molstar
Version:
A comprehensive macromolecular library.
206 lines (205 loc) • 8.11 kB
JavaScript
;
/**
* 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.isQuaternaryAmine = isQuaternaryAmine;
exports.isTertiaryAmine = isTertiaryAmine;
exports.isImide = isImide;
exports.isAmide = isAmide;
exports.isSulfonium = isSulfonium;
exports.isSulfonicAcid = isSulfonicAcid;
exports.isSulfate = isSulfate;
exports.isPhosphate = isPhosphate;
exports.isHalocarbon = isHalocarbon;
exports.isCarbonyl = isCarbonyl;
exports.isCarboxylate = isCarboxylate;
exports.isGuanidine = isGuanidine;
exports.isAcetamidine = isAcetamidine;
exports.isPolar = isPolar;
exports.hasPolarNeighbour = hasPolarNeighbour;
exports.hasAromaticNeighbour = hasAromaticNeighbour;
const types_1 = require("../../../mol-model/structure/model/properties/atomic/types");
const types_2 = require("../../../mol-model/structure/model/types");
const util_1 = require("./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 (types_2.BondType.is(16 /* BondType.Flag.Aromatic */, edgeProps.flags[i]))
return true;
}
return false;
}
function bondToCarbonylCount(structure, unit, index) {
let carbonylCount = 0;
(0, util_1.eachBondedAtom)(structure, unit, index, (unit, index) => {
if (isCarbonyl(structure, unit, index))
carbonylCount += 1;
});
return carbonylCount;
}
//
/**
* Nitrogen in a quaternary amine
*/
function isQuaternaryAmine(structure, unit, index) {
return ((0, util_1.typeSymbol)(unit, index) === "N" /* Elements.N */ &&
(0, util_1.bondCount)(structure, unit, index) === 4 &&
(0, util_1.bondToElementCount)(structure, unit, index, "H" /* Elements.H */) === 0);
}
/**
* Nitrogen in a tertiary amine
*/
function isTertiaryAmine(structure, unit, index, idealValence) {
return ((0, util_1.typeSymbol)(unit, index) === "N" /* Elements.N */ &&
(0, util_1.bondCount)(structure, unit, index) === 4 &&
idealValence === 3);
}
/**
* Nitrogen in an imide
*/
function isImide(structure, unit, index) {
let flag = false;
if ((0, util_1.typeSymbol)(unit, index) === "N" /* Elements.N */ &&
((0, util_1.bondCount)(structure, unit, index) - (0, util_1.bondToElementCount)(structure, unit, index, "H" /* Elements.H */)) === 2) {
flag = bondToCarbonylCount(structure, unit, index) === 2;
}
return flag;
}
/**
* Nitrogen in an amide
*/
function isAmide(structure, unit, index) {
let flag = false;
if ((0, util_1.typeSymbol)(unit, index) === "N" /* Elements.N */ &&
((0, util_1.bondCount)(structure, unit, index) - (0, util_1.bondToElementCount)(structure, unit, index, "H" /* Elements.H */)) === 2) {
flag = bondToCarbonylCount(structure, unit, index) === 1;
}
return flag;
}
/**
* Sulfur in a sulfonium group
*/
function isSulfonium(structure, unit, index) {
return ((0, util_1.typeSymbol)(unit, index) === "S" /* Elements.S */ &&
(0, util_1.bondCount)(structure, unit, index) === 3 &&
(0, util_1.bondToElementCount)(structure, unit, index, "H" /* Elements.H */) === 0);
}
/**
* Sulfur in a sulfonic acid or sulfonate group
*/
function isSulfonicAcid(structure, unit, index) {
return ((0, util_1.typeSymbol)(unit, index) === "S" /* Elements.S */ &&
(0, util_1.bondToElementCount)(structure, unit, index, "O" /* Elements.O */) === 3);
}
/**
* Sulfur in a sulfate group
*/
function isSulfate(structure, unit, index) {
return ((0, util_1.typeSymbol)(unit, index) === "S" /* Elements.S */ &&
(0, util_1.bondToElementCount)(structure, unit, index, "O" /* Elements.O */) === 4);
}
/**
* Phosphor in a phosphate group
