molstar 3.0.0 → 3.0.1

package/lib/commonjs/mol-model/structure/model/properties/atomic/hierarchy.d.ts

@@ -1,244 +0,0 @@
-/**
- * Copyright (c) 2017-2021 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>
- */
-import { Column, Table } from '../../../../../mol-data/db';
-import { Segmentation } from '../../../../../mol-data/int';
-import { ElementSymbol, MoleculeType, PolymerType } from '../../types';
-import { ChainIndex, EntityIndex, ResidueIndex, ElementIndex } from '../../indexing';
-import { SortedRanges } from '../../../../../mol-data/int/sorted-ranges';
-export declare const AtomsSchema: {
-    /**
-     * The chemical element of this atom site.
-     * For mmCIF files, this points to atom_type.symbol in the ATOM_TYPE category.
-     */
-    type_symbol: Column.Schema.Aliased<ElementSymbol>;
-    /**
-     * A component of the identifier for this atom site.
-     * This is a standardized name for the atom within its residue.
-     * For mmCIF files, this points to chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
-     */
-    label_atom_id: Column.Schema.Str;
-    /**
-     * An alternative identifier for label_atom_id that may be provided by an author
-     * in order to match the identification used in the publication that describes the structure.
-     */
-    auth_atom_id: Column.Schema.Str;
-    /**
-     * A component of the identifier for this atom site.
-     * Identifies an alternative conformation for this atom site.
-     */
-    label_alt_id: Column.Schema.Str;
-    /**
-     * A component of the identifier for this atom site.
-     * For mmCIF files, this points to chem_comp.id in the CHEM_COMP category.
-     */
-    label_comp_id: Column.Schema.Str;
-    /**
-     * An alternative identifier for atom_site.label_comp_id that may be provided by an author
-     * in order to match the identification used in the publication that describes the structure.
-     */
-    auth_comp_id: Column.Schema.Str;
-    /**
-     * The net integer charge assigned to this atom.
-     * This is the formal charge assignment normally found in chemical diagrams.
-     */
-    pdbx_formal_charge: Column.Schema.Int;
-};
-export declare type AtomsSchema = typeof AtomsSchema;
-export declare type Atoms = Table<AtomsSchema>;
-export declare const ResiduesSchema: {
-    /**
-     * The group of atoms to which the atom site belongs. This data item is provided for
-     * compatibility with the original Protein Data Bank format, and only for that purpose.
-     */
-    group_PDB: Column.Schema.Aliased<"ATOM" | "HETATM">;
-    /**
-     * For mmCIF files, this points to entity_poly_seq.num in the ENTITY_POLY_SEQ category.
-     */
-    label_seq_id: Column.Schema.Int;
-    /**
-     * An alternative identifier for atom_site.label_seq_id that may be provided by an author
-     * in order to match the identification used in the publication that describes the structure.
-     */
-    auth_seq_id: Column.Schema.Int;
-    /**
-     * PDB insertion code.
-     */
-    pdbx_PDB_ins_code: Column.Schema.Str;
-};
-export declare type ResiduesSchema = typeof ResiduesSchema;
-export declare type Residues = Table<ResiduesSchema>;
-export declare const ChainsSchema: {
-    /**
-     * A component of the identifier for this atom site.
-     * For mmCIF files, this points to struct_asym.id in the STRUCT_ASYM category.
-     */
-    label_asym_id: Column.Schema.Str;
-    /**
-     * An alternative identifier for atomsite.label_asym_id that may be provided by an author
-     * in order to match the identification used in the publication that describes the structure.
-     */
-    auth_asym_id: Column.Schema.Str;
-    /**
-     * For mmCIF files, this points to _entity.id in the ENTITY category.
-     */
-    label_entity_id: Column.Schema.Str;
-};
-export declare type ChainsSchema = typeof ChainsSchema;
-export declare type Chains = Table<ChainsSchema>;
-export interface AtomicData {
-    atoms: Atoms;
-    /**
-     * The index of this atom in the input data.
-     * Required because of sorting of atoms.
-     */
-    atomSourceIndex: Column<number>;
-    residues: Residues;
-    chains: Chains;
-}
-export interface AtomicDerivedData {
-    readonly atom: {
-        readonly atomicNumber: ArrayLike<number>;
-    };
-    readonly residue: {
-        readonly traceElementIndex: ArrayLike<ElementIndex | -1>;
-        readonly directionFromElementIndex: ArrayLike<ElementIndex | -1>;
-        readonly directionToElementIndex: ArrayLike<ElementIndex | -1>;
-        readonly moleculeType: ArrayLike<MoleculeType>;
-        readonly polymerType: ArrayLike<PolymerType>;
-    };
-}
-export interface AtomicSegments {
-    /** Maps residueIndex to a range of atoms [segments[rI], segments[rI + 1]) */
-    residueAtomSegments: Segmentation<ElementIndex, ResidueIndex>;
-    /**
-     * Maps chainIndex to a range of atoms [segments[cI], segments[cI + 1]),
