3dmol/src/parsers/ParserOptionsSpec.ts

JavaScript/TypeScript molecular visualization library

/**
* File formats supported by 3Dmol.js
* @typedef FileFormats
* @category Parsers
* @prop cdjson,json  Chemical JSON format
* @prop cube Gaussian cube format
* @prop gro  Gromacs topology format, need to add coordinates to resulting model.
* @prop mcif,cif Crystallographic Information File, the successor to PDB that makes you miss the PDB file format
* @prop mmtf Macromolecular Transmission Format, the successor to PDB that is totally awesome
* @prop mol2 Sybyl Mol2 format
* @prop pdb The venerable Protein Data Bank format
* @prop pqr Like PDB but with partial charges which are read into the partialcharge atom property
* @prop prmtop Amber topology file, must add coordinates
* @prop sdf MDL MOL format, supports multiple models and meta data
* @prop vasp VASP format (CONTCAR, POSCAR)
* @prop xyz XYZ cartesian coordinates format
*/

import { AtomStyleSpec } from "GLModel";


/**
  * Parser options specification. Used to specify the options of a GLModel.  Depending on the input file format, not all fields may be defined.
  * @category Parsers
  */
 export interface ParserOptionsSpec {
  /** true if you want to add to a new frame and false otherwise ; supported by all */
  frames?: boolean;
  /** object specifying the vibration behavior ; supported by all */
  vibrate?: {
    /** vibrate.frames - number of frames to be created, default to 10 ; supported by all */
    frames?: number;
    /** vibrate.amplitude -amplitude of distortion, default to 1 (full) ; supported by all */
    amplitude?: number
  };
  /** specifies whether or not multiple models are being defined ; supported by xyz,sdf, or mol2 */
  multimodel?: boolean;
  /** specifies weather or not the model is of one molecule ; Supported by xyz , sdf , mol2 */
  onemol?: boolean;
  /** do not strip hydrogens ; supported by sdf,mol2 */
  keepH?: boolean;
  /** used to define ChemDoodle styles ; supported by cdjson */
  parseStyle?: unknown;
  /** boolean dictating weather or not to do assembly ; supported by mcif, pdb */
  doAssembly?: boolean;
  /**  Set to true if you wish to duplicate assembly atoms otherwise false ; supported by all formats with symmetries.  Not duplicating will result in faster rendering but it will not be possible to individually style symmetries. */
  duplicateAssemblyAtoms?: boolean;
  /** Set to true with duplicateAssemblyAtoms to individually wrap atoms (from symmetries) into unit cell  */
  wrapAtoms?: boolean;
  /** shift symmetry mates so their centroid is in the unit cell */
  normalizeAssembly?: boolean;
  /** do not detect bonds between symmetries generated with duplicateAssemblyAtoms (cif only - other formats never make bonds between symmetries) */
  dontConnectDuplicatedAtoms?: boolean;
  /** boolean dictating the presence of a secondary structure ; supported by pdb */
  noSecondaryStructure?: boolean;
  /** do not compute ss ; supported by pdb, mmtf, cif */
  noComputeSecondaryStructure?: boolean;
  /** maximum distance used for identifying hydrogen bonds when computing secondary structure; supported by pdb, mmtf, cif */
  hbondCutoff?: number;
  /** which alternate location to select, if present; '*' to load all ; supported by pdb */
  altLoc?: string;
  /** index of the assembly in symmetry ; supported by mmtf */
  assemblyIndex?: number;
  /** for formats without explicit bonds (e.g. PDB, xyz) infer bonding (default true).  */
  assignBonds?: boolean;
  /** for formats without explicit bonds, if assigning bonds to not assign bonds to common cations */
  unboundCations?: boolean;
  /** set model to this style after parsing */
  style?: AtomStyleSpec;
 };