*/
function isPhosphate(structure, unit, index) {
return ((0, util_1.typeSymbol)(unit, index) === "P" /* Elements.P */ &&
(0, util_1.bondToElementCount)(structure, unit, index, "O" /* Elements.O */) === (0, util_1.bondCount)(structure, unit, index));
}
/**
* Halogen with one bond to a carbon
*/
function isHalocarbon(structure, unit, index) {
return ((0, types_1.isHalogen)((0, util_1.typeSymbol)(unit, index)) &&
(0, util_1.bondCount)(structure, unit, index) === 1 &&
(0, util_1.bondToElementCount)(structure, unit, index, "C" /* Elements.C */) === 1);
}
/**
* Carbon in a carbonyl/acyl group
*
* TODO currently only checks intra bonds for group detection
*/
function isCarbonyl(structure, unit, index) {
let flag = false;
if ((0, util_1.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 && (0, util_1.typeSymbol)(unit, b[i]) === "O" /* Elements.O */) {
flag = true;
break;
}
}
}
return flag;
}
/**
* Carbon in a carboxylate group
*/
function isCarboxylate(structure, unit, index) {
let terminalOxygenCount = 0;
if ((0, util_1.typeSymbol)(unit, index) === "C" /* Elements.C */ &&
(0, util_1.bondToElementCount)(structure, unit, index, "O" /* Elements.O */) === 2 &&
(0, util_1.bondToElementCount)(structure, unit, index, "C" /* Elements.C */) === 1) {
(0, util_1.eachBondedAtom)(structure, unit, index, (unit, index) => {
if ((0, util_1.typeSymbol)(unit, index) === "O" /* Elements.O */ &&
(0, util_1.bondCount)(structure, unit, index) - (0, util_1.bondToElementCount)(structure, unit, index, "H" /* Elements.H */) === 1) {
terminalOxygenCount += 1;
}
});
}
return terminalOxygenCount === 2;
}
/**
* Carbon in a guanidine group
*/
function isGuanidine(structure, unit, index) {
let terminalNitrogenCount = 0;
if ((0, util_1.typeSymbol)(unit, index) === "C" /* Elements.C */ &&
(0, util_1.bondCount)(structure, unit, index) === 3 &&
(0, util_1.bondToElementCount)(structure, unit, index, "N" /* Elements.N */) === 3) {
(0, util_1.eachBondedAtom)(structure, unit, index, (unit, index) => {
if ((0, util_1.bondCount)(structure, unit, index) - (0, util_1.bondToElementCount)(structure, unit, index, "H" /* Elements.H */) === 1) {
terminalNitrogenCount += 1;
}
});
}
return terminalNitrogenCount === 2;
}
/**
* Carbon in a acetamidine group
*/
function isAcetamidine(structure, unit, index) {
let terminalNitrogenCount = 0;
if ((0, util_1.typeSymbol)(unit, index) === "C" /* Elements.C */ &&
(0, util_1.bondCount)(structure, unit, index) === 3 &&
(0, util_1.bondToElementCount)(structure, unit, index, "N" /* Elements.N */) === 2 &&
(0, util_1.bondToElementCount)(structure, unit, index, "C" /* Elements.C */) === 1) {
(0, util_1.eachBondedAtom)(structure, unit, index, (unit, index) => {
if ((0, util_1.bondCount)(structure, unit, index) - (0, util_1.bondToElementCount)(structure, unit, index, "H" /* Elements.H */) === 1) {
terminalNitrogenCount += 1;
}
});
}
return terminalNitrogenCount === 2;
}
const PolarElements = new Set(['N', 'O', 'S', 'F', 'CL', 'BR', 'I']);
function isPolar(element) { return PolarElements.has(element); }
function hasPolarNeighbour(structure, unit, index) {
let flag = false;
(0, util_1.eachBondedAtom)(structure, unit, index, (unit, index) => {
if (isPolar((0, util_1.typeSymbol)(unit, index)))
flag = true;
});
return flag;
}
function hasAromaticNeighbour(structure, unit, index) {
let flag = false;
(0, util_1.eachBondedAtom)(structure, unit, index, (unit, index) => {
if (isAromatic(unit, index))
flag = true;
});
return flag;
}