static.kuangkie.hydrogen.bundle.908845ef105919970172.js Maven / Gradle / Ivy
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this.atoms.forEach((function(n,r){n.fragment===t&&e.add(r)})),e}},{key:"getFragment",value:function(t){return this.clone(this.getFragmentIds(t),null,!0)}},{key:"mergeInto",value:function(t,e,n,r,o,i,a,s,l){var c=this;e=e||new et(this.atoms.keys()),n=n||new et(this.bonds.keys()),a=a||new et(this.simpleObjects.keys()),s=s||new et(this.texts.keys()),l=l||new et(this.rgroupAttachmentPoints.keys()),i=i||new Map,n=n.filter((function(t){var n=c.bonds.get(t);return e.has(n.begin)&&e.has(n.end)}));var d=new et;this.atoms.forEach((function(t,n){e.has(n)&&d.add(t.fragment)}));var h=new Map;this.frags.forEach((function(e,n){d.has(n)&&h.set(n,t.frags.add(null))}));var f=[];this.rgroups.forEach((function(e,n){var r=o;if(r||(e.frags.forEach((function(t,e){f.push(e),d.has(e)&&(r=!0)})),r)){var i=t.rgroups.get(n);i?e.frags.forEach((function(t,e){f.push(e),d.has(e)&&i.frags.add(h.get(e))})):t.rgroups.set(n,e.clone(h))}})),this.atoms.forEach((function(n,r){e.has(r)&&-1===f.indexOf(n.fragment)&&i.set(r,t.atoms.add(n.clone(h)))})),this.atoms.forEach((function(n,r){e.has(r)&&-1!==f.indexOf(n.fragment)&&i.set(r,t.atoms.add(n.clone(h)))})),h.forEach((function(e,n){var r=c.frags.get(n);r&&r instanceof vt&&t.frags.set(e,c.frags.get(n).clone(i))}));var p=new Map;return this.bonds.forEach((function(e,r){n.has(r)&&p.set(r,t.bonds.add(e.clone(i)))})),this.sgroups.forEach((function(n){if(!n.atoms.some((function(t){return!e.has(t)}))){n=Zt.clone(n,i);var r=t.sgroups.add(n);n.id=r,n.atoms.forEach((function(e){var n=t.atoms.get(e);n&&n.sgs.add(r)})),"DAT"===n.type?t.sGroupForest.insert(n,-1,[]):t.sGroupForest.insert(n)}})),this.functionalGroups.forEach((function(e){e=Lt.clone(e),t.functionalGroups.add(e)})),a.forEach((function(e){t.simpleObjects.add(c.simpleObjects.get(e).clone())})),s.forEach((function(e){t.texts.add(c.texts.get(e).clone())})),l.forEach((function(e){var n=c.rgroupAttachmentPoints.get(e);u()(null!=n),t.rgroupAttachmentPoints.add(n.clone(i))})),r||(t.isReaction=this.isReaction,this.rxnArrows.forEach((function(e){t.rxnArrows.add(e.clone())})),this.rxnPluses.forEach((function(e){t.rxnPluses.add(e.clone())}))),t.name=this.name,t}},{key:"prepareLoopStructure",value:function(){this.initHalfBonds(),this.initNeighbors(),this.updateHalfBonds(Array.from(this.atoms.keys())),this.sortNeighbors(Array.from(this.atoms.keys())),this.findLoops()}},{key:"atomAddToSGroup",value:function(t,e){Zt.addAtom(this.sgroups.get(t),e,this),this.atoms.get(e).sgs.add(t)}},{key:"calcConn",value:function(t){for(var e=0,n=0;n1e-4?o:new $(1,0),e.norm=e.dir.turnLeft(),e.ang=e.dir.oxAngle(),e.loop<0&&(e.loop=-1)}},{key:"initHalfBonds",value:function(){var t=this;this.halfBonds.clear(),this.bonds.forEach((function(e,n){t.bondInitHalfBonds(n,e)}))}},{key:"setHbNext",value:function(t,e){this.halfBonds.get(this.halfBonds.get(t).contra).next=e}},{key:"halfBondSetAngle",value:function(t,e){var n=this.halfBonds.get(t),r=this.halfBonds.get(e);r.rightCos=$.dot(r.dir,n.dir),n.leftCos=$.dot(r.dir,n.dir),r.rightSin=$.cross(r.dir,n.dir),n.leftSin=$.cross(r.dir,n.dir),n.leftNeighbor=e,r.rightNeighbor=t}},{key:"atomAddNeighbor",value:function(t){var e,n=this.halfBonds.get(t),r=this.atoms.get(n.begin);for(e=0;en.ang);++e);r.neighbors.splice(e,0,t);var o=r.neighbors[(e+1)%r.neighbors.length],i=r.neighbors[(e+r.neighbors.length-1)%r.neighbors.length];this.setHbNext(i,t),this.setHbNext(t,o),this.halfBondSetAngle(t,i),this.halfBondSetAngle(o,t)}},{key:"atomSortNeighbors",value:function(t){var e=this,n=this.atoms.get(t),r=this.halfBonds;n.neighbors.sort((function(t,e){return r.get(t).ang-r.get(e).ang})).forEach((function(t,r){var o=n.neighbors[(r+1)%n.neighbors.length];e.halfBonds.get(e.halfBonds.get(t).contra).next=o,e.halfBondSetAngle(o,t)}))}},{key:"sortNeighbors",value:function(t){var e=this;t?t.forEach((function(t){e.atomSortNeighbors(t)})):this.atoms.forEach((function(t,n){e.atomSortNeighbors(n)}))}},{key:"atomUpdateHalfBonds",value:function(t){var e=this;this.atoms.get(t).neighbors.forEach((function(t){e.halfBondUpdate(t),e.halfBondUpdate(e.halfBonds.get(t).contra)}))}},{key:"updateHalfBonds",value:function(t){var e=this;t?t.forEach((function(t){e.atomUpdateHalfBonds(t)})):this.atoms.forEach((function(t,n){e.atomUpdateHalfBonds(n)}))}},{key:"sGroupsRecalcCrossBonds",value:function(){var t=this;this.sgroups.forEach((function(t){t.xBonds=[],t.neiAtoms=[]})),this.bonds.forEach((function(e,n){var r=t.atoms.get(e.begin),o=t.atoms.get(e.end);r.sgs.forEach((function(r){if(!o.sgs.has(r)){var i=t.sgroups.get(r);i.xBonds.push(n),Qt(i.neiAtoms,e.end)}})),o.sgs.forEach((function(o){if(!r.sgs.has(o)){var i=t.sgroups.get(o);i.xBonds.push(n),Qt(i.neiAtoms,e.begin)}}))}))}},{key:"sGroupDelete",value:function(t){var e=this;this.sgroups.get(t).atoms.forEach((function(n){e.atoms.get(n).sgs.delete(t)})),this.sGroupForest.remove(t),this.sgroups.delete(t)}},{key:"atomSetPos",value:function(t,e){this.atoms.get(t).pp=e}},{key:"rxnPlusSetPos",value:function(t,e){this.rxnPluses.get(t).pp=e}},{key:"rxnArrowSetPos",value:function(t,e){var n=this.rxnArrows.get(t);n&&(n.pos=e)}},{key:"simpleObjectSetPos",value:function(t,e){this.simpleObjects.get(t).pos=e}},{key:"textSetPosition",value:function(t,e){var n=this.texts.get(t);n&&(n.position=e)}},{key:"getCoordBoundingBox",value:function(t){var e=null;function n(t){e?t instanceof Array?t.forEach((function(t){e.min=$.min(e.min,t),e.max=$.max(e.max,t)})):(e.min=$.min(e.min,t),e.max=$.max(e.max,t)):e={min:t,max:t}}var r=!t||0===t.size;return this.atoms.forEach((function(e,o){(r||t.has(o))&&n(e.pp)})),r&&(this.rxnPluses.forEach((function(t){n(t.pp)})),this.rxnArrows.forEach((function(t){n(t.pos)})),this.simpleObjects.forEach((function(t){n(t.pos)})),this.texts.forEach((function(t){n(t.position)}))),!e&&r&&(e={min:new $(0,0),max:new $(1,1)}),e}},{key:"getCoordBoundingBoxObj",value:function(){var t=null;return this.atoms.forEach((function(e){var n;n=e.pp,t?(t.min=$.min(t.min,n),t.max=$.max(t.max,n)):t={min:new $(n),max:new $(n)}})),t}},{key:"getBondLengthData",value:function(){var t=this,e=0,n=0;return this.bonds.forEach((function(r){e+=$.dist(t.atoms.get(r.begin).pp,t.atoms.get(r.end).pp),n++})),{cnt:n,totalLength:e}}},{key:"getAvgBondLength",value:function(){var t=this.getBondLengthData();return t.cnt>0?t.totalLength/t.cnt:-1}},{key:"getAvgClosestAtomDistance",value:function(){var t,e,n,r=0,o=0,i=Array.from(this.atoms.keys());for(e=0;eo)&&(t=o));r+=t}return i.length>0?r/i.length:-1}},{key:"checkBondExists",value:function(t,e){return void 0!==this.bonds.find((function(n,r){return r.begin===t&&r.end===e||r.end===t&&r.begin===e}))}},{key:"findConnectedComponent",value:function(t){for(var e=this,n=[t],r=new et;n.length>0;){var o=n.pop();r.add(o),this.atoms.get(o).neighbors.forEach((function(t){var o=e.halfBonds.get(t).end;r.has(o)||n.push(o)}))}return r}},{key:"findConnectedComponents",value:function(t){var e=this;this.halfBonds.size||(this.initHalfBonds(),this.initNeighbors(),this.updateHalfBonds(Array.from(this.atoms.keys())),this.sortNeighbors(Array.from(this.atoms.keys())));var n=new et,r=[];return this.atoms.forEach((function(o,i){if((t||o.fragment<0)&&!n.has(i)){var a=e.findConnectedComponent(i);r.push(a),n=n.union(a)}})),r}},{key:"markFragment",value:function(t,e){var n=this,r=new vt([],void 0,e),o=this.frags.add(r);t.forEach((function(t){var e=n.atoms.get(t);e.stereoLabel&&r.updateStereoAtom(n,t,o,!0),e.fragment=o}))}},{key:"markFragments",value:function(t){var e=this;this.findConnectedComponents().forEach((function(n){e.markFragment(n,t)}))}},{key:"scale",value:function(t){var e=this;1!==t&&(this.atoms.forEach((function(e){e.pp=e.pp.scaled(t)})),this.rxnPluses.forEach((function(e){e.pp=e.pp.scaled(t)})),this.rxnArrows.forEach((function(e){e.pos=e.pos.map((function(e){return e.scaled(t)}))})),this.sgroups.forEach((function(e){e.pp=e.pp?e.pp.scaled(t):null})),this.texts.forEach((function(n){e.rxnArrows.size&&(n.pos=n.pos.map((function(e){return e.scaled(t)})),n.position=n.position.scaled(t))})))}},{key:"rescale",value:function(){var t=this.getAvgBondLength();t<0&&!this.isReaction&&(t=this.getAvgClosestAtomDistance()),t<.001&&(t=1);var e=1/t;this.scale(e)}},{key:"loopHasSelfIntersections",value:function(t){for(var e=0;e0&&t===s){r.partitionLoop(n).forEach((function(t){var e;r.loopIsInner(t)&&!r.loopHasSelfIntersections(t)?(e=Math.min.apply(Math,(0,h.Z)(t)),r.loops.set(e,new Ft(t,r,r.loopIsConvex(t)))):e=-2,t.forEach((function(t){r.halfBonds.get(t).loop=e,i.add(r.halfBonds.get(t).bid)})),e>=0&&o.push(e)}));break}n.push(t)}})),{newLoops:o,bondsToMark:Array.from(i)}}},{key:"calcImplicitHydrogen",value:function(t){var e=this.atoms.get(t),n=this.calcConn(e),o=(0,r.Z)(n,2),i=o[0],a=o[1],s=i;if(e.badConn=!1,a)if("C"===e.label&&0===e.charge){if(3===i)return void(e.implicitH=-st(e.radical));if(2===i)return void(e.implicitH=1-st(e.radical))}else{if("O"===e.label&&0===e.charge||"N"===e.label&&0===e.charge&&3===i||"N"===e.label&&1===e.charge&&3===i||"S"===e.label&&0===e.charge&&3===i)return void(e.implicitH=0);e.hasImplicitH||s++}if(s<0||e.isQuery())e.implicitH=0;else if(e.explicitValence>=0){var u=_.get(e.label);e.implicitH=u?e.explicitValence-e.calcValenceMinusHyd(s):0,e.implicitH<0&&(e.implicitH=0,e.badConn=!0)}else e.calcValence(s)}},{key:"setImplicitHydrogen",value:function(t){var e=this;this.sgroups.forEach((function(t){"MRV_IMPLICIT_H"===t.data.fieldName&&(e.atoms.get(t.atoms[0]).hasImplicitH=!0)})),t?t.forEach((function(t){e.atoms.get(t)&&e.calcImplicitHydrogen(t)})):this.atoms.forEach((function(t,n){e.calcImplicitHydrogen(n)}))}},{key:"atomGetNeighbors",value:function(t){var e,n=this;return null===(e=this.atoms.get(t))||void 0===e?void 0:e.neighbors.map((function(t){var e=n.halfBonds.get(t);return{aid:e.end,bid:e.bid}}))}},{key:"getComponents",value:function(){var t=this,e=this.findConnectedComponents(!0),n=[],r=null;this.rxnArrows.forEach((function(t){r=t.center().x})),this.rxnPluses.forEach((function(t){n.push(t.pp.x)})),null!==r&&n.push(r),n.sort((function(t,e){return t-e}));var o=[];e.forEach((function(e){for(var r=t.getCoordBoundingBox(e),i=$.lc2(r.min,.5,r.max,.5),a=0;i.x>n[a];)++a;o[a]=o[a]||new et,o[a]=o[a].union(e)}));var i=[],a=[];return o.forEach((function(e){e&&(1===t.defineRxnFragmentTypeForAtomset(e,r||0)?i.push(e):a.push(e))})),{reactants:i,products:a}}},{key:"defineRxnFragmentTypeForAtomset",value:function(t,e){var n=this.getCoordBoundingBox(t);return $.lc2(n.min,.5,n.max,.5).x1&&void 0!==arguments[1]?arguments[1]:0,n={};return G(n,"type",t.type),G(n,"topology",t.topology),G(n,"reactingCenterStatus",t.center),G(n,"stereo",t.stereo),G(n,"cip",t.cip),G(n,"begin",t.atoms[0]+e),G(n,"end",t.atoms[1]+e),new dt(n)}function fe(t,e){(null==e||e>t.length)&&(e=t.length);for(var n=0,r=new Array(e);n=t.length?{done:!0}:{done:!1,value:t[r++]}},e:function(t){throw t},f:o}}throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method.")}var i,a=!0,s=!1;return{s:function(){n=n.call(t)},n:function(){var t=n.next();return a=t.done,t},e:function(t){s=!0,i=t},f:function(){try{a||null==n.return||n.return()}finally{if(s)throw i}}}}(t.rgroups.entries());try{for(i.s();!(e=i.n()).done;){var a=(0,r.Z)(e.value,2),s=a[0],u=a[1];u.frags.forEach((function(t){return o.add(t)}));var l=Array.from(u.frags.values()).reduce((function(e,n){return e.union(t.getFragmentIds(n))}),new et);n.push({type:"rgroup",fragment:t.clone(l),center:me(t,l),data:{rgnumber:s,rgroup:u}})}}catch(t){i.e(t)}finally{i.f()}var c=Array.from(t.frags.keys()).filter((function(t){return!o.has(t)}));return function(t,e,n){var r=function(t,e,n){var r=new Map;return e.forEach((function(e){var o=n.getFragmentIds(e),i=!1;o.forEach((function(t){var o;null===(o=n.atoms.get(t))||void 0===o||o.sgs.forEach((function(t){i=!0;var n=r.get(t);n?n.add(e):r.set(t,new et([e]))}))})),i||t.push({type:"molecule",fragment:n.clone(o),center:me(n,o)})})),r}(t,e,n);et.unionIntersections(Array.from(r.values())).forEach((function(e){var r=new et;e.forEach((function(t){r=r.union(n.getFragmentIds(t))})),t.push({type:"molecule",fragment:n.clone(r),center:me(n,r)})}))}(n,c,t),t.rxnArrows.forEach((function(t){n.push({type:"arrow",center:t.pos[0],data:{mode:t.mode,pos:t.pos,height:t.height}})})),t.rxnPluses.forEach((function(t){n.push({type:"plus",center:t.pp,data:{}})})),t.simpleObjects.forEach((function(t){n.push({type:"simpleObject",center:t.pos[0],data:{mode:t.mode,pos:t.pos}})})),t.texts.forEach((function(t){n.push({type:"text",center:t.position,data:{content:t.content,position:t.position,pos:t.pos}})})),n.forEach((function(t){if(t.fragment){var e=Array.from(t.fragment.sgroups.values()).filter((function(t){return t.atoms.every((function(t){return void 0!