add component atom

src/mol-model-formats/structure/property/bonds/atom.ts

@@ -0,0 +1,92 @@
+/**
+ * Copyright (c) 2020 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
+ */
+
+import { Model } from '../../../../mol-model/structure/model/model';
+import { CustomPropertyDescriptor } from '../../../../mol-model/custom-property';
+import { CifWriter } from '../../../../mol-io/writer/cif';
+import { Table } from '../../../../mol-data/db';
+import { FormatPropertyProvider } from '../../common/property';
+import { CCD_Schema } from '../../../../mol-io/reader/cif/schema/ccd';
+
+export interface ComponentAtom {
+    readonly data: Table<CCD_Schema['chem_comp_atom']>
+    readonly entries: ReadonlyMap<string, ComponentAtom.Entry>
+}
+
+export namespace ComponentAtom {
+    export const Descriptor: CustomPropertyDescriptor = {
+        name: 'chem_comp_atom',
+        cifExport: {
+            prefix: '',
+            categories: [{
+                name: 'chem_comp_atom',
+                instance(ctx) {
+                    const p = Provider.get(ctx.firstModel);
+                    if (!p) return CifWriter.Category.Empty;
+                    const chem_comp_atom = p.data;
+                    if (!chem_comp_atom) return CifWriter.Category.Empty;
+
+                    const comp_names = ctx.structures[0].uniqueResidueNames;
+                    const { comp_id, _rowCount } = chem_comp_atom;
+                    const indices: number[] = [];
+                    for (let i = 0; i < _rowCount; i++) {
+                        if (comp_names.has(comp_id.value(i))) indices[indices.length] = i;
+                    }
+
+                    return CifWriter.Category.ofTable(chem_comp_atom, indices);
+                }
+            }]
+        }
+    };
+
+    export const Provider = FormatPropertyProvider.create<ComponentAtom>(Descriptor);
+
+    export function chemCompAtomFromTable(model: Model, table: Table<CCD_Schema['chem_comp_atom']>): Table<CCD_Schema['chem_comp_atom']> {
+        return Table.pick(table, CCD_Schema.chem_comp_atom, (i: number) => {
+            return model.properties.chemicalComponentMap.has(table.comp_id.value(i));
+        });
+    }
+
+    export function getEntriesFromChemCompAtom(data: Table<CCD_Schema['chem_comp_atom']>) {
+        const entries: Map<string, Entry> = new Map();
+
+        function addEntry(id: string) {
+            let e = new Entry(id);
+            entries.set(id, e);
+            return e;
+        }
+
+        const { comp_id, atom_id, charge, pdbx_stereo_config, _rowCount } = data;
+
+        let entry = addEntry(comp_id.value(0)!);
+        for (let i = 0; i < _rowCount; i++) {
+            const name = atom_id.value(i)!;
+            const id = comp_id.value(i)!;
+            const ch = charge.value(i)!;
+            const stereo = pdbx_stereo_config.value(i)!;
+
+            if (entry.id !== id) {
+                entry = addEntry(id);
+            }
+
+            entry.add(name, ch, stereo);
+        }
+
+        return entries;
+    }
+
+    export class Entry {
+        readonly map: Map<string, { charge: number, stereo_config: CCD_Schema['chem_comp_atom']['pdbx_stereo_config']['T'] }> = new Map();
+
+        add(a: string, charge: number, stereo_config: CCD_Schema['chem_comp_atom']['pdbx_stereo_config']['T']) {
+            this.map.set(a, { charge, stereo_config });
+        }
+
+        constructor(public readonly id: string) { }
+    }
+}