-     *
-     * residues of i-th chain are accessed like this:
-     * const rI = residueAtomSegments.index, offsets = chainAtomSegments.offsets;
-     * const start = rI[offsets[i]], const end = rI[offsets[i + 1] - 1] + 1;
-     * for (let j = start; j < end; i++) { }
-     */
-    chainAtomSegments: Segmentation<ElementIndex, ChainIndex>;
-}
-export interface AtomicIndex {
-    /** @returns index or -1 if not present. */
-    getEntityFromChain(cI: ChainIndex): EntityIndex;
-    /** @returns index or -1 if not present. */
-    findEntity(label_asym_id: string): EntityIndex;
-    /**
-     * Find chain using label_ mmCIF properties
-     * @returns index or -1 if not present.
-     */
-    findChainLabel(key: AtomicIndex.ChainLabelKey): ChainIndex;
-    /**
-     * Find chain using auth_ mmCIF properties
-     * @returns index or -1 if not present.
-     */
-    findChainAuth(key: AtomicIndex.ChainAuthKey): ChainIndex;
-    /**
-     * Index of the 1st occurence of this residue.
-     * auth_seq_id is used because label_seq_id is undefined for "ligands" in mmCIF.
-     * @param key.pdbx_PDB_ins_code Empty string for undefined
-     * @returns index or -1 if not present.
-     */
-    findResidue(key: AtomicIndex.ResidueKey): ResidueIndex;
-    findResidue(label_entity_id: string, label_asym_id: string, auth_seq_id: number, pdbx_PDB_ins_code?: string): ResidueIndex;
-    /**
-     * Index of the 1st occurence of this residue.
-     * @param key.pdbx_PDB_ins_code Empty string for undefined
-     * @returns index or -1 if not present.
-     */
-    findResidueAuth(key: AtomicIndex.ResidueAuthKey): ResidueIndex;
-    /**
-     * Find the residue index where the spefied residue should be inserted to maintain the ordering (entity_id, asym_id, seq_id, ins_code).
-     * Useful for determining ranges for sequence-level annotations.
-     * @param key.pdbx_PDB_ins_code Use empty string for undefined
-     */
-    findResidueInsertion(key: AtomicIndex.ResidueLabelKey): ResidueIndex;
-    /**
-     * Find element index of an atom.
-     * @param key
-     * @returns index or -1 if the atom is not present.
-     */
-    findAtom(key: AtomicIndex.AtomKey): ElementIndex;
-    /**
-     * Find element index of an atom.
-     * @param key
-     * @returns index or -1 if the atom is not present.
-     */
-    findAtomAuth(key: AtomicIndex.AtomAuthKey): ElementIndex;
-    /**
-     * Find element index of an atom on a given residue.
-     * @returns index or -1 if the atom is not present.
-     */
-    findAtomOnResidue(residueIndex: ResidueIndex, label_atom_id: string, label_alt_id?: string): ElementIndex;
-    /**
-     * Find element index of any given atom on a given residue.
-     * @returns first found index or -1 if none of the given atoms are present.
-     */
-    findAtomsOnResidue(residueIndex: ResidueIndex, label_atom_ids: Set<string>): ElementIndex;
-    /**
-     * Find element index of an atom on a given residue.
-     * @returns index or -1 if the atom is not present.
-     */
-    findElementOnResidue(residueIndex: ResidueIndex, type_symbol: ElementSymbol): ElementIndex;
-}
-export declare namespace AtomicIndex {
-    interface ChainLabelKey {
-        label_entity_id: string;
-        label_asym_id: string;
-    }
-    interface ChainAuthKey {
-        auth_asym_id: string;
-        auth_seq_id: number;
-    }
-    interface ResidueKey {
-        label_entity_id: string;
-        label_asym_id: string;
-        auth_seq_id: number;
-        pdbx_PDB_ins_code?: string;
-    }
-    function EmptyResidueKey(): ResidueKey;
-    interface ResidueAuthKey {
-        auth_asym_id: string;
-        auth_comp_id: string;
-        auth_seq_id: number;
-        pdbx_PDB_ins_code?: string;
-    }
-    interface ResidueLabelKey {
-        label_entity_id: string;
-        label_asym_id: string;
-        label_seq_id: number;
-        pdbx_PDB_ins_code?: string;
-    }
-    interface AtomKey extends ResidueKey {
-        label_atom_id: string;
-        label_alt_id?: string;
-    }
-    interface AtomAuthKey extends ResidueAuthKey {
-        auth_atom_id: string;
-        label_alt_id?: string;
-    }
-}
-export interface AtomicRanges {
-    polymerRanges: SortedRanges<ElementIndex>;
-    gapRanges: SortedRanges<ElementIndex>;
-    cyclicPolymerMap: Map<ResidueIndex, ResidueIndex>;
-}
-declare type _Hierarchy = AtomicData & AtomicSegments;
-export interface AtomicHierarchy extends _Hierarchy {
-    index: AtomicIndex;
-    derived: AtomicDerivedData;
-}
-export declare namespace AtomicHierarchy {
-    /** Start residue inclusive */
-    function chainStartResidueIndex(segs: AtomicSegments, cI: ChainIndex): ResidueIndex;
-    /** End residue exclusive */
-    function chainEndResidueIndexExcl(segs: AtomicSegments, cI: ChainIndex): ResidueIndex;
-    function chainResidueCount(segs: AtomicSegments, cI: ChainIndex): number;
-}
-export {};

