File size: 9,326 Bytes
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import { IAtom } from "@/UI/Navigation/TreeView/TreeInterfaces";
import { makeEasyParser } from "./index";
import { EasyParserPDB } from "./EasyParserPDB";
import { EasyParserMol2 } from "./EasyParserMol2";
import { EasyParserSDF } from "./EasyParserSDF";
import { EasyParserIAtomList } from "./EasyParserIAtomList";
import { EasyParserGLModel } from "./EasyParserGLModel";
import { GLModel } from "@/UI/Panels/Viewer/GLModelType";
// Mock data for testing
const pdbContent = `
ATOM 1 N ALA A 1 27.222 18.520 27.241 1.00 20.00 N
ATOM 2 CA ALA A 1 27.827 19.324 28.257 1.00 20.00 C
HETATM 1039 ZN ZN A 201 24.620 20.301 30.824 1.00 23.32 ZN
`;
const mol2Content = `
@<TRIPOS>MOLECULE
MyMol
5 4 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 C1 1.0000 2.0000 3.0000 C.3 1 LIG1 -0.1
2 N1 1.5000 2.5000 3.5000 N.4 1 LIG1 -0.5
3 O1 2.0000 3.0000 4.0000 O.2 1 LIG1 -0.4
4 H1 0.5000 1.5000 2.5000 H 1 LIG1 0.1
5 H2 1.2000 2.2000 3.2000 H 1 LIG1 0.1
@<TRIPOS>BOND
1 1 2 1
2 2 3 2
3 1 4 1
4 1 5 1
`;
const sdfV2000Content = `
MyMolecule
-ISIS- 08212314022D
3 2 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 2 0 0 0 0
M END
$$$$
`;
const sdfV3000Content = `
MyV3000Mol
-ISIS- 08212314033D
0 0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 2 1 0 0 0
M V30 BEGIN ATOM
M V30 1 C 1.0 2.0 3.0 0
M V30 2 N 2.0 3.0 4.0 0 CHG=1
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 END BOND
M V30 END CTAB
M END
$$$$
`;
const flatSdfContent = `
FlatMolecule
-ISIS- 08212314042D
2 1 0 0 0 0 0 0 0 0999 V2000
1.2345 5.6789 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2345 -5.6789 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
M END
$$$$
`;
const iAtomListContent: IAtom[] = [
{ resn: 'ALA', chain: 'A', resi: 1, x: 1, y: 1, z: 1, elem: 'C', bonds: [], bondOrder: [] },
{ resn: 'LYS', chain: 'B', resi: 2, x: 2, y: 2, z: 2, elem: 'N', bonds: [], bondOrder: [] }
];
const mockGLModel: GLModel = {
selectedAtoms: () => iAtomListContent,
removeAtoms: () => {},
hide: () => {},
show: () => {},
setStyle: () => {},
setClickable: () => {},
setHoverable: () => {},
id: 123
};
describe("EasyParser Factory and Classes", () => {
describe("makeEasyParser factory", () => {
it("should create EasyParserPDB for .pdb files", () => {
const fileInfo = new FileInfo({ name: "protein.pdb", contents: pdbContent });
const parser = makeEasyParser(fileInfo);
expect(parser).toBeInstanceOf(EasyParserPDB);
});
it("should create EasyParserMol2 for .mol2 files", () => {
const fileInfo = new FileInfo({ name: "ligand.mol2", contents: mol2Content });
const parser = makeEasyParser(fileInfo);
expect(parser).toBeInstanceOf(EasyParserMol2);
});
it("should create EasyParserSDF for .sdf files", () => {
const fileInfo = new FileInfo({ name: "compound.sdf", contents: sdfV2000Content });
const parser = makeEasyParser(fileInfo);
expect(parser).toBeInstanceOf(EasyParserSDF);
});
it("should create EasyParserIAtomList for IAtom[]", () => {
const parser = makeEasyParser(iAtomListContent);
expect(parser).toBeInstanceOf(EasyParserIAtomList);
expect(parser.length).toBe(2);
});
it("should create EasyParserGLModel for GLModel", () => {
const parser = makeEasyParser(mockGLModel);
expect(parser).toBeInstanceOf(EasyParserGLModel);
expect(parser.length).toBe(2);
});
});
describe("EasyParserPDB", () => {
const fileInfo = new FileInfo({ name: "protein.pdb", contents: pdbContent });
const parser = new EasyParserPDB(fileInfo);
it("should load 3 atom lines", () => {
expect(parser.length).toBe(3);
});
it("should parse an ATOM line correctly", () => {
const atom = parser.getAtom(0);
expect(atom.serial).toBe(1);
expect(atom.atom).toBe("N");
expect(atom.resn).toBe("ALA");
