TmMolStar/src/tmdet-extension/debug-utils.ts

/**
 * Copyright (C) 2022, Protein Bioinformatics Research Group, RCNS
 *
 * Licensed under CC BY-NC 4.0, see LICENSE file for more info.
 *
 * @author Gabor Tusnady <tusnady.gabor@ttk.hu>
 * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
 */

import { mmCIF_Database } from "molstar/lib/mol-io/reader/cif/schema/mmcif";
import { Mat4, Vec3 } from "molstar/lib/mol-math/linear-algebra";
import { MmcifFormat } from "molstar/lib/mol-model-formats/structure/mmcif";
import { Model } from "molstar/lib/mol-model/structure";
import { AtomicConformation } from "molstar/lib/mol-model/structure/model/properties/atomic";
import { createStructureRepresentationParams } from "molstar/lib/mol-plugin-state/helpers/structure-representation-params";
import { StateTransforms } from "molstar/lib/mol-plugin-state/transforms";
import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context";
import { Expression } from "molstar/lib/mol-script/language/expression";
import { Color } from "molstar/lib/mol-util/color";
import { rotateCamera as RC } from "./camera";
import { TmDetDescriptorCache } from "./prop";
import { getChainExpression as GCE, getCurrentHierarchy as GCH, transformationForStateTransform, transformWholeModel } from "./transformation";
import { PDBTMTransformationMatrix } from "./types";

export namespace DebugUtil {
    let plugin: PluginUIContext;
    let logEnabled = false;

    export function init(ctx: PluginUIContext) {
        plugin = ctx;
    }

    //
    // logging
    //
    export function enableLog() {
        logEnabled = true;
        console.log('DebugUtil Enabled', logEnabled);
    }

    export function disableLog() {
        logEnabled = false;
    }

    export function log(...args: any[]) {
        if (logEnabled) {
            console.log(...args);
        }
    }

    //
    //
    // lin.alg.
    //

    export function transformVector(v: Vec3, matrix: Mat4): Vec3 {
        const result = Vec3.transformMat4(Vec3(), v, matrix);
        log("transformVector: Input v & matrix:", v, Mat4.makeTable(matrix));
        log("transformVector: Result vector:", result);
        return result;
    }

    export function descriptorMxToMat4(matrix: PDBTMTransformationMatrix): Mat4 {
        log("descriptorMxToMat4: Input:", matrix);
        const result = transformationForStateTransform(matrix);
        log("descriptorMxToMat4: Result:", result);
        return result;
    }


    //
    // structure utils
    //

    export const getChainExpression = GCE;

    export function getCellOfFirstStructure() {
        return getCell();
    }

    export function getCell(structureIndex: number = 0, modelIndex: number = 0) {
        return getCurrentHierarchy().models[structureIndex].structures[modelIndex].cell;
    }

    export function getCurrentHierarchy() {
        return GCH(plugin);
    }

    export function getModelOfFirstStructure() {
        return getCellOfFirstStructure().obj?.data.model;
    }

    // in case of mmCIF format
    export function dumpAtomProperties(authAtomId: number) {
        const model: Model|undefined = getModelOfFirstStructure();
        log("First model:", model);
        if(!model) {
            return;
        }

        const rowCount = model.atomicHierarchy.atoms._rowCount;
        const conformation: AtomicConformation = model.atomicConformation;
        const db: mmCIF_Database = (model.sourceData as MmcifFormat).data.db;
        const atom_site = db.atom_site;
        for (let index = 0; index < rowCount; index++) {
            if (conformation.atomId.value(index) == authAtomId) {
                log("Model Atom Conformation:", {
                    atomIdParameter: authAtomId,
                    atomId: conformation.atomId.value(index),
                    coords: [
                        conformation.x[index],
                        conformation.y[index],
                        conformation.z[index]
                    ],
                    xyzDefined: conformation.xyzDefined
                });

                log("Atom Source Data (mmCIF database):", {
                    authId: atom_site.auth_atom_id.value(index),
                    compId: atom_site.auth_comp_id.value(index),
                    authAsymId: atom_site.auth_asym_id.value(index),
                    authSeqId: atom_site.auth_seq_id.value(index),
                    coords: [
                        atom_site.Cartn_x.value(index),
                        atom_site.Cartn_y.value(index),
                        atom_site.Cartn_z.value(index)
                    ]
                });
            }
        }
    }


    export function getCachesOfEachStructure() {
        let sIndex = 0;
        getCurrentHierarchy().structures.forEach(struct => {
            let cIndex = 0;
            struct.components.forEach(component => {
                log(`struct: ${sIndex}; component: ${cIndex}`, component.cell.cache);
                cIndex++;
            });
            sIndex++;
        });
    }

    export function color(expression: Expression, color: number[], structureIndex: number = 0, modelIndex: number = 0) {
        const structure = getCell(structureIndex, modelIndex);
        const stateBuilder = plugin.build().to(structure);
        stateBuilder.apply(
            StateTransforms.Model.StructureSelectionFromExpression,
            { expression: expression }
        )
        .apply(
            StateTransforms.Representation.StructureRepresentation3D,
            createStructureRepresentationParams(plugin, structure.obj?.data, {
                type: 'ball-and-stick',
                color: 'uniform', colorParams: { value: Color.fromArray(color, 0) }
            })
        );
        stateBuilder.commit();
    }

    export function transform(entityId: string) {
        const tmx = TmDetDescriptorCache.get(entityId)?.additional_entry_annotations.membrane.transformation_matrix;
        transformWholeModel(plugin, tmx!);
    }

    //
    // Camera
    //
    export function rotateCamera() {
        RC(plugin);
    }

    export function requestCameraReset() {
        requestAnimationFrame(() => plugin.canvas3d?.requestCameraReset({ durationMs: 1000 }));
    }
}