package/lib/commonjs/mol-model/structure/model/properties/atomic/hierarchy.js

@@ -1,110 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2017-2021 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>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.AtomicHierarchy = exports.AtomicIndex = exports.ChainsSchema = exports.ResiduesSchema = exports.AtomsSchema = void 0;
-var db_1 = require("../../../../../mol-data/db");
-var mmcif_1 = require("../../../../../mol-io/reader/cif/schema/mmcif");
-exports.AtomsSchema = {
-    /**
-     * The chemical element of this atom site.
-     * For mmCIF files, this points to atom_type.symbol in the ATOM_TYPE category.
-     */
-    type_symbol: db_1.Column.Schema.Aliased(mmcif_1.mmCIF_Schema.atom_site.type_symbol),
-    /**
-     * A component of the identifier for this atom site.
-     * This is a standardized name for the atom within its residue.
-     * For mmCIF files, this points to chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
-     */
-    label_atom_id: mmcif_1.mmCIF_Schema.atom_site.label_atom_id,
-    /**
-     * An alternative identifier for label_atom_id that may be provided by an author
-     * in order to match the identification used in the publication that describes the structure.
-     */
-    auth_atom_id: mmcif_1.mmCIF_Schema.atom_site.auth_atom_id,
-    /**
-     * A component of the identifier for this atom site.
-     * Identifies an alternative conformation for this atom site.
-     */
-    label_alt_id: mmcif_1.mmCIF_Schema.atom_site.label_alt_id,
-    /**
-     * A component of the identifier for this atom site.
-     * For mmCIF files, this points to chem_comp.id in the CHEM_COMP category.
-     */
-    label_comp_id: mmcif_1.mmCIF_Schema.atom_site.label_comp_id,
-    /**
-     * An alternative identifier for atom_site.label_comp_id that may be provided by an author
-     * in order to match the identification used in the publication that describes the structure.
-     */
-    auth_comp_id: mmcif_1.mmCIF_Schema.atom_site.auth_comp_id,
-    /**
-     * The net integer charge assigned to this atom.
-     * This is the formal charge assignment normally found in chemical diagrams.
-     */
-    pdbx_formal_charge: mmcif_1.mmCIF_Schema.atom_site.pdbx_formal_charge,
-    // id, occupancy and B_iso_or_equiv are part of conformation
-};
-exports.ResiduesSchema = {
-    /**
-     * The group of atoms to which the atom site belongs. This data item is provided for
-     * compatibility with the original Protein Data Bank format, and only for that purpose.
-     */
-    group_PDB: mmcif_1.mmCIF_Schema.atom_site.group_PDB,
-    /**
-     * For mmCIF files, this points to entity_poly_seq.num in the ENTITY_POLY_SEQ category.
-     */
-    label_seq_id: mmcif_1.mmCIF_Schema.atom_site.label_seq_id,
-    /**
-     * An alternative identifier for atom_site.label_seq_id that may be provided by an author
-     * in order to match the identification used in the publication that describes the structure.
-     */
-    auth_seq_id: mmcif_1.mmCIF_Schema.atom_site.auth_seq_id,
-    /**
-     * PDB insertion code.
-     */
-    pdbx_PDB_ins_code: mmcif_1.mmCIF_Schema.atom_site.pdbx_PDB_ins_code,
-    // comp_id is part of atoms because of microheterogeneity
-};
-exports.ChainsSchema = {
-    /**
-     * A component of the identifier for this atom site.
-     * For mmCIF files, this points to struct_asym.id in the STRUCT_ASYM category.
-     */
-    label_asym_id: mmcif_1.mmCIF_Schema.atom_site.label_asym_id,
-    /**
-     * An alternative identifier for atomsite.label_asym_id that may be provided by an author
-     * in order to match the identification used in the publication that describes the structure.
-     */
-    auth_asym_id: mmcif_1.mmCIF_Schema.atom_site.auth_asym_id,
-    /**
-     * For mmCIF files, this points to _entity.id in the ENTITY category.
-     */
-    label_entity_id: mmcif_1.mmCIF_Schema.atom_site.label_entity_id
-};
-var AtomicIndex;
-(function (AtomicIndex) {
-    function EmptyResidueKey() { return { label_entity_id: '', label_asym_id: '', auth_seq_id: 0, pdbx_PDB_ins_code: void 0 }; }
-    AtomicIndex.EmptyResidueKey = EmptyResidueKey;
-})(AtomicIndex = exports.AtomicIndex || (exports.AtomicIndex = {}));
-var AtomicHierarchy;
-(function (AtomicHierarchy) {
-    /** Start residue inclusive */
-    function chainStartResidueIndex(segs, cI) {
-        return segs.residueAtomSegments.index[segs.chainAtomSegments.offsets[cI]];
-    }
-    AtomicHierarchy.chainStartResidueIndex = chainStartResidueIndex;
-    /** End residue exclusive */
-    function chainEndResidueIndexExcl(segs, cI) {
-        return segs.residueAtomSegments.index[segs.chainAtomSegments.offsets[cI + 1] - 1] + 1;
-    }
-    AtomicHierarchy.chainEndResidueIndexExcl = chainEndResidueIndexExcl;
-    function chainResidueCount(segs, cI) {
-        return chainEndResidueIndexExcl(segs, cI) - chainStartResidueIndex(segs, cI);
-    }
-    AtomicHierarchy.chainResidueCount = chainResidueCount;
-})(AtomicHierarchy = exports.AtomicHierarchy || (exports.AtomicHierarchy = {}));
-//# sourceMappingURL=hierarchy.js.map