==t}))})),n=new Kt;e.forEach((function(t,e){n.set(e,t)})),t.fragment.sgroups=n}})),n}function me(t,e){var n=t.getCoordBoundingBox(e);return $.centre(n.min,n.max)}function ve(t,e){var n=Object.keys(t);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(t);e&&(r=r.filter((function(e){return Object.getOwnPropertyDescriptor(t,e).enumerable}))),n.push.apply(n,r)}return n}function ge(t){for(var e=1;ee)throw new Error("number does not fit");return r.padStart(e)},parseDecimalInt:function(t){var e=parseInt(t,10);return isNaN(e)?0:e},partitionLine:function(t,e,n){for(var r=[],o=0,i=0;o=t.length?{done:!0}:{done:!1,value:t[r++]}},e:function(t){throw t},f:o}}throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method.")}var i,a=!0,s=!1;return{s:function(){n=n.call(t)},n:function(){var t=n.next();return a=t.done,t},e:function(t){s=!0,i=t},f:function(){try{a||null==n.return||n.return()}finally{if(s)throw i}}}}function Ae(t,e){(null==e||e>t.length)&&(e=t.length);for(var n=0,r=new Array(e);n=0);var b=Pe.parseDecimalInt(v),w=b>0?b-1:void 0;c.push(new re(y,w,g))}return{sGroupId:s,attachmentPoints:c}}};function Ve(t){var e=Pe.partitionLine(t,Pe.fmtInfo.atomLinePartition),n={pp:new $(parseFloat(e[0]),-parseFloat(e[1]),parseFloat(e[2])),label:e[4].trim(),explicitValence:Pe.fmtInfo.valenceMap[Pe.parseDecimalInt(e[10])],massDifference:Pe.parseDecimalInt(e[5]),charge:Pe.fmtInfo.chargeMap[Pe.parseDecimalInt(e[6])],hCount:Pe.parseDecimalInt(Pe.parseDecimalInt(e[8])),stereoCare:0!==Pe.parseDecimalInt(e[9]),aam:Pe.parseDecimalInt(e[14]),invRet:Pe.parseDecimalInt(e[15]),exactChangeFlag:Pe.parseDecimalInt(e[16])};return new at(n)}function We(t){var e=Pe.partitionLine(t,Pe.fmtInfo.bondLinePartition),n={begin:Pe.parseDecimalInt(e[0])-1,end:Pe.parseDecimalInt(e[1])-1,type:Pe.fmtInfo.bondTypeMap[Pe.parseDecimalInt(e[2])],stereo:Pe.fmtInfo.bondStereoMap[Pe.parseDecimalInt(e[3])],xxx:e[4],topology:Pe.fmtInfo.bondTopologyMap[Pe.parseDecimalInt(e[5])],reactingCenterStatus:Pe.parseDecimalInt(e[6])};return new dt(n)}function Ye(t){for(var e=Pe.partitionLine(t,Pe.fmtInfo.atomListHeaderPartition),n=Pe.parseDecimalInt(e[0])-1,r="T"===e[2].trim(),o=Pe.parseDecimalInt(e[4].trim()),i=t.slice(Pe.fmtInfo.atomListHeaderLength),a=[],s=Pe.fmtInfo.atomListHeaderItemLength,u=0;u0&&(A.ifthen=E),A.resth=1===P,A.range=O,i[x]=A}else if("APO"===m)a.get("attachmentPoints")||a.set("attachmentPoints",Ue.readKeyValuePairs(v));else if("ALS"===m){var R=(t=Pe.partitionLine(v,[1,3,3,1,1,1]),r=Pe.partitionLineFixed(v.slice(10),4,!1),s=Pe.parseDecimalInt(t[1])-1,u=Pe.parseDecimalInt(t[2]),l="T"===t[4].trim(),c=function(t){for(var e=[],n=0;n=0){var E=v[x-1];"GEN"===E.type&&(w.atoms=[].slice.call(E.atoms))}}}for(y in v)Ue.loadSGroup(o,v[y],b);var P=[];for(y in v)Zt.filter(o,v[y],b),0!==v[y].atoms.length||v[y].allAtoms||P.push(+y);for(r=0;r0&&"$MOL"===t[0].substr(0,4);){t=t.slice(1);for(var u=0;u0&&(f.ifthen=c),f.resth=1===d,f.range=h,r[i]=f,o++}}}Object.keys(n).forEach((function(e){n[e].forEach((function(n){n.rgroups.set(e,new Gt(r[e]));var o=n.frags.add({});n.rgroups.get(e).frags.add(o),n.atoms.forEach((function(t){t.fragment=o})),n.mergeInto(t)}))}))}function on(t){for(var e=[],n=0,r=0,o=-1,i=!1;ro+1&&e.push(t.slice(o+1,r)),o=r)}return r>o+1&&e.push(t.slice(o+1,r)),e}function an(t,e){var n=t.indexOf(e);return[t.slice(0,n),t.slice(n+1)]}function sn(t){for(var e=[],n=0,r=!1,o=0;o0&&e.push(t.trim()),e}function un(t,e){if(!t)return null;var n=[],r=(t=(t=t.trim()).substr(1,t.length-2)).split(" ");e=e||0;for(var o=1;o2?n[2]-0:0;function a(e){for(var n=e;n=0?Pe.paddedNum(i.nCharnCharsToDisplay,3):"ALL")+" 1 "+(i.tagChar||" ")+" "+Pe.paddedNum(i.daspPos,1)+" ";return s.push(c),(l=i.fieldValue,l.replace(vn,"\n")).replace(/\n*$/,"").split("\n").forEach((function(t){for(;t.length>69;)s.push("M SCD "+o+" "+t.slice(0,69)),t=t.slice(69);s.push("M SED "+o+" "+t)})),s.join("\n")},GEN:function(t,e,n,r,o){var i=(n[t.id]+"").padStart(3),a=[];return(a=(a=(a=a.concat(pn("SAL",i,t.atoms,r))).concat(pn("SBL",i,t.bonds,o))).concat(mn(e,t,i))).join("\n")}};function pn(t,e,n,r){if(!n)return[];for(var o=[],i=0;i1&&"V3000"===r[1])return cn.parseRxn3000(t,e);var o=Ke.parseRxn2000(t,e,n);return o.name=t[1].trim(),o},prepareForSaving:hn,saveToMolfile:fn},yn=function(){function t(){(0,o.Z)(this,t),this.molecule=null,this.molfile=null,this.reaction=!1,this.mapping={},this.bondMapping={}}return(0,i.Z)(t,[{key:"parseCTFile",value:function(t){var e,n=t.molfileLines,r=t.shouldReactionRelayout,o=t.ignoreChiralFlag;return(e=0===n[0].search("\\$RXN")?gn.parseRxn(n,r,o):gn.parseMol(n,o)).initHalfBonds(),e.initNeighbors(),e.bindSGroupsToFunctionalGroups(),e}},{key:"prepareSGroups",value:function(t,e){var n,r=this.molecule,o=[],i=0;if(null===(n=this.molecule)||void 0===n||n.sGroupForest.getSGroupsBFS().reverse().forEach((function(n){var a=r.sgroups.get(n),s=!1;try{gn.prepareForSaving[a.type](a,r)}catch(e){if(!t||"number"!=typeof e.id)throw new Error("Error: ".concat(e.message));s=!0}(s||!e&&/^INDIGO_.+_DESC$/i.test(a.data.fieldName))&&(i+=+s,o.push(a.id))}),this),i)throw new Error("Warning: "+i+" invalid S-groups were detected. They will be omitted.");for(var a=0;a0)throw new Error("Reactions with r-groups are not supported at the moment");var s=e.getComponents(),u=s.reactants,l=s.products,c=u.concat(l);this.molfile="$RXN\n"+e.name+"\n\n\n"+Pe.paddedNum(u.length,3)+Pe.paddedNum(l.length,3)+Pe.paddedNum(0,3)+"\n";for(var d=0;d0){if(!r){var m=(new t).getCTab(e.getScaffold(),e.rgroups);return this.molfile="$MDL REV 1\n$MOL\n$HDR\n"+e.name+"\n\n\n$END HDR\n",this.molfile+="$CTAB\n"+m+"$END CTAB\n",e.rgroups.forEach((function(n,r){a.molfile+="$RGP\n",a.writePaddedNumber(r,3),a.molfile+="\n",n.frags.forEach((function(n){var r=(new t).getCTab(e.getFragment(n));a.molfile+="$CTAB\n"+r+"$END CTAB\n"})),a.molfile+="$END RGP\n"})),this.molfile+="$END MOL\n",this.molfile}e=e.getScaffold()}return this.molecule=e.clone(),this.prepareSGroups(n,o),this.writeHeader(),this.writeCTab2000(void 0,i),this.molfile}},{key:"writeHeader",value:function(){var t=new Date;this.writeCR(),this.writeWhiteSpace(2),this.write("Ketcher"),this.writeWhiteSpace(),this.writeCR((t.getMonth()+1+"").padStart(2)+(t.getDate()+"").padStart(2)+(t.getFullYear()%100+"").padStart(2)+(t.getHours()+"").padStart(2)+(t.getMinutes()+"").padStart(2)+"2D 1 1.00000 0.00000 0"),this.writeCR()}},{key:"write",value:function(t){this.molfile+=t}},{key:"writeCR",value:function(t){0===arguments.length&&(t=""),this.molfile+=t+"\n"}},{key:"writeWhiteSpace",value:function(){var t=arguments.length>0&&void 0!==arguments[0]?arguments[0]:0;0===arguments.length&&(t=1),this.write(" ".repeat(Math.max(t,0)))}},{key:"writePadded",value:function(t,e){this.write(t),this.writeWhiteSpace(e-t.length)}},{key:"writePaddedNumber",value:function(t,e){var n=(t-0).toString();this.writeWhiteSpace(e-n.length),this.write(n)}},{key:"writePaddedFloat",value:function(t,e,n){this.write(Pe.paddedNum(t,e,n))}},{key:"writeCTab2000Header",value:function(t){this.writePaddedNumber(this.molecule.atoms.size,3),this.writePaddedNumber(this.molecule.bonds.size,3),this.writePaddedNumber(0,3),this.writePaddedNumber(0,3);var e=Array.from(this.molecule.frags.values()).some((function(t){return!!t&&t.enhancedStereoFlag===ct.Abs}));this.writePaddedNumber(e||t?1:0,3),this.writePaddedNumber(0,3),this.writePaddedNumber(0,3),this.writePaddedNumber(0,3),this.writePaddedNumber(0,3),this.writePaddedNumber(0,3),this.writePaddedNumber(999,3),this.writeCR(" V2000")}},{key:"writeCTab2000",value:function(t,e){var n=this;this.writeCTab2000Header(e),this.mapping={};var r=1,o=[],i=[];for(this.molecule.atoms.forEach((function(t,e){var a=t.label;null!=t.atomList?(a="L",o.push(e)):t.pseudo?t.pseudo.length>3&&(a="A",i.push({id:e,value:"'".concat(t.pseudo,"'")})):t.alias?i.push({id:e,value:t.alias}):_.get(t.label)||-1!==["A","Q","X","*","R#"].indexOf(t.label)||(a="C",i.push({id:e,value:t.label})),n.writeAtom(t,a),n.mapping[e]=r++}),this),this.bondMapping={},r=1,this.molecule.bonds.forEach((function(t,e){n.bondMapping[e]=r++,n.writeBond(t)}),this);i.length>0;)this.writeAtomProps(i[0]),i.splice(0,1);var a=[],s=[],u=[],l=[],c=[],d=[],h=[],f=[],p=[];this.molecule.atoms.forEach((function(t,e){if(0!==t.charge&&a.push([e,t.charge]),0!==t.isotope&&s.push([e,t.isotope]),0!==t.radical&&u.push([e,t.radical]),null!=t.rglabel&&"R#"===t.label)for(var n=0;n<32;n++)t.rglabel&1<0||t.range.length>0){var n=" 1 "+Pe.paddedNum(e,3)+" "+Pe.paddedNum(t.ifthen,3)+" "+Pe.paddedNum(t.resth?1:0,3)+" "+t.range;c.push(n)}})),this.writeAtomPropList("M CHG",a),this.writeAtomPropList("M ISO",s),this.writeAtomPropList("M RAD",u),this.writeAtomPropList("M RGP",l);for(var m=0;m0)for(var v=0;v=0&&(n.write("M SPL"),n.writePaddedNumber(1,3),n.writeWhiteSpace(1),n.writePaddedNumber(t,3),n.writeWhiteSpace(1),n.writePaddedNumber(x[o],3),n.writeCR()),"SRU"===r.type&&r.data.connectivity){var i=" ".concat(t.toString().padStart(3)," ").concat((r.data.connectivity||"").padEnd(3));n.write("M SCN"),n.writePaddedNumber(1,3),n.write(i.toUpperCase()),n.writeCR()}"SRU"===r.type&&(n.write("M SMT "),n.writePaddedNumber(t,3),n.writeWhiteSpace(),n.write(r.data.subscript||"n"),n.writeCR()),r.getAttachmentPoints().forEach((function(e){n.writeSGroupAttachmentPointLine(t,e)})),n.writeCR(gn.saveToMolfile[r.type](r,n.molecule,x,n.mapping,n.bondMapping))},A=1;A0;){for(var r=[];e.length>0&&r.length<8;)r.push(e[0]),e.splice(0,1);this.write(t),this.writePaddedNumber(r.length,3),r.forEach((function(t){n.writeWhiteSpace(),n.writePaddedNumber(n.mapping[t[0]],3),n.writeWhiteSpace(),n.writePaddedNumber(t[1],3)})),this.writeCR()}}},{key:"writeSGroupAttachmentPointLine",value:function(t,e){var n;this.write("M SAP"),this.writeWhiteSpace(1),this.writePaddedNumber(t,3),this.writePaddedNumber(1,3),this.writeWhiteSpace(1);var r=this.mapping[e.atomId];this.writePaddedNumber(r,3),this.writeWhiteSpace(1);var o=null!==(n=this.mapping[e.leaveAtomId])&&void 0!==n?n:0;this.writePaddedNumber(o,3),this.writeWhiteSpace(1);var i=e.attachmentId?e.attachmentId.slice(0,2):" ";this.writePadded(i,2),this.writeCR()}}]),t}();function bn(t,e){var n=Object.keys(t);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(t);e&&(r=r.filter((function(e){return Object.getOwnPropertyDescriptor(t,e).enumerable}))),n.push.apply(n,r)}return n}function wn(t){for(var e=1;e0?1:-1},En.prototype.samesides=function(t,e,n,r){return this.sameside(this.molecule.atoms.get(t).pp,this.molecule.atoms.get(e).pp,this.molecule.atoms.get(n).pp,this.molecule.atoms.get(r).pp)},En.prototype.sortSubstituents=function(t){var e=this.molecule.atoms.get(t[0]).pureHydrogen(),n=t[1]<0||this.molecule.atoms.get(t[1]).pureHydrogen(),r=this.molecule.atoms.get(t[2]).pureHydrogen(),o=t[3]<0||this.molecule.atoms.get(t[3]).pureHydrogen();return!(e&&n||r&&o||(n?t[1]=-1:e?(t[0]=t[1],t[1]=-1):t[0]>t[1]&&Pn(t,0,1),o?t[3]=-1:r?(t[2]=t[3],t[3]=-1):t[2]>t[3]&&Pn(t,2,3),0))},En.prototype.isGeomStereoBond=function(t,e){var n=this.molecule.bonds.get(t);if(n.type!==dt.PATTERN.TYPE.DOUBLE)return!1;var r=this.molecule.atoms.get(n.begin).label,o=this.molecule.atoms.get(n.end).label;if("C"!==r&&"N"!==r&&"Si"!==r&&"Ge"!==r)return!1;if("C"!==o&&"N"!==o&&"Si"!==o&&"Ge"!==o)return!1;var i,a,s=this.getNeighbors.call(this.context,n.begin),u=this.getNeighbors.call(this.context,n.end);if(s.length<2||s.length>3||u.length<2||u.length>3)return!1;for(e[0]=-1,e[1]=-1,e[2]=-1,e[3]=-1,i=0;i=0&&n.vertices[f].branches--}n.vertices[s].branches++,n.vertices[d].parent_vertex=s,n.vertices[d].parent_edge=h,n.vertices[d].dfs_state=1,r.push(d)}}};!a(););},On.prototype.edgeClosingCycle=function(t){return 0!==this.edges[t].closing_cycle},On.prototype.numBranches=function(t){return this.vertices[t].branches},On.prototype.numOpeningCycles=function(t){return this.edges[t].opening_cycles},On.prototype.toString=function(){var t="";return this.v_seq.forEach((function(e){t+=e.idx+" -> "})),t+="*"},An.prototype.each=function(t,e){this.atoms.forEach(t,e)},An.prototype.buildFromBonds=function(t){var e=this,n=this.molecule.atoms,r=this.molecule.bonds,o=new et;n.forEach((function(t,i){var a=e.getNeighbors.call(e.context,i);if(2!==a.length)return!1;var s=a[0],u=a[1];if([i,s.aid,u.aid].findIndex((function(t){return["C","Si"].indexOf(n.get(t).label)<0}),e)>=0)return!1;if([s.bid,u.bid].findIndex((function(t){return r.get(t).type!==dt.PATTERN.TYPE.DOUBLE}),e)>=0)return!1;var l=e.getNeighbors.call(e.context,s.aid).filter((function(t){return t.aid!==i})),c=e.getNeighbors.call(e.context,u.aid).filter((function(t){return t.aid!==i}));return!(l.length<1||l.length>2||c.length<1||c.length>2||l.concat(c).findIndex((function(t){return r.get(t.bid).type!