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import { getMoleculesFromStore } from "@/Store/StoreExternalAccess";
import { TreeNode } from "@/TreeNodes/TreeNode/TreeNode";
import { TreeNodeList } from "@/TreeNodes/TreeNodeList/TreeNodeList";
import {
IAtom,
SelectedType,
TreeNodeType,
} from "@/UI/Navigation/TreeView/TreeInterfaces";
import { convertFileInfosOpenBabel } from "@/FileSystem/OpenBabel/OpenBabel";
import { FileInfo } from "@/FileSystem/FileInfo";
// Mock dependencies
jest.mock("@/Store/StoreExternalAccess", () => ({
getMoleculesFromStore: jest.fn(),
}));
jest.mock("@/FileSystem/OpenBabel/OpenBabel", () => ({
convertFileInfosOpenBabel: jest.fn(),
}));
// Mock the module that uses `import.meta.url` to prevent compilation errors in Jest.
// This also breaks a circular dependency by delaying the instantiation of TreeNodeList.
jest.mock(
"@/FileSystem/LoadSaveMolModels/ParseMolModels/ParseMolModelsUtils",
() => ({
parseMolecularModelFromTexts: jest.fn().mockImplementation(() => {
// Dynamically require TreeNodeList inside the mock implementation
// to break the circular dependency at module load time.
const {
TreeNodeList,
} = require("@/TreeNodes/TreeNodeList/TreeNodeList");
return Promise.resolve(new TreeNodeList([]));
}),
})
);
describe("MoleculeInput component filtering", () => {
beforeEach(() => {
// Clear mocks before each test
(getMoleculesFromStore as jest.Mock).mockClear();
(convertFileInfosOpenBabel as jest.Mock).mockClear();
// Mock the implementation for OpenBabel to just pass through the PDB content
// This simulates a format conversion from PDB to PDB.
(convertFileInfosOpenBabel as jest.Mock).mockImplementation(
async (fileInfos: FileInfo[], targetFormat: string) => {
// This test only deals with pdb and pdbqt which are text based.
if (
targetFormat === "pdb" ||
targetFormat === "pdbqt" ||
targetFormat === "pdbqtlig"
) {
return fileInfos.map((fi) => fi.contents);
}
return [];
}
);
// --- Create a mock TreeNodeList representing a parsed PDB file ---
// This structure mimics a protein with associated metal and solvent.
const proteinAtom: IAtom = {
serial: 1,
atom: "CA",
resn: "GLY",
chain: "A",
resi: 1,
elem: "C",
x: 1,
y: 1,
z: 1,
bonds: [],
bondOrder: [],
};
const metalAtom: IAtom = {
serial: 2,
atom: "ZN",
resn: "ZN",
chain: "A",
resi: 201,
elem: "ZN",
hetflag: true,
x: 2,
y: 2,
z: 2,
bonds: [],
bondOrder: [],
};
const solventAtom: IAtom = {
serial: 3,
atom: "O",
resn: "HOH",
chain: "A",
resi: 301,
elem: "O",
hetflag: true,
x: 3,
y: 3,
z: 3,
bonds: [],
bondOrder: [],
};
const nucleicAtom: IAtom = {
serial: 4,
atom: "P",
resn: "A",
chain: "B",
resi: 1,
elem: "P",
x: 4,
y: 4,
z: 4,
bonds: [],
bondOrder: [],
};
// Terminal nodes that hold the actual molecular data
const proteinTerminalNode = new TreeNode({
title: "Protein Chain A",
type: TreeNodeType.Protein,
model: [proteinAtom],
visible: true,
selected: SelectedType.False,
treeExpanded: false,
focused: false,
viewerDirty: false,
src: "test.pdb",
});
const metalTerminalNode = new TreeNode({
title: "ZN",
type: TreeNodeType.Metal,
model: [metalAtom],
visible: true,
selected: SelectedType.False,
treeExpanded: false,
focused: false,
viewerDirty: false,
src: "test.pdb",
});
const solventTerminalNode = new TreeNode({
title: "HOH",
type: TreeNodeType.Solvent,
model: [solventAtom],
visible: true,
selected: SelectedType.False,
treeExpanded: false,
focused: false,
viewerDirty: false,
src: "test.pdb",
});
const nucleicTerminalNode = new TreeNode({
title: "NA Chain B",
type: TreeNodeType.Nucleic,
model: [nucleicAtom],
visible: true,
selected: SelectedType.False,
treeExpanded: false,
focused: false,
viewerDirty: false,
src: "test.pdb",
});
// The root node containing the hierarchy
const rootNode = new TreeNode({
title: "MyMolecule",
visible: true,
selected: SelectedType.False,
treeExpanded: true,
focused: false,
viewerDirty: false,
nodes: new TreeNodeList([
proteinTerminalNode,
metalTerminalNode,
solventTerminalNode,
nucleicTerminalNode,
]),
src: "test.pdb",
});
proteinTerminalNode.parentId = rootNode.id;
metalTerminalNode.parentId = rootNode.id;
