molstar 3.3.1 → 3.6.0

package/lib/mol-io/common/netcdf/reader.js

@@ -0,0 +1,456 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Adapted from https://github.com/cheminfo-js/netcdfjs
+ * MIT License, Copyright (c) 2016 cheminfo
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { IOBuffer } from '../io-buffer';
+/**
+ * Throws a non-valid NetCDF exception if the statement it's true
+ */
+function notNetcdf(statement, reason) {
+    if (statement) {
+        throw new TypeError('Not a valid NetCDF v3.x file: ' + reason);
+    }
+}
+/**
+ * Moves 1, 2, or 3 bytes to next 4-byte boundary
+ */
+function padding(buffer) {
+    if ((buffer.offset % 4) !== 0) {
+        buffer.skip(4 - (buffer.offset % 4));
+    }
+}
+/**
+ * Reads the name
+ */
+function readName(buffer) {
+    // Read name
+    var nameLength = buffer.readUint32();
+    var name = buffer.readChars(nameLength);
+    // validate name
+    // TODO
+    // Apply padding
+    padding(buffer);
+    return name;
+}
+var types = {
+    BYTE: 1,
+    CHAR: 2,
+    SHORT: 3,
+    INT: 4,
+    FLOAT: 5,
+    DOUBLE: 6
+};
+/**
+ * Parse a number into their respective type
+ */
+function num2str(type) {
+    switch (Number(type)) {
+        case types.BYTE:
+            return 'byte';
+        case types.CHAR:
+            return 'char';
+        case types.SHORT:
+            return 'short';
+        case types.INT:
+            return 'int';
+        case types.FLOAT:
+            return 'float';
+        case types.DOUBLE:
+            return 'double';
+        default:
+            return 'undefined';
+    }
+}
+/**
+ * Parse a number type identifier to his size in bytes
+ */
+function num2bytes(type) {
+    switch (Number(type)) {
+        case types.BYTE:
+            return 1;
+        case types.CHAR:
+            return 1;
+        case types.SHORT:
+            return 2;
+        case types.INT:
+            return 4;
+        case types.FLOAT:
+            return 4;
+        case types.DOUBLE:
+            return 8;
+        default:
+            return -1;
+    }
+}
+/**
+ * Reverse search of num2str
+ */
+function str2num(type) {
+    switch (String(type)) {
+        case 'byte':
+            return types.BYTE;
+        case 'char':
+            return types.CHAR;
+        case 'short':
+            return types.SHORT;
+        case 'int':
+            return types.INT;
+        case 'float':
+            return types.FLOAT;
+        case 'double':
+            return types.DOUBLE;
+        default:
+            return -1;
+    }
+}
+/**
+ * Auxiliary function to read numeric data
+ */
+function readNumber(size, bufferReader) {
+    if (size !== 1) {
+        var numbers = new Array(size);
+        for (var i = 0; i < size; i++) {
+            numbers[i] = bufferReader();
+        }
+        return numbers;
+    }
+    else {
+        return bufferReader();
+    }
+}
+/**
+ * Given a type and a size reads the next element
+ */
+function readType(buffer, type, size) {
+    switch (type) {
+        case types.BYTE:
+            return buffer.readBytes(size);
+        case types.CHAR:
+            return trimNull(buffer.readChars(size));
+        case types.SHORT:
+            return readNumber(size, buffer.readInt16.bind(buffer));
+        case types.INT:
+            return readNumber(size, buffer.readInt32.bind(buffer));
+        case types.FLOAT:
+            return readNumber(size, buffer.readFloat32.bind(buffer));
+        case types.DOUBLE:
+            return readNumber(size, buffer.readFloat64.bind(buffer));
+        default:
+            notNetcdf(true, 'non valid type ' + type);
+            return undefined;
+    }
+}
+/**
+ * Removes null terminate value
+ */
+function trimNull(value) {
+    if (value.charCodeAt(value.length - 1) === 0) {
+        return value.substring(0, value.length - 1);
+    }
+    return value;
+}
+// const STREAMING = 4294967295;
+/**
+ * Read data for the given non-record variable
+ */
+function nonRecord(buffer, variable) {
+    // variable type