==dt.PATTERN.TYPE.SINGLE}),e)>=0||l.concat(c).findIndex((function(t){return r.get(t.bid).stereo===dt.PATTERN.STEREO.EITHER}),e)>=0||(o.add(s.aid).add(u.aid),0))})),o.size>0&&n.forEach((function(t,n){if(!o.has(n)){var r=e.getNeighbors.call(e.context,n),i=!1;r.find((function(t){var e=this.molecule.bonds.get(t.bid);return e.type===dt.PATTERN.TYPE.SINGLE&&e.begin===n&&(e.stereo===dt.PATTERN.STEREO.UP||e.stereo===dt.PATTERN.STEREO.DOWN)&&(i=!0,!0)}),e),i&&e.buildOneCenter(n)}}))},An.allowed_stereocenters=[{elem:"C",charge:0,degree:3,n_double_bonds:0,implicit_degree:4},{elem:"C",charge:0,degree:4,n_double_bonds:0,implicit_degree:4},{elem:"Si",charge:0,degree:3,n_double_bonds:0,implicit_degree:4},{elem:"Si",charge:0,degree:4,n_double_bonds:0,implicit_degree:4},{elem:"N",charge:1,degree:3,n_double_bonds:0,implicit_degree:4},{elem:"N",charge:1,degree:4,n_double_bonds:0,implicit_degree:4},{elem:"N",charge:0,degree:3,n_double_bonds:0,implicit_degree:3},{elem:"S",charge:0,degree:4,n_double_bonds:2,implicit_degree:4},{elem:"S",charge:1,degree:3,n_double_bonds:0,implicit_degree:3},{elem:"S",charge:0,degree:3,n_double_bonds:1,implicit_degree:3},{elem:"P",charge:0,degree:3,n_double_bonds:0,implicit_degree:3},{elem:"P",charge:1,degree:4,n_double_bonds:0,implicit_degree:4},{elem:"P",charge:0,degree:4,n_double_bonds:1,implicit_degree:4}],An.prototype.buildOneCenter=function(t){var e=this,n=this.molecule.atoms.get(t),r=this.getNeighbors.call(this.context,t),o=r.length,i=-1,a={group:0,type:0,pyramid:[]},s=[],u=0,l=0;a.pyramid[0]=-1,a.pyramid[1]=-1,a.pyramid[2]=-1,a.pyramid[3]=-1;var c=0;if(o>4)throw new Error("stereocenter with %d bonds are not supported"+o);if(r.forEach((function(t,r){var o=e.molecule.atoms.get(t.aid),i=e.molecule.bonds.get(t.bid);if(s[r]={edge_idx:t.bid,nei_idx:t.aid,rank:t.aid,vec:$.diff(o.pp,n.pp).yComplement()},o.pureHydrogen()?(c++,s[r].rank=1e4):"H"===o.label&&(s[r].rank=5e3),!s[r].vec.normalize())throw new Error("zero bond length");if(i.type===dt.PATTERN.TYPE.TRIPLE)throw new Error("non-single bonds not allowed near stereocenter");if(i.type===dt.PATTERN.TYPE.AROMATIC)throw new Error("aromatic bonds not allowed near stereocenter");i.type===dt.PATTERN.TYPE.DOUBLE&&l++})),An.allowed_stereocenters.find((function(t){return t.elem===n.label&&t.charge===n.charge&&t.degree===o&&t.n_double_bonds===l&&(i=t.implicit_degree,!0)})),-1===i)throw new Error("unknown stereocenter configuration: "+n.label+", charge "+n.charge+", "+o+" bonds ("+l+" double)");if(4===o&&c>1)throw new Error(c+" hydrogens near stereocenter");if(3===o&&4===i&&c>0)throw new Error("have hydrogen(s) besides implicit hydrogen near stereocenter");if(4===o){s[0].rank>s[1].rank&&Rn(s,0,1),s[1].rank>s[2].rank&&Rn(s,1,2),s[2].rank>s[3].rank&&Rn(s,2,3),s[1].rank>s[2].rank&&Rn(s,1,2),s[0].rank>s[1].rank&&Rn(s,0,1),s[1].rank>s[2].rank&&Rn(s,1,2);for(var d,h,f=-1,p=-1,m=-1,v=-1,g=0,y=0;y<4;y++){var b=this.getBondStereo(t,s[y].edge_idx);if(b===dt.PATTERN.STEREO.UP||b===dt.PATTERN.STEREO.DOWN){f=y,g=b;break}}if(-1===f)throw new Error("none of 4 bonds going from stereocenter is stereobond");if(-1===p&&((d=An.xyzzy(s[f].vec,s[(f+1)%4].vec,s[(f+2)%4].vec))+(h=An.xyzzy(s[f].vec,s[(f+1)%4].vec,s[(f+3)%4].vec))!==3&&d+h!==12||(p=(f+1)%4,m=(f+2)%4,v=(f+3)%4)),-1===p&&((d=An.xyzzy(s[f].vec,s[(f+2)%4].vec,s[(f+1)%4].vec))+(h=An.xyzzy(s[f].vec,s[(f+2)%4].vec,s[(f+3)%4].vec))!==3&&d+h!==12||(p=(f+2)%4,m=(f+1)%4,v=(f+3)%4)),-1===p&&((d=An.xyzzy(s[f].vec,s[(f+3)%4].vec,s[(f+1)%4].vec))+(h=An.xyzzy(s[f].vec,s[(f+3)%4].vec,s[(f+2)%4].vec))!==3&&d+h!==12||(p=(f+3)%4,m=(f+2)%4,v=(f+1)%4)),-1===p)throw new Error("internal error: can not find opposite bond");if(g===dt.PATTERN.STEREO.UP&&this.getBondStereo(t,s[p].edge_idx)===dt.PATTERN.STEREO.DOWN)throw new Error("stereo types of the opposite bonds mismatch");if(g===dt.PATTERN.STEREO.DOWN&&this.getBondStereo(t,s[p].edge_idx)===dt.PATTERN.STEREO.UP)throw new Error("stereo types of the opposite bonds mismatch");if(g===this.getBondStereo(t,s[m].edge_idx))throw new Error("stereo types of non-opposite bonds match");if(g===this.getBondStereo(t,s[v].edge_idx))throw new Error("stereo types of non-opposite bonds match");u=3===f||3===p?g:g===dt.PATTERN.STEREO.UP?dt.PATTERN.STEREO.DOWN:dt.PATTERN.STEREO.UP;var w=An.sign(s[0].vec,s[1].vec,s[2].vec);u===dt.PATTERN.STEREO.UP&&w>0||u===dt.PATTERN.STEREO.DOWN&&w<0?(a.pyramid[0]=s[0].nei_idx,a.pyramid[1]=s[1].nei_idx,a.pyramid[2]=s[2].nei_idx):(a.pyramid[0]=s[0].nei_idx,a.pyramid[1]=s[2].nei_idx,a.pyramid[2]=s[1].nei_idx),a.pyramid[3]=s[3].nei_idx}else if(3===o){s[0].rank>s[1].rank&&Rn(s,0,1),s[1].rank>s[2].rank&&Rn(s,1,2),s[0].rank>s[1].rank&&Rn(s,0,1);var x=this.getBondStereo(t,s[0].edge_idx),E=this.getBondStereo(t,s[1].edge_idx),P=this.getBondStereo(t,s[2].edge_idx),O=0,A=0;if(O+=x===dt.PATTERN.STEREO.UP?1:0,O+=E===dt.PATTERN.STEREO.UP?1:0,O+=P===dt.PATTERN.STEREO.UP?1:0,A+=x===dt.PATTERN.STEREO.DOWN?1:0,A+=E===dt.PATTERN.STEREO.DOWN?1:0,A+=P===dt.PATTERN.STEREO.DOWN?1:0,4===i){if(3===O)throw new Error("all 3 bonds up near stereoatom");if(3===A)throw new Error("all 3 bonds down near stereoatom");if(0===O&&0===A)throw new Error("no up/down bonds near stereoatom -- indefinite case");if(1===O&&1===A)throw new Error("one bond up, one bond down -- indefinite case");if(g=0,2===O)u=dt.PATTERN.STEREO.DOWN;else if(2===A)u=dt.PATTERN.STEREO.UP;else{for(f=-1,m=-1,v=-1,y=0;y<3;y++){var R=this.getBondStereo(t,s[y].edge_idx);if(R===dt.PATTERN.STEREO.UP||R===dt.PATTERN.STEREO.DOWN){f=y,g=R,m=(y+1)%3,v=(y+2)%3;break}}if(-1===f)throw new Error("internal error: can not find up or down bond");var S=An.xyzzy(s[m].vec,s[v].vec,s[f].vec);if(3===S||4===S)throw new Error("degenerate case for 3 bonds near stereoatom");u=1===S?g:g===dt.PATTERN.STEREO.UP?dt.PATTERN.STEREO.DOWN:dt.PATTERN.STEREO.UP}var T=An.sign(s[0].vec,s[1].vec,s[2].vec);u===dt.PATTERN.STEREO.UP&&T>0||u===dt.PATTERN.STEREO.DOWN&&T<0?(a.pyramid[0]=s[0].nei_idx,a.pyramid[1]=s[1].nei_idx,a.pyramid[2]=s[2].nei_idx):(a.pyramid[0]=s[0].nei_idx,a.pyramid[1]=s[2].nei_idx,a.pyramid[2]=s[1].nei_idx),a.pyramid[3]=-1}else{var k;if(A>0&&O>0)throw new Error("one bond up, one bond down -- indefinite case");if(0===A&&0===O)throw new Error("no up-down bonds attached to stereocenter");k=O>0?1:-1,1!==An.xyzzy(s[0].vec,s[1].vec,s[2].vec)&&1!==An.xyzzy(s[0].vec,s[2].vec,s[1].vec)&&1!==An.xyzzy(s[2].vec,s[1].vec,s[0].vec)||(k=-k),An.sign(s[0].vec,s[1].vec,s[2].vec)===k?(a.pyramid[0]=s[0].nei_idx,a.pyramid[1]=s[2].nei_idx,a.pyramid[2]=s[1].nei_idx):(a.pyramid[0]=s[0].nei_idx,a.pyramid[1]=s[1].nei_idx,a.pyramid[2]=s[2].nei_idx),a.pyramid[3]=-1}}this.atoms.set(t,a)},An.prototype.getBondStereo=function(t,e){var n=this.molecule.bonds.get(e);return t!==n.begin?0:n.stereo},An.xyzzy=function(t,e,n){var r=.001,o=$.cross(t,e),i=$.dot(t,e),a=$.cross(t,n),s=$.dot(t,n);if(Math.abs(o)0?4:8}return o*a<-r*r||s.001)return 1;if(r<-.001)return-1;throw new Error("degenerate triangle")},An.isPyramidMappingRigid=function(t){var e=t.slice(),n=!0;return e[0]>e[1]&&(Rn(e,0,1),n=!n),e[1]>e[2]&&(Rn(e,1,2),n=!n),e[2]>e[3]&&(Rn(e,2,3),n=!n),e[1]>e[2]&&(Rn(e,1,2),n=!n),e[0]>e[1]&&(Rn(e,0,1),n=!n),e[1]>e[2]&&(Rn(e,1,2),n=!n),n},Sn._Atom=function(t){this.neighbours=[],this.aromatic=!1,this.lowercase=!1,this.chirality=0,this.branch_cnt=0,this.paren_written=!1,this.h_count=t,this.parent=-1},Sn.prototype.isBondInRing=function(t){return this.inLoop[t]},Sn.prototype.saveMolecule=function(t,e){var n,r,o,i=this;e||(this.ignoreErrors=e),(t=t.clone(void 0,void 0,!t.hasRxnArrow(),void 0,void 0,void 0)).initHalfBonds(),t.initNeighbors(),t.sortNeighbors(),t.setImplicitHydrogen(),t.sgroups.forEach((function(e){if("MUL"===e.type)try{Zt.prepareMulForSaving(e,t)}catch(t){throw Error("Bad s-group ("+t.message+")")}})),this.atoms=new Array(t.atoms.size),t.atoms.forEach((function(t,e){i.atoms[e]=new Sn._Atom(t.implicitH)}));var a=["B","C","N","O","P","S","Se","As"];t.bonds.forEach((function(e,n){e.type===dt.PATTERN.TYPE.AROMATIC&&(i.atoms[e.begin].aromatic=!0,-1!==a.indexOf(t.atoms.get(e.begin).label)&&(i.atoms[e.begin].lowercase=!0),i.atoms[e.end].aromatic=!0,-1!==a.indexOf(t.atoms.get(e.end).label)&&(i.atoms[e.end].lowercase=!0)),i.atoms[e.begin].neighbours.push({aid:e.end,bid:n}),i.atoms[e.end].neighbours.push({aid:e.begin,bid:n})})),this.inLoop=function(){t.prepareLoopStructure();var e=new et;t.loops.forEach((function(n){if(n.hbs.length<=6){var r=n.hbs.map((function(e){return t.halfBonds.get(e).bid}));e=e.union(new et(r))}}));var n={};return e.forEach((function(t){n[t]=1})),n}(),this.touchedCistransbonds=0,this.markCisTrans(t);var s=t.getComponents(),u=s.reactants.concat(s.products),l=new On(t,this.atoms,u,s.reactants.length);for(l.walk(),this.atoms.forEach((function(t){t.neighbours=[]})),n=0;n=0){var p=this.atoms[d],m=l.numOpeningCycles(h);for(r=0;r=4)throw new Error("internal: pyramid overflow");a[s++]=o;break}if(4===s)s=a[0],a[0]=a[1],a[1]=a[2],a[2]=a[3],a[3]=s;else if(3!==s)throw new Error("cannot calculate chirality");An.isPyramidMappingRigid(a)?i.atoms[e].chirality=1:i.atoms[e].chirality=2}))}catch(t){}var g=[];g.push(0);var y=!0;for(n=0;n=0){for(l.numBranches(f)>1&&this.atoms[f].branch_cnt>0&&this.atoms[f].paren_written&&(this.smiles+=")"),m=l.numOpeningCycles(h),r=0;r=0){var w=l.numBranches(f);if(w>1&&this.atoms[f].branch_cntw)throw new Error("unexpected branch")}var x=t.bonds.get(h),E=0;if(x.type===dt.PATTERN.TYPE.SINGLE&&(E=this.calcBondDirection(t,h,f)),1===E&&d===x.end||2===E&&d===x.begin?this.smiles+="/":2===E&&d===x.end||1===E&&d===x.begin?this.smiles+="\\":x.type===dt.PATTERN.TYPE.ANY?this.smiles+="~":x.type===dt.PATTERN.TYPE.DOUBLE?this.smiles+="=":x.type===dt.PATTERN.TYPE.TRIPLE?this.smiles+="#":x.type===dt.PATTERN.TYPE.SINGLE_OR_AROMATIC?this.smiles+="-,:":x.type===dt.PATTERN.TYPE.DOUBLE_OR_AROMATIC?this.smiles+="=,:":x.type===dt.PATTERN.TYPE.SINGLE_OR_DOUBLE?this.smiles+="-,=":x.type!==dt.PATTERN.TYPE.AROMATIC||this.atoms[x.begin].lowercase&&this.atoms[x.end].lowercase&&this.isBondInRing(h)?x.type===dt.PATTERN.TYPE.SINGLE&&this.atoms[x.begin].aromatic&&this.atoms[x.end].aromatic&&(this.smiles+="-"):this.smiles+=":",l.edgeClosingCycle(h)){for(r=1;r>":"."),y=!1,this.writtenComponents++;b&&(this.writeAtom(t,d,this.atoms[d].aromatic,this.atoms[d].lowercase,this.atoms[d].chirality),this.writtenAtoms.push(c.idx))}return this.comma=!1,this.writeRadicals(t),this.comma&&(this.smiles+="|"),this.smiles},Sn.prototype.writeCycleNumber=function(t){if(t>0&&t<10)this.smiles+=t;else if(t>=10&&t<100)this.smiles+="%"+t;else{if(!(t>=100&&t<1e3))throw new Error("bad cycle number: "+t);this.smiles+="%%"+t}},Sn.prototype.writeAtom=function(t,e,n,r,o){var i,a=t.atoms.get(e),s=!1,u=-1;if("A"!==a.label)if("R"!==a.label&&"R#"!==a.label){i=a.aam,"C"!==a.label&&"P"!==a.label&&"N"!==a.label&&"S"!==a.label&&"O"!==a.label&&"Cl"!==a.label&&"F"!==a.label&&"Br"!==a.label&&"B"!==a.label&&"I"!==a.label&&(s=!0),(a.explicitValence>=0||0!==a.radical||o>0||n&&"C"!==a.label&&"O"!==a.label||n&&"C"===a.label&&this.atoms[e].neighbours.length<3&&0===this.atoms[e].h_count)&&(u=this.atoms[e].h_count);var l=a.label;if(a.atomList&&!a.atomList.notList?(l=a.atomList.label(),s=!1):a.isPseudo()||a.atomList&&a.atomList.notList?(l="*",s=!1):(o||0!==a.charge||a.isotope>0||u>=0||i>0)&&(s=!0),s&&(-1===u&&(u=this.atoms[e].h_count),this.smiles+="["),a.isotope>0&&(this.smiles+=a.isotope),this.smiles+=r?l.toLowerCase():l,o>0&&(this.smiles+=1===o?"@":"@@",a.implicitH>1))throw new Error(a.implicitH+" implicit H near stereocenter");"H"!==a.label&&(u>1||0===u&&!s?this.smiles+="H"+u:1===u&&(this.smiles+="H")),a.charge>1?this.smiles+="+"+a.charge:a.charge<-1?this.smiles+=a.charge:1===a.charge?this.smiles+="+":-1===a.charge&&(this.smiles+="-"),i>0&&(this.smiles+=":"+i),s&&(this.smiles+="]")}else this.smiles+="[*]";else this.smiles+="*"},Sn.prototype.markCisTrans=function(t){var e=this;this.cis_trans=new En(t,(function(t){return this.atoms[t].neighbours}),this),this.cis_trans.build(),this.dbonds=new Array(t.bonds.size),t.bonds.forEach((function(t,n){e.dbonds[n]={ctbond_beg:-1,ctbond_end:-1,saved:0}})),this.cis_trans.each((function(n,r){var o=t.bonds.get(r);if(0!==n.parity&&!e.isBondInRing(r)){var i=e.atoms[o.begin].neighbours,a=e.atoms[o.end].neighbours,s=!0,u=!0;if(i.forEach((function(e){e.bid!==r&&t.bonds.get(e.bid).type===dt.PATTERN.TYPE.SINGLE&&(s=!1)})),a.forEach((function(e){e.bid!==r&&t.bonds.get(e.bid).type===dt.PATTERN.TYPE.SINGLE&&(u=!1)})),s||u)return;i.forEach((function(n){n.bid!==r&&(t.bonds.get(n.bid).begin===o.begin?e.dbonds[n.bid].ctbond_beg=r:e.dbonds[n.bid].ctbond_end=r)})),a.forEach((function(n){n.bid!==r&&(t.bonds.get(n.bid).begin===o.end?e.dbonds[n.bid].ctbond_beg=r:e.dbonds[n.bid].ctbond_end=r)}))}}))},Sn.prototype.updateSideBonds=function(t,e){var n=t.bonds.get(e),r=this.cis_trans.getSubstituents(e),o=this.cis_trans.getParity(e),i=[-1,-1,-1,-1];i[0]=t.findBondId(r[0],n.begin),-1!==r[1]&&(i[1]=t.findBondId(r[1],n.begin)),i[2]=t.findBondId(r[2],n.end),-1!==r[3]&&(i[3]=t.findBondId(r[3],n.end));var a=0,s=0,u=0,l=0;if(0!==this.dbonds[i[0]].saved&&(1===this.dbonds[i[0]].saved&&t.bonds.get(i[0]).begin===n.begin||2===this.dbonds[i[0]].saved&&t.bonds.get(i[0]).end===n.begin?a++:s++),-1!==i[1]&&0!==this.dbonds[i[1]].saved&&(2===this.dbonds[i[1]].saved&&t.bonds.get(i[1]).begin===n.begin||1===this.dbonds[i[1]].saved&&t.bonds.get(i[1]).end===n.begin?a++:s++),0!==this.dbonds[i[2]].saved&&(1===this.dbonds[i[2]].saved&&t.bonds.get(i[2]).begin===n.end||2===this.dbonds[i[2]].saved&&t.bonds.get(i[2]).end===n.end?u++:l++),-1!==i[3]&&0!==this.dbonds[i[3]].saved&&(2===this.dbonds[i[3]].saved&&t.bonds.get(i[3]).begin===n.end||1===this.dbonds[i[3]].saved&&t.bonds.get(i[3]).end===n.end?u++:l++),o===En.PARITY.CIS?