package/lib/commonjs/mol-model/structure/model/properties/atomic/measures.d.ts

@@ -1,21 +0,0 @@
-/**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-import { ElementSymbol } from '../../types';
-export declare const AtomicNumbers: {
-    [e: string]: number | undefined;
-};
-export declare const ElementVdwRadii: {
-    [e: number]: number | undefined;
-};
-export declare const ElementAtomWeights: {
-    [e: number]: number | undefined;
-};
-export declare const DefaultVdwRadius = 1.7;
-export declare const DefaultAtomWeight = 10.81;
-export declare const DefaultAtomNumber = 0;
-export declare function VdwRadius(element: ElementSymbol): number;
-export declare function AtomWeight(element: ElementSymbol): number;
-export declare function AtomNumber(element: ElementSymbol): number;

package/lib/commonjs/mol-model/structure/model/properties/atomic/measures.js

@@ -1,38 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.AtomNumber = exports.AtomWeight = exports.VdwRadius = exports.DefaultAtomNumber = exports.DefaultAtomWeight = exports.DefaultVdwRadius = exports.ElementAtomWeights = exports.ElementVdwRadii = exports.AtomicNumbers = void 0;
-exports.AtomicNumbers = {
-    'H': 1, 'D': 1, 'T': 1, 'HE': 2, 'LI': 3, 'BE': 4, 'B': 5, 'C': 6, 'N': 7, 'O': 8, 'F': 9, 'NE': 10, 'NA': 11, 'MG': 12, 'AL': 13, 'SI': 14, 'P': 15, 'S': 16, 'CL': 17, 'AR': 18, 'K': 19, 'CA': 20, 'SC': 21, 'TI': 22, 'V': 23, 'CR': 24, 'MN': 25, 'FE': 26, 'CO': 27, 'NI': 28, 'CU': 29, 'ZN': 30, 'GA': 31, 'GE': 32, 'AS': 33, 'SE': 34, 'BR': 35, 'KR': 36, 'RB': 37, 'SR': 38, 'Y': 39, 'ZR': 40, 'NB': 41, 'MO': 42, 'TC': 43, 'RU': 44, 'RH': 45, 'PD': 46, 'AG': 47, 'CD': 48, 'IN': 49, 'SN': 50, 'SB': 51, 'TE': 52, 'I': 53, 'XE': 54, 'CS': 55, 'BA': 56, 'LA': 57, 'CE': 58, 'PR': 59, 'ND': 60, 'PM': 61, 'SM': 62, 'EU': 63, 'GD': 64, 'TB': 65, 'DY': 66, 'HO': 67, 'ER': 68, 'TM': 69, 'YB': 70, 'LU': 71, 'HF': 72, 'TA': 73, 'W': 74, 'RE': 75, 'OS': 76, 'IR': 77, 'PT': 78, 'AU': 79, 'HG': 80, 'TL': 81, 'PB': 82, 'BI': 83, 'PO': 84, 'AT': 85, 'RN': 86, 'FR': 87, 'RA': 88, 'AC': 89, 'TH': 90, 'PA': 91, 'U': 92, 'NP': 93, 'PU': 94, 'AM': 95, 'CM': 96, 'BK': 97, 'CF': 98, 'ES': 99, 'FM': 100, 'MD': 101, 'NO': 102, 'LR': 103, 'RF': 104, 'DB': 105, 'SG': 106, 'BH': 107, 'HS': 108, 'MT': 109
-};
-// http://dx.doi.org/10.1021/jp8111556 (or 2.0)
-exports.ElementVdwRadii = {
