File size: 17,295 Bytes
71174bc | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 | import { IFileInfo } from "@/FileSystem/Types";
import { EasyParserParent } from "./EasyParserParent";
import { IAtom } from "@/UI/Navigation/TreeView/TreeInterfaces";
import { GLModel } from "@/UI/Panels/Viewer/GLModelType";
interface ISDFBond {
atomIndex1: number; // 0-indexed based on order in SDF atom block
atomIndex2: number; // 0-indexed based on order in SDF atom block
bondType: number;
}
/**
* A parser for SDF (Structure-Data File) files.
* Parses atom and bond information from the first molecule in an SDF string.
* Supports both V2000 and V3000 formats.
*/
export class EasyParserSDF extends EasyParserParent {
private _parsedBonds: ISDFBond[] = [];
// Maps 0-based index in this._atoms to original 1-based index from SDF
private _atomOrderToSdfIndex: Map<number, number> = new Map();
// Maps original 1-based SDF index to 0-based index in this._atoms
private _sdfIndexToAtomOrder: Map<number, number> = new Map();
private _isV3000: boolean;
constructor(src: IFileInfo | GLModel | IAtom[]) {
super(undefined);
this._isV3000 = (src as IFileInfo).contents.includes("V3000");
this._load(src);
}
/**
* Load the source.
*
* @param {IFileInfo | GLModel | IAtom[]} src The source to parse.
*/
_load(src: IFileInfo | GLModel | IAtom[]): void {
// Ensure fields are initialized before doing anything else
if (!this._parsedBonds) {
this._parsedBonds = [];
}
if (!this._atomOrderToSdfIndex) {
this._atomOrderToSdfIndex = new Map();
}
if (!this._sdfIndexToAtomOrder) {
this._sdfIndexToAtomOrder = new Map();
}
const lines = (src as IFileInfo).contents.split(/\r?\n/);
this._atoms = [];
this._parsedBonds = [];
this._atomOrderToSdfIndex.clear();
this._sdfIndexToAtomOrder.clear();
if (this._isV3000) {
this._parseV3000(lines);
} else {
this._parseV2000(lines);
}
}
/**
* Parses a V3000 formatted SDF file from an array of lines.
*
* @param {string[]} lines The lines of the SDF file.
* @private
*/
private _parseV3000(lines: string[]): void {
let inAtomBlock = false;
let inBondBlock = false;
let atomOrder = 0;
for (const line of lines) {
if (line.startsWith("M V30 END ATOM")) {
inAtomBlock = false;
continue;
}
if (line.startsWith("M V30 END BOND")) {
inBondBlock = false;
continue;
}
if (inAtomBlock) {
this._atoms.push(line);
// V3000 atom lines: M V30 <index> <elem> <x> <y> <z> <mass_diff> [properties...]
const parts = line.trim().match(/\S+/g); // Using match for robustness.
if (parts && parts.length >= 3) {
const sdfIndex = parseInt(parts[2], 10);
if (!isNaN(sdfIndex)) {
this._atomOrderToSdfIndex.set(atomOrder, sdfIndex);
this._sdfIndexToAtomOrder.set(sdfIndex, atomOrder);
atomOrder++;
}
}
} else if (inBondBlock) {
// V3000 bond lines: M V30 <idx> <type> <atom1_idx> <atom2_idx> [properties...]
const parts = line.trim().match(/\S+/g); // Using match for robustness.
if (parts && parts.length >= 6) {
const bondType = parseInt(parts[3], 10);
const sdfAtomIdx1 = parseInt(parts[4], 10);
const sdfAtomIdx2 = parseInt(parts[5], 10);
const atomOrderIdx1 = this._sdfIndexToAtomOrder.get(sdfAtomIdx1);
const atomOrderIdx2 = this._sdfIndexToAtomOrder.get(sdfAtomIdx2);
if (
atomOrderIdx1 !== undefined &&
atomOrderIdx2 !== undefined &&
!isNaN(bondType)
) {
this._parsedBonds.push({
atomIndex1: atomOrderIdx1,
atomIndex2: atomOrderIdx2,
bondType: bondType,
});
}
}
}
if (line.startsWith("M V30 BEGIN ATOM")) {
inAtomBlock = true;
}
if (line.startsWith("M V30 BEGIN BOND")) {
inBondBlock = true;
}
}
}
/**
* Parses a V2000 formatted SDF file from an array of lines.
*
* @param {string[]} lines The lines of the SDF file.