(a+=u,s+=l):(a+=l,s+=u),a>0&&s>0)throw new Error("incompatible cis-trans configuration");return(0!==a||0!==s)&&(a>0&&(this.dbonds[i[0]].saved=t.bonds.get(i[0]).begin===n.begin?1:2,-1!==i[1]&&(this.dbonds[i[1]].saved=t.bonds.get(i[1]).begin===n.begin?2:1),this.dbonds[i[2]].saved=t.bonds.get(i[2]).begin===n.end==(o===En.PARITY.CIS)?1:2,-1!==i[3]&&(this.dbonds[i[3]].saved=t.bonds.get(i[3]).begin===n.end==(o===En.PARITY.CIS)?2:1)),s>0&&(this.dbonds[i[0]].saved=t.bonds.get(i[0]).begin===n.begin?2:1,-1!==i[1]&&(this.dbonds[i[1]].saved=t.bonds.get(i[1]).begin===n.begin?1:2),this.dbonds[i[2]].saved=t.bonds.get(i[2]).begin===n.end==(o===En.PARITY.CIS)?2:1,-1!==i[3]&&(this.dbonds[i[3]].saved=t.bonds.get(i[3]).begin===n.end==(o===En.PARITY.CIS)?1:2)),!0)},Sn.prototype.calcBondDirection=function(t,e,n){var r,o=this;if(-1===this.dbonds[e].ctbond_beg&&-1===this.dbonds[e].ctbond_end)return 0;if(t.bonds.get(e).type!==dt.PATTERN.TYPE.SINGLE)throw new Error("internal: directed bond type "+t.bonds.get(e).type);for(;r=0,this.cis_trans.each((function(e,n){0===e.parity||o.isBondInRing(n)||o.updateSideBonds(t,n)&&r++})),r!==this.touchedCistransbonds;)this.touchedCistransbonds=r;return 0===this.dbonds[e].saved&&(n===t.bonds.get(e).begin?this.dbonds[e].saved=1:this.dbonds[e].saved=2),this.dbonds[e].saved},Sn.prototype.writeRadicals=function(t){var e,n,r=new Array(this.writtenAtoms.length);for(e=0;e [ \d]*<(\S+)>/);if(n){var r=n[1],o=e.split("\n")[1].trim();t[r]=Number.isFinite(o)?+o:o.toString()}return t}),{});n.push({struct:s,props:u})}}return n}},{key:"serialize",value:function(t){var e=new xn(this.molSerializerOptions);return t.reduce((function(t,n){return t+=e.serialize(n.struct),Object.keys(n.props).forEach((function(e){t+="> <".concat(e,">\n"),t+="".concat(n.props[e],"\n\n")})),"".concat(t,"$$$$\n")}),"")}}]),t}();!function(t){t.Mol="chemical/x-mdl-molfile",t.Rxn="chemical/x-mdl-rxnfile",t.DaylightSmiles="chemical/x-daylight-smiles",t.ExtendedSmiles="chemical/x-chemaxon-cxsmiles",t.DaylightSmarts="chemical/x-daylight-smarts",t.InChI="chemical/x-inchi",t.InChIAuxInfo="chemical/x-inchi-aux",t.InChIKey="chemical/x-inchi-key",t.CDX="chemical/x-cdx",t.CDXML="chemical/x-cdxml",t.CML="chemical/x-cml",t.KET="chemical/x-indigo-ket",t.UNKNOWN="chemical/x-unknown",t.SDF="chemical/x-sdf"}(Cn||(Cn={}));var Mn=Math.PI/12;function Nn(t,e){var n=$.diff(e,t);return Math.atan2(n.y,n.x)}function _n(t,e){return e&&(t=Nn(t,e)),Math.round(t/Mn)*Mn}function Dn(t){var e=Math.round(t/Math.PI*180);return e>180?e-=360:e<=-180&&(e+=360),e}var Ln={calcAngle:Nn,fracAngle:_n,degrees:Dn,setFracAngle:function(t){Mn=Math.PI/180*t},mergeBondsParams:function(t,e,n,r){var o=t.atoms.get(e.begin),i=n.atoms.get(r.begin),a=t.atoms.get(e.end),s=n.atoms.get(r.end),u=Nn(o.pp,a.pp)-Nn(i.pp,s.pp),l=Math.abs(Dn(u)%180),c=$.dist(o.pp,a.pp)/$.dist(i.pp,s.pp);return{merged:!(0,E.inRange)(l,10,170)&&(0,E.inRange)(c,.8,1.2),angle:u,scale:c,cross:Math.abs(Dn(u))>90}},calcNewAtomPos:function(t,e,n){var r=new $(1,0).rotate(n?Nn(t,e):_n(t,e));return r.add_(t),r}};S().el.translateAbs=function(t,e){this.delta=this.delta||new $,this.delta.x+=t-0,this.delta.y+=e-0,this.transform("t"+this.delta.x.toString()+","+this.delta.y.toString())},S().st.translateAbs=function(t,e){this.forEach((function(n){n.translateAbs(t,e)}))};var jn,Fn,Gn,Hn=function(){function t(e){(0,o.Z)(this,t),this.type=e,this.paths=[],this.boxes=[],this.boundingBox=null,this.oldBoundingBox=null,this.exts=[]}return(0,i.Z)(t,[{key:"add",value:function(t,e,n){this.paths.push(t),e&&(this.boxes.push(e),this.boundingBox=null==this.boundingBox?e:Et.union(this.boundingBox,e)),n&&this.exts.push(n)}},{key:"clear",value:function(){this.paths=[],this.boxes=[],this.exts=[],null!==this.boundingBox&&(this.oldBoundingBox=this.boundingBox.clone()),this.boundingBox=null}},{key:"translate",value:function(){if(arguments.length>2)throw new Error("One vector or two scalar arguments expected");if(1===arguments.length){var t=arguments.length<=0?void 0:arguments[0];this.translate(t.x,t.y)}else{for(var e=arguments.length<=0?void 0:arguments[0],n=arguments.length<=1?void 0:arguments[1],r=new $(e,n),o=0;o0?(a<0||i[a]i[s]?s:a,d=i[a]>i[s]?a:s;return i[c]+Math.abs(o[c])*(i[d]-i[c])/(Math.abs(o[c])+Math.abs(o[d]))},calcCoordinates:function(t,e,n){var r={pos1:null,pos2:null},o={x:e.x-t.x,y:e.y-t.y},i=(Math.pow(n,2)-o.x*o.x-o.y*o.y-Math.pow(n,2))/-2,a=o.x*o.x+o.y*o.y;if(0!==o.x){var s=-2*o.y*i,u=s*s-4*a*(i*i-n*n*o.x*o.x);u>0&&(r.pos1={x:0,y:0},r.pos2={x:0,y:0},r.pos1.y=(-s+Math.sqrt(u))/(2*a),r.pos2.y=(-s-Math.sqrt(u))/(2*a),r.pos1.x=(i-r.pos1.y*o.y)/o.x,r.pos2.x=(i-r.pos2.y*o.y)/o.x)}else r.pos1={x:0,y:0},r.pos2={x:0,y:0},r.pos1.y=i/o.y,r.pos2.y=i/o.y,r.pos1.x=-Math.sqrt(Math.pow(n,2)-Math.pow(i,2)/Math.pow(o.y,2)),r.pos2.x=Math.sqrt(Math.pow(n,2)-Math.pow(i,2)/Math.pow(o.y,2));return null!==r.pos1&&(r.pos1.x+=t.x,r.pos1.y+=t.y),null!==r.pos2&&(r.pos2.x+=t.x,r.pos2.y+=t.y),r},drawCIPLabel:function(t){var e=t.atomOrBond,n=t.position,r=t.restruct,o=t.visel,i=r.render,a=i.options,s=i.paper,u=s.set(),l=function(t){var e=t.paper,n=t.cipLabelPosition,r=t.atomOrBond,o=t.options,i=e.text(n.x,n.y,"(".concat(r.cip,")")).attr({font:o.font,"font-size":o.fontsz}),a=i.getBBox(),s=e.set(),u=e.rect(a.x-1,a.y-1,a.width+2,a.height+2,3,3).attr({fill:"#fff",stroke:"#fff"});return s.push(u.toFront(),i.toFront()),{path:s,text:i,rectangle:u}}({paper:s,cipLabelPosition:n.scaled(a.scale),atomOrBond:e,options:a}),c=Un(l.path.getBBox());return l.path.translateAbs(.5*c.width,-.5*c.height),u.push(l.path.toFront()),r.addReObjectPath(jn.additionalInfo,o,u,null,!0),l},updateHalfBondCoordinates:function(t,e,n){return t.p.y!==e.p.y||(t.p.xe.p.x&&(t.p.x=t.p.x-n)),[t,e]}};function Wn(t,e){var n=Object.keys(t);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(t);e&&(r=r.filter((function(e){return Object.getOwnPropertyDescriptor(t,e).enumerable}))),n.push.apply(n,r)}return n}function Yn(t){for(var e=1;e=0?1:-1,c=10*l,d=5*l,h=4*l,f=s.x+n,p="M".concat(H(s.x),",").concat(H(s.y))+"A".concat(n/2,",").concat(u,",",0,",",0,",").concat(l>0?1:0,",").concat(H(f),",").concat(H(s.y))+"L".concat(H(f-d),",").concat(H(s.y-c))+"l".concat(H(d),",").concat(H(h))+"l".concat(H(d),",").concat(H(-h))+"l".concat(H(-d),",").concat(c),m=k()(p).rotate(o,s.x,s.y).toString();return t.path(m).attr(Yn(Yn({},i.lineattr),a&&{stroke:i.arrowSnappingStyle.stroke}))}(t,e,n,o,i,s);case _t.EllipticalArcFilledTriangle:return function(t,e,n,o,i,a){var s=(0,r.Z)(e.pos,1)[0],u=e.height,l=u>=0?1:-1,c=10*l,d=5*l,h=s.x+n,f="M".concat(H(s.x),",").concat(H(s.y))+"A".concat(n/2,",").concat(u,",",0,",",0,",").concat(l>0?1:0,",").concat(H(h),",").concat(H(s.y))+"L".concat(H(h-d),",").concat(H(s.y-c))+"l".concat(H(c),",").concat(H(0))+"l".concat(H(-d),",").concat(H(c)),p=k()(f).rotate(o,s.x,s.y).toString();return t.path(p).attr(Yn(Yn({},i.lineattr),a&&{stroke:i.arrowSnappingStyle.stroke}))}(t,e,n,o,i,s);case _t.EllipticalArcOpenAngle:return function(t,e,n,o,i,a){var s=(0,r.Z)(e.pos,1)[0],u=e.height,l=u>=0?1:-1,c=5*l,d=7*l,h=s.x+n,f="M".concat(H(s.x),",").concat(H(s.y))+"A".concat(n/2,",").concat(u,",",0,",",0,",").concat(l>0?1:0,",").concat(H(h),",").concat(H(s.y))+"L".concat(H(h-c),",").concat(H(s.y-d))+"M".concat(H(h),",").concat(H(s.y))+"L".concat(H(h+c),", ").concat(H(s.y-d)),p=k()(f).rotate(o,s.x,s.y).toString();return t.path(p).attr(Yn(Yn({},i.lineattr),a&&{stroke:i.arrowSnappingStyle.stroke}))}(t,e,n,o,i,s);case _t.EllipticalArcOpenHalfAngle:return function(t,e,n,o,i,a){var s=(0,r.Z)(e.pos,1)[0],u=e.height,l=u>=0?1:-1,c=5*l,d=7*l,h=s.x+n,f="M".concat(H(s.x),",").concat(H(s.y))+"A".concat(n/2,",").concat(u,",",0,",",0,",").concat(l>0?1:0,", ").concat(H(h),",").concat(H(s.y))+"L".concat(H(h+c),", ").concat(H(s.y-d)),p=k()(f).rotate(o,s.x,s.y).toString();return t.path(p).attr(Yn(Yn({},i.lineattr),a&&{stroke:i.arrowSnappingStyle.stroke}))}(t,e,n,o,i,s)}},plus:function(t,e,n){var r=n.scale/5;return t.path("M{0},{4}L{0},{5}M{2},{1}L{3},{1}",H(e.x),H(e.y),H(e.x-r),H(e.x+r),H(e.y-r),H(e.y+r)).attr(n.lineattr)},aromaticBondPaths:function(t,e,n,r,o,i){return[i&&1&o?$n(t,n,i):qn(t,n),i&&2&o?$n(e,r,i):qn(e,r)]},bondSingle:function(t,e,n,r,o){var i=arguments.length>5&&void 0!==arguments[5]?arguments[5]:"#000",a=e.p,s=n.p;return t.path(qn(a,s)).attr(r.lineattr).attr({fill:i,stroke:i}).attr(o?r.bondSnappingStyle:{})},bondSingleUp:function(t,e,n,r,o,i){var a=arguments.length>6&&void 0!==arguments[6]?arguments[6]:"#000";return t.path("M{0},{1}L{2},{3}L{4},{5}Z",H(e.x),H(e.y),H(n.x),H(n.y),H(r.x),H(r.y)).attr(o.lineattr).attr({fill:a,stroke:a}).attr(i?o.bondSnappingStyle:{})},bondSingleStereoBold:function(t,e,n,r,o,i,a){var s=arguments.length>7&&void 0!==arguments[7]?arguments[7]:"#000";return t.path("M{0},{1}L{2},{3}L{4},{5}L{6},{7}Z",H(e.x),H(e.y),H(n.x),H(n.y),H(r.x),H(r.y),H(o.x),H(o.y)).attr(i.lineattr).attr({stroke:s,fill:s}).attr(a?i.bondSnappingStyle:{})},bondDoubleStereoBold:function(t,e,n,r,o,i){var a=arguments.length>6&&void 0!==arguments[6]?arguments[6]:"#000";return t.set([e,t.path("M{0},{1}L{2},{3}",H(n.x),H(n.y),H(r.x),H(r.y)).attr(o.lineattr).attr({stroke:a,fill:a}).attr(i?o.bondSnappingStyle:{})])},bondSingleDown:function(t,e,n,r,o,i,a){for(var s,u=arguments.length>7&&void 0!==arguments[7]?arguments[7]:"#000",l=e.p,c=e.norm,d=.7*i.stereoBond,h="",f=0;f7&&void 0!==arguments[7]?arguments[7]:"#000",u=e.p,l=e.norm,c=.7*i.stereoBond,d="M"+H(u.x)+","+H(u.y),h=u,f=0;f5&&void 0!==arguments[5]?arguments[5]:"#000",a=e.p,s=n.p,u=e.norm,l=a.addScaled(u,r.bondSpace),c=s.addScaled(u,r.bondSpace),d=a.addScaled(u,-r.bondSpace),h=s.addScaled(u,-r.bondSpace);return t.path(qn(a,s)+qn(l,c)+qn(d,h)).attr(r.lineattr).attr({fill:i,stroke:i}).attr(o?r.bondSnappingStyle:{})},bondAromatic:function(t,e,n,r,o){var i=t.path(e[0]).attr(r.lineattr).attr(o?r.bondSnappingStyle:{}),a=t.path(e[1]).attr(r.lineattr).attr(o?r.bondSnappingStyle:{});return null!=n&&(n>0?i:a).attr({"stroke-dasharray":"- "}),t.set([i,a])},bondAny:function(t,e,n,r,o){var i=e.p,a=n.p;return t.path(qn(i,a)).attr(r.lineattr).attr({"stroke-dasharray":"- "}).attr(o?r.bondSnappingStyle:{})},bondHydrogen:function(t,e,n,r,o){var i=e.p,a=n.p;return t.path(qn(i,a)).attr(r.lineattr).attr({"stroke-dasharray":".","stroke-linecap":"square"}).attr(o?r.bondSnappingStyle:{})},bondDative:function(t,e,n,r,o){var i=e.p,a=n.p;return t.path(qn(i,a)).attr(r.lineattr).attr({"arrow-end":"block-midium-long"}).attr(o?r.bondSnappingStyle:{})},reactingCenter:function(t,e,n){for(var r="",o=0;o1||this.showLabel&&0!==this.a.implicitH?this.getLabeledSelectionContour(t):this.getUnlabeledSelectionContour(t)}},{key:"makeHoverPlate",value:function(t){var e=this.a,n=t.options,r=t.ctab.sgroups,o=t.ctab.molecule.functionalGroups;return Lt.isAtomInContractedFunctionalGroup(e,r,o,!0)?null:this.getSelectionContour(t).attr(n.hoverStyle)}},{key:"makeSelectionPlate",value:function(t){var e=this.a,n=t.render,r=n.options,o=n.ctab.sgroups,i=n.ctab.molecule.functionalGroups;return Lt.isAtomInContractedFunctionalGroup(e,o,i,!0)?null:this.getSelectionContour(n).attr(r.selectionStyle)}},{key:"getShiftedSegmentPosition",value:function(t,e){for(var n=gt.obj2scaled(this.a.pp,t),r=0,o=this.visel.exts,i=0;i0?n.addScaled(e,r+3*t.lineWidth):n}},{key:"hasAttachmentPoint",value:function(){return Boolean(this.a.attachmentPoints)}},{key:"show",value:function(t,e,n){var r,o=t.molecule.atoms.get(e),i=t.molecule.sgroups,a=t.molecule.functionalGroups,s=t.render,u=gt.obj2scaled(this.a.pp,s.options);if(Lt.isAtomInContractedFunctionalGroup(o,i,a,!1)){var l=t.molecule.getGroupFromAtomId(e);if((null==l?void 0:l.getContractedPosition(t.molecule).atomId)===e){var c=s.paper.text(u.x,u.y,l.data.name).attr({"font-weight":700,"font-size":14});t.addReObjectPath(jn.data,this.visel,c,u,!0)}}else{var d,h,f,p,m,v,g;this.hydrogenOnTheLeft=function(t,e){if(0===e.a.neighbors.length){if("D"===e.a.label||"T"===e.a.label)return!1;var n=_.get(e.a.label);return!n||Boolean(n.leftH)}if(1===e.a.neighbors.length){var r=e.a.neighbors[0];return t.halfBonds.get(r).dir.x>0}return!1}(t.molecule,this),this.showLabel=function(t,e,n){var r=Boolean(n.a.attachmentPoints),o="c"===n.a.label.toLowerCase(),i=e.showHydrogenLabels!==Kn.Off&&e.showHydrogenLabels!==Kn.Hetero,a=0===n.a.neighbors.length||n.a.neighbors.length<2&&i;if(r&&o)return!1;if(a||e.carbonExplicitly||e.showHydrogenLabels===Kn.On||n.a.alias||0!==n.a.isotope||0!==n.a.radical||0!==n.a.charge||n.a.explicitValence>=0||null!==n.a.atomList||null!==n.a.rglabel||n.a.badConn&&e.showValenceWarnings||"c"!==n.a.label.toLowerCase())return!0;if(2===n.a.neighbors.length){var s=n.a.neighbors[0],u=n.a.neighbors[1],l=t.molecule.halfBonds.get(s),c=t.molecule.halfBonds.get(u),d=t.bonds.get(l.bid),h=t.bonds.get(c.bid);if(d.b.type===h.b.type&&d.b.stereo===dt.PATTERN.STEREO.NONE&&h.b.stereo===dt.PATTERN.STEREO.NONE&&Math.abs($.cross(l.dir,c.dir))<.2)return!0}return!1}(t,s.options,this),this.color="black";var y=null;if(this.showLabel&&(g=function(t,e,n,r){var o={};if(o.text=function(t){if(null!