-    1: 1.1, 2: 1.4, 3: 1.81, 4: 1.53, 5: 1.92, 6: 1.7, 7: 1.55, 8: 1.52, 9: 1.47, 10: 1.54, 11: 2.27, 12: 1.73, 13: 1.84, 14: 2.1, 15: 1.8, 16: 1.8, 17: 1.75, 18: 1.88, 19: 2.75, 20: 2.31, 21: 2.3, 22: 2.15, 23: 2.05, 24: 2.05, 25: 2.05, 26: 2.05, 27: 2.0, 28: 2.0, 29: 2.0, 30: 2.1, 31: 1.87, 32: 2.11, 33: 1.85, 34: 1.9, 35: 1.83, 36: 2.02, 37: 3.03, 38: 2.49, 39: 2.4, 40: 2.3, 41: 2.15, 42: 2.1, 43: 2.05, 44: 2.05, 45: 2.0, 46: 2.05, 47: 2.1, 48: 2.2, 49: 2.2, 50: 1.93, 51: 2.17, 52: 2.06, 53: 1.98, 54: 2.16, 55: 3.43, 56: 2.68, 57: 2.5, 58: 2.48, 59: 2.47, 60: 2.45, 61: 2.43, 62: 2.42, 63: 2.4, 64: 2.38, 65: 2.37, 66: 2.35, 67: 2.33, 68: 2.32, 69: 2.3, 70: 2.28, 71: 2.27, 72: 2.25, 73: 2.2, 74: 2.1, 75: 2.05, 76: 2.0, 77: 2.0, 78: 2.05, 79: 2.1, 80: 2.05, 81: 1.96, 82: 2.02, 83: 2.07, 84: 1.97, 85: 2.02, 86: 2.2, 87: 3.48, 88: 2.83, 89: 2.0, 90: 2.4, 91: 2.0, 92: 2.3, 93: 2.0, 94: 2.0, 95: 2.0, 96: 2.0, 97: 2.0, 98: 2.0, 99: 2.0, 100: 2.0, 101: 2.0, 102: 2.0, 103: 2.0, 104: 2.0, 105: 2.0, 106: 2.0, 107: 2.0, 108: 2.0, 109: 2.0
-};
-// https://doi.org/10.1515/pac-2015-0305 (table 2, 3, and 4)
-exports.ElementAtomWeights = {
-    1: 1.008, 2: 4.0026, 3: 6.94, 4: 9.0122, 5: 10.81, 6: 10.81, 7: 14.007, 8: 15.999, 9: 18.998, 10: 20.180, 11: 22.990, 12: 24.305, 13: 26.982, 14: 28.085, 15: 30.974, 16: 32.06, 17: 35.45, 18: 39.948, 19: 39.098, 20: 40.078, 21: 44.956, 22: 47.867, 23: 50.942, 24: 51.996, 25: 54.938, 26: 55.845, 27: 58.933, 28: 58.693, 29: 63.546, 30: 65.38, 31: 69.723, 32: 72.630, 33: 74.922, 34: 78.971, 35: 79.904, 36: 83.798, 37: 85.468, 38: 87.62, 39: 88.906, 40: 91.224, 41: 92.906, 42: 95.95, 43: 96.906, 44: 101.07, 45: 102.91, 46: 106.42, 47: 107.87, 48: 112.41, 49: 114.82, 50: 118.71, 51: 121.76, 52: 127.60, 53: 127.60, 54: 131.29, 55: 132.91, 56: 137.33, 57: 138.91, 58: 140.12, 59: 140.91, 60: 144.24, 61: 144.912, 62: 150.36, 63: 151.96, 64: 157.25, 65: 158.93, 66: 162.50, 67: 164.93, 68: 167.26, 69: 168.93, 70: 173.05, 71: 174.97, 72: 178.49, 73: 180.95, 74: 183.84, 75: 186.21, 76: 190.23, 77: 192.22, 78: 195.08, 79: 196.97, 80: 200.59, 81: 204.38, 82: 207.2, 83: 208.98, 84: 1.97, 85: 2.02, 86: 2.2, 87: 3.48, 88: 2.83, 89: 2.0, 90: 232.04, 91: 231.04, 92: 238.03, 93: 237.048, 94: 244.064, 95: 243.061, 96: 247.070, 97: 247.070, 98: 251.079, 99: 252.083, 100: 257.095, 101: 258.098, 102: 259.101, 103: 262.110, 104: 267.122, 105: 270.131, 106: 271.134, 107: 270.133, 108: 270.134, 109: 278.156
-};
-exports.DefaultVdwRadius = 1.7; // C
-exports.DefaultAtomWeight = 10.81; // C
-exports.DefaultAtomNumber = 0;
-function VdwRadius(element) {
-    var i = exports.AtomicNumbers[element];
-    return i === void 0 ? exports.DefaultVdwRadius : exports.ElementVdwRadii[i];
-}
-exports.VdwRadius = VdwRadius;
-function AtomWeight(element) {
-    var i = exports.AtomicNumbers[element];
-    return i === void 0 ? exports.DefaultAtomWeight : exports.ElementAtomWeights[i];
-}
-exports.AtomWeight = AtomWeight;
-function AtomNumber(element) {
-    var i = exports.AtomicNumbers[element];
-    return i === void 0 ? exports.DefaultAtomNumber : i;
-}
-exports.AtomNumber = AtomNumber;
-//# sourceMappingURL=measures.js.map

