moorhen 0.0.1 → 0.6.2

package/types/libcoot.d.ts

@@ -0,0 +1,450 @@
+
+import { emscriptem } from "./emscriptem";
+import { gemmi } from "./gemmi"
+
+// Warning: do not import moorhen namespace otherwise worker code breaks during transpilation
+
+declare global {
+    function print(arg0: string): void;
+    function createRSRModule(arg0: any): Promise<any>;
+    function createCCP4Module(arg0: any): Promise<libcootApi.CCP4ModuleType>;    
+}
+
+export namespace libcootApi {
+    type CCP4ModuleType = {
+        get_sequence_info(gemmiStructure: gemmi.Structure, molName: string): emscriptem.vector<SequenceEntry>;
+        get_atom_info_for_selection(gemmiStructure: gemmi.Structure, arg1: string, arg2: string): emscriptem.vector<AtomInfo>;
+        structure_is_ligand(gemmiStructure: gemmi.Structure): boolean;
+        count_residues_in_selection(gemmiStructure: gemmi.Structure, selection: gemmi.Selection): number;
+        remove_non_selected_residues(gemmiStructure: gemmi.Structure, selection: gemmi.Selection): gemmi.Structure;
+        check_polymer_type(polymerConst: emscriptem.instance<number>): {value: number};
+        remove_ligands_and_waters_chain(chain: gemmi.Chain): void;
+        gemmi_setup_entities(gemmiStructure: gemmi.Structure): void;
+        remove_ligands_and_waters_structure(gemmiStructure: gemmi.Structure): void;
+        remove_hydrogens_structure(gemmiStructure: gemmi.Structure): void;
+        read_structure_from_string(pdbData: string | ArrayBuffer, molName: string): gemmi.Structure;
+        get_mtz_columns(fileName: string): emscriptem.vector<string>;
+        FS_createDataFile(arg0: string, fileName: string, byteArray: Uint8Array, arg3: boolean, arg4: boolean): void;
+        getElementNameAsString: (arg0: emscriptem.instance<string>) => string;
+        FS_unlink: (arg0: string) => void;
+        cif_parse_string: (arg0: gemmi.cifDocument, arg1: string) => void;
+        get_pdb_string_from_gemmi_struct: (arg0:gemmi.Structure) => string;
+        Selection: { new(cid: string): gemmi.Selection };
+        NeighborSearch: { new(model: gemmi.Model, unitCell: gemmi.UnitCell, radius: number): gemmi.NeighborSearch };
+        Position: { new(x: number, y: number, z: number): gemmi.Position };
+        Fractional: { new(x: number, y: number, z: number): gemmi.Fractional };
+        cifDocument: { new(): gemmi.cifDocument }
+    }
+    type SequenceResInfo = {
+        resNum: number;
+        resCode: string;
+        cid: string;
+    }
+    type SequenceEntry = {
+        type: number;
+        name: string;
+        chain: string;
+        sequence: emscriptem.vector<SequenceResInfo>;
+    
+    }
+    // We need to define AtomInfo here because we cannot import moorhen namespace otherwise worker code breaks during transpilation
+    type AtomInfo = {
+        x: number;
+        y: number;
+        z: number;
+        charge: number;
+        element: emscriptem.instance<string>;
+        symbol: string;
+        tempFactor: number;
+        serial: number;
+        name: string;
+        has_altloc: boolean;
+        alt_loc: string;
+        mol_name: string;
+        chain_id: string;
+        res_no: string;
+        res_name: string;
+        label: string;
+    }
+    interface AutoReadMtzInfo extends emscriptem.instance<AutoReadMtzInfo> {
+        idx: number;
+        F: string;
+        phi: string;
+        w: string;
+        F_obs: string;
+        sigF_obs: string;
+        Rfree: string;
+        weights_used: boolean;
+    }
+    interface CootPhiPsi extends emscriptem.instance<CootPhiPsi> {
+        ins_code: string;
+        residue_number: number;
+        chain_id: string;
+        phi: () => number;
+        psi: () => number;
+    }
+    interface CootPhiPsiProbT extends emscriptem.instance<CootPhiPsiProbT> {
+        phi_psi: CootPhiPsi;
+        is_allowed_flag: boolean;
+        residue_name: () => string;
+    }
+    interface InterestingPlaceT extends emscriptem.instance<InterestingPlaceT> {
+        feature_type: string;
+        residue_spec: ResidueSpecT;
+        x: number;
+        y: number;
+        z: number;
+        button_label: string;
+        feature_value: number;
+        badness: number;
+    }
+    interface InterestingPlaceDataJS extends ResidueSpecJS {
+        featureType: string;
+        featureValue: number;