==t.atomList)return t.atomList.label();if(t.pseudo)return t.pseudo;if(t.alias)return t.alias;if("R#"===t.label&&null!==t.rglabel){for(var e="",n=0;n<32;n++)t.rglabel&1<1?1:n.zoom),f=-g.rbb.width/2*(n.zoom>1?1:n.zoom),p=Math.floor(this.a.implicitH),m="H"===g.text,v="D"===g.text||"T"===g.text,t.addReObjectPath(jn.data,this.visel,g.path,u,!0)),n.showAtomIds){(y={}).text=e.toString();var b=this.hydrogenOnTheLeft?$.lc(u,1,new $({x:-2,y:0,z:0}),6):$.lc(u,1,new $({x:2,y:0,z:0}),6);this.showLabel&&(b=$.lc(b,1,new $({x:1,y:-3,z:0}),6)),y.path=s.paper.text(b.x,b.y,y.text).attr({font:n.font,"font-size":n.fontszsub,fill:"#070"}),y.rbb=Vn.relBox(y.path.getBBox()),Jn.recenterText(y.path,y.rbb),t.addReObjectPath(jn.indices,this.visel,y.path,u)}if(this.showLabel&&(!this.a.pseudo||v)){var w=null;if(m&&p>0&&(w=function(t,e,n,r){var o=gt.obj2scaled(t.a.pp,e.options),i=e.options,a=.5*i.lineWidth,s={};return s.text=(n+1).toString(),s.path=e.paper.text(o.x,o.y,s.text).attr({font:i.font,"font-size":i.fontszsub,fill:t.color}),s.rbb=Vn.relBox(s.path.getBBox()),Jn.recenterText(s.path,s.rbb),nr(s.path,s.rbb,r+.5*s.rbb.width+a,.2*t.label.rbb.height),s}(this,s,p,h),h+=w.rbb.width+d,t.addReObjectPath(jn.data,this.visel,w.path,u,!0)),0!==this.a.radical){var x=function(t,e){var n,r=gt.obj2scaled(t.a.pp,e.options),o=e.options,i=e.paper,a={};switch(t.a.radical){case 1:a.path=i.set(),n=1.6*o.lineWidth,a.path.push(Jn.radicalBullet(i,r.add(new $(-n,0)),o),Jn.radicalBullet(i,r.add(new $(n,0)),o)),a.path.attr("fill",t.color);break;case 2:a.path=i.set(),a.path.push(Jn.radicalBullet(i,r,o)),a.path.attr("fill",t.color);break;case 3:a.path=i.set(),n=1.6*o.lineWidth,a.path.push(Jn.radicalCap(i,r.add(new $(-n,0)),o),Jn.radicalCap(i,r.add(new $(n,0)),o)),a.path.attr("stroke",t.color)}a.rbb=Vn.relBox(a.path.getBBox());var s=-.5*(t.label.rbb.height+a.rbb.height);return 3===t.a.radical&&(s-=o.lineWidth/2),nr(a.path,a.rbb,0,s),a}(this,s);t.addReObjectPath(jn.data,this.visel,x.path,u,!0)}if(0!==this.a.isotope){var E=function(t,e,n){var r=gt.obj2scaled(t.a.pp,e.options),o=e.options,i=.5*o.lineWidth,a={};return a.text=t.a.isotope.toString(),a.path=e.paper.text(r.x,r.y,a.text).attr({font:o.font,"font-size":o.fontszsub,fill:t.color}),a.rbb=Vn.relBox(a.path.getBBox()),Jn.recenterText(a.path,a.rbb),nr(a.path,a.rbb,n-.5*a.rbb.width-i,-.3*t.label.rbb.height),a}(this,s,f);f-=E.rbb.width+d,t.addReObjectPath(jn.data,this.visel,E.path,u,!0)}if(!m&&!this.a.alias&&p>0&&function(t,e){var n,r;return t===Kn.On||t===Kn.Terminal&&e.a.neighbors.length<2||t===Kn.Hetero&&"c"!==(null===(n=e.label)||void 0===n?void 0:n.text.toLowerCase())||t===Kn.TerminalAndHetero&&(e.a.neighbors.length<2||"c"!==(null===(r=e.label)||void 0===r?void 0:r.text.toLowerCase()))}(n.showHydrogenLabels,this)){var P=function(t,e,n,r){var o=r.hydroIndex,i=t.hydrogenOnTheLeft,a=gt.obj2scaled(t.a.pp,e.options),s=e.options,u=.5*s.lineWidth,l=r.hydrogen;return l.text="H",l.path=e.paper.text(a.x,a.y,l.text).attr({font:s.font,"font-size":s.fontsz,fill:t.color}),l.rbb=Vn.relBox(l.path.getBBox()),Jn.recenterText(l.path,l.rbb),i||(nr(l.path,l.rbb,r.rightMargin+.5*l.rbb.width+u,0),r.rightMargin+=l.rbb.width+u),n>1&&((o={}).text=n.toString(),o.path=e.paper.text(a.x,a.y,o.text).attr({font:s.font,"font-size":s.fontszsub,fill:t.color}),o.rbb=Vn.relBox(o.path.getBBox()),Jn.recenterText(o.path,o.rbb),i||(nr(o.path,o.rbb,r.rightMargin+.5*o.rbb.width*(s.zoom>1?1:s.zoom)+u,.2*t.label.rbb.height),r.rightMargin+=o.rbb.width+u)),i&&(null!=o&&(nr(o.path,o.rbb,r.leftMargin-.5*o.rbb.width-u,.2*t.label.rbb.height),r.leftMargin-=o.rbb.width+u),nr(l.path,l.rbb,r.leftMargin-.5*l.rbb.width*(n>1&&s.zoom<1?s.zoom:1)-u,0),r.leftMargin-=l.rbb.width+u),Object.assign(r,{hydrogen:l,hydroIndex:o})}(this,s,p,{hydrogen:{},hydroIndex:w,rightMargin:h,leftMargin:f}),O=P.hydrogen;w=P.hydroIndex,h=P.rightMargin,f=P.leftMargin,t.addReObjectPath(jn.data,this.visel,O.path,u,!0),null!=w&&t.addReObjectPath(jn.data,this.visel,w.path,u,!0)}if(0!==this.a.charge&&n.showCharge){var A=function(t,e,n){var r=gt.obj2scaled(t.a.pp,e.options),o=e.options,i=.5*o.lineWidth,a={text:""},s=Math.abs(t.a.charge);return 1!==s&&(a.text=s.toString()),t.a.charge<0?a.text+="–":a.text+="+",a.path=e.paper.text(r.x,r.y,a.text).attr({font:o.font,"font-size":o.fontszsub,fill:t.color}),a.rbb=Vn.relBox(a.path.getBBox()),Jn.recenterText(a.path,a.rbb),nr(a.path,a.rbb,n+.5*a.rbb.width+i,-.3*t.label.rbb.height),a}(this,s,h);h+=A.rbb.width+d,t.addReObjectPath(jn.data,this.visel,A.path,u,!0)}if(this.a.explicitValence>=0&&n.showValence){var R=function(t,e,n){var r=gt.obj2scaled(t.a.pp,e.options),o=e.options,i=.5*o.lineWidth,a={};if(a.text={0:"0",1:"I",2:"II",3:"III",4:"IV",5:"V",6:"VI",7:"VII",8:"VIII",9:"IX",10:"X",11:"XI",12:"XII",13:"XIII",14:"XIV"}[t.a.explicitValence],!a.text)throw new Error("invalid valence "+t.a.explicitValence.toString());return a.text="("+a.text+")",a.path=e.paper.text(r.x,r.y,a.text).attr({font:o.font,"font-size":o.fontszsub,fill:t.color}),a.rbb=Vn.relBox(a.path.getBBox()),Jn.recenterText(a.path,a.rbb),nr(a.path,a.rbb,n+.5*a.rbb.width+i,-.3*t.label.rbb.height),a}(this,s,h);h+=R.rbb.width+d,t.addReObjectPath(jn.data,this.visel,R.path,u,!0)}if(this.a.badConn&&n.showValenceWarnings){var S=function(t,e,n,r){var o=gt.obj2scaled(t.a.pp,e.options),i=.5*e.options.lineWidth,a={},s=o.y+t.label.rbb.height/2+i;return a.path=e.paper.path("M{0},{1}L{2},{3}",H(o.x+n),H(s),H(o.x+r),H(s)).attr(e.options.lineattr).attr({stroke:"#F00"}),a.rbb=Vn.relBox(a.path.getBBox()),a}(this,s,f,h);t.addReObjectPath(jn.warnings,this.visel,S.path,u,!0)}y&&nr(y.path,y.rbb,-.5*g.rbb.width-.5*y.rbb.width-d,.3*g.rbb.height)}this.setHover(this.hover,s);var T=this.a.stereoLabel,k=function(t){var e="";if(t.a.aam>0&&(e+=t.a.aam),t.a.invRet>0)if(e.length>0&&(e+=","),1===t.a.invRet)e+="Inv";else{if(2!==t.a.invRet)throw new Error("Invalid value for the invert/retain flag");e+="Ret"}if(t.a.exactChangeFlag>0){if(e.length>0&&(e+=","),1!==t.a.exactChangeFlag)throw new Error("Invalid value for the exact change flag");e+="ext"}return e}(this),B=this.a.pseudo?"":function(t){var e="";if(0!==t.a.ringBondCount)if(t.a.ringBondCount>0)e+="rb"+t.a.ringBondCount.toString();else if(-1===t.a.ringBondCount)e+="rb0";else{if(-2!==t.a.ringBondCount)throw new Error("Ring bond count invalid");e+="rb*"}if(0!==t.a.substitutionCount)if(e.length>0&&(e+=","),t.a.substitutionCount>0)e+="s"+t.a.substitutionCount.toString();else if(-1===t.a.substitutionCount)e+="s0";else{if(-2!==t.a.substitutionCount)throw new Error("Substitution count invalid");e+="s*"}if(t.a.unsaturatedAtom>0){if(e.length>0&&(e+=","),1!==t.a.unsaturatedAtom)throw new Error("Unsaturated atom invalid value");e+="u"}return t.a.hCount>0&&(e.length>0&&(e+=","),e+="H"+(t.a.hCount-1).toString()),e}(this),C=Number(null===(r=t.atoms.get(e))||void 0===r?void 0:r.a.fragment),Z=t.molecule.frags.get(C),M=function(t,e,n,r){if(!t)return!1;var o=t.match(/\D+/g)[0];if(n&&o===J.Abs)return!1;if(n&&o!==J.Abs)return!0;switch(e){case Gn.Off:return!1;case Gn.On:return!0;case Gn.Classic:return!(r!==ct.Mixed&&o!==J.Or);case Gn.IUPAC:return!(r!==ct.Mixed||o===J.Abs);default:return!0}}(T,n.stereoLabelStyle,n.ignoreChiralFlag,null==Z?void 0:Z.enhancedStereoFlag),N="";if(M&&(N="".concat(T,"\n")),B.length>0&&(N+="".concat(B,"\n")),k.length>0&&(N+=".".concat(k,".")),N.length>0){var D=_.get(this.a.label),L=s.paper.text(u.x,u.y,N).attr({font:n.font,"font-size":n.fontszsub,fill:n.atomColoring&&D?I[this.a.label]:"#000"});if(T){var j=function(t,e){return e&&t.colorStereogenicCenters!==Fn.Off&&t.colorStereogenicCenters!==Fn.BondsOnly?er(t,e):"#000"}(s.options,T);L.node.childNodes[0].setAttribute("fill",j);var F=function(t,e){var n=e.match(/\D+/g)[0],r=+e.replace(n,"");return t.autoFadeOfStereoLabels&&n!==J.Abs&&t.colorStereogenicCenters!==Fn.Off&&t.colorStereogenicCenters!==Fn.BondsOnly?Math.max(1-(r-1)/10,.3):1}(s.options,T);L.node.childNodes[0].setAttribute("fill-opacity",F)}var G=Vn.relBox(L.getBBox());Jn.recenterText(L,G);for(var z=this.visel,U=3,V=this.bisectLargestSector(t.molecule),W=0;Wo&&(o=n[a],i=e[a]);return{neighborAngle:i,largestAngle:o}}},{key:"bisectLargestSector",value:function(t){var e,n=this.getLargestSectorFromNeighbors(t),r=n.largestAngle;return e=n.neighborAngle+r/2,new $(Math.cos(e),Math.sin(e))}}],[{key:"isSelectable",value:function(){return!0}}]),a}(zn);function er(t,e){switch(e.match(/\D+/g)[0]){case J.And:return t.colorOfAndCenters;case J.Or:return t.colorOfOrCenters;case J.Abs:return t.colorOfAbsoluteCenters;default:return"#000"}}function nr(t,e,n,r){t.translateAbs(n,r),e.x+=n,e.y+=r}function rr(t,e){var n=Object.keys(t);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(t);e&&(r=r.filter((function(e){return 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e=this.b,n=t.ctab,r=t.options,o=r.bondThickness,i=r.doubleBondWidth,a=r.stereoBondWidth,s=i+o,u=n.molecule.halfBonds.get(e.hb1).p,l=n.molecule.halfBonds.get(e.hb2).p,c=e.stereo!==dt.PATTERN.STEREO.NONE&&e.stereo!==dt.PATTERN.STEREO.CIS_TRANS,d=c?0:-2,h=$.getLinePoint(l,u,d),f=$.getLinePoint(u,l,d),p=c?.5*a:s+.5,m=c?a+1*s/a:s+.5,v=$.getLinePoint(h,f,m),g=$.getLinePoint(f,h,p),y=h.add(new $(m,0)),b=f.add(new $(p,0)),w=v.add(new $(m,0)),x=g.add(new $(p,0)),E=e.angle,P=y.rotateAroundOrigin(E+90,new $(h.x,h.y)),O=y.rotateAroundOrigin(E-90,new $(h.x,h.y)),A=w.rotateAroundOrigin(E+90,v),R=w.rotateAroundOrigin(E-90,v),S=b.rotateAroundOrigin(E+90,f),T=b.rotateAroundOrigin(E-90,f);return[A,P,S,x.rotateAroundOrigin(E+90,g),x.rotateAroundOrigin(E-90,g),T,R,O]}},{key:"getSelectionContour",value:function(t){var e=t.paper,n=this.getSelectionPoints(t),o=(0,r.Z)(n,8),i=o[0],a=o[1],s=o[2],u=o[3],l=o[4],c=o[5],d=o[6],h=o[7],f="\n M ".concat(a.x," ").concat(a.y,"\n L ").concat(s.x," ").concat(s.y,"\n C ").concat(u.x," ").concat(u.y,", ").concat(l.x," ").concat(l.y,", ").concat(c.x," ").concat(c.y,"\n L ").concat(h.x," ").concat(h.y,"\n C ").concat(d.x," ").concat(d.y,", ").concat(i.x," ").concat(i.y,", ").concat(a.x," ").concat(a.y,"\n ");return e.path(f)}},{key:"makeHoverPlate",value:function(t){var e=t.ctab,n=t.options;u.bondRecalc(this,e,n);var r=this.b,o=e.sgroups,i=e.molecule.functionalGroups;return Lt.isBondInContractedFunctionalGroup(r,o,i)?null:this.getSelectionContour(t).attr(function(t){for(var e=1;e=0&&r[1]>=0}(e,this,t),u.bondRecalc(this,t,n),function(t,e){var n=t.b.hb1,r=t.b.hb2;if(!n&&0!==n||!r&&0!==r)t.doubleBondShift=fr(e,t);else{var o=e.halfBonds.get(n).loop,i=e.halfBonds.get(r).loop;if(o>=0&&i>=0){var a=e.loops.get(o).dblBonds,s=e.loops.get(i).dblBonds,u=e.loops.get(o).hbs.length,l=e.loops.get(i).hbs.length;t.doubleBondShift=function(t,e,n,r){return 6===t&&6!==e&&(n>1||1===r)?-1:6===e&&6!==t&&(r>1||1===n)?1:e*n>t*r?-1:e*nt?-1:1}(u,l,a,s)}else t.doubleBondShift=o>=0?-1:i>=0?1:fr(e,t)}}(this,o),c&&d){var h=t.isSnappingBond(e);this.path=function(t,e,n,r,o){var i,a,s,u=null,l=t.render,c=t.molecule,d=!(null!==(i=t.atoms.get(n.begin))&&void 0!==i&&i.showLabel),h=!(null!==(a=t.atoms.get(r.begin))&&void 0!==a&&a.showLabel);switch(e.b.type){case dt.PATTERN.TYPE.SINGLE:switch(e.b.stereo){case dt.PATTERN.STEREO.UP:ar(n.bid,e,t),u=e.boldStereo&&e.neihbid1>=0&&e.neihbid2>=0?ur(l,n,r,e,c,o):function(t,e,n,r,o,i){var a=e.p,s=n.p,u=e.norm,l=t.options,c=.7*l.stereoBond,d=s.addScaled(u,c),h=s.addScaled(u,-c);if(r.neihbid2>=0){var f=cr(n,r.neihbid2,l.stereoBond,o);d=f[0],h=f[1]}return Jn.bondSingleUp(t.paper,a,d,h,l,i,sr(l,r,o))}(l,n,r,e,c,o);break;case dt.PATTERN.STEREO.DOWN:u=function(t,e,n,r,o,i){var a=e.p,s=n.p,u=t.options,l=s.sub(a),c=l.length()+.2;l=l.normalized();var d=1.2*u.lineWidth,h=Math.max(Math.floor((c-u.lineWidth)/(u.lineWidth+d)),0)+2,f=c/(h-1);return Jn.bondSingleDown(t.paper,e,l,h,f,u,i,sr(u,r,o))}(l,n,r,e,c,o);break;case dt.PATTERN.STEREO.EITHER:u=function(t,e,n,r,o,i){var a=e.p,s=n.p,u=t.options,l=s.sub(a),c=l.length();l=l.normalized();var d=.6*u.lineWidth,h=Math.max(Math.floor((c-u.lineWidth)/(u.lineWidth+d)),0)+2,f=c/(h-.5);return Jn.bondSingleEither(t.paper,e,l,h,f,u,i,sr(u,r,o))}(l,n,r,e,c,o);break;default:u=Jn.bondSingle(l.paper,n,r,l.options,o,sr(l.options,e,c))}break;case dt.PATTERN.TYPE.DOUBLE:ar(n.bid,e,t),u=e.b.stereo===dt.PATTERN.STEREO.NONE&&e.boldStereo&&e.neihbid1>=0&&e.neihbid2>=0?function(t,e,n,r,o,i,a,s){var u=e.p,l=n.p,c=e.norm,d=r.doubleBondShift,h=1.5*t.options.stereoBond,f=u.addScaled(c,h*d),p=l.addScaled(c,h*d);d>0?(i&&(f=f.addScaled(e.dir,h*lr(e.rightCos,e.rightSin))),a&&(p=p.addScaled(e.dir,-h*lr(n.leftCos,n.leftSin)))):d<0&&(i&&(f=f.addScaled(e.dir,h*lr(e.leftCos,e.leftSin))),a&&(p=p.addScaled(e.dir,-h*lr(n.rightCos,n.rightSin))));var m=ur(t,e,n,r,o,s);return Jn.bondDoubleStereoBold(t.paper,m,f,p,t.options,s,sr(t.options,r,o))}(l,n,r,e,c,d,h,o):function(t,e,n,r,o,i,a){var s=r.b.stereo===dt.PATTERN.STEREO.CIS_TRANS,u=e.p,l=n.p,c=e.norm,d=s?0:r.doubleBondShift,h=t.options,f=h.bondSpace/2,p=f+d*f,m=d*f-f,v=u.addScaled(c,p),g=l.addScaled(c,p),y=u.addScaled(c,m),b=l.addScaled(c,m);return d>0?