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molstar

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A comprehensive macromolecular library.

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/** * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info. * * @author Alexander Rose <alexander.rose@weirdbyte.de> */ import { isHalogen } from '../../../mol-model/structure/model/properties/atomic/types'; import { BondType } from '../../../mol-model/structure/model/types'; import { eachBondedAtom, bondCount, typeSymbol, bondToElementCount } from './util'; function isAromatic(unit, index) { // TODO also extend unit.rings with geometry/composition-based aromaticity detection and use it here in addition const { offset, edgeProps } = unit.bonds; for (let i = offset[index], il = offset[index + 1]; i < il; ++i) { if (BondType.is(16 /* BondType.Flag.Aromatic */, edgeProps.flags[i])) return true; } return false; } function bondToCarbonylCount(structure, unit, index) { let carbonylCount = 0; eachBondedAtom(structure, unit, index, (unit, index) => { if (isCarbonyl(structure, unit, index)) carbonylCount += 1; }); return carbonylCount; } // /** * Nitrogen in a quaternary amine */ export function isQuaternaryAmine(structure, unit, index) { return (typeSymbol(unit, index) === "N" /* Elements.N */ && bondCount(structure, unit, index) === 4 && bondToElementCount(structure, unit, index, "H" /* Elements.H */) === 0); } /** * Nitrogen in a tertiary amine */ export function isTertiaryAmine(structure, unit, index, idealValence) { return (typeSymbol(unit, index) === "N" /* Elements.N */ && bondCount(structure, unit, index) === 4 && idealValence === 3); } /** * Nitrogen in an imide */ export function isImide(structure, unit, index) { let flag = false; if (typeSymbol(unit, index) === "N" /* Elements.N */ && (bondCount(structure, unit, index) - bondToElementCount(structure, unit, index, "H" /* Elements.H */)) === 2) { flag = bondToCarbonylCount(structure, unit, index) === 2; } return flag; } /** * Nitrogen in an amide */ export function isAmide(structure, unit, index) { let flag = false; if (typeSymbol(unit, index) === "N" /* Elements.N */ && (bondCount(structure, unit, index) - bondToElementCount(structure, unit, index, "H" /* Elements.H */)) === 2) { flag = bondToCarbonylCount(structure, unit, index) === 1; } return flag; } /** * Sulfur in a sulfonium group */ export function isSulfonium(structure, unit, index) { return (typeSymbol(unit, index) === "S" /* Elements.S */ && bondCount(structure, unit, index) === 3 && bondToElementCount(structure, unit, index, "H" /* Elements.H */) === 0); } /** * Sulfur in a sulfonic acid or sulfonate group */ export function isSulfonicAcid(structure, unit, index) { return (typeSymbol(unit, index) === "S" /* Elements.S */ && bondToElementCount(structure, unit, index, "O" /* Elements.O */) === 3); } /** * Sulfur in a sulfate group */ export function isSulfate(structure, unit, index) { return (typeSymbol(unit, index) === "S" /* Elements.S */ && bondToElementCount(structure, unit, index, "O" /* Elements.O */) === 4); } /** * Phosphor in a phosphate group */ export function isPhosphate(structure, unit, index) { return (typeSymbol(unit, index) === "P" /* Elements.P */ && bondToElementCount(structure, unit, index, "O" /* Elements.O */) === bondCount(structure, unit, index)); } /** * Halogen with one bond to a carbon */ export function isHalocarbon(structure, unit, index) { return (isHalogen(typeSymbol(unit, index)) && bondCount(structure, unit, index) === 1 && bondToElementCount(structure, unit, index, "C" /* Elements.C */) === 1); } /** * Carbon in a carbonyl/acyl group * * TODO currently only checks intra bonds for group detection */ export function isCarbonyl(structure, unit, index) { let flag = false; if (typeSymbol(unit, index) === "C" /* Elements.C */) { const { offset, edgeProps, b } = unit.bonds; for (let i = offset[index], il = offset[index + 1]; i < il; ++i) { if (edgeProps.order[i] === 2 && typeSymbol(unit, b[i]) === "O" /* Elements.O */) { flag = true; break; } } } return flag; } /** * Carbon in a carboxylate group */ export function isCarboxylate(structure, unit, index) { let terminalOxygenCount = 0; if (typeSymbol(unit, index) === "C" /* Elements.C */ && bondToElementCount(structure, unit, index, "O" /* Elements.O */) === 2 && bondToElementCount(structure, unit, index, "C" /* Elements.C */) === 1) { eachBondedAtom(structure, unit, index, (unit, index) => { if (typeSymbol(unit, index) === "O" /* Elements.O */ && bondCount(structure, unit, index) - bondToElementCount(structure, unit, index, "H" /* Elements.H */) === 1) { terminalOxygenCount += 1; } }); } return terminalOxygenCount === 2; } /** * Carbon in a guanidine group */ export function isGuanidine(structure, unit, index) { let terminalNitrogenCount = 0; if (typeSymbol(unit, index) === "C" /* Elements.C */ && bondCount(structure, unit, index) === 3 && bondToElementCount(structure, unit, index, "N" /* Elements.N */) === 3) { eachBondedAtom(structure, unit, index, (unit, index) => { if (bondCount(structure, unit, index) - bondToElementCount(structure, unit, index, "H" /* Elements.H */) === 1) { terminalNitrogenCount += 1; } }); } return terminalNitrogenCount === 2; } /** * Carbon in a acetamidine group */ export function isAcetamidine(structure, unit, index) { let terminalNitrogenCount = 0; if (typeSymbol(unit, index) === "C" /* Elements.C */ && bondCount(structure, unit, index) === 3 && bondToElementCount(structure, unit, index, "N" /* Elements.N */) === 2 && bondToElementCount(structure, unit, index, "C" /* Elements.C */) === 1) { eachBondedAtom(structure, unit, index, (unit, index) => { if (bondCount(structure, unit, index) - bondToElementCount(structure, unit, index, "H" /* Elements.H */) === 1) { terminalNitrogenCount += 1; } }); } return terminalNitrogenCount === 2; } const PolarElements = new Set(['N', 'O', 'S', 'F', 'CL', 'BR', 'I']); export function isPolar(element) { return PolarElements.has(element); } export function hasPolarNeighbour(structure, unit, index) { let flag = false; eachBondedAtom(structure, unit, index, (unit, index) => { if (isPolar(typeSymbol(unit, index))) flag = true; }); return flag; } export function hasAromaticNeighbour(structure, unit, index) { let flag = false; eachBondedAtom(structure, unit, index, (unit, index) => { if (isAromatic(unit, index)) flag = true; }); return flag; }