* @private
*/
private _parseV2000(lines: string[]): void {
let atomCount = 0;
let bondCount = 0;
let countsLineIndex = -1;
const currentAtomBlockLines: string[] = [];
// Find the counts line (typically 4th line, 0-indexed) for the first molecule
for (let i = 0; i < lines.length; i++) {
const line = lines[i];
if (i >= 3 && line.trim().endsWith("V2000")) {
const parts = line.trim().split(/\s+/);
if (parts.length >= 2) {
const numAtoms = parseInt(parts[0], 10);
const numBonds = parseInt(parts[1], 10);
if (!isNaN(numAtoms) && !isNaN(numBonds)) {
atomCount = numAtoms;
bondCount = numBonds;
countsLineIndex = i;
break;
}
}
}
if (line.trim() === "$$$$") {
// End of the first molecule block
break;
}
}
if (countsLineIndex === -1) {
// Attempt a heuristic parse for atoms if no counts line is found, this is less reliable
let inMoleculeBlock = false;
for (let i = 0; i < lines.length; ++i) {
const line = lines[i];
if (line.includes("M END") || line.trim() === "$$$$") {
break;
}
// Heuristic: Atom lines have X, Y, Z coords and an element symbol.
// Example: " -0.6664 -0.2064 0.1642 C 0 0 0 0 0 0 0 0 0 0 0 0"
if (
line.match(
/^\s*-?\d+\.\d{4}\s+-?\d+\.\d{4}\s+-?\d+\.\d{4}\s+\w/
)
) {
// Assume past header
if (!inMoleculeBlock && i > 2) {
inMoleculeBlock = true;
}
if (inMoleculeBlock) {
currentAtomBlockLines.push(line);
}
} else if (
inMoleculeBlock &&
currentAtomBlockLines.length > 0 &&
!line.match(/^\s*\d+\s+\d+\s+\d+/)
) {
// If we were reading atoms and the next line doesn't look like a bond or atom, stop.
break;
}
}
this._atoms = currentAtomBlockLines;
// Note: Bond parsing is skipped in this heuristic fallback as it's unreliable without counts.
return;
}
// Extract atom lines
const atomBlockStartIndex = countsLineIndex + 1;
for (let i = 0; i < atomCount; i++) {
const atomLineIndex = atomBlockStartIndex + i;
if (atomLineIndex < lines.length) {
currentAtomBlockLines.push(lines[atomLineIndex]);
// Map the 0-indexed position in our _atoms array to the original 1-based SDF atom index
this._atomOrderToSdfIndex.set(i, i + 1);
} else {
// console.warn("SDF parsing: Atom count in counts line exceeds available lines in file.");
break;
}
}
this._atoms = currentAtomBlockLines;
// Extract bond lines
const bondBlockStartIndex = atomBlockStartIndex + atomCount;
for (let i = 0; i < bondCount; i++) {
const bondLineIndex = bondBlockStartIndex + i;
if (bondLineIndex < lines.length) {
const line = lines[bondLineIndex];
// SDF bond line: aaabbbttt... (atom1_idx, atom2_idx, bond_type)
// Atom indices are 1-based in SDF format.
const atomIdx1 = parseInt(line.substring(0, 3).trim(), 10) - 1; // Convert to 0-indexed
const atomIdx2 = parseInt(line.substring(3, 6).trim(), 10) - 1; // Convert to 0-indexed
const bondType = parseInt(line.substring(6, 9).trim(), 10);
if (!isNaN(atomIdx1) && !isNaN(atomIdx2) && !isNaN(bondType)) {
this._parsedBonds.push({
atomIndex1: atomIdx1,
atomIndex2: atomIdx2,
bondType,
});
}
} else {
// console.warn("SDF parsing: Bond count in counts line exceeds available lines in file.");
break;
}
}
}
/**
* Parse an atom line string from SDF into an IAtom object. This method is
* called by the `getAtom` method of the parent class.
*
* @param {string} atomStr The atom line string.
* @param {number} [atomParserIndex] The 0-based index of this atom in the
* parser's `_atoms` list. This parameter
* is required by EasyParserSDF.
* @returns {IAtom | undefined} The parsed atom, or undefined if parsing
* fails.
*/
_parseAtomStr(
atomStr: string,
atomParserIndex?: number
): IAtom | undefined {
if (this._isV3000) {
return this._parseV3000AtomStr(atomStr, atomParserIndex);
} else {
return this._parseV2000AtomStr(atomStr, atomParserIndex);
}
}
/**
* Parses a V3000 atom line string into an IAtom object.
*
* @param {string} atomStr The V3000 atom line string.
* @param {number} [atomParserIndex] The 0-based index of this atom.
* @returns {IAtom | undefined} The parsed atom.
* @private
*/
private _parseV3000AtomStr(
atomStr: string,
atomParserIndex?: number
): IAtom | undefined {
// M V30 <index> <elem> <x> <y> <z> <mass_diff> [key=val] ...