solventTerminalNode.parentId = rootNode.id;
nucleicTerminalNode.parentId = rootNode.id;
const mockMolecules = new TreeNodeList([rootNode]);
(getMoleculesFromStore as jest.Mock).mockReturnValue(mockMolecules);
});
it("should include protein, metal, solvent, and nucleic acid by default", async () => {
const params: IMoleculeInputParams = {
considerProteins: true,
considerCompounds: false, // Ensure we are only testing protein-related components
proteinFormat: "pdb",
// Defaults are includeMetalsAsProtein: true, includeSolventAsProtein: true
};
const moleculeInput = new MoleculeInput(params);
const result =
(await moleculeInput.getProtAndCompoundPairs()) as FileInfo[];
expect(result).toHaveLength(1);
const pdbContent = result[0].contents;
expect(pdbContent).toMatch(/ATOM\s+.*\s+CA\s+GLY\s+/); // Protein
expect(pdbContent).toMatch(/HETATM\s+.*\s+ZN\s+ZN\s+/); // Metal
expect(pdbContent).toMatch(/HETATM\s+.*\s+O\s+HOH\s+/); // Solvent
expect(pdbContent).toMatch(/HETATM\s+.*\s+P\s+A\s+/); // Nucleic Acid
});
it("should exclude metals when includeMetalsAsProtein is false", async () => {
const params: IMoleculeInputParams = {
considerProteins: true,
considerCompounds: false,
proteinFormat: "pdb",
includeMetalsAsProtein: false,
includeSolventAsProtein: true,
};
const moleculeInput = new MoleculeInput(params);
const result =
(await moleculeInput.getProtAndCompoundPairs()) as FileInfo[];
expect(result).toHaveLength(1);
const pdbContent = result[0].contents;
expect(pdbContent).toMatch(/ATOM\s+.*\s+CA\s+GLY\s+/); // Protein
expect(pdbContent).not.toMatch(/HETATM\s+.*\s+ZN\s+ZN\s+/); // Metal excluded
expect(pdbContent).toMatch(/HETATM\s+.*\s+O\s+HOH\s+/); // Solvent included
expect(pdbContent).toMatch(/HETATM\s+.*\s+P\s+A\s+/); // Nucleic Acid included
});
it("should exclude solvent when includeSolventAsProtein is false", async () => {
const params: IMoleculeInputParams = {
considerProteins: true,
considerCompounds: false,
proteinFormat: "pdb",
includeMetalsAsProtein: true,
includeSolventAsProtein: false,
};
const moleculeInput = new MoleculeInput(params);
const result =
(await moleculeInput.getProtAndCompoundPairs()) as FileInfo[];
expect(result).toHaveLength(1);
const pdbContent = result[0].contents;
expect(pdbContent).toMatch(/ATOM\s+.*\s+CA\s+GLY\s+/); // Protein
expect(pdbContent).toMatch(/HETATM\s+.*\s+ZN\s+ZN\s+/); // Metal included
expect(pdbContent).not.toMatch(/HETATM\s+.*\s+O\s+HOH\s+/); // Solvent excluded
expect(pdbContent).toMatch(/HETATM\s+.*\s+P\s+A\s+/); // Nucleic Acid included
});
it("should exclude nucleic acids when includeNucleicAsProtein is false", async () => {
const params: IMoleculeInputParams = {
considerProteins: true,
considerCompounds: false,
proteinFormat: "pdb",
includeNucleicAsProtein: false,
};
const moleculeInput = new MoleculeInput(params);
const result =
(await moleculeInput.getProtAndCompoundPairs()) as FileInfo[];
expect(result).toHaveLength(1);
const pdbContent = result[0].contents;
expect(pdbContent).toMatch(/ATOM\s+.*\s+CA\s+GLY\s+/); // Protein
expect(pdbContent).toMatch(/HETATM\s+.*\s+ZN\s+ZN\s+/); // Metal included
expect(pdbContent).toMatch(/HETATM\s+.*\s+O\s+HOH\s+/); // Solvent included
expect(pdbContent).not.toMatch(/HETATM\s+.*\s+P\s+A\s+/); // Nucleic Acid excluded
});
it("should exclude both metal and solvent when both flags are false", async () => {
const params: IMoleculeInputParams = {
considerProteins: true,
considerCompounds: false,
proteinFormat: "pdb",
includeMetalsAsProtein: false,
includeSolventAsProtein: false,
};
const moleculeInput = new MoleculeInput(params);
const result =
(await moleculeInput.getProtAndCompoundPairs()) as FileInfo[];
expect(result).toHaveLength(1);
const pdbContent = result[0].contents;
expect(pdbContent).toMatch(/ATOM\s+.*\s+CA\s+GLY\s+/); // Protein
expect(pdbContent).not.toMatch(/HETATM\s+.*\s+ZN\s+ZN\s+/); // Metal excluded
expect(pdbContent).not.toMatch(/HETATM\s+.*\s+O\s+HOH\s+/); // Solvent excluded
expect(pdbContent).toMatch(/HETATM\s+.*\s+P\s+A\s+/); // Nucleic Acid included
});
});
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