File size: 4,547 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 | import { FileInfo } from "@/FileSystem/FileInfo";
import { convertFileInfosOpenBabel } from "@/FileSystem/OpenBabel/OpenBabel";
import { TreeNodeList } from "@/TreeNodes/TreeNodeList/TreeNodeList";
import { _convertTreeNodeListToPDB } from "./_ConvertTreeNodeListToPDB";
import { TreeNode } from "@/TreeNodes/TreeNode/TreeNode";
import { GLModel } from "@/UI/Panels/Viewer/GLModelType";
import { IAtom } from "@/UI/Navigation/TreeView/TreeInterfaces";
import { IFileInfo } from "@/FileSystem/Types";
import { getFileNameParts } from "@/FileSystem/FilenameManipulation";
// function bondOrdersAssigned(treeNodes: TreeNode[]): boolean {
// const bondOrders: Set<number> = new Set();
// for (const treeNode of treeNodes) {
// const atoms = getAtomsOfModel(treeNode.model as GLModel);
// for (const atom of atoms) {
// for (const bondOrder of atom.bondOrder) {
// bondOrders.add(bondOrder);
// }
// }
// }
// return !(bondOrders.size === 1 && bondOrders.has(1));
// }
/**
* Given a list of mol containers, convert them to a specified molecular format.
* Don't call this function directly. Instead, use TreeNodeList.toFileInfos().
*
* @param {TreeNodeList} treeNodeList The list of mol containers.
* @param {string} targetExt The extension of the format to convert
* to.
* @param {boolean} [merge=false] Whether to merge the models into a
* single PDB string.
* @returns {FileInfo[]} The text-formatted (e.g., PDB, MOL2) strings.
*/
export function _convertTreeNodeList(
treeNodeList: TreeNodeList,
targetExt: string,
merge = true
): Promise<FileInfo[]> {
targetExt = targetExt.toLowerCase();
// let calculateBondOrders = false;
// if (formatInf.hasBondOrders === true) {
// // Sometimes a molecule might not have bond orders assigned, even if the
// // format supports it. In this case, use PDB as an intermediary because
// // they will force conversion via open babel, which will assign bond
// // orders for you.
// if (!bondOrdersAssigned(treeNodeList)) {
// calculateBondOrders = true;
// } else {
// // Use MOL2 as intermediary. First, convert the mol containers to a MOL2
// // string.
// molTxts = convertTreeNodeToMol2(treeNodeList, merge);
// intermediaryExt = "mol2";
// // If MOL2 is destination format, just return that
// if (formatInf.primaryExt === "mol2") {
// return Promise.resolve(molTxts);
// }
// }
// }
// if (formatInf.hasBondOrders !== true || calculateBondOrders) {
// Get all the models from the tree nodes.
const mols = treeNodeList.filters
.keepModels()
.map((treeNode: TreeNode) => treeNode.model as GLModel | IAtom[] | IFileInfo[]);
const allModelsAreIFileInfos = mols.every((mol) => {
return mol.contents && mol.name;
})
let fileInfos: FileInfo[] = [];
if (merge || !allModelsAreIFileInfos) {
// If you need to merge the molecules, or if the models are not
// IFileInfos, go through a PDB intermediate.
// Use PDB as intermediary. First, convert the mol containers to a PDB
// string.
let molTxts: string[] = [];
molTxts = _convertTreeNodeListToPDB(treeNodeList, merge);
fileInfos = molTxts.map(
(molTxt: string, idx: number) =>
new FileInfo({
name: `tmpmol${idx}.pdb`,
contents: molTxt,
})
);
} else {
// If the models are already IFileInfos (and no merging), just use them.
fileInfos = mols.map((mol: IFileInfo, idx: number) => {
const {ext} = getFileNameParts(mol.name);
mol.name = `tmpmol${idx}.${ext}`;
return new FileInfo(mol)
});
}
return convertFileInfosOpenBabel(fileInfos, targetExt).then(
(contents: string[]) => {
return contents.map((content: string) => {
return new FileInfo({
name: `tmpmol.${targetExt}`,
contents: content,
});
});
}
);
// const promises = fileInfos.map((fileInfo: FileInfo) =>
// fileInfo.convertFromPDBTxt(targetExt)
// );
// return Promise.all(promises);
}
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