ply spec

src/mol-io/reader/_spec/mol2.spec.ts

@@ -265,10 +265,10 @@ describe('mol2 reader', () => {
         expect(molecule.num_subst).toBe(0);
         expect(molecule.num_feat).toBe(0);
         expect(molecule.num_sets).toBe(0);
-        expect(molecule.mol_type).toBe("SMALL")
-        expect(molecule.charge_type).toBe("GASTEIGER");
-        expect(molecule.status_bits).toBe("");
-        expect(molecule.mol_comment).toBe("");
+        expect(molecule.mol_type).toBe('SMALL')
+        expect(molecule.charge_type).toBe('GASTEIGER');
+        expect(molecule.status_bits).toBe('');
+        expect(molecule.mol_comment).toBe('');
 
         // required atom fields
         expect(atoms.count).toBe(26);
@@ -277,7 +277,7 @@ describe('mol2 reader', () => {
         expect(atoms.x.value(0)).toBeCloseTo(1.7394, 0.001);
         expect(atoms.y.value(0)).toBeCloseTo(-2.1169, 0.0001);
         expect(atoms.z.value(0)).toBeCloseTo(-1.0893, 0.0001);
-        expect(atoms.atom_type.value(0)).toBe("O.3");
+        expect(atoms.atom_type.value(0)).toBe('O.3');
 
         // optional atom fields
         expect(atoms.subst_id.value(0)).toBe(1);
@@ -316,10 +316,10 @@ describe('mol2 reader', () => {
         expect(molecule.num_subst).toBe(0);
         expect(molecule.num_feat).toBe(0);
         expect(molecule.num_sets).toBe(0);
-        expect(molecule.mol_type).toBe("SMALL")
-        expect(molecule.charge_type).toBe("GASTEIGER");
-        expect(molecule.status_bits).toBe("");
-        expect(molecule.mol_comment).toBe("");
+        expect(molecule.mol_type).toBe('SMALL')
+        expect(molecule.charge_type).toBe('GASTEIGER');
+        expect(molecule.status_bits).toBe('');
+        expect(molecule.mol_comment).toBe('');
 
         // required atom fields
         expect(atoms.count).toBe(26);
@@ -328,7 +328,7 @@ describe('mol2 reader', () => {
         expect(atoms.x.value(0)).toBeCloseTo(1.7394, 0.001);
         expect(atoms.y.value(0)).toBeCloseTo(-2.1169, 0.0001);
         expect(atoms.z.value(0)).toBeCloseTo(-1.0893, 0.0001);
-        expect(atoms.atom_type.value(0)).toBe("O.3");
+        expect(atoms.atom_type.value(0)).toBe('O.3');
 
         // optional atom fields
         expect(atoms.subst_id.value(0)).toBe(1);
@@ -367,10 +367,10 @@ describe('mol2 reader', () => {
         expect(molecule.num_subst).toBe(0);
         expect(molecule.num_feat).toBe(0);
         expect(molecule.num_sets).toBe(0);
-        expect(molecule.mol_type).toBe("SMALL")
-        expect(molecule.charge_type).toBe("GASTEIGER");
-        expect(molecule.status_bits).toBe("");
-        expect(molecule.mol_comment).toBe("");
+        expect(molecule.mol_type).toBe('SMALL')
+        expect(molecule.charge_type).toBe('GASTEIGER');
+        expect(molecule.status_bits).toBe('');
+        expect(molecule.mol_comment).toBe('');
 
         // required atom fields
         expect(atoms.count).toBe(26);
@@ -379,7 +379,7 @@ describe('mol2 reader', () => {
         expect(atoms.x.value(0)).toBeCloseTo(1.7394, 0.001);
         expect(atoms.y.value(0)).toBeCloseTo(-2.1169, 0.0001);
         expect(atoms.z.value(0)).toBeCloseTo(-1.0893, 0.0001);
-        expect(atoms.atom_type.value(0)).toBe("O.3");
+        expect(atoms.atom_type.value(0)).toBe('O.3');
 
         // optional atom fields
         expect(atoms.subst_id.value(0)).toBe(0);

src/mol-io/reader/_spec/ply.spec.ts

@@ -56,6 +56,60 @@ end_header
 3 3 5 4
 `
 
+const plyCubeString = `ply
+format ascii 1.0
+comment test cube
+element vertex 24
+property float32 x
+property float32 y
+property float32 z
+property uint32 material_index
+element face 6
+property list uint8 int32 vertex_indices
+element material 6
+property uint8 red
+property uint8 green
+property uint8 blue
+end_header
+-1 -1 -1 0
+1 -1 -1 0
+1 1 -1 0
+-1 1 -1 0
+1 -1 1 1
+-1 -1 1 1
+-1 1 1 1
+1 1 1 1
+1 1 1 2
+1 1 -1 2
+1 -1 -1 2
+1 -1 1 2
+-1 1 -1 3
+-1 1 1 3
+-1 -1 1 3
+-1 -1 -1 3
+-1 1 1 4
+-1 1 -1 4
+1 1 -1 4
+1 1 1 4
+1 -1 1 5
+1 -1 -1 5
+-1 -1 -1 5
+-1 -1 1 5
+4 0 1 2 3
+4 4 5 6 7
+4 8 9 10 11
+4 12 13 14 15
+4 16 17 18 19
+4 20 21 22 23
+255 0 0
+0 255 0
+0 0 255
+255 255 0
+0 255 255
+255 0 255
+`
+
+
 describe('ply reader', () => {
     it('basic', async () => {
         const parsed = await Ply(plyString).run();
@@ -66,13 +120,33 @@ describe('ply reader', () => {
         if (!vertex) return
         const x = vertex.getProperty('x')
         if (!x) return
-        console.log('x', x.toArray())
+        expect(x.value(0)).toEqual(130.901)
+
+        const face = plyFile.getElement('face') as PlyList
+        if (!face) return
+        expect(face.value(0)).toEqual({ count: 3, entries: [0, 2, 1]})
+        expect(face.value(1)).toEqual({ count: 3, entries: [3, 5, 4]})
+
+        expect.assertions(3)
+    });
+
+    it('material', async () => {
+        const parsed = await Ply(plyCubeString).run();
+        if (parsed.isError) return;
+        const plyFile = parsed.result;
+
+        const vertex = plyFile.getElement('vertex') as PlyTable
+        if (!vertex) return
+        expect(vertex.rowCount).toBe(24)
 
         const face = plyFile.getElement('face') as PlyList
         if (!face) return
-        const f0 = face.value(0)
-        console.log('f0', f0)
-        const f1 = face.value(1)
-        console.log('f1', f1)
+        expect(face.rowCount).toBe(6)
+
+        const material = plyFile.getElement('face') as PlyTable
+        if (!material) return
+        expect(face.rowCount).toBe(6)
+
+        expect.assertions(3)
     });
 });

src/mol-io/reader/cif/data-model.ts

@@ -199,7 +199,7 @@ export namespace CifField {
 
     export function ofColumn(column: Column<any>): CifField {
         const { rowCount, valueKind, areValuesEqual } = column;
-        
+
         let str: CifField['str']
         let int: CifField['int']
         let float: CifField['float']
@@ -219,7 +219,6 @@ export namespace CifField {
             default:
                 throw new Error('unsupported')
         }
-                
 
         return {
             __array: void 0,