+        buttonLabel: string;
+        badness: number;
+        coordX: number;
+        coordY: number;
+        coordZ: number;
+    }
+    interface HBondAtom extends emscriptem.instance<HBondAtom> {
+        serial: number;
+        x: number;
+        y: number;
+        z: number;
+        charge: number;
+        occ: number;
+        b_iso: number;
+        element: string;
+        name: string;
+        model: number;
+        chain: string;
+        res_no: number;
+        residue_name: string;
+        altLoc: number | string;
+    }
+    interface MoorhenHBond extends emscriptem.instance<MoorhenHBond> {
+        hb_hydrogen: HBondAtom;
+        donor: HBondAtom;
+        acceptor: HBondAtom;
+        donor_neigh: HBondAtom;
+        acceptor_neigh: HBondAtom;
+        angle_1: number;
+        angle_2: number;
+        angle_3: number;
+        dist: number;
+        ligand_atom_is_donor: boolean;
+        hydrogen_is_ligand_atom: boolean;
+        bond_has_hydrogen_flag: boolean;
+    }
+    interface HistogramInfo extends emscriptem.instance<HistogramInfo> {
+        base: number;
+        bin_width: number;
+        counts: emscriptem.vector<number>;
+    }
+    type HistogramInfoJS = {
+        base: number;
+        bin_width: number;
+        counts: number[];
+    }
+    type AutoReadMtzInfoJS = {
+        idx: number;
+        F: string;
+        phi: string;
+        w: string;
+        F_obs: string;
+        sigF_obs: string;
+        Rfree: string;
+        weights_used: boolean;
+    }
+    type HBondJS = {
+        hb_hydrogen: libcootApi.HBondAtom;
+        donor: libcootApi.HBondAtom;
+        acceptor: libcootApi.HBondAtom;
+        donor_neigh: libcootApi.HBondAtom;
+        acceptor_neigh: libcootApi.HBondAtom;
+        angle_1: number;
+        angle_2: number;
+        angle_3: number;
+        dist: number;
+        ligand_atom_is_donor: boolean;
+        hydrogen_is_ligand_atom: boolean;
+        bond_has_hydrogen_flag: boolean;     
+    }
+    interface MMRCCStatsJS {
+        "All atoms": DensityCorrelationStatsInfoJS[];
+        "Side-chains": DensityCorrelationStatsInfoJS[];
+    }
+    interface DensityCorrelationStatsInfoJS {
+        resNum: number;
+        insCode: string;
+        modelNumber: number;
+        chainId: string;
+        n: number;
+        correlation: number;
+    }
+    interface DensityCorrelationStatsInfoT extends emscriptem.instance<DensityCorrelationStatsInfoT> {
+        n: number;
+        sum_xy: number;
+        sum_sqrd_x: number;
+        sum_sqrd_y: number;
+        sum_x: number;
+        sum_y: number;
+        correlation: () => number;
+    }
+    interface CootCartesian extends emscriptem.instance<CootCartesian> {
+        x: () => number;
+        y: () => number;
+        z: () => number;
+    }
+    interface CootCartesianPair extends emscriptem.instance<CootCartesianPair> {
+        getStart: () => CootCartesian;
+        getFinish: () => CootCartesian;
+        amplitude: () => number;
+        size: number;
+    }
+    interface Generic3dLinesBondsBoxT extends emscriptem.instance<Generic3dLinesBondsBoxT> {
+        line_segments: emscriptem.vector<emscriptem.vector<CootCartesianPair>>;
+    }
+    type Generic3dLinesBondsBoxJS = {
+        start: { x: number; y: number; z: number };
+        end: { x: number; y: number; z: number };
+        dist: number;
+    }
+    type RotamerInfoJS = {
+        name: string;
+        rank: number;
+        status: string;
+        richardson_probability: number;
+    }
+    interface SimpleMeshT extends emscriptem.instance<SimpleMeshT> {
+        vertices: emscriptem.vector<VncVertex>;
+        triangles: emscriptem.vector<gTriangle>;
+    }
+    interface SimpleMeshJS {
+        prim_types: [[string]];
+        useIndices?: [[boolean]];
+        idx_tri: [[number[]]];
+        vert_tri: [[number[]]];
+        additional_norm_tri?: [[number[]]];
+        norm_tri: [[number[]]];
+        col_tri: [[number[]]];
+    }
+    interface SymmetryData extends emscriptem.instance<SymmetryData> {
+        cell: CellTranslation;
+        symm_trans: emscriptem.vector<PairType<SymmetryTransT, CellTranslation>>;
+    }
+    interface CellTranslation extends emscriptem.instance<CellTranslation> {
+        us: number;
+        vs: number;
+        ws: number;
+    }