+    var type = str2num(variable.type);
+    // size of the data
+    var size = variable.size / num2bytes(type);
+    // iterates over the data
+    var data = new Array(size);
+    for (var i = 0; i < size; i++) {
+        data[i] = readType(buffer, type, 1);
+    }
+    return data;
+}
+/**
+ * Read data for the given record variable
+ */
+function record(buffer, variable, recordDimension) {
+    // variable type
+    var type = str2num(variable.type);
+    var width = variable.size ? variable.size / num2bytes(type) : 1;
+    // size of the data
+    // TODO streaming data
+    var size = recordDimension.length;
+    // iterates over the data
+    var data = new Array(size);
+    var step = recordDimension.recordStep;
+    for (var i = 0; i < size; i++) {
+        var currentOffset = buffer.offset;
+        data[i] = readType(buffer, type, width);
+        buffer.seek(currentOffset + step);
+    }
+    return data;
+}
+// Grammar constants
+var ZERO = 0;
+var NC_DIMENSION = 10;
+var NC_VARIABLE = 11;
+var NC_ATTRIBUTE = 12;
+/**
+ * Read the header of the file
+ * Returns object with the fields:
+ *  - `recordDimension`: Number with the length of record dimension
+ *  - `dimensions`: List of dimensions
+ *  - `globalAttributes`: List of global attributes
+ *  - `variables`: List of variables
+ */
+function header(buffer, version) {
+    // Length of record dimension
+    // sum of the varSize's of all the record variables.
+    var header = { recordDimension: { length: buffer.readUint32() } };
+    // Version
+    header.version = version;
+    // List of dimensions
+    var dimList = dimensionsList(buffer);
+    header.recordDimension.id = dimList.recordId;
+    header.recordDimension.name = dimList.recordName;
+    header.dimensions = dimList.dimensions;
+    // List of global attributes
+    header.globalAttributes = attributesList(buffer);
+    // List of variables
+    var variables = variablesList(buffer, dimList.recordId, version);
+    header.variables = variables.variables;
+    header.recordDimension.recordStep = variables.recordStep;
+    return header;
+}
+/**
+ * List of dimensions
+ */
+function dimensionsList(buffer) {
+    var dimensions, recordId, recordName;
+    var dimList = buffer.readUint32();
+    if (dimList === ZERO) {
+        notNetcdf((buffer.readUint32() !== ZERO), 'wrong empty tag for list of dimensions');
+        return [];
+    }
+    else {
+        notNetcdf((dimList !== NC_DIMENSION), 'wrong tag for list of dimensions');
+        // Length of dimensions
+        var dimensionSize = buffer.readUint32();
+        dimensions = new Array(dimensionSize);
+        for (var dim = 0; dim < dimensionSize; dim++) {
+            // Read name
+            var name_1 = readName(buffer);
+            // Read dimension size
+            var size = buffer.readUint32();
+            if (size === 0) {
+                recordId = dim;
+                recordName = name_1;
+            }
+            dimensions[dim] = {
+                name: name_1,
+                size: size
+            };
+        }
+        return {
+            dimensions: dimensions,
+            recordId: recordId,
+            recordName: recordName
+        };
+    }
+}
+/**
+ * List of attributes
+ */
+function attributesList(buffer) {
+    var attributes;
+    var gAttList = buffer.readUint32();
+    if (gAttList === ZERO) {
+        notNetcdf((buffer.readUint32() !== ZERO), 'wrong empty tag for list of attributes');
+        return [];
+    }
+    else {
+        notNetcdf((gAttList !== NC_ATTRIBUTE), 'wrong tag for list of attributes');
+        // Length of attributes
+        var attributeSize = buffer.readUint32();
+        attributes = new Array(attributeSize);
+        for (var gAtt = 0; gAtt < attributeSize; gAtt++) {
+            // Read name
+            var name_2 = readName(buffer);
+            // Read type
+            var type = buffer.readUint32();
+            notNetcdf(((type < 1) || (type > 6)), 'non valid type ' + type);
+            // Read attribute
