File size: 2,678 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 | // Originally, I repurposed the 3dmol.js parser for when plugins need to access
// information about atoms. But I came to realize that this is overkill. I'm now
// going to create a minimal parser for PDB and MOL2 files instead, since these
// are the formats that molmoda uses internally for protein and compound files,
// respectively. It doens't need to have a lot of functionality. It just needs
// to be light on memory.
import { IFileInfo } from "@/FileSystem/Types";
import { EasyParserParent } from "./EasyParserParent";
import { IAtom } from "@/UI/Navigation/TreeView/TreeInterfaces";
/**
* A parser for MOL2 files.
*/
export class EasyParserMol2 extends EasyParserParent {
/**
* Load the source.
*
* @param {IFileInfo} src The source to parse.
*/
_load(src: IFileInfo): void {
if (src.contents.indexOf("@<TRIPOS>ATOM") === -1) {
throw new Error("MOL2 file does not contain @<TRIPOS>ATOM section. Incorrect format?");
}
const prts = src.contents.split("@<TRIPOS>ATOM");
let atoms = prts[1].split("@<TRIPOS>")[0];
// While first char is newline, remove it
while (atoms[0] === "\n") {
atoms = atoms.slice(1);
}
// Trim the right side.
atoms = atoms.trimRight();
this._atoms = atoms.split("\n").map((atom: string) => atom.trim());
}
/**
* Parse an atom.
*
* @param {string} atomStr The string to parse.
* @param {number} [atomParserIndex] Optional: The 0-based index of this atom in the parser's internal list.
* @returns {IAtom} The parsed atom.
*/
_parseAtomStr(atomStr: string, atomParserIndex?: number): IAtom {
// Atom looks like this:
// " 31 C4 39.2670 22.5690 13.2440 C.ar 501 ATP501 0.1692"
// Split by spaces.
const [serialOrig, atomName, xOrig, yOrig, zOrig, elemOrig, resiOrig, resn, bOrig] = atomStr.split(/\s+/);
const serial = parseInt(serialOrig);
const x = parseFloat(xOrig);
const y = parseFloat(yOrig);
const z = parseFloat(zOrig);
const elem = elemOrig.split(".")[0]
const resi = parseInt(resiOrig);
const b = parseFloat(bOrig);
// In this context, b is the charge.
// Some not specified
const chain = "A";
const altLoc = " ";
return {
resn,
chain,
resi,
x,
y,
z,
bondOrder: [],
bonds: [],
elem,
serial,
altLoc,
b,
atom: atomName,
};
}
} |