package/lib/commonjs/mol-model/structure/model/properties/atomic/types.d.ts

@@ -1,155 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-import { ElementSymbol } from '../../types';
-/**
- * Enum of element symbols
- */
-export declare const enum Elements {
-    H = "H",
-    D = "D",
-    T = "T",
-    HE = "HE",
-    LI = "LI",
-    BE = "BE",
-    B = "B",
-    C = "C",
-    N = "N",
-    O = "O",
-    F = "F",
-    NE = "NE",
-    NA = "NA",
-    MG = "MG",
-    AL = "AL",
-    SI = "SI",
-    P = "P",
-    S = "S",
-    CL = "CL",
-    AR = "AR",
-    K = "K",
-    CA = "CA",
-    SC = "SC",
-    TI = "TI",
-    V = "V",
-    CR = "CR",
-    MN = "MN",
-    FE = "FE",
-    CO = "CO",
-    NI = "NI",
-    CU = "CU",
-    ZN = "ZN",
-    GA = "GA",
-    GE = "GE",
-    AS = "AS",
-    SE = "SE",
-    BR = "BR",
-    KR = "KR",
-    RB = "RB",
-    SR = "SR",
-    Y = "Y",
-    ZR = "ZR",
-    NB = "NB",
-    MO = "MO",
-    TC = "TC",
-    RU = "RU",
-    RH = "RH",
-    PD = "PD",
-    AG = "AG",
-    CD = "CD",
-    IN = "IN",
-    SN = "SN",
-    SB = "SB",
-    TE = "TE",
-    I = "I",
-    XE = "XE",
-    CS = "CS",
-    BA = "BA",
-    LA = "LA",
-    CE = "CE",
-    PR = "PR",
-    ND = "ND",
-    PM = "PM",
-    SM = "SM",
-    EU = "EU",
-    GD = "GD",
-    TB = "TB",
-    DY = "DY",
-    HO = "HO",
-    ER = "ER",
-    TM = "TM",
-    YB = "YB",
-    LU = "LU",
-    HF = "HF",
-    TA = "TA",
-    W = "W",
-    RE = "RE",
-    OS = "OS",
-    IR = "IR",
-    PT = "PT",
-    AU = "AU",
-    HG = "HG",
-    TL = "TL",
-    PB = "PB",
-    BI = "BI",
-    PO = "PO",
-    AT = "AT",
-    RN = "RN",
-    FR = "FR",
-    RA = "RA",
-    AC = "AC",
-    TH = "TH",
-    PA = "PA",
-    U = "U",
-    NP = "NP",
-    PU = "PU",
-    AM = "AM",
-    CM = "CM",
-    BK = "BK",
-    CF = "CF",
-    ES = "ES",
-    FM = "FM",
-    MD = "MD",
-    NO = "NO",
-    LR = "LR",
-    RF = "RF",
-    DB = "DB",
-    SG = "SG",
-    BH = "BH",
-    HS = "HS",
-    MT = "MT",
-    DS = "DS",
-    RG = "RG",
-    CN = "CN",
-    NH = "NH",
-    FL = "FL",
-    MC = "MC",
-    LV = "LV",
-    TS = "TS",
-    OG = "OG"
-}
-export declare const ElementNames: {
-    [k: string]: string;
-};
-export declare const AlkaliMetals: Set<ElementSymbol>;
-export declare function isAlkaliMetal(element: ElementSymbol): boolean;
-export declare const AlkalineEarthMetals: Set<ElementSymbol>;
-export declare function isAlkalineEarthMetal(element: ElementSymbol): boolean;
-export declare const PolyatomicNonmetals: Set<ElementSymbol>;
-export declare function isPolyatomicNonmetal(element: ElementSymbol): boolean;
-export declare const DiatomicNonmetals: Set<ElementSymbol>;
-export declare function isDiatomicNonmetal(element: ElementSymbol): boolean;
-export declare const NobleGases: Set<ElementSymbol>;
-export declare function isNobleGas(element: ElementSymbol): boolean;
-export declare const PostTransitionMetals: Set<ElementSymbol>;
-export declare function isPostTransitionMetal(element: ElementSymbol): boolean;
-export declare const Metalloids: Set<ElementSymbol>;
-export declare function isMetalloid(element: ElementSymbol): boolean;
-export declare const Halogens: Set<ElementSymbol>;
-export declare function isHalogen(element: ElementSymbol): boolean;
-export declare function isTransitionMetal(element: ElementSymbol): boolean;
-export declare function isLanthanide(element: ElementSymbol): boolean;
-export declare function isActinide(element: ElementSymbol): boolean;
-export declare function isMetal(element: ElementSymbol): boolean;
-export declare function isNonmetal(element: ElementSymbol): boolean;