(o&&(v=v.addScaled(e.dir,h.bondSpace*lr(e.rightCos,e.rightSin))),i&&(g=g.addScaled(e.dir,-h.bondSpace*lr(n.leftCos,n.leftSin)))):d<0&&(o&&(y=y.addScaled(e.dir,h.bondSpace*lr(e.leftCos,e.leftSin))),i&&(b=b.addScaled(e.dir,-h.bondSpace*lr(n.rightCos,n.rightSin)))),Jn.bondDouble(t.paper,v,y,g,b,s,h,a)}(l,n,r,e,d,h,o);break;case dt.PATTERN.TYPE.TRIPLE:u=Jn.bondTriple(l.paper,n,r,l.options,o);break;case dt.PATTERN.TYPE.AROMATIC:var f,p;u=n.loop>=0&&(null===(f=c.loops.get(n.loop))||void 0===f?void 0:f.aromatic)||r.loop>=0&&(null===(p=c.loops.get(r.loop))||void 0===p?void 0:p.aromatic)?Jn.bondSingle(l.paper,n,r,l.options,o):dr(l,n,r,e,d,h,o);break;case dt.PATTERN.TYPE.SINGLE_OR_DOUBLE:u=function(t,e,n,r){var o=e.p,i=n.p,a=t.options,s=$.dist(o,i)/Number((a.bondSpace+a.lineWidth).toFixed());return 1&s||(s+=1),Jn.bondSingleOrDouble(t.paper,e,n,s,a,r)}(l,(s=Vn.updateHalfBondCoordinates(n,r,1))[0],s[1],o);break;case dt.PATTERN.TYPE.SINGLE_OR_AROMATIC:u=dr(l,n,r,e,d,h,o);break;case dt.PATTERN.TYPE.DOUBLE_OR_AROMATIC:u=dr(l,(s=Vn.updateHalfBondCoordinates(n,r,-1))[0],s[1],e,d,h,o);break;case dt.PATTERN.TYPE.ANY:s=Vn.updateHalfBondCoordinates(n,r,-1),u=Jn.bondAny(l.paper,s[0],s[1],l.options,o);break;case dt.PATTERN.TYPE.HYDROGEN:s=Vn.updateHalfBondCoordinates(n,r,1),u=Jn.bondHydrogen(l.paper,s[0],s[1],l.options,o);break;case dt.PATTERN.TYPE.DATIVE:u=Jn.bondDative(l.paper,n,r,l.options,o);break;default:throw new Error("Bond type "+e.b.type+" not supported")}if(u){var m=l.options.previewOpacity;u.attr({opacity:e.b.isPreview?m:1})}return u}(t,this,c,d,h),this.rbb=Vn.relBox(this.path.getBBox()),t.addReObjectPath(jn.bondSkeleton,this.visel,this.path,null,!0);var f={};f.path=function(t,e,n,r){var o=n.p,i=r.p,a=i.add(o).scaled(.5),s=i.sub(o).normalized(),u=s.rotateSC(1,0),l=[],c=t.options.lineWidth,d=t.options.bondSpace/2,h=c,f=2*c,p=1.5*d,m=1.5*d,v=3*d,g=.2;switch(e.b.reactingCenterStatus){case dt.PATTERN.REACTING_CENTER.NOT_CENTER:l.push(a.addScaled(u,v).addScaled(s,g*v)),l.push(a.addScaled(u,-v).addScaled(s,-.2*v)),l.push(a.addScaled(u,v).addScaled(s,-.2*v)),l.push(a.addScaled(u,-v).addScaled(s,g*v));break;case dt.PATTERN.REACTING_CENTER.CENTER:l.push(a.addScaled(u,v).addScaled(s,g*v).addScaled(s,h)),l.push(a.addScaled(u,-v).addScaled(s,-.2*v).addScaled(s,h)),l.push(a.addScaled(u,v).addScaled(s,g*v).addScaled(s,-h)),l.push(a.addScaled(u,-v).addScaled(s,-.2*v).addScaled(s,-h)),l.push(a.addScaled(s,p).addScaled(u,m)),l.push(a.addScaled(s,-p).addScaled(u,m)),l.push(a.addScaled(s,p).addScaled(u,-m)),l.push(a.addScaled(s,-p).addScaled(u,-m));break;case dt.PATTERN.REACTING_CENTER.MADE_OR_BROKEN:l.push(a.addScaled(u,v).addScaled(s,f)),l.push(a.addScaled(u,-v).addScaled(s,f)),l.push(a.addScaled(u,v).addScaled(s,-f)),l.push(a.addScaled(u,-v).addScaled(s,-f));break;case dt.PATTERN.REACTING_CENTER.ORDER_CHANGED:l.push(a.addScaled(u,v)),l.push(a.addScaled(u,-v));break;case dt.PATTERN.REACTING_CENTER.MADE_OR_BROKEN_AND_CHANGED:l.push(a.addScaled(u,v).addScaled(s,f)),l.push(a.addScaled(u,-v).addScaled(s,f)),l.push(a.addScaled(u,v).addScaled(s,-f)),l.push(a.addScaled(u,-v).addScaled(s,-f)),l.push(a.addScaled(u,v)),l.push(a.addScaled(u,-v));break;default:return null}return Jn.reactingCenter(t.paper,l,t.options)}(r,this,c,d),f.path&&(f.rbb=Vn.relBox(f.path.getBBox()),t.addReObjectPath(jn.data,this.visel,f.path,null,!0));var p={};p.path=function(t,e,n,r){var o=t.options,i=null;if(e.b.topology===dt.PATTERN.TOPOLOGY.RING)i="rng";else{if(e.b.topology!==dt.PATTERN.TOPOLOGY.CHAIN)return null;i="chn"}var a=n.p,s=r.p,u=s.add(a).scaled(.5),l=s.sub(a).normalized().rotateSC(1,0),c=o.lineWidth;e.doubleBondShift>0?l=l.scaled(-e.doubleBondShift):0===e.doubleBondShift&&(c+=o.bondSpace/2);var d=new $(2,1).scaled(o.bondSpace);e.b.type===dt.PATTERN.TYPE.TRIPLE&&(c+=o.bondSpace);var h=u.add(new $(l.x*(d.x+c),l.y*(d.y+c)));return Jn.topologyMark(t.paper,h,i,o)}(r,this,c,d),p.path&&(p.rbb=Vn.relBox(p.path.getBBox()),t.addReObjectPath(jn.data,this.visel,p.path,null,!0)),this.setHover(this.hover,r);var m=null,v=.6*n.subFontSize;n.showBondIds&&(m=hr(e,l,c,d,v,.5,.5,c.norm),t.addReObjectPath(jn.indices,this.visel,m)),n.showHalfBondIds&&(m=hr(this.b.hb1,l,c,d,v,.8,.2,c.norm),t.addReObjectPath(jn.indices,this.visel,m),m=hr(this.b.hb2,l,c,d,v,.2,.8,d.norm),t.addReObjectPath(jn.indices,this.visel,m)),n.showLoopIds&&!n.showBondIds&&(m=hr(c.loop,l,c,d,v,.5,.5,d.norm),t.addReObjectPath(jn.indices,this.visel,m),m=hr(d.loop,l,c,d,v,.5,.5,c.norm),t.addReObjectPath(jn.indices,this.visel,m));var g=t.molecule.highlights,y=!1,b="";if(g.forEach((function(t){var n,r=null===(n=t.bonds)||void 0===n?void 0:n.includes(e);y=y||r,r&&(b=t.color)})),y){var w={fill:b,stroke:b,"stroke-width":7*n.lineattr["stroke-width"],"stroke-linecap":"round"},x=gt.obj2scaled(this.b.center,t.render.options),E=function(t,e,n){var r={x:e.p.x,y:e.p.y},o={x:n.p.x,y:n.p.y},i=t.render.paper,a="M".concat(r.x,",").concat(r.y," L").concat(o.x,",").concat(o.y);return i.path(a)}(t,c,d);E.attr(w),t.addReObjectPath(jn.hovering,this.visel,E,x,!0)}i.cip&&(this.cip=Vn.drawCIPLabel({atomOrBond:i,position:i.center,restruct:r.ctab,visel:this.visel}))}}}}],[{key:"isSelectable",value:function(){return!0}},{key:"bondRecalc",value:function(t,e,n){var r=e.render,o=e.atoms.get(t.b.begin),i=e.atoms.get(t.b.end);if(o&&i&&void 0!==t.b.hb1&&void 0!==t.b.hb2){var a=gt.obj2scaled(o.a.pp,r.options),s=gt.obj2scaled(i.a.pp,r.options),u=e.molecule.halfBonds.get(t.b.hb1),l=e.molecule.halfBonds.get(t.b.hb2);null!=u&&u.dir&&null!=l&&l.dir&&(u.p=o.getShiftedSegmentPosition(n,u.dir),l.p=i.getShiftedSegmentPosition(n,l.dir),t.b.center=$.lc2(o.a.pp,.5,i.a.pp,.5),t.b.len=$.dist(a,s),t.b.sb=5*n.lineWidth,t.b.sa=Math.max(t.b.sb,t.b.len/2-2*n.lineWidth),t.b.angle=180*Math.atan2(u.dir.y,u.dir.x)/Math.PI)}}}]),u}(zn);function ir(t,e,n,r){return t.neighbors.findIndex((function(t){var o=r.molecule.halfBonds.get(t);if(!o||o.bid===e)return!1;var i=r.bonds.get(o.bid);return!!i&&(i.b.type===dt.PATTERN.TYPE.SINGLE&&i.b.stereo===dt.PATTERN.STEREO.UP?i.b.end===o.begin||i.boldStereo&&n:!(i.b.type!==dt.PATTERN.TYPE.DOUBLE||i.b.stereo!==dt.PATTERN.STEREO.NONE||!n||!i.boldStereo))}))}function ar(t,e,n){var r,o,i=[e.b.begin,e.b.end].map((function(e){var r=n.molecule.atoms.get(e);if(!r)return-1;var o=ir(r,t,!0,n);return o<0?-1:r.neighbors[o]}));e.neihbid1=null!==(r=n.atoms.get(e.b.begin))&&void 0!==r&&r.showLabel?-1:i[0],e.neihbid2=null!==(o=n.atoms.get(e.b.end))&&void 0!==o&&o.showLabel?-1:i[1]}function sr(t,e,n){var r,o,i="#000";if(0===e.b.stereo)return i;var a=null===(r=n.atoms.get(e.b.begin))||void 0===r?void 0:r.stereoLabel,s=null===(o=n.atoms.get(e.b.end))||void 0===o?void 0:o.stereoLabel,u="";return a&&!s?u=a:!a&&s&&(u=s),u&&t.colorStereogenicCenters!==Fn.Off&&t.colorStereogenicCenters!==Fn.LabelsOnly?er(t,u):i}function ur(t,e,n,r,o,i){var a=t.options,s=cr(e,r.neihbid1,a.stereoBond,o),u=cr(n,r.neihbid2,a.stereoBond,o),l=s[0],c=s[1],d=u[0],h=u[1];return Jn.bondSingleStereoBold(t.paper,l,c,d,h,a,i,sr(a,r,o))}function lr(t,e){return e<0||Math.abs(t)>.9?0:e/(1-t)}function cr(t,e,n,r){var o=r.halfBonds.get(e),i=$.dot(t.dir,o.dir),a=$.cross(t.dir,o.dir),s=Math.sqrt(.5*(1-i)),u=o.dir.rotateSC((a>=0?-1:1)*s,Math.sqrt(.5*(1+i))),l=t.p.addScaled(u,.7*n/(s+.3)),c=t.p.addScaled(u.negated(),.7*n/(s+.3));return a>0?[l,c]:[c,l]}function dr(t,e,n,r,o,i,a){var s=[.125,.125,.005,.125],u=0,l=null,c=t.options,d=r.doubleBondShift;r.b.type===dt.PATTERN.TYPE.SINGLE_OR_AROMATIC&&(u=d>0?1:2,l=s.map((function(t){return t*c.scale}))),r.b.type===dt.PATTERN.TYPE.DOUBLE_OR_AROMATIC&&(u=3,l=s.map((function(t){return t*c.scale})));var h=function(t,e,n,r,o,i,a,s){var u=t.p,l=e.p,c=t.norm,d=i/2,h=d+n*d,f=n*d-d,p=u.addScaled(c,h),m=l.addScaled(c,h),v=u.addScaled(c,f),g=l.addScaled(c,f);return n>0?(r&&(p=p.addScaled(t.dir,i*lr(t.rightCos,t.rightSin))),o&&(m=m.addScaled(t.dir,-i*lr(e.leftCos,e.leftSin)))):n<0&&(r&&(v=v.addScaled(t.dir,i*lr(t.leftCos,t.leftSin))),o&&(g=g.addScaled(t.dir,-i*lr(e.rightCos,e.rightSin)))),Jn.aromaticBondPaths(p,v,m,g,a,s)}(e,n,d,o,i,c.bondSpace,u,l);return Jn.bondAromatic(t.paper,h,d,c,a)}function hr(t,e,n,r,o,i,a,s){var u=$.lc(n.p,i,r.p,a,s,o),l=e.text(u.x,u.y,t.toString()),c=Vn.relBox(l.getBBox());return Jn.recenterText(l,c),l}function fr(t,e){if(!e.b.hb1&&0!==e.b.hb1||!e.b.hb2&&0!==e.b.hb2)return 0;var n=t.halfBonds.get(e.b.hb1),r=t.halfBonds.get(e.b.hb2);if(!n||!r)return 0;var o=(n.leftSin>.3?1:0)+(r.rightSin>.3?1:0),i=(r.leftSin>.3?1:0)+(n.rightSin>.3?1:0);return o>i?-1:o.3?1:0)+(n.rightSin>.3?1:0)==1?1:0}var pr=new WeakMap,mr=function(t){(0,f.Z)(s,t);var e,n,r=(e=s,n=function(){if("undefined"==typeof Reflect||!Reflect.construct)return!1;if(Reflect.construct.sham)return!1;if("function"==typeof Proxy)return!0;try{return Boolean.prototype.valueOf.call(Reflect.construct(Boolean,[],(function(){}))),!0}catch(t){return!1}}(),function(){var t,r=(0,m.Z)(e);if(n){var o=(0,m.Z)(this).constructor;t=Reflect.construct(r,arguments,o)}else t=r.apply(this,arguments);return(0,p.Z)(this,t)});function s(){var 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o=$.diff(e[1],e[0]),i=o.x/2,a=o.y/2,s=t.paper.ellipse(H(e[0].x+i),H(e[0].y+a),H(Math.abs(i)+n/8),H(Math.abs(a)+n/8));if(r.push({path:this.getHoverPathStyle(s,t,!0),stylesApplied:!0}),Math.abs(i)-n/8>0&&Math.abs(a)-n/8>0){var u=t.paper.ellipse(H(e[0].x+i),H(e[0].y+a),H(Math.abs(i)-n/8),H(Math.abs(a)-n/8));r.push({path:this.getHoverPathStyle(u,t,!1),stylesApplied:!0})}break;case zt.rectangle:var l=t.paper.rect(H(Math.min(e[0].x,e[1].x)-n/8),H(Math.min(e[0].y,e[1].y)-n/8),H(Math.max(e[0].x,e[1].x)-Math.min(e[0].x,e[1].x)+n/4),H(Math.max(e[0].y,e[1].y)-Math.min(e[0].y,e[1].y)+n/4));if(r.push({path:this.getHoverPathStyle(l,t,!0),stylesApplied:!0}),Math.max(e[0].x,e[1].x)-Math.min(e[0].x,e[1].x)-n/4>0&&Math.max(e[0].y,e[1].y)-Math.min(e[0].y,e[1].y)-n/4>0){var c=t.paper.rect(H(Math.min(e[0].x,e[1].x)+n/8),H(Math.min(e[0].y,e[1].y)+n/8),H(Math.max(e[0].x,e[1].x)-Math.min(e[0].x,e[1].x)-n/4),H(Math.max(e[0].y,e[1].y)-Math.min(e[0].y,e[1].y)-n/4));r.push({path:this.getHoverPathStyle(c,t,!1),stylesApplied:!0})}break;case zt.line:var d=[],h=Math.atan((e[1].y-e[0].y)/(e[1].x-e[0].x)),f={x:0,y:0},p={x:0,y:0},m=e[0].x>e[1].x?-1:1;f.x=e[0].x-m*(n/8*Math.cos(h)),f.y=e[0].y-m*(n/8*Math.sin(h)),p.x=e[1].x+m*(n/8*Math.cos(h)),p.y=e[1].y+m*(n/8*Math.sin(h)),d.push("M",f.x+m*n/8*Math.sin(h),f.y-m*n/8*Math.cos(h)),d.push("L",p.x+m*n/8*Math.sin(h),p.y-m*n/8*Math.cos(h)),d.push("L",p.x-m*n/8*Math.sin(h),p.y+m*n/8*Math.cos(h)),d.push("L",f.x-m*n/8*Math.sin(h),f.y+m*n/8*Math.cos(h)),d.push("L",f.x+m*n/8*Math.sin(h),f.y-m*n/8*Math.cos(h)),r.push({path:this.getHoverPathStyle(t.paper.path(d),t,!0),stylesApplied:!0});break;default:throw new Error("Unsupported shape type")}return r}},{key:"drawHover",value:function(t){var e=this.hoverPath(t).map((function(e){return e.stylesApplied?e.path:e.path.attr(t.options.hoverStyle)}));return t.ctab.addReObjectPath(jn.hovering,this.visel,e),e}},{key:"makeSelectionPlate",value:function(t,e,n){var r=this,o=this.item.pos.map((function(e){return gt.obj2scaled(e,t.render.options)||new $})),i=this.getReferencePoints(),a=t.render.options.scale;return this.selectionSet=t.render.paper.set(),this.selectionPointsSet=t.render.paper.set(),this.selectionSet.push(Ir(this.item.mode,e,o).attr(n.selectionStyleSimpleObject)),i.forEach((function(e){var n=gt.obj2scaled(e,t.render.options);r.selectionPointsSet.push(t.render.paper.circle(n.x,n.y,a/8).attr({fill:"black"}))})),t.addReObjectPath(jn.selectionPlate,this.visel,this.selectionPointsSet),this.selectionSet}},{key:"togglePoints",value:function(t){var e,n;t?null===(e=this.selectionPointsSet)||void 0===e||e.show():null===(n=this.selectionPointsSet)||void 0===n||n.hide()}},{key:"show",value:function(t,e){var n=t.render,r=this.item.pos.map((function(t){return gt.obj2scaled(t,e)||new $})),o=Ir(this.item.mode,n.paper,r),i=e.offset;null!=i&&o.translateAbs(i.x,i.y),this.visel.add(o,Et.fromRelBox(Vn.relBox(o.getBBox())))}}],[{key:"isSelectable",value:function(){return!0}}]),a}(zn);function Zr(t,e){var n;if((e.xMath.max(t[0].x,t[1].x))&&(e.yMath.max(t[0].y,t[1].y)))n=Math.min($.dist(t[0],e),$.dist(t[1],e));else{var r=$.dist(t[0],t[1]),o=$.dist(t[0],e),i=$.dist(t[1],e),a=(r+o+i)/2;n=2/r*Math.sqrt(a*(a-r)*(a-o)*(a-i))}return n}function Ir(t,e,n){var r;switch(t){case zt.ellipse:r=Jn.ellipse(e,n);break;case zt.rectangle:r=Jn.rectangle(e,n);break;case zt.line:r=Jn.line(e,n);break;default:throw new Error("Unsupported shape type")}return r}var Mr=function(t){(0,f.Z)(a,t);var e,n,r=(e=a,n=function(){if("undefined"==typeof Reflect||!Reflect.construct)return!1;if(Reflect.construct.sham)return!1;if("function"==typeof Proxy)return!0;try{return Boolean.prototype.valueOf.call(Reflect.construct(Boolean,[],(function(){}))),!0}catch(t){return!1}}(),function(){var t,r=(0,m.Z)(e);if(n){var o=(0,m.Z)(this).constructor;t=Reflect.construct(r,arguments,o)}else t=r.apply(this,arguments);return(0,p.Z)(this,t)});function a(t){var e;return(0,o.Z)(this,a),(e=r.call(this,"loop")).loop=t,e.centre=new $,e.radius=new $,e}return(0,i.Z)(a,[{key:"show",value:function(t,e,n){var r=this,o=t.render.paper,i=t.molecule,a=this.loop;this.centre=new $,a.hbs.forEach((function(e){var o=i.halfBonds.get(e),s=t.bonds.get(o.bid),u=gt.obj2scaled(t.atoms.get(o.begin).a.pp,n);s.b.type!