const parts = atomStr.trim().match(/\S+/g);
if (!parts || parts.length < 7) return undefined;
const sdfIndex = parseInt(parts[2], 10);
const elem = parts[3];
const x = parseFloat(parts[4]);
const y = parseFloat(parts[5]);
const z = parseFloat(parts[6]);
// parts[7] is mass difference, which we can ignore for now
let charge = 0;
// Look for charge property in remaining parts
for (let i = 8; i < parts.length; i++) {
if (parts[i].startsWith("CHG=")) {
charge = parseInt(parts[i].substring(4), 10);
if (isNaN(charge)) charge = 0;
break;
}
}
if (isNaN(x) || isNaN(y) || isNaN(z)) return undefined;
const bonds: number[] = [];
const bondOrder: number[] = [];
if (atomParserIndex !== undefined) {
this._parsedBonds.forEach((bond) => {
if (bond.atomIndex1 === atomParserIndex) {
bonds.push(bond.atomIndex2);
bondOrder.push(bond.bondType);
} else if (bond.atomIndex2 === atomParserIndex) {
bonds.push(bond.atomIndex1);
bondOrder.push(bond.bondType);
}
});
}
return {
x,
y,
z,
elem,
serial: sdfIndex,
atom: elem,
resn: "UNL",
chain: "A",
resi: 1,
altLoc: " ",
b: charge,
bonds,
bondOrder,
};
}
/**
* Parses a V2000 atom line string into an IAtom object.
*
* @param {string} atomStr The V2000 atom line string.
* @param {number} [atomParserIndex] The 0-based index of this atom.
* @returns {IAtom | undefined} The parsed atom.
* @private
*/
private _parseV2000AtomStr(
atomStr: string,
atomParserIndex?: number
): IAtom | undefined {
// SDF atom line format (V2000):
// Columns Content
// 1-10 x-coordinate
// 11-20 y-coordinate
// 21-30 z-coordinate
// 32-34 Atom symbol (left-justified)
// 35-36 Mass difference (dd) from default isotope mass. (+/- relative to default)
// 37-39 Charge (ccc): 0 (uncharged or not specified), 1 (+3), 2 (+2), 3 (+1), 4 (doublet radical), 5 (-1), 6 (-2), 7 (-3)
// ... more fields exist but are not parsed by this basic parser for now.
// Basic check
if (atomStr.length < 34) {
return undefined;
}
// atomParserIndex is essential for SDF bond parsing, ensure it's provided.
if (atomParserIndex === undefined) {
// This case should ideally not be reached if getAtom in parent always passes it.
// console.error("EasyParserSDF._parseAtomStr: atomParserIndex is undefined. This is required for SDF parsing.");
return undefined;
}
const x = parseFloat(atomStr.substring(0, 10).trim());
const y = parseFloat(atomStr.substring(10, 20).trim());
const z = parseFloat(atomStr.substring(20, 30).trim());
const elem = atomStr.substring(31, 34).trim(); // Atom symbol
let charge = 0;
if (atomStr.length >= 39) {
const chargeCode = parseInt(atomStr.substring(36, 39).trim(), 10);
switch (chargeCode) {
case 1:
charge = 3;
break;
case 2:
charge = 2;
break;
case 3:
charge = 1;
break;
// case 4: // doublet radical, charge is still 0. We don't store radical info in IAtom.
case 5:
charge = -1;
break;
case 6:
charge = -2;
break;
case 7:
charge = -3;
break;
default:
charge = 0;
break; // Includes 0 for uncharged
}
}
const bonds: number[] = [];
const bondOrder: number[] = [];
// atomParserIndex is the 0-based index of the current atom line in this._atoms
this._parsedBonds.forEach((bond) => {
if (bond.atomIndex1 === atomParserIndex) {
bonds.push(bond.atomIndex2);
bondOrder.push(bond.bondType);
} else if (bond.atomIndex2 === atomParserIndex) {
bonds.push(bond.atomIndex1);
bondOrder.push(bond.bondType);
}
});
const originalSdfAtomNumber =
this._atomOrderToSdfIndex.get(atomParserIndex);
return {
x,
y,
z,
elem,
serial: originalSdfAtomNumber, // Use original 1-based SDF atom number for serial
atom: elem, // In SDF, atom name is usually the element symbol
resn: "UNL", // SDF doesn't typically have residue names
chain: "A", // SDF doesn't typically have chains
resi: 1, // SDF doesn't typically have residue indices
altLoc: " ", // SDF doesn't have alternate locations in the same way as PDB
b: charge, // Using 'b' for charge for consistency with EasyParserMol2
bonds,
bondOrder,
// hetflag, etc. are not typically part of basic SDF atom lines
};
}
/**
* Get the atom at the given 0-based index.
* Overrides parent to pass the index to `_parseAtomStr` for context.
*
* @param {number} idx The 0-based index of the atom in the internal list.
* @returns {IAtom} The parsed atom object.
* @throws {Error} if parsing fails.
*/
getAtom(idx: number): IAtom {
const atomEntry = this._atoms[idx];
// If it's not a string, it's already been parsed and cached.
if (typeof atomEntry !== "string") {
return atomEntry as IAtom;
}
// Parse the string representation of the atom.
const parsedAtom = this._parseAtomStr(atomEntry as string, idx);
if (parsedAtom === undefined) {
throw new Error(
`Failed to parse SDF atom line at index ${idx}: "${atomEntry}"`
);
}
// Cache the parsed atom object to avoid re-parsing.
this._atoms[idx] = parsedAtom;
return parsedAtom;
}
}
|