+            var size = buffer.readUint32();
+            var value = readType(buffer, type, size);
+            // Apply padding
+            padding(buffer);
+            attributes[gAtt] = {
+                name: name_2,
+                type: num2str(type),
+                value: value
+            };
+        }
+    }
+    return attributes;
+}
+/**
+ * List of variables
+ */
+function variablesList(buffer, recordId, version) {
+    var varList = buffer.readUint32();
+    var recordStep = 0;
+    var variables;
+    if (varList === ZERO) {
+        notNetcdf((buffer.readUint32() !== ZERO), 'wrong empty tag for list of variables');
+        return [];
+    }
+    else {
+        notNetcdf((varList !== NC_VARIABLE), 'wrong tag for list of variables');
+        // Length of variables
+        var variableSize = buffer.readUint32();
+        variables = new Array(variableSize);
+        for (var v = 0; v < variableSize; v++) {
+            // Read name
+            var name_3 = readName(buffer);
+            // Read dimensionality of the variable
+            var dimensionality = buffer.readUint32();
+            // Index into the list of dimensions
+            var dimensionsIds = new Array(dimensionality);
+            for (var dim = 0; dim < dimensionality; dim++) {
+                dimensionsIds[dim] = buffer.readUint32();
+            }
+            // Read variables size
+            var attributes = attributesList(buffer);
+            // Read type
+            var type = buffer.readUint32();
+            notNetcdf(((type < 1) && (type > 6)), 'non valid type ' + type);
+            // Read variable size
+            // The 32-bit varSize field is not large enough to contain the
+            // size of variables that require more than 2^32 - 4 bytes,
+            // so 2^32 - 1 is used in the varSize field for such variables.
+            var varSize = buffer.readUint32();
+            // Read offset
+            var offset = buffer.readUint32();
+            if (version === 2) {
+                notNetcdf((offset > 0), 'offsets larger than 4GB not supported');
+                offset = buffer.readUint32();
+            }
+            // Count amount of record variables
+            if (dimensionsIds[0] === recordId) {
+                recordStep += varSize;
+            }
+            variables[v] = {
+                name: name_3,
+                dimensions: dimensionsIds,
+                attributes: attributes,
+                type: num2str(type),
+                size: varSize,
+                offset: offset,
+                record: (dimensionsIds[0] === recordId)
+            };
+        }
+    }
+    return {
+        variables: variables,
+        recordStep: recordStep
+    };
+}
+/**
+ * Reads a NetCDF v3.x file
+ * https://www.unidata.ucar.edu/software/netcdf/docs/file_format_specifications.html
+ */
+var NetcdfReader = /** @class */ (function () {
+    function NetcdfReader(data) {
+        var buffer = new IOBuffer(data);
+        buffer.setBigEndian();
+        // Validate that it's a NetCDF file
+        notNetcdf((buffer.readChars(3) !== 'CDF'), 'should start with CDF');
+        // Check the NetCDF format
+        var version = buffer.readByte();
+        notNetcdf((version > 2), 'unknown version');
+        // Read the header
+        this.header = header(buffer, version);
+        this.buffer = buffer;
+    }
+    Object.defineProperty(NetcdfReader.prototype, "version", {
+        /**
+         * Version for the NetCDF format
+         */
+        get: function () {
+            if (this.header.version === 1) {
+                return 'classic format';
+            }
+            else {
+                return '64-bit offset format';
+            }
+        },
+        enumerable: false,
+        configurable: true
+    });
+    Object.defineProperty(NetcdfReader.prototype, "recordDimension", {
+        get: function () {
+            return this.header.recordDimension;
+        },
+        enumerable: false,
+        configurable: true
+    });
