File size: 4,291 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 | import { getMoleculesFromStore } from "@/Store/StoreExternalAccess";
import { TreeNodeList } from "@/TreeNodes/TreeNodeList/TreeNodeList";
import { getTerminalNodesToConsider } from "@/UI/Navigation/TreeView/TreeUtils";
import { IMolsToConsider, ICompiledNodes } from "./Types";
import { TreeNodeType } from "@/UI/Navigation/TreeView/TreeInterfaces";
import { TreeNode } from "@/TreeNodes/TreeNode/TreeNode";
/**
* Runs the job when the user wants to save in a non-molmoda format, by
* molecule.
*
* @param {IMolsToConsider} molsToConsider The molecules to save.
* @param {boolean} separateComponents Whether to separate components into different files.
* @returns {ICompiledNodes} The compiled nodes organized by type and grouping.
*/
export function compileByMolecule(
molsToConsider: IMolsToConsider,
separateComponents: boolean
): ICompiledNodes {
// Not using molmoda format. Create ZIP file with protein and small
// molecules.
const byType = new Map<TreeNodeType, TreeNodeList[]>();
const nodeGroups: TreeNodeList[] = [];
const compoundsNodes = new TreeNodeList();
getMoleculesFromStore().forEach((topLevelNode) => {
// Get all descendants for this molecule
const allNodes = new TreeNodeList([topLevelNode]);
if (topLevelNode.nodes) {
allNodes.extend(topLevelNode.nodes);
}
// Filter based on user selection (visible, selected, etc.)
let terminalNodes = getTerminalNodesToConsider(
molsToConsider,
allNodes
);
// Remove undefineds, regions
terminalNodes = terminalNodes.filters.removeUndefined();
terminalNodes = terminalNodes.filters.keepRegions(false);
if (terminalNodes.length === 0) return;
if (separateComponents) {
// Group by type
const nodesByType = new Map<TreeNodeType, TreeNodeList>();
// Helper lists for legacy output
const nonCompoundNodesForThisMol = new TreeNodeList();
terminalNodes.forEach((node) => {
const type = node.type || TreeNodeType.Other;
if (!nodesByType.has(type)) {
nodesByType.set(type, new TreeNodeList());
}
nodesByType.get(type)?.push(node);
// Legacy population
if (type === TreeNodeType.Compound) {
compoundsNodes.push(node);
} else {
nonCompoundNodesForThisMol.push(node);
}
});
// Process each type for byType map
nodesByType.forEach((nodes, type) => {
if (!byType.has(type)) {
byType.set(type, []);
}
// Compounds are always saved individually (one file per compound)
if (type === TreeNodeType.Compound) {
nodes.forEach((node) => {
byType.get(type)?.push(new TreeNodeList([node]));
});
} else {
// Other components (Protein, Nucleic, Metal, etc.) are grouped per top-level molecule.
// So all chains of Protein A go into one file.
byType.get(type)?.push(nodes);
}
});
// Legacy: Add non-compound nodes group
if (nonCompoundNodesForThisMol.length > 0) {
nodeGroups.push(nonCompoundNodesForThisMol);
}
} else {
// Lump everything for this molecule into one group under 'Other' (or mix)
if (!byType.has(TreeNodeType.Other)) {
byType.set(TreeNodeType.Other, []);
}
byType.get(TreeNodeType.Other)?.push(terminalNodes);
// For legacy compatibility, if we aren't separating, we treat everything as a "non-compound" group usually,
// or we separate compounds if they exist?
// Original behavior for !keepCompoundsSeparate was grouping everything into nodeGroups.
// But usually keepCompoundsSeparate passed to compileByMolecule was true in the calling code of compileMolModels.
// In compileMolModels (original), if !keepCompoundsSeparate, it grouped everything.
// Here, if separateComponents is false, we put everything in nodeGroups.
nodeGroups.push(terminalNodes);
}
});
return { byType, nodeGroups, compoundsNodes };
}
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