package/lib/commonjs/mol-model/structure/model/properties/atomic/types.js

@@ -1,70 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.isNonmetal = exports.isMetal = exports.isActinide = exports.isLanthanide = exports.isTransitionMetal = exports.isHalogen = exports.Halogens = exports.isMetalloid = exports.Metalloids = exports.isPostTransitionMetal = exports.PostTransitionMetals = exports.isNobleGas = exports.NobleGases = exports.isDiatomicNonmetal = exports.DiatomicNonmetals = exports.isPolyatomicNonmetal = exports.PolyatomicNonmetals = exports.isAlkalineEarthMetal = exports.AlkalineEarthMetals = exports.isAlkaliMetal = exports.AlkaliMetals = exports.ElementNames = void 0;
-var measures_1 = require("./measures");
-exports.ElementNames = {
-    H: 'Hydrogen', HE: 'Helium', LI: 'Lithium', BE: 'Beryllium', B: 'Boron', C: 'Carbon', N: 'Nitrogen', O: 'Oxygen', F: 'Fluorine', NE: 'Neon', NA: 'Sodium', MG: 'Magnesium', AL: 'Aluminum', SI: 'Silicon', P: 'Phosphorus', S: 'Sulfur', CL: 'Chlorine', AR: 'Argon', K: 'Potassium', CA: 'Calcium', SC: 'Scandium', TI: 'Titanium', V: 'Vanadium', CR: 'Chromium', MN: 'Manganese', FE: 'Iron', CO: 'Cobalt', NI: 'Nickel', CU: 'Copper', ZN: 'Zinc', GA: 'Gallium', GE: 'Germanium', AS: 'Arsenic', SE: 'Selenium', BR: 'Bromine', KR: 'Krypton', RB: 'Rubidium', SR: 'Strontium', Y: 'Yttrium', ZR: 'Zirconium', NB: 'Niobium', MO: 'Molybdenum', TC: 'Technetium', RU: 'Ruthenium', RH: 'Rhodium', PD: 'Palladium', AG: 'Silver', CD: 'Cadmium', IN: 'Indium', SN: 'Tin', SB: 'Antimony', TE: 'Tellurium', I: 'Iodine', XE: 'Xenon', CS: 'Cesium', BA: 'Barium', LA: 'Lanthanum', CE: 'Cerium', PR: 'Praseodymium', ND: 'Neodymium', PM: 'Promethium', SM: 'Samarium', EU: 'Europium', GD: 'Gadolinium', TB: 'Terbium', DY: 'Dysprosium', HO: 'Holmium', ER: 'Erbium', TM: 'Thulium', YB: 'Ytterbium', LU: 'Lutetium', HF: 'Hafnium', TA: 'Tantalum', W: 'Wolfram', RE: 'Rhenium', OS: 'Osmium', IR: 'Iridium', PT: 'Platinum', AU: 'Gold', HG: 'Mercury', TL: 'Thallium', PB: 'Lead', BI: 'Bismuth', PO: 'Polonium', AT: 'Astatine', RN: 'Radon', FR: 'Francium', RA: 'Radium', AC: 'Actinium', TH: 'Thorium', PA: 'Protactinium', U: 'Uranium', NP: 'Neptunium', PU: 'Plutonium', AM: 'Americium', CM: 'Curium', BK: 'Berkelium', CF: 'Californium', ES: 'Einsteinium', FM: 'Fermium', MD: 'Mendelevium', NO: 'Nobelium', LR: 'Lawrencium', RF: 'Rutherfordium', DB: 'Dubnium', SG: 'Seaborgium', BH: 'Bohrium', HS: 'Hassium', MT: 'Meitnerium', DS: 'Darmstadtium', RG: 'Roentgenium', CN: 'Copernicium', NH: 'Nihonium', FL: 'Flerovium', MC: 'Moscovium', LV: 'Livermorium', TS: 'Tennessine', OG: 'Oganesson'
-};
-exports.AlkaliMetals = new Set(['LI', 'NA', 'K', 'RB', 'CS', 'FR']);
-function isAlkaliMetal(element) { return exports.AlkaliMetals.has(element); }
-exports.isAlkaliMetal = isAlkaliMetal;
-exports.AlkalineEarthMetals = new Set(['BE', 'MG', 'CA', 'SR', 'BA', 'RA']);
-function isAlkalineEarthMetal(element) { return exports.AlkalineEarthMetals.has(element); }