+    Object.defineProperty(NetcdfReader.prototype, "dimensions", {
+        get: function () {
+            return this.header.dimensions;
+        },
+        enumerable: false,
+        configurable: true
+    });
+    Object.defineProperty(NetcdfReader.prototype, "globalAttributes", {
+        get: function () {
+            return this.header.globalAttributes;
+        },
+        enumerable: false,
+        configurable: true
+    });
+    Object.defineProperty(NetcdfReader.prototype, "variables", {
+        get: function () {
+            return this.header.variables;
+        },
+        enumerable: false,
+        configurable: true
+    });
+    /**
+     * Checks if a variable is available
+     * @param {string|object} variableName - Name of the variable to check
+     * @return {Boolean} - Variable existence
+     */
+    NetcdfReader.prototype.hasDataVariable = function (variableName) {
+        return this.header.variables && this.header.variables.findIndex(function (val) { return val.name === variableName; }) !== -1;
+    };
+    /**
+     * Retrieves the data for a given variable
+     * @param {string|object} variableName - Name of the variable to search or variable object
+     * @return {Array} - List with the variable values
+     */
+    NetcdfReader.prototype.getDataVariable = function (variableName) {
+        var _a;
+        var variable;
+        if (typeof variableName === 'string') {
+            // search the variable
+            variable = (_a = this.header.variables) === null || _a === void 0 ? void 0 : _a.find(function (val) { return val.name === variableName; });
+        }
+        else {
+            variable = variableName;
+        }
+        // throws if variable not found
+        if (variable === undefined)
+            throw new Error('variable not found');
+        // go to the offset position
+        this.buffer.seek(variable.offset);
+        if (variable.record) {
+            // record variable case
+            return record(this.buffer, variable, this.header.recordDimension);
+        }
+        else {
+            // non-record variable case
+            return nonRecord(this.buffer, variable);
+        }
+    };
+    return NetcdfReader;
+}());
+export { NetcdfReader };

package/lib/mol-io/reader/cif/schema/bird.d.ts

@@ -1,7 +1,7 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.356, IHM 1.17, MA 1.3.5.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.357, IHM 1.17, MA 1.3.6.
  *
  * @author molstar/ciftools package
  */
@@ -50,7 +50,7 @@ export declare const BIRD_Schema: {
         /**
          * Defines the structural classification of the entity.
          */
-        type: Schema.Aliased<"Unknown" | "Amino acid" | "Aminoglycoside" | "Anthracycline" | "Anthraquinone" | "Ansamycin" | "Chalkophore" | "Chromophore" | "Glycopeptide" | "Cyclic depsipeptide" | "Cyclic lipopeptide" | "Cyclic peptide" | "Heterocyclic" | "Imino sugar" | "Keto acid" | "Lipoglycopeptide" | "Lipopeptide" | "Macrolide" | "Non-polymer" | "Nucleoside" | "Oligopeptide" | "Oligosaccharide" | "Peptaibol" | "Peptide-like" | "Polycyclic" | "Polypeptide" | "Polysaccharide" | "Quinolone" | "Thiolactone" | "Thiopeptide" | "Siderophore" | "Chalkophore, Polypeptide">;
+        type: Schema.Aliased<"unknown" | "non-polymer" | "peptide-like" | "macrolide" | "amino acid" | "aminoglycoside" | "anthracycline" | "anthraquinone" | "ansamycin" | "chalkophore" | "chromophore" | "glycopeptide" | "cyclic depsipeptide" | "cyclic lipopeptide" | "cyclic peptide" | "heterocyclic" | "imino sugar" | "keto acid" | "lipoglycopeptide" | "lipopeptide" | "nucleoside" | "oligopeptide" | "oligosaccharide" | "peptaibol" | "polycyclic" | "polypeptide" | "polysaccharide" | "quinolone" | "thiolactone" | "thiopeptide" | "siderophore" | "chalkophore, polypeptide">;
         /**
          * Evidence for the assignment of _pdbx_reference_molecule.type
          */
@@ -58,7 +58,7 @@ export declare const BIRD_Schema: {
         /**
          * Broadly defines the function of the entity.