expect(atom.chain).toBe("A");
expect(atom.resi).toBe(1);
expect(atom.x).toBe(27.222);
expect(atom.y).toBe(18.520);
expect(atom.z).toBe(27.241);
expect(atom.b).toBe(20.00);
expect(atom.elem).toBe("N");
expect(atom.hetflag).toBe(false);
});
it("should parse a HETATM line correctly", () => {
const atom = parser.getAtom(2);
expect(atom.serial).toBe(1039);
expect(atom.atom).toBe("ZN");
expect(atom.elem).toBe("Zn");
expect(atom.hetflag).toBe(true);
});
});
describe("EasyParserMol2", () => {
const fileInfo = new FileInfo({ name: "ligand.mol2", contents: mol2Content });
const parser = new EasyParserMol2(fileInfo);
it("should load 5 atoms", () => {
expect(parser.length).toBe(5);
});
it("should parse a MOL2 atom line correctly", () => {
const atom = parser.getAtom(1);
expect(atom.serial).toBe(2);
expect(atom.atom).toBe("N1");
expect(atom.x).toBe(1.5);
expect(atom.y).toBe(2.5);
expect(atom.z).toBe(3.5);
expect(atom.elem).toBe("N");
expect(atom.resn).toBe("LIG1");
expect(atom.b).toBe(-0.5); // Charge
});
});
describe("EasyParserSDF", () => {
it("should correctly parse V2000 format", () => {
const fileInfo = new FileInfo({ name: "v2000.sdf", contents: sdfV2000Content });
const parser = new EasyParserSDF(fileInfo);
expect(parser.length).toBe(3);
const atom1 = parser.getAtom(0);
expect(atom1.elem).toBe("C");
expect(atom1.x).toBe(0.0);
const atom2 = parser.getAtom(1);
expect(atom2.bonds).toEqual([0]); // Bonded to first atom (index 0)
expect(atom2.bondOrder).toEqual([1]); // Single bond
});
it("should correctly parse V3000 format", () => {
const fileInfo = new FileInfo({ name: "v3000.sdf", contents: sdfV3000Content });
const parser = new EasyParserSDF(fileInfo);
expect(parser.length).toBe(2);
const atom1 = parser.getAtom(0);
expect(atom1.elem).toBe("C");
expect(atom1.x).toBe(1.0);
expect(atom1.bonds).toEqual([1]);
expect(atom1.bondOrder).toEqual([1]);
const atom2 = parser.getAtom(1);
expect(atom2.elem).toBe("N");
expect(atom2.b).toBe(1); // Charge
});
});
describe("EasyParserParent functionality", () => {
it("isFlat() should return true for 2D structures", () => {
const fileInfo = new FileInfo({ name: "flat.sdf", contents: flatSdfContent });
const parser = makeEasyParser(fileInfo);
expect(parser.isFlat()).toBe(true);
});
it("isFlat() should return false for 3D structures", () => {
const fileInfo = new FileInfo({ name: "3d.pdb", contents: pdbContent });
const parser = makeEasyParser(fileInfo);
expect(parser.isFlat()).toBe(false);
});
it("isWithinDistance() should work correctly", () => {
const atoms1: IAtom[] = [{ resn: 'A', chain: 'A', resi: 1, x: 0, y: 0, z: 0, elem: 'C', bonds: [], bondOrder: [] }];
const atoms2: IAtom[] = [{ resn: 'B', chain: 'B', resi: 1, x: 5, y: 0, z: 0, elem: 'N', bonds: [], bondOrder: [] }];
const atoms3: IAtom[] = [{ resn: 'C', chain: 'C', resi: 1, x: 11, y: 0, z: 0, elem: 'O', bonds: [], bondOrder: [] }];
const parser1 = new EasyParserIAtomList(atoms1);
const parser2 = new EasyParserIAtomList(atoms2);
const parser3 = new EasyParserIAtomList(atoms3);
expect(parser1.isWithinDistance(parser2, 6)).toBe(true);
expect(parser1.isWithinDistance(parser3, 10)).toBe(false);
});
it("getUniqueResidues() should return unique names and IDs", () => {
const atoms: IAtom[] = [
{ resn: 'ALA', chain: 'A', resi: 10, elem: 'C', x: 0, y: 0, z: 0, bonds: [], bondOrder: [] },
{ resn: 'ALA', chain: 'A', resi: 10, elem: 'N', x: 0, y: 0, z: 0, bonds: [], bondOrder: [] },
{ resn: 'LYS', chain: 'A', resi: 11, elem: 'C', x: 0, y: 0, z: 0, bonds: [], bondOrder: [] },
];
const parser = new EasyParserIAtomList(atoms);
const { names, ids } = parser.getUniqueResidues();
expect(Array.from(names)).toEqual(['ALA', 'LYS']);
expect(Array.from(ids)).toEqual([10, 11]);
});
});
}); |