+    interface SymmetryTransT extends emscriptem.instance<SymmetryTransT> {
+        x: () => number;
+        y: () => number;
+        z: () => number;
+        is_identity: () => boolean;
+        str: () => string;
+        isym: () => number;
+        symm_as_string: string;
+    }
+    type PairType<T1, T2> = {
+        first: T1;
+        second: T2;
+    }
+    interface ClipperCoordOrth extends emscriptem.instance<ClipperCoordOrth> {
+        x: () => number;
+        y: () => number;
+        z: () => number;
+    }
+    interface MapMoleculeCentreInfo extends emscriptem.instance<MapMoleculeCentreInfo> {
+        success: boolean;
+        updated_centre: ClipperCoordOrth;
+        suggested_contour_level: number;
+        suggested_radius: number;
+        sum_of_densities: number;
+    }
+    type MapMoleculeCentreInfoJS = {
+        success: boolean;
+        updated_centre: [number, number, number];
+        suggested_contour_level: number;
+        suggested_radius: number;
+    }
+    interface ResidueSpecT extends emscriptem.instance<ResidueSpecT> {
+        model_number: number;
+        chain_id: string;
+        res_no: number;
+        ins_code: string;    
+    }
+    interface ResidueSpecJS {
+        resNum: number;
+        insCode: string;
+        modelNumber: number;
+        chainId: string;
+    }
+    interface AtomSpecT extends emscriptem.instance<ResidueSpecT> {
+        chain_id: string;
+        res_no: number;
+        ins_code: string;
+        atom_name: string;
+        alt_conf: string;
+        int_user_data: number;
+        float_user_data: number;
+        string_user_data: string;
+        model_number: number;
+    }
+    interface AtomSpecJS {
+        chain_id: string;
+        res_no: number;
+        ins_code: string;
+        atom_name: string;
+        alt_conf: string;
+        int_user_data: number;
+        float_user_data: number;
+        string_user_data: string;
+        model_number: number;
+    }
+    interface ResidueValidationInformationT extends emscriptem.instance<ResidueValidationInformationT> {
+        label: string;
+        residue_spec: ResidueSpecT;
+        function_value: number;
+    }
+    interface ChainValidationInformationT extends emscriptem.instance<ChainValidationInformationT> {
+        chain_id: string;
+        rviv: emscriptem.vector<ResidueValidationInformationT>;
+    }
+    interface ValidationInformationT extends emscriptem.instance<ValidationInformationT> {
+        get_index_for_chain: (arg0: string) => number;
+        empty: () => boolean;
+        name: string;
+        cviv: emscriptem.vector<ChainValidationInformationT>;
+    }
+    type ValidationInformationJS = {
+        chainId: string;
+        insCode: string;
+        seqNum: number;
+        restype: string;
+        value: number;
+        label?: string;
+    }
+    interface SuperposeResultsT extends emscriptem.instance<SuperposeResultsT> {
+        superpose_info: string;
+        alignment: PairType<string, string>;
+        alignment_info_vec: emscriptem.vector<ValidationInformationT>;
+        aligned_pairs: emscriptem.vector<PairType<ResidueValidationInformationT, ResidueValidationInformationT>>;
+    }
+    type SuperposeResultsJS = {
+        referenceSequence: string,
+        movingSequence: string,
+        supperposeInfo: string,
+        alignedPairsData: {reference: ValidationInformationJS, moving: ValidationInformationJS}[],
+    }
+    interface InstancedDataType extends emscriptem.instance<InstancedDataType> {
+        position: [number, number, number];
+        size: [number, number, number];
+        colour: [number, number, number, number];
+        orientation: [[number, number, number, number], [number, number, number, number], [number, number, number, number], [number, number, number, number]];
+    }
+    interface gTriangle extends emscriptem.instance<gTriangle> {
+        point_id: [number, number, number];
+    }
+    interface VncVertex extends emscriptem.instance<VncVertex> {
+        pos: [number, number, number];
+        normal: [number, number, number];
+        color: [number, number, number, number];
+    }
+    interface InstancedGeomT extends emscriptem.instance<InstancedGeomT> {
+        vertices: emscriptem.vector<VncVertex>;
+        triangles: emscriptem.vector<gTriangle>;
+        name: string;
+        instancing_data_A: emscriptem.vector<InstancedDataType>;
