File size: 2,532 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 | import type { TreeNodeList } from "@/TreeNodes/TreeNodeList/TreeNodeList";
import { parseMolecularModelFromTexts } from "./ParseMolModelsUtils";
import { IFormatInfo } from "../Types/MolFormats";
import { FileInfo } from "@/FileSystem/FileInfo";
import { IGen3DOptions, convertFileInfosOpenBabel } from "@/FileSystem/OpenBabel/OpenBabel";
/**
* Uses OpenBabel to parse the a molecular-model file.
*
* @param {FileInfo} fileInfo The file to parse.
* @param {IFormatInfo} formatInfo The format of the file.
* @param {boolean} [desalt=false] Whether to desalt the
* molecules.
* @param {IGen3DOptions} [gen3D=undefined] Whether and how to generate 3D
* coordinates.
* @param {boolean} [surpressMsgs=false] Whether to surpress messages.
* @returns {Promise<TreeNodeList>} A promise that resolves when the file is
* parsed. The promise resolves to an array of TreeNode objects, one for each
* frame. Can also resolve void.
*/
export function parseUsingOpenBabel(
fileInfo: FileInfo,
formatInfo: IFormatInfo,
desalt = false,
gen3D?: IGen3DOptions,
surpressMsgs?: boolean
): Promise<TreeNodeList> {
const targetFormat = formatInfo.hasBondOrders ? "mol2" : "pdb";
// Convert it to MOL2 format and load that using 3dmoljs.
return convertFileInfosOpenBabel([fileInfo], targetFormat, gen3D, undefined, desalt, surpressMsgs)
.then((contents: string[]) => {
const hasMultipleFrames = contents.length > 1;
const fileInfos = contents.map((c, i) => {
// Separate basename and extension.
// Need to account for multiple frames.
let { name } = fileInfo;
if (hasMultipleFrames) {
// const prts = getFileNameParts(fileInfo.name);
// name = `(frame ${i + 1}) ${prts.basename}.${prts.ext}`;
name = `(frame${i + 1}) ${fileInfo.name}`;
}
return new FileInfo({
contents: c,
name: name,
});
});
return parseMolecularModelFromTexts(
fileInfos,
targetFormat
);
})
.catch((err) => {
// It's a catch block for the promise returned by
// convertMolFormatOpenBabel.
throw err;
});
}
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