          */
-        class: Schema.Aliased<"Antagonist" | "Antibiotic" | "Anticancer" | "Anticoagulant" | "Antifungal" | "Antigen" | "Antiinflammatory" | "Antimicrobial" | "Antineoplastic" | "Antiparasitic" | "Antiretroviral" | "Anthelmintic" | "Antithrombotic" | "Antitumor" | "Antiviral" | "CASPASE inhibitor" | "Chaperone binding" | "Enzyme inhibitor" | "Drug delivery" | "Glycan component" | "Growth factor" | "Immunosuppressant" | "Inducer" | "Inhibitor" | "Lantibiotic" | "Metabolism" | "Metal transport" | "Nutrient" | "Oxidation-reduction" | "Protein binding" | "Receptor" | "Substrate analog" | "Synthetic opioid" | "Thrombin inhibitor" | "Transition state mimetic" | "Transport activator" | "Trypsin inhibitor" | "Toxin" | "Unknown" | "Water retention" | "Anticoagulant, Antithrombotic" | "Antibiotic, Antimicrobial" | "Antibiotic, Anthelmintic" | "Antibiotic, Antineoplastic" | "Antimicrobial, Antiretroviral" | "Antimicrobial, Antitumor" | "Antimicrobial, Antiparasitic, Antibiotic" | "Thrombin inhibitor, Trypsin inhibitor">;
+        class: Schema.Aliased<"unknown" | "antagonist" | "antibiotic" | "anticancer" | "anticoagulant" | "antifungal" | "antigen" | "antiinflammatory" | "antimicrobial" | "antineoplastic" | "antiparasitic" | "antiretroviral" | "anthelmintic" | "antithrombotic" | "antitumor" | "antiviral" | "caspase inhibitor" | "chaperone binding" | "enzyme inhibitor" | "drug delivery" | "glycan component" | "growth factor" | "immunosuppressant" | "inducer" | "inhibitor" | "lantibiotic" | "metabolism" | "metal transport" | "nutrient" | "oxidation-reduction" | "protein binding" | "receptor" | "substrate analog" | "synthetic opioid" | "thrombin inhibitor" | "transition state mimetic" | "transport activator" | "trypsin inhibitor" | "toxin" | "water retention" | "anticoagulant, antithrombotic" | "antibiotic, antimicrobial" | "antibiotic, anthelmintic" | "antibiotic, antineoplastic" | "antimicrobial, antiretroviral" | "antimicrobial, antitumor" | "antimicrobial, antiparasitic, antibiotic" | "thrombin inhibitor, trypsin inhibitor">;
         /**
          * Evidence for the assignment of _pdbx_reference_molecule.class
          */
@@ -91,7 +91,7 @@ export declare const BIRD_Schema: {
         /**
          * Defines the current PDB release status for this molecule definition.
          */
-        release_status: Schema.Aliased<"WAIT" | "REL" | "HOLD" | "OBS">;
+        release_status: Schema.Aliased<"wait" | "rel" | "hold" | "obs">;
         /**
          * Assigns the identifier for the reference molecule which have been replaced
          * by this reference molecule.
@@ -392,11 +392,11 @@ export declare const BIRD_Schema: {
         /**
          * A flag to indicate that this monomer is observed in the instance example.
          */
-        observed: Schema.Aliased<"N" | "Y">;
+        observed: Schema.Aliased<"y" | "n">;
         /**
          * A flag to indicate that sequence heterogeneity at this monomer position.
          */
-        hetero: Schema.Aliased<"N" | "Y">;
+        hetero: Schema.Aliased<"y" | "n">;
     };
     /**
      * Additional features associated with the reference entity.
@@ -479,7 +479,7 @@ export declare const BIRD_Schema: {
         /**
          * An identifier for the wwPDB site creating or modifying the molecule.