+        instancing_data_B: emscriptem.vector<InstancedDataType>;
+    }
+    interface InstancedMeshT extends emscriptem.instance<InstancedMeshT> {
+        geom: emscriptem.vector<InstancedGeomT>;
+        markup: SimpleMeshT;
+    }
+    type InstancedMeshJS = {
+        prim_types: any;
+        idx_tri: any;
+        vert_tri: any;
+        norm_tri: any
+        col_tri: any;
+        instance_use_colors: any;
+        instance_sizes: any;
+        instance_origins: any;
+        instance_orientations: any;
+    }
+    interface MovedAtomT extends emscriptem.instance<MovedAtomT> {
+        atom_name: string;
+        alt_conf: string;
+        x: number;
+        y: number;
+        z: number;
+        index: number;
+    }
+    interface MovedResidueT extends emscriptem.instance<MovedResidueT> {
+        add_atom: (arg: MovedAtomT) => void;
+        chain_id: string;
+        res_no: number;
+        ins_code: string;
+        moved_atoms: emscriptem.vector<MovedAtomT>
+    }
+    interface RamaData extends emscriptem.instance<RamaData> {
+        chainId: string;
+        insCode: string;
+        seqNum: number;
+        restype: string;
+        phi: number;
+        psi: number;
+        isOutlier: boolean;
+        is_pre_pro: boolean;
+    }
+    type RamaDataJS = {
+        chainId: string;
+        insCode: string;
+        seqNum: number;
+        restype: string;
+        isOutlier: boolean;
+        phi: number;
+        psi: number;
+        is_pre_pro: boolean;
+    }
+    type CootModule = {
+        SmilesToPDB(arg0: string, arg1: string, arg2: number, arg3: number): PairType<string, string>;
+        FS: {
+            readFile(tempFilename: string, arg1: { encoding: string; }): string | Uint8Array;
+            mkdir: (arg0: string) => void; 
+        };
+        FS_unlink(tempFilename: string): void;
+        FS_createDataFile(arg0: string, arg1: string, arg2: Uint8Array | string, arg3: boolean, arg4: boolean, arg5?: boolean): void;
+        molecules_container_js: { new(verbose: boolean): MoleculesContainerJS };
+        Vectormoved_residue_t: { new(): emscriptem.vector<MovedResidueT>};
+        moved_residue_t: { new(arg0: string, arg1: number, arg2: string): MovedResidueT};
+        moved_atom_t: { new(arg0: string, arg1: string, arg2: number, arg3: number, arg4: number, arg5: number): MovedAtomT};
+        MapIntFloat3: { new(): emscriptem.map<[number, number, number], number>};
+        VectorStringUInt_pair: { new(): emscriptem.vector<{ first: string, second: number }>};
+        getRamachandranData(arg0: string, arg1: string): emscriptem.vector<RamaData>
+    }
+    interface MoleculesContainerJS {
+        close_molecule(molNo: number): number;
+        copy_fragment_using_residue_range(molNo: number, chainId: string, res_no_start: number, res_no_end: number): number;
+        writeCCP4Map(molNo: number, tempFilename: string): void;
+        writeCIFASCII(molNo: number, tempFilename: string): void;
+        writePDBASCII(molNo: number, tempFilename: string): void;
+        set_map_sampling_rate(arg0: number): void;
+        fill_rotamer_probability_tables(): void;
+        set_user_defined_atom_colour_by_selection(imol: number, indexedResiduesVec: emscriptem.vector<{ first: string; second: number; }>, nonCarbon: boolean): void;
+        set_user_defined_bond_colours(imol: number, colourMap: emscriptem.map<[number, number, number], number>): void;
+        read_ccp4_map(arg0: string, arg2: boolean): number;
+        associate_data_mtz_file_with_map(arg0: number, arg1: string, arg2: string, arg3: string, arg5: string): void;
+        read_mtz(arg0: string, arg1: string, arg2: string, arg3: string, arg4: boolean, arg5: boolean): number;
+        replace_map_by_mtz_from_file(arg0: number, arg1: string, arg2: string, arg3: string, arg4: string, arg5: boolean): number;
+        replace_molecule_by_model_from_file(imol: number, tempFilename: string): void;
+        import_cif_dictionary(tempFilename: string, associatedMolNo: number): number;
+        auto_read_mtz(tempFilename: string): emscriptem.vector<number>;
+        read_pdb(tempFilename: string): number;
+        set_show_timings: (arg0: boolean) => void;
+        new_positions_for_atoms_in_residues: (arg0: number, arg1: emscriptem.vector<MovedResidueT>) => number;
+    }       
+}