-exports.isAlkalineEarthMetal = isAlkalineEarthMetal;
-exports.PolyatomicNonmetals = new Set(['C', 'P', 'S', 'SE']);
-function isPolyatomicNonmetal(element) { return exports.PolyatomicNonmetals.has(element); }
-exports.isPolyatomicNonmetal = isPolyatomicNonmetal;
-exports.DiatomicNonmetals = new Set(['H', 'N', 'O', 'F', 'CL', 'BR', 'I']);
-function isDiatomicNonmetal(element) { return exports.DiatomicNonmetals.has(element); }
-exports.isDiatomicNonmetal = isDiatomicNonmetal;
-exports.NobleGases = new Set(['HE', 'NE', 'AR', 'KR', 'XE', 'RN']);
-function isNobleGas(element) { return exports.NobleGases.has(element); }
-exports.isNobleGas = isNobleGas;
-exports.PostTransitionMetals = new Set(['ZN', 'GA', 'CD', 'IN', 'SN', 'HG', 'TI', 'PB', 'BI', 'PO', 'CN']);
-function isPostTransitionMetal(element) { return exports.PostTransitionMetals.has(element); }
-exports.isPostTransitionMetal = isPostTransitionMetal;
-exports.Metalloids = new Set(['B', 'SI', 'GE', 'AS', 'SB', 'TE', 'AT']);
-function isMetalloid(element) { return exports.Metalloids.has(element); }
-exports.isMetalloid = isMetalloid;
-exports.Halogens = new Set(['F', 'CL', 'BR', 'I', 'AT']);
-function isHalogen(element) { return exports.Halogens.has(element); }
-exports.isHalogen = isHalogen;
-function isTransitionMetal(element) {
-    var no = (0, measures_1.AtomNumber)(element);
-    return ((no >= 21 && no <= 29) ||
-        (no >= 39 && no <= 47) ||
-        (no >= 72 && no <= 79) ||
-        (no >= 104 && no <= 108));
-}
-exports.isTransitionMetal = isTransitionMetal;
-function isLanthanide(element) {
-    var no = (0, measures_1.AtomNumber)(element);
-    return no >= 57 && no <= 71;
-}
-exports.isLanthanide = isLanthanide;
-function isActinide(element) {
-    var no = (0, measures_1.AtomNumber)(element);
-    return no >= 89 && no <= 103;
-}
-exports.isActinide = isActinide;
-function isMetal(element) {
-    return (isAlkaliMetal(element) ||
-        isAlkalineEarthMetal(element) ||
-        isLanthanide(element) ||
-        isActinide(element) ||
-        isTransitionMetal(element) ||
-        isPostTransitionMetal(element));
-}
-exports.isMetal = isMetal;
-function isNonmetal(element) {
-    return (isDiatomicNonmetal(element) ||
-        isPolyatomicNonmetal(element) ||
-        isNobleGas(element));
-}
-exports.isNonmetal = isNonmetal;
-//# sourceMappingURL=types.js.map

package/lib/commonjs/mol-model/structure/model/properties/atomic.d.ts

@@ -1,8 +0,0 @@
-/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-export * from './atomic/conformation';
-export * from './atomic/hierarchy';
-export * from './atomic/measures';

package/lib/commonjs/mol-model/structure/model/properties/atomic.js

@@ -1,12 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./atomic/conformation"), exports);
-(0, tslib_1.__exportStar)(require("./atomic/hierarchy"), exports);
-(0, tslib_1.__exportStar)(require("./atomic/measures"), exports);
-//# sourceMappingURL=atomic.js.map