          */
-        processing_site: Schema.Aliased<"RCSB" | "PDBE" | "BMRB" | "PDBJ" | "PDBC">;
+        processing_site: Schema.Aliased<"RCSB" | "PDBE" | "PDBJ" | "BMRB" | "PDBC">;
         /**
          * The action associated with this audit record.
          */

package/lib/mol-io/reader/cif/schema/bird.js

@@ -1,7 +1,7 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.356, IHM 1.17, MA 1.3.5.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.357, IHM 1.17, MA 1.3.6.
  *
  * @author molstar/ciftools package
  */
@@ -9,6 +9,7 @@ import { Column } from '../../../../mol-data/db';
 var Schema = Column.Schema;
 var str = Schema.str;
 var float = Schema.float;
+var lstr = Schema.lstr;
 var Aliased = Schema.Aliased;
 var int = Schema.int;
 export var BIRD_Schema = {
@@ -54,7 +55,7 @@ export var BIRD_Schema = {
         /**
          * Defines the structural classification of the entity.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * Evidence for the assignment of _pdbx_reference_molecule.type
          */
@@ -62,7 +63,7 @@ export var BIRD_Schema = {
         /**
          * Broadly defines the function of the entity.
          */
-        class: Aliased(str),
+        class: Aliased(lstr),
         /**
          * Evidence for the assignment of _pdbx_reference_molecule.class
          */
@@ -74,7 +75,7 @@ export var BIRD_Schema = {
         /**
          * Defines how this entity is represented in PDB data files.
          */
-        represent_as: Aliased(str),
+        represent_as: Aliased(lstr),
         /**
          * For entities represented as single molecules, the identifier
          * corresponding to the chemical definition for the molecule.
@@ -95,7 +96,7 @@ export var BIRD_Schema = {
         /**
          * Defines the current PDB release status for this molecule definition.
          */
-        release_status: Aliased(str),
+        release_status: Aliased(lstr),
         /**
          * Assigns the identifier for the reference molecule which have been replaced
          * by this reference molecule.
@@ -125,7 +126,7 @@ export var BIRD_Schema = {
         /**
          * Defines the polymer characteristic of the entity.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * Additional details about this entity.
          */
@@ -245,7 +246,7 @@ export var BIRD_Schema = {
         /**
          * The bond order target for the chemical linkage.
          */
-        value_order: Aliased(str),
+        value_order: Aliased(lstr),
         /**
          * The entity component identifier for the first of two entities containing the linkage.
          */
@@ -331,7 +332,7 @@ export var BIRD_Schema = {
         /**
          * The bond order target for the non-standard linkage.
          */
-        value_order: Aliased(str),
+        value_order: Aliased(lstr),
     },
     /**
      * Data items in the PDBX_REFERENCE_ENTITY_POLY category record details about
@@ -396,11 +397,11 @@ export var BIRD_Schema = {
         /**
          * A flag to indicate that this monomer is observed in the instance example.
          */
-        observed: Aliased(str),
+        observed: Aliased(lstr),
         /**
          * A flag to indicate that sequence heterogeneity at this monomer position.
          */
-        hetero: Aliased(str),
+        hetero: Aliased(lstr),
     },
     /**
      * Additional features associated with the reference entity.

package/lib/mol-io/reader/cif/schema/ccd-extras.d.ts

@@ -8,5 +8,5 @@ export declare const ccd_chemCompAtom_schema: {
     comp_id: import("../../../../mol-data/db/column").Column.Schema.Str;
     atom_id: import("../../../../mol-data/db/column").Column.Schema.Str;
     charge: import("../../../../mol-data/db/column").Column.Schema.Int;
-    pdbx_stereo_config: import("../../../../mol-data/db/column").Column.Schema.Aliased<"N" | "R" | "S">;
+    pdbx_stereo_config: import("../../../../mol-data/db/column").Column.Schema.Aliased<"s" | "r" | "n">;
 };