
-  toMmcif(): string;
-  /**
-   * Translates all atoms by the given vector (x, y, z in Å).
-   */
-  translate(x: number, y: number, z: number): void;
-  /**
-   * Returns the number of atoms.
-   */
-  readonly atomCount: number;
-  /**
-   * Returns the number of chains.
-   */
-  readonly chainCount: number;
-  /**
-   * Returns the number of residues.
-   */
-  readonly residueCount: number;
+    rotateY(radians: number): void;
+    /**
+     * Rotates around the Z axis (angle in radians).
+     */
+    rotateZ(radians: number): void;
+    /**
+     * Solvates the structure with water and ions.
+     */
+    solvate(config?: SolvateConfig | null): void;
+    /**
+     * Serializes to mmCIF format.
+     */
+    toMmcif(): string;
+    /**
+     * Serializes to mmCIF format as bytes.
+     */
+    toMmcifBytes(): Uint8Array;
+    /**
+     * Serializes to PDB format.
+     */
+    toPdb(): string;
+    /**
+     * Serializes to PDB format as bytes.
+     */
+    toPdbBytes(): Uint8Array;
+    /**
+     * Builds a Topology from this structure.
+     */
+    toTopology(config?: TopologyConfig | null, templates?: Template[] | null): Topology;
+    /**
+     * Translates all atoms by the given vector (x, y, z in Å).
+     */
+    translate(x: number, y: number, z: number): void;
+    /**
+     * Returns the number of atoms.
+     */
+    readonly atomCount: number;
+    /**
+     * Returns the number of chains.
+     */
+    readonly chainCount: number;
+    /**
+     * Returns the number of residues.
+     */
+    readonly residueCount: number;
 }
 
+/**
+ * A residue or ligand template for topology building.
+ */
 export class Template {
-  private constructor();
-  free(): void;
-  [Symbol.dispose](): void;
-  /**
-   * Parses a MOL2 byte array into a Template.
-   */
-  static fromMol2Bytes(content: Uint8Array): Template;
-  /**
-   * Parses a MOL2 string into a Template.
-   */
-  static fromMol2(content: string): Template;
-  /**
-   * Returns the template name (residue code).
-   */
-  readonly name: string;
+    private constructor();
+    free(): void;
+    [Symbol.dispose](): void;
+    /**
+     * Parses a MOL2 string into a Template.
+     */
+    static fromMol2(content: string): Template;
+    /**
+     * Parses a MOL2 byte array into a Template.
+     */
+    static fromMol2Bytes(content: Uint8Array): Template;
+    /**
+     * Returns the template name (residue code).
+     */
+    readonly name: string;
 }
 
+/**
+ * A structure with bond connectivity information.
+ */
 export class Topology {
-  private constructor();
-  free(): void;
-  [Symbol.dispose](): void;
-  /**
-   * Serializes to PDB format as bytes.
-   */
-  toPdbBytes(): Uint8Array;
-  /**
-   * Creates a Topology from a Structure.
-   */
-  static fromStructure(structure: Structure, config?: TopologyConfig | null, templates?: Template[] | null): Topology;
-  /**
-   * Serializes to mmCIF format as bytes.
-   */
-  toMmcifBytes(): Uint8Array;
-  /**
-   * Serializes to PDB format with CONECT records.
-   */
-  toPdb(): string;
-  /**
-   * Serializes to mmCIF format with struct_conn records.
-   */
-  toMmcif(): string;
-  /**
-   * Returns the number of bonds.
-   */
-  readonly bondCount: number;
-  /**
-   * Returns a copy of the underlying structure.
-   */
-  readonly structure: Structure;
+    private constructor();
+    free(): void;
+    [Symbol.dispose](): void;
+    /**
+     * Creates a Topology from a Structure.
+     */
+    static fromStructure(structure: Structure, config?: TopologyConfig | null, templates?: Template[] | null): Topology;
+    /**
+     * Serializes to mmCIF format with struct_conn records.
+     */
+    toMmcif(): string;
+    /**
+     * Serializes to mmCIF format as bytes.
+     */
+    toMmcifBytes(): Uint8Array;
+    /**
+     * Serializes to PDB format with CONECT records.
+     */
+    toPdb(): string;
+    /**
+     * Serializes to PDB format as bytes.
+     */
+    toPdbBytes(): Uint8Array;
+    /**
+     * Returns the number of bonds.
+     */
+    readonly bondCount: number;
+    /**
+     * Returns a copy of the underlying structure.
+     */
+    readonly structure: Structure;
 }
 
 /**

package/bio_forge_wasm.js

@@ -1,5 +1,9 @@
+/* @ts-self-types="./bio_forge_wasm.d.ts" */
+
 import * as wasm from "./bio_forge_wasm_bg.wasm";
-export * from "./bio_forge_wasm_bg.js";
 import { __wbg_set_wasm } from "./bio_forge_wasm_bg.js";
 __wbg_set_wasm(wasm);
 wasm.__wbindgen_start();
+export {
+    Structure, Template, Topology, init
+} from "./bio_forge_wasm_bg.js";