==dt.PATTERN.TYPE.AROMATIC&&(a.aromatic=!1),r.centre.add_(u)})),a.convex=!0;for(var s=0;s0&&(a.convex=!1)}if(this.centre=this.centre.scaled(1/a.hbs.length),this.radius=-1,a.hbs.forEach((function(e){var o=i.halfBonds.get(e),a=gt.obj2scaled(t.atoms.get(o.begin).a.pp,n),s=gt.obj2scaled(t.atoms.get(o.end).a.pp,n),u=$.diff(s,a).rotateSC(1,0).normalized(),l=$.dot($.diff(a,r.centre),u);r.radius=r.radius<0?l:Math.min(r.radius,l)})),this.radius*=.7,a.aromatic){var c=null;if(a.convex&&n.aromaticCircle)c=o.circle(this.centre.x,this.centre.y,this.radius).attr({stroke:"#000","stroke-width":n.lineattr["stroke-width"]});else{for(var d="",h=0;he.getRowWidth(t)?n:t}),t[0]),a=i[i.length-1],s=a.getBBox().x+a.getBBox().width,u=t[t.length-1],l=Math.max.apply(Math,(0,h.Z)(u.map((function(t){return t.getBBox().y+t.getBBox().height}))));return{p0:new $(n,o),p1:new $(s,l)}}},{key:"getRowWidth",value:function(t){return t.reduce((function(t,e){return t+e.getBBox().width}),0)}},{key:"drawHover",value:function(t){if(!this.paths.length)return null;var e=this.hoverPath(t).attr(t.options.hoverStyle);return t.ctab.addReObjectPath(jn.hovering,this.visel,e),e}},{key:"makeSelectionPlate",value:function(t,e,n){return this.paths.length&&e?this.hoverPath(t.render).attr(n.selectionStyle):null}},{key:"show",value:function(t,e,n){var o=this,i=t.render,s=i.paper,u=gt.obj2scaled(this.item.position,n),l=0;this.paths=[];var c=this.item.content?JSON.parse(this.item.content):null;c&&(c.blocks.forEach((function(t){var e=o.getRanges(t,n),i=0,c=[];e.forEach((function(e){var o=(0,r.Z)(e,3),d=o[0],h=o[1],f=o[2];t.text=t.text.replace(/[^\S\r\n]/g," ");var p=s.text(u.x,u.y,t.text.substring(d,h+1)||" ").attr(function(t){for(var e=1;e=t.length?{done:!0}:{done:!1,value:t[r++]}},e:function(t){throw t},f:o}}throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method.")}var i,a=!0,s=!1;return{s:function(){n=n.call(t)},n:function(){var t=n.next();return a=t.done,t},e:function(t){s=!0,i=t},f:function(){try{a||null==n.return||n.return()}finally{if(s)throw i}}}}function $r(t,e){(null==e||e>t.length)&&(e=t.length);for(var n=0,r=new Array(e);n0;){var i=r.pop();o.add(i);var a=this.atoms.get(i);a&&(a.component>=0&&e.add(a.component),a.a.neighbors.forEach((function(t){var e=n.molecule.halfBonds.get(t);if(e){var i=e.end;o.has(i)||r.push(i)}})))}return o}},{key:"addConnectedComponent",value:function(t){var e=this,n=this.connectedComponents.add(t),r=new et,o=this.getConnectedComponent(Array.from(t),r);r.delete(n);var i=-1;return o.forEach((function(t){var r=e.atoms.get(t);r&&(r.component=n,-1!==r.a.rxnFragmentType&&(i=r.a.rxnFragmentType))})),this.ccFragmentType.set(n,i),n}},{key:"removeConnectedComponent",value:function(t){var e=this;return this.connectedComponents.get(t).forEach((function(t){var n=e.atoms.get(t);n&&(n.component=-1)})),this.connectedComponents.delete(t)}},{key:"assignConnectedComponents",value:function(){var t=this;this.atoms.forEach((function(e,n){if(!(e.component>=0)){var r=new et,o=t.getConnectedComponent(n,r);r.forEach((function(e){t.removeConnectedComponent(e)})),t.addConnectedComponent(o)}}))}},{key:"initLayers",value:function(){for(var t in jn)this.layers[jn[t]]=this.render.paper.rect(0,0,10,10).attr({class:t+"Layer",fill:"#000",opacity:"0.0"}).toFront()}},{key:"addReObjectPath",value:function(t,e,n){var r=this,o=arguments.length>3&&void 0!==arguments[3]?arguments[3]:null,i=arguments.length>4&&void 0!==arguments[4]&&arguments[4];n&&this.layers[t].node.parentNode&&(Array.isArray(n)?n:[n]).forEach((function(n){var a=r.render.options.offset,s=i?Et.fromRelBox(Vn.relBox(n.getBBox())):null,u=o&&s?s.translate(o.negated()):null;null!==a&&(n.translateAbs(a.x,a.y),s=s?s.translate(a):null),e.add(n,s,u),n.insertBefore(r.layers[jn[t]])}))}},{key:"clearMarks",value:function(){var e=this;Object.keys(t.maps).forEach((function(t){e[t+"Changed"]=new Map})),this.structChanged=!1}},{key:"markItemRemoved",value:function(){this.structChanged=!0}},{key:"markBond",value:function(t,e){this.markItem("bonds",t,e)}},{key:"markAtom",value:function(t,e){this.markItem("atoms",t,e)}},{key:"markItem",value:function(t,e,n){var r=this[t+"Changed"],o=r.has(e)?Math.max(n,r.get(e)):n;r.set(e,o),this[t].has(e)&&this.clearVisel(this[t].get(e).visel)}},{key:"clearVisel",value:function(t){t.paths.forEach((function(t){t.remove()})),t.clear()}},{key:"eachItem",value:function(e){var n=this;Object.keys(t.maps).forEach((function(t){n[t].forEach(e)}))}},{key:"getSelectionBoxCenter",value:function(t){var e,n,r,o=null,i=qr(null!==(n=t.atoms)&&void 0!==n?n:[]);try{for(i.s();!(r=i.n()).done;){var s=r.value,u=this.atoms.get(s).a.pp,l=new Et(u,u);o=null==o?l:Et.union(o,l)}}catch(t){i.e(t)}finally{i.f()}var c=function(t){for(var e=1;e0}))})),this.sgroups.forEach((function(t){n.clearVisel(t.visel),t.hovering=null,t.selectionPlate=null})),this.frags.forEach((function(t){n.clearVisel(t.visel)})),this.rgroups.forEach((function(t){n.clearVisel(t.visel)})),e&&(this.clearConnectedComponents(),this.molecule.initHalfBonds(),this.molecule.initNeighbors());var r=Array.from(this.atomsChanged.keys());this.molecule.updateHalfBonds(r),this.molecule.sortNeighbors(r),this.assignConnectedComponents(),this.initialized=!0,this.showMonomers(),this.showPolymerBonds(),this.verifyLoops();var o=e||this.structChanged;return o&&this.updateLoops(),this.showAtoms(),this.showBonds(),this.showRgroupAttachmentPoints(),o&&this.showLoops(),this.showReactionSymbols(),this.showSGroups(),this.showFragments(),this.showRGroups(),this.showEnhancedFlags(),this.showSimpleObjects(),this.showTexts(),this.clearMarks(),!0}},{key:"updateLoops",value:function(){var t=this;this.reloops.forEach((function(e){t.clearVisel(e.visel)}));var e=this.molecule.findLoops();e.bondsToMark.forEach((function(e){t.markBond(e,1)})),e.newLoops.forEach((function(e){t.reloops.set(e,new Mr(t.molecule.loops.get(e)))}))}},{key:"showLoops",value:function(){var t=this,e=this.render.options;this.reloops.forEach((function(n,r){n.show(t,r,e)}))}},{key:"showSimpleObjects",value:function(){var t=this,e=this.render.options;this.simpleObjectsChanged.forEach((function(n,r){var o=t.simpleObjects.get(r);o&&o.show(t,e)}))}},{key:"showTexts",value:function(){var t=this,e=this.render.options;this.textsChanged.forEach((function(n,r){var o=t.texts.get(r);o&&o.show(t,r,e)}))}},{key:"showReactionSymbols",value:function(){var t=this,e=this.render.options;this.rxnArrowsChanged.forEach((function(n,r){var o=t.rxnArrows.get(r);o&&o.show(t,r,e)})),this.rxnPlusesChanged.forEach((function(n,r){var o=t.rxnPluses.get(r);o&&o.show(t,r,e)}))}},{key:"showSGroups",value:function(){var t=this;this.molecule.sGroupForest.getSGroupsBFS().reverse().forEach((function(e){var n=t.sgroups.get(e);n&&n.show(t)}))}},{key:"showFragments",value:function(){var t=this;this.frags.forEach((function(e,n){var r=e.draw(t.render,n);r&&t.addReObjectPath(jn.data,e.visel,r,null,!0)}))}},{key:"showRGroups",value:function(){var t=this,e=this.render.options;this.rgroups.forEach((function(n,r){n.show(t,r,e)}))}},{key:"loopRemove",value:function(t){var e=this,n=this.reloops.get(t);if(n){this.clearVisel(n.visel);var r=[];n.loop.hbs.forEach((function(t){var n=e.molecule.halfBonds.get(t);n&&(n.loop=-1,e.markBond(n.bid,1),e.markAtom(n.begin,1),r.push(n.bid))})),this.reloops.delete(t),this.molecule.loops.delete(t)}}},{key:"verifyLoops",value:function(){var t=this;this.reloops.forEach((function(e,n){e.isValid(t.molecule,n)||t.loopRemove(n)}))}},{key:"getRGroupAttachmentPointsVBoxByAtomIds",value:function(t){var e=this,n=null;return t.forEach((function(t){var r,o=e.molecule.getRGroupAttachmentPointsByAtomId(t).reduce((function(t,n){var r=e.rgroupAttachmentPoints.get(n);u()(null!=r);var o=r.getVBoxObj(e.render);return t&&o?Et.union(t,o):o}),null);n=n&&o?Et.union(n,o):null!==(r=n)&&void 0!==r?r:o})),n}},{key:"showRgroupAttachmentPoints",value:function(){var t=this;this.rgroupAttachmentPoints.forEach((function(e,n){var r=t.rgroupAttachmentPoints.get(n);null!=r&&r.visel&&t.clearVisel(r.visel);var o=null==r?void 0:r.item.atomId,i=t.molecule.getGroupFromAtomId(o);Boolean(null==i?void 0:i.isContracted())||null==r||r.show(t)}))}},{key:"showAtoms",value:function(){var t=this,e=this.render.options;this.atomsChanged.forEach((function(n,r){var o=t.atoms.get(r);o&&o.show(t,r,e)}))}},{key:"showMonomers",value:function(){var t=this;this.monomers.forEach((function(e){e.remove(),e.show(t.render.theme)}))}},{key:"showPolymerBonds",value:function(){this.polymerBonds.forEach((function(t){t.remove(),t.show()}))}},{key:"showEnhancedFlags",value:function(){var t=this,e=this.render.options;this.enhancedFlagsChanged.forEach((function(n,r){var o=t.enhancedFlags.get(r);o&&o.show(t,r,e)}))}},{key:"showBonds",value:function(){var t=this,e=this.render.options;this.bondsChanged.forEach((function(n,r){var o=t.bonds.get(r);o&&o.show(t,r,e)}))}},{key:"setSelection",value:function(e){var n=this,o=[];Object.keys(t.maps).forEach((function(i){var a=n[i].values(),s=(0,r.Z)(a,1)[0];(t.maps[i].isSelectable()||s instanceof Sr)&&n[i].forEach((function(t,r){var a,s;if(t instanceof tr){var u,l,c=qr(t.a.sgs.values());try{for(c.s();!(l=c.n()).done;)u=l.value}catch(t){c.e(t)}finally{c.f()}o.push({selected:t.selected,sgroup:u})}if(t instanceof Sr&&Lt.isContractedFunctionalGroup(null==t||null===(a=t.item)||void 0===a?void 0:a.id,n.molecule.functionalGroups)){var d=o.filter((function(e){var n;return e.sgroup===(null==t||null===(n=t.item)||void 0===n?void 0:n.id)}));t.selected=d.length>0&&d[0].selected}var h=null!=e&&e[i]?e[i].indexOf(r)>-1:t.selected;null===e&&(h=!1),n.showItemSelection(t,h),null===(s=t.selectionPlate)||void 0===s||s.toBack()}))}))}},{key:"showItemSelection",value:function(t,e){var n=function(t){var e,n,r,o;return t&&null!==t.selectionPlate&&(!(null!==(e=t.selectionPlate)&&void 0!==e&&e.items)&&!(null!==(n=t.selectionPlate)&&void 0!==n&&n.removed)||Array.isArray(null===(r=t.selectionPlate)||void 0===r?void 0:r.items)&&!(null!==(o=t.selectionPlate[0])&&void 0!==o&&o.removed))}(t);if(t.selected=e,t instanceof Rr&&(t.sgroup.selected=e),e){if(!n){var r=this.render,o=r.options,i=r.paper;t.selectionPlate=t.makeSelectionPlate(this,i,o),this.addReObjectPath(jn.selectionPlate,t.visel,t.selectionPlate),"function"==typeof t.makeAdditionalInfo&&(t.additionalInfo=t.makeAdditionalInfo(this),this.addReObjectPath(jn.additionalInfo,t.visel,t.additionalInfo))}var a,s;t.selectionPlate&&(t.selectionPlate.show(),null===(a=t.additionalInfo)||void 0===a||a.show(),null===(s=t.cip)||void 0===s||s.rectangle.attr({fill:"#7f7",stroke:"#7f7"}),t.togglePoints&&t.togglePoints(!0))}else if(n&&t.selectionPlate){var u,l;t.selectionPlate.hide(),t.togglePoints&&t.togglePoints(!1),null===(u=t.additionalInfo)||void 0===u||u.hide(),null===(l=t.cip)||void 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n.action=n.action.mergeWith(aa(t,e.type,[i.begin,i.end],e.attrs)),n.selection.bonds.push(r),n}),{action:new Di,selection:{atoms:n,bonds:[]}})}(e,n,r,o);var i,a=(i=e.molecule,(o.bonds||[]).reduce((function(t,e){var n=i.bonds.get(e);return t.concat([n.begin,n.end])}),[])),s=(0,B.uniq)(r.concat(a));return t===Rt.Fragment?fa(e,n,s,Array.from(e.atoms.keys())):t===Rt.Multifragment?function(t,e,n){var r=va(t.molecule,n);return{action:aa(t,e.type,n,e.attrs),selection:{atoms:n,bonds:r}}}(e,n,s):t===Rt.Group?fa(e,n,s,s):t===Rt.Atom?function(t,e,n){return n.reduce((function(n,r){return n.action=n.action.mergeWith(aa(t,e.type,[r],e.attrs)),n}),{action:new Di,selection:{atoms:n,bonds:[]}})}(e,n,s):{action:aa(e,n.type,s,n.attrs)}}function fa(t,e,n,r){var o=new et(n.map((function(e){return t.atoms.get(e).a.fragment})));return Array.from(o).reduce((function(n,o){var i=r.reduce((function(e,n){var r=t.atoms.get(n).a;return o===r.fragment&&e.push(n),e}),[]),a=va(t.molecule,i);return n.action=n.action.mergeWith(aa(t,e.type,i,e.attrs)),n.selection.atoms=n.selection.atoms.concat(i),n.selection.bonds=n.selection.bonds.concat(a),n}),{action:new Di,selection:{atoms:[],bonds:[]}})}function pa(t,e,n){var r=Yi(e,n);return r.length>0&&(r.forEach((function(e){t.addOp(new Pi(e,n))})),!0)}function ma(t,e,n){var r=e.molecule,o=new Map;n.forEach((function(t){Yi(e,t).forEach((function(t){o.set(t,o.has(t)?o.get(t)+1:1)}))})),o.forEach((function(n,o){var i=e.sgroups.get(o).item;if(Zt.getAtoms(e.molecule,i).length===n){var a=r.sgroups.get(o);t.mergeWith(la(o,a.getAttrs())),t.addOp(new Ti(o)),a.getAttachmentPoints().forEach((function(e){t.addOp(new ia(o,e))})),t.addOp(new Ci(o))}}))}function va(t,e){var n=new et(e);return Array.from(t.bonds.keys()).filter((function(e){var r=t.bonds.get(e);return n.has(r.begin)&&n.has(r.end)}))}function ga(t,e){var n=Object.keys(t);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(t);e&&(r=r.filter((function(e){return 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r.perform(t)}function qa(t,e){var n=function(t,e){var n=t.rgroupAttachmentPoints.get(e);u()(null!=n);var r=n.atomId,o=t.atoms.get(r),i=null==o?void 0:o.attachmentPoints,a=Q.None;if(i===Q.BothSides){var s=n.type;"primary"===s?a=Q.SecondSideOnly:"secondary"===s&&(a=Q.FirstSideOnly)}return{atomId:r,newAttachmentPoints:a}}(t.molecule,e),r=Sa(t,n.atomId,{attachmentPoints:n.newAttachmentPoints},null),o=new Di;return o.addOp(new ei(e)),o.perform(t).mergeWith(r)}function $a(t,e){return Qa(t,{atoms:[e]})}function Xa(t,e){var n=arguments.length>2&&void 0!==arguments[2]?arguments[2]:[],r=new Di,o=t.molecule.bonds.get(e),i=[];return r.addOp(new Bo(e)),n.includes(o.begin)||0!==Wi(t,o.begin)||(pa(r,t,o.begin)&&i.push(o.begin),r.addOp(new Ao(o.begin))),n.includes(o.end)||0!==Wi(t,o.end)||(pa(r,t,o.end)&&i.push(o.end),r.addOp(new Ao(o.end))),ma(r,t,i),(r=r.perform(t)).addOp(new Yo([o.begin,o.end]).perform(t)),r.mergeWith(xa(t,o,!1)),r.operations.reverse(),r}function Ka(t,e){var n=t.molecule.getBondFragment(e),r=Xa(t,e);return Va(t,n).mergeWith(r)}function Qa(t,e){u()(null!=!!e);var n=new Di,r=[],o=[],i=function(t){return St.reduce((function(e,n){return e[n]=t[n]||[],e}),{})}(e);i.sgroups.forEach((function(e){var n=t.sgroups.get(e).item.atoms;i.atoms=i.atoms.concat(n),t.molecule.bonds.forEach((function(t,e){n.indexOf(t.begin)>=0&&n.indexOf(t.end)>=0&&i.bonds.push(e)}))})),i.atoms=Array.from(new Set(i.atoms)),i.bonds=Array.from(new Set(i.bonds)),i.atoms.forEach((function(e){t.molecule.atomGetNeighbors(e).forEach((function(t){-1===i.bonds.indexOf(t.bid)&&(i.bonds=i.bonds.concat([t.bid]))}))}));var a=new Di;i.bonds.forEach((function(e){var n=t.molecule.getBondFragment(e);o.indexOf(n)<0&&o.push(n),a.mergeWith(Xa(t,e,i.atoms))}));var s=[];i.atoms.forEach((function(e){var i=t.molecule.atoms.get(e).fragment;o.indexOf(i)<0&&o.push(i),pa(n,t,e)&&r.push(e),n.addOp(new Ao(e)),t.molecule.getRGroupAttachmentPointsByAtomId(e).forEach((function(t){n.addOp(new ei(t)),s.push(t)}))})),ma(n,t,r),i.rxnArrows.forEach((function(t){n.addOp(new fi(t))})),i.rxnPluses.forEach((function(t){n.addOp(new ci(t))})),i.simpleObjects.forEach((function(t){n.addOp(new vi(t))})),i.texts.forEach((function(t){n.addOp(new Mi(t))}));var l=new Di;i.rgroupAttachmentPoints.forEach((function(e){s.includes(e)||l.mergeWith(qa(t,e))})),(n=n.perform(t)).mergeWith(a).mergeWith(l);for(var c=o.map((function(e){return Gt.findRGroupByFragment(t.molecule.rgroups,e)}));o.length>0;)n=Va(t,o.pop(),c).mergeWith(n);return n}function Ja(t,e,n){var r=arguments.length>3&&void 0!==arguments[3]?arguments[3]:0,o=function(t){if(1===t.sgroups.size){var e=t.sgroups.keys().next().value,n=t.sgroups.get(e);if(n.isContracted())return n.getContractedPosition(t).position}if(t.atoms.size>0){var r=1e50,o=r,i=-r,a=-o;return t.atoms.forEach((function(t){r=Math.min(r,t.pp.x),o=Math.min(o,t.pp.y),i=Math.max(i,t.pp.x),a=Math.max(a,t.pp.y)})),new $((r+i)/2,(o+a)/2)}return t.rxnArrows.size>0?t.rxnArrows.get(0).center():t.rxnPluses.size>0?t.rxnPluses.get(0).pp:t.simpleObjects.size>0?t.simpleObjects.get(0).center():t.texts.size>0?t.texts.get(0).position:new $(0,0)}(e),i=$.diff(n,o),a=new Di,s=new Map,u=new Map,l={atoms:[],bonds:[]};return e.atoms.forEach((function(e,i){u.has(e.fragment)||u.set(e.fragment,a.addOp(new Fo(null,e.fragment.properties).perform(t)).frid);var c=Object.assign(e.clone(),{fragment:u.get(e.fragment)}),d=new Oo(c,$.diff(e.pp,o).rotate(r).add(n)).perform(t);a.addOp(d),s.set(i,d.data.aid),l.atoms.push(d.data.aid),a.mergeWith(Ya(t,c.attachmentPoints,d.data.aid))})),e.frags.forEach((function(e,n){e&&(e.properties&&a.addOp(new Go(u.get(n),e.properties).perform(t)),e.stereoAtoms.forEach((function(e){return a.addOp(new Uo(u.get(n),s.get(e)).perform(t))})))})),e.bonds.forEach((function(e){var n=new ko(s.get(e.begin),s.get(e.end),e).perform(t);a.addOp(n),l.bonds.push(n.data.bid)})),l.atoms.forEach((function(e){a.addOp(new Yo([e]).perform(t))})),e.sgroups.forEach((function(n){var r=t.molecule.sgroups.newId(),o=n.atoms.map((function(t){return s.get(t)})),u=n.cloneAttachmentPoints(s);n.isNotContractible(e)&&n.setAttr("expanded",!0),da(t,n.type,o,n.data,r,u,n.pp?n.pp.add(i):null,"SUP"===n.type?n.isExpanded():null,n.data.name).operations.reverse().forEach((function(t){a.addOp(t)}))})),e.rxnArrows.forEach((function(e){a.addOp(new hi(e.pos.map((function(t){return t.add(i)})),e.mode).perform(t))})),e.rxnPluses.forEach((function(e){a.addOp(new li(e.pp.add(i)).perform(t))})),e.simpleObjects.forEach((function(e){a.addOp(new mi(e.pos.map((function(t){return t.add(i)})),e.mode).perform(t))})),e.texts.forEach((function(e){a.addOp(new Ii(e.content,e.position.add(i),e.pos.map((function(t){return t.add(i)}))).perform(t))})),e.rgroups.forEach((function(n,r){n.frags.forEach((function(e,n){a.addOp(new Xo(r,u.get(n)).perform(t))}));var o=e.rgroups.get(r).ifthen,i=e.rgroups.get(o)?o:0;a.mergeWith(ta(t,r,n.getAttrs())).mergeWith(na(t,i,n.ifthen))})),a.operations.reverse(),[a,l]}function ts(t,e,n){var r=new Di;return r.addOp(new hi(e,n)),r.perform(t)}function es(t,e,n,r,o,i){var a=new Di;return a.addOp(new ii(e,n,r,o,!1,i)),a.perform(t)}function ns(t,e){var n=new Di;return n.addOp(new fi(e)),n.perform(t)}function rs(t,e){var n=new Di;return n.addOp(new li(e).perform(t)),n}function os(t,e){var n=new Di;return n.addOp(new ci(e)),n.perform(t)}function is(t,e,n,o){var i=new Di,a=e||Xi(t.molecule);return i.mergeWith(function(t,e,n,r){var o,i=t.molecule,a=new Di;return null==e||null===(o=e.atoms)||void 0===o||o.forEach((function(t){var e=i.atoms.get(t);if(e){var o=as(e.pp,r,n);a.addOp(new Eo(t,o))}})),Qi(i,(null==e?void 0:e.atoms)||[]).forEach((function(t){if(t.pp){var e=as(t.pp,r,n);a.addOp(new Ai(t.id,e))}})),null!=e&&e.bonds&&function(t,e,n){t.forEach((function(t){var r=e.bonds.get(t);r&&r.type===dt.PATTERN.TYPE.SINGLE&&(r.stereo!==dt.PATTERN.STEREO.UP?r.stereo===dt.PATTERN.STEREO.DOWN&&n.addOp(new Ro(t,"stereo",dt.PATTERN.STEREO.UP)):n.addOp(new Ro(t,"stereo",dt.PATTERN.STEREO.DOWN)))}))}(e.bonds,i,a),a.perform(t)}(t,a,n,o)),a.rxnArrows&&i.mergeWith(function(t,e,n,o){var i=new Di;return e.forEach((function(e){var a=t.molecule.rxnArrows.get(e);if(a){var s=(0,r.Z)(a.pos,2),u=s[0],l=s[1].sub(u).oxAngle(),c=l-Math.PI/2,d="vertical"===n?-2*l:-2*c;i.addOp(new ri(e,d,a.center()));var h=as(a.center(),o,n);i.addOp(new ni(e,h))}})),i.perform(t)}(t,a.rxnArrows,n,o)),a.rxnPluses&&i.mergeWith(function(t,e,n,r){var o=new Di;return e.forEach((function(e){var i=t.molecule.rxnPluses.get(e);if(i){var a=as(i.pp,r,n);o.addOp(new si(e,a))}})),o.perform(t)}(t,a.rxnPluses,n,o)),a.texts&&i.mergeWith(function(t,e,n,r){var o=new Di;return e.forEach((function(e){var i=t.molecule.texts.get(e);if(i){var a=i.pos[0],s=i.pos[2],u=as($.centre(a,s),r,n);o.addOp(new _i(e,u))}})),o.perform(t)}(t,a.texts,n,o)),i}function as(t,e,n){var r=new $;return"horizontal"===n?r.x=e.x>t.x?2*(e.x-t.x):-2*(t.x-e.x):r.y=e.y>t.y?2*(e.y-t.y):-2*(t.y-e.y),r}function ss(t,e,n,r){var o=t.molecule,i=new Di;return e||(e=Xi(o)),e.atoms&&(e.atoms.forEach((function(t){var e=o.atoms.get(t);i.addOp(new Eo(t,us(e.pp,n,r)))})),e.sgroupData||Qi(o,e.atoms).forEach((function(t){i.addOp(new Ai(t.id,us(t.pp,n,r)))}))),e.rxnArrows&&e.rxnArrows.forEach((function(t){i.addOp(new ri(t,r,n))})),e.rxnPluses&&e.rxnPluses.forEach((function(t){var e=o.rxnPluses.get(t);i.addOp(new si(t,us(e.pp,n,r)))})),e.texts&&e.texts.forEach((function(t){var e=o.texts.get(t);i.addOp(new _i(t,us(e.position,n,r)))})),e.sgroupData&&e.sgroupData.forEach((function(t){var e=o.sgroups.get(t);i.addOp(new Ai(t,us(e.pp,n,r)))})),e.enhancedFlags&&e.enhancedFlags.forEach((function(e){var o=e,a=t.molecule.frags.get(o);i.addOp(new No(e,us(a.stereoFlagPosition||vt.getDefaultStereoFlagPosition(t.molecule,o),n,r)))})),i.perform(t)}function us(t,e,n){var r=t.sub(e);return(r=r.rotate(n)).add_(e),r.sub(t)}function ls(t,e){var n=new Di;return n.addOp(new vi(e)),n.perform(t)}function cs(t,e,n,r){var o=new Di;return o.addOp(new mi(e,n,r)),o.perform(t)}function ds(t,e,n,r,o,i){var a=new Di;return a.addOp(new bi(e,n,r,o,!1,i)),a.perform(t)}function hs(t,e){var n=Object.keys(t);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(t);e&&(r=r.filter((function(e){return Object.getOwnPropertyDescriptor(t,e).enumerable}))),n.push.apply(n,r)}return n}function fs(t){for(var e=1;e5&&void 0!==arguments[5]&&arguments[5],a=new Di,s=e.molecule,u=t.molecule,l=e.molecule.isSingleGroup(),c=u.atoms.get(n),d=n,f=null;if(o){var p=function(t,e,n){var r=new Di,o=Vi(t,e,"fragment"),i=null;if(null===n){var a=Ki(t,e),s=ba(t,{type:1},e,a.atom,void 0,a.pos.get_xy0());(r=s[0]).operations.reverse(),i=s[2]}else{var u=new Oo({label:"C",fragment:o},new $(1,0).rotate(n).add(t.molecule.atoms.get(e).pp).get_xy0()).perform(t);r.addOp(u),r.addOp(new ko(e,u.data.aid,{type:1}).perform(t)),i=u.data.aid}return{action:r,aid1:i}}(t,n,r);a=p.action,d=p.aid1,c=u.atoms.get(d),f=Ln.calcAngle(u.atoms.get(n).pp,c.pp)-e.angle0}else null===r&&(r=Ln.calcAngle(c.pp,Ki(t,n).pos)),f=r-e.angle0;var m=new Map,v=s.atoms.get(e.aid).pp,g=Vi(t,n,"fragment"),y={atoms:[],bonds:[]};return s.atoms.forEach((function(n,r){var o=at.getAttrHash(n);if(o.fragment=g,r===e.aid)a.mergeWith(Sa(t,d,o,!0)),m.set(r,d),y.atoms.push(d);else{var i=$.diff(n.pp,v).rotate(f).add(c.pp),s=new Oo(o,i.get_xy0()).perform(t);a.addOp(s),m.set(r,s.data.aid),y.atoms.push(s.data.aid)}})),l||Ca(a,t,y.atoms,n),s.bonds.forEach((function(e){var n=new ko(m.get(e.begin),m.get(e.end),e).perform(t);a.addOp(n),new Ro(n.data.bid,"isPreview",i).perform(t),y.bonds.push(n.data.bid)})),s.sgroups.forEach((function(e){var n=t.molecule.sgroups.newId(),r=e.atoms.map((function(t){return m.get(t)})),o=e.cloneAttachmentPoints(m);da(t,e.type,r,fs(fs({},e.data),{},{expanded:!!i||e.data.expanded}),n,o,c.pp,"SUP"===e.type?e.isExpanded():null,e.data.name).operations.reverse().forEach((function(t){a.addOp(t)}))})),a.operations.reverse(),a.addOp(new Yo([].concat((0,h.Z)(y.atoms),[n])).perform(t)),a.mergeWith(xa(t,t.molecule.bonds.get(y.bonds[0]))),[a,y]}function bs(t,e,n,r,o,i){var a=arguments.length>6&&void 0!==arguments[6]&&arguments[6];return i?function(t,e,n,r,i){var s=function(t,e,n){return ws(t,e,n,o,a)}(t,e,n);return Promise.resolve(s)}(t,e,n):ws(t,e,n,o)}function ws(t,e,n,r){var o=arguments.length>4&&void 0!==arguments[4]&&arguments[4],i=new Di,a=e.molecule,s=t.molecule,u=s.bonds.get(n),l=a.bonds.get(e.bid),c=a.atoms.get(r?l.end:l.begin),d=new Map([[l.begin,r?u.end:u.begin],[l.end,r?u.begin:u.end]]),f={begin:r?l.end:l.begin,end:r?l.begin:l.end},p=Ln.mergeBondsParams(s,u,a,f),m=p.angle,v=p.scale,g=s.getBondFragment(n),y={atoms:[],bonds:[]};a.atoms.forEach((function(e,n){var r=at.getAttrHash(e);if(r.fragment=g,n!==l.begin&&n!==l.end){var o=$.diff(e.pp,c.pp).rotate(m).scaled(v).add(s.atoms.get(u.begin).pp),a=Ui.atom(t,o,null,.1);if(null===a){var h=new Oo(r,o).perform(t);i.addOp(h),d.set(n,h.data.aid),y.atoms.push(h.data.aid)}else d.set(n,a.id),i.mergeWith(Sa(t,d.get(n),r,!0))}else i.mergeWith(Sa(t,d.get(n),r,!0))})),Ca(i,t,y.atoms,u.begin);var b=function(t,e,n,r){var o=t.name===ps,i=t.name===ms;if(t.bonds.size&&(o||i)){var a=dt.getBondNeighbourIds(e,n),s=a.beginBondIds,u=a.endBondIds;if(1!==s.length||1!==u.length)return null;var l=e.bonds.get(s[0]),c=e.bonds.get(u[0]);if(!l||!c)throw new Error("Incorrect bond id was provided");if(o)return dt.getBenzeneConnectingBondType(r,l,c);if(i)return dt.getCyclopentadieneFusingBondType(r,l,c)}return null}(a,s,n,u),w=null!==b;return a.bonds.forEach((function(e,r){var c=s.findBondId(d.get(e.begin),d.get(e.end)),h=null;if(null===c){var f=new ko(d.get(e.begin),d.get(e.end),e).perform(t);i.addOp(f);var p=f.data.bid;if(h=p,w){var m=a.name===ps,v=a.name===ms;if(m){var g=vs.includes(r)?dt.PATTERN.TYPE.DOUBLE:dt.PATTERN.TYPE.SINGLE;i.addOp(new Ro(p,"type",g).perform(t))}if(v){var x=dt.getBondNeighbourIds(s,n),E=x.beginBondIds,P=x.endBondIds,O=s.bonds.get(E[0]),A=s.bonds.get(P[0]),R=dt.getCyclopentadieneDoubleBondIndexes(u,O,A).includes(r)?dt.PATTERN.TYPE.DOUBLE:dt.PATTERN.TYPE.SINGLE;i.addOp(new Ro(p,"type",R).perform(t))}}y.bonds.push(p)}else{var S=u.type>l.type?u:l;i.mergeWith(wa(t,c,S,!0)),w&&b&&i.addOp(new Ro(n,"type",b).perform(t)),h=n}i.addOp(new Ro(h,"isPreview",o).perform(t))})),y.atoms.length&&i.addOp(new Yo([u.begin,u.end].concat((0,h.Z)(y.atoms))).perform(t)),y.bonds.length&&i.mergeWith(xa(t,t.molecule.bonds.get(y.bonds[0]))),i.operations.reverse(),[i,y]}function xs(t,e,n,r){var o=new Di;return o.addOp(new Ii(e,n,r)),o.perform(t)}function Es(t,e,n){var r=new Di;return r.addOp(new Ni(e,n)),r.perform(t)}function Ps(t,e){var n=new Di;return n.addOp(new Mi(e)),n.perform(t)}function Os(t){var e=function(){if("undefined"==typeof Reflect||!Reflect.construct)return!1;if(Reflect.construct.sham)return!1;if("function"==typeof Proxy)return!0;try{return Boolean.prototype.valueOf.call(Reflect.construct(Boolean,[],(function(){}))),!0}catch(t){return!1}}();return function(){var n,r=(0,m.Z)(t);if(e){var o=(0,m.Z)(this).constructor;n=Reflect.construct(r,arguments,o)}else n=r.apply(this,arguments);return(0,p.Z)(this,n)}}var As=function(t){(0,f.Z)(n,t);var e=Os(n);function n(t,r,i,a){var 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