chython 2.4__cp312-cp312-win_amd64.whl

chython/algorithms/calculate2d/clean2d.js

@@ -0,0 +1 @@
+!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.$=e():t.$=e()}(self,(function(){return(()=>{var t={348:t=>{class e{static clone(t){let i=Array.isArray(t)?Array():{};for(let r in t){let n=t[r];"function"==typeof n.clone?i[r]=n.clone():i[r]="object"==typeof n?e.clone(n):n}return i}static equals(t,e){if(t.length!==e.length)return!1;let i=t.slice().sort(),r=e.slice().sort();for(var n=0;n<i.length;n++)if(i[n]!==r[n])return!1;return!0}static print(t){if(0==t.length)return"";let e="(";for(let i=0;i<t.length;i++)e+=t[i].id?t[i].id+", ":t[i]+", ";return e=e.substring(0,e.length-2),e+")"}static each(t,e){for(let i=0;i<t.length;i++)e(t[i])}static get(t,e,i){for(let r=0;r<t.length;r++)if(t[r][e]==i)return t[r]}static contains(t,e){if(e.property||e.func){if(e.func){for(let i=0;i<t.length;i++)if(e.func(t[i]))return!0}else for(let i=0;i<t.length;i++)if(t[i][e.property]==e.value)return!0}else for(let i=0;i<t.length;i++)if(t[i]==e.value)return!0;return!1}static intersection(t,e){let i=new Array;for(let r=0;r<t.length;r++)for(let n=0;n<e.length;n++)t[r]===e[n]&&i.push(t[r]);return i}static unique(t){let e={};return t.filter((function(t){return void 0===e[t]&&(e[t]=!0)}))}static count(t,e){let i=0;for(let r=0;r<t.length;r++)t[r]===e&&i++;return i}static toggle(t,e){let i=Array(),r=!1;for(let n=0;n<t.length;n++)t[n]!==e?i.push(t[n]):r=!0;return r||i.push(e),i}static remove(t,e){let i=Array();for(let r=0;r<t.length;r++)t[r]!==e&&i.push(t[r]);return i}static removeUnique(t,e){let i=t.indexOf(e);return i>-1&&t.splice(i,1),t}static removeAll(t,e){return t.filter((function(t){return-1===e.indexOf(t)}))}static merge(t,e){let i=new Array(t.length+e.length);for(let e=0;e<t.length;e++)i[e]=t[e];for(let r=0;r<e.length;r++)i[t.length+r]=e[r];return i}static containsAll(t,e){let i=0;for(let r=0;r<t.length;r++)for(let n=0;n<e.length;n++)t[r]===e[n]&&i++;return i===e.length}static sortByAtomicNumberDesc(t){let e=t.map((function(t,e){return{index:e,value:t.atomicNumber.split(".").map(Number)}}));return e.sort((function(t,e){let i=Math.min(e.value.length,t.value.length),r=0;for(;r<i&&e.value[r]===t.value[r];)r++;return r===i?e.value.length-t.value.length:e.value[r]-t.value[r]})),e.map((function(e){return t[e.index]}))}static deepCopy(t){let i=Array();for(let r=0;r<t.length;r++){let n=t[r];i[r]=n instanceof Array?e.deepCopy(n):n}return i}}t.exports=e},427:(t,e,i)=>{const r=i(348);i(843),i(421);class n{constructor(t,e="-"){this.element=1===t.length?t.toUpperCase():t,this.drawExplicit=!1,this.ringbonds=Array(),this.rings=Array(),this.bondType=e,this.branchBond=null,this.isBridge=!1,this.isBridgeNode=!1,this.originalRings=Array(),this.bridgedRing=null,this.anchoredRings=Array(),this.bracket=null,this.plane=0,this.attachedPseudoElements={},this.hasAttachedPseudoElements=!1,this.isDrawn=!0,this.isConnectedToRing=!1,this.neighbouringElements=Array(),this.isPartOfAromaticRing=t!==this.element,this.bondCount=0,this.chirality="",this.isStereoCenter=!1,this.priority=0,this.mainChain=!1,this.hydrogenDirection="down",this.subtreeDepth=1,this.hasHydrogen=!1,this.class=void 0}addNeighbouringElement(t){this.neighbouringElements.push(t)}attachPseudoElement(t,e,i=0,r=0){null===i&&(i=0),null===r&&(r=0);let n=i+t+r;this.attachedPseudoElements[n]?this.attachedPseudoElements[n].count+=1:this.attachedPseudoElements[n]={element:t,count:1,hydrogenCount:i,previousElement:e,charge:r},this.hasAttachedPseudoElements=!0}getAttachedPseudoElements(){let t={},e=this;return Object.keys(this.attachedPseudoElements).sort().forEach((function(i){t[i]=e.attachedPseudoElements[i]})),t}getAttachedPseudoElementsCount(){return Object.keys(this.attachedPseudoElements).length}isHeteroAtom(){return"C"!==this.element&&"H"!==this.element}addAnchoredRing(t){r.contains(this.anchoredRings,{value:t})||this.anchoredRings.push(t)}getRingbondCount(){return this.ringbonds.length}backupRings(){this.originalRings=Array(this.rings.length);for(let t=0;t<this.rings.length;t++)this.originalRings[t]=this.rings[t]}restoreRings(){this.rings=Array(this.originalRings.length);for(let t=0;t<this.originalRings.length;t++)this.rings[t]=this.originalRings[t]}haveCommonRingbond(t,e){for(let i=0;i<t.ringbonds.length;i++)for(let r=0;r<e.ringbonds.length;r++)if(t.ringbonds[i].id==e.ringbonds[r].id)return!0;return!1}neighbouringElementsEqual(t){if(t.length!==this.neighbouringElements.length)return!1;t.sort(),this.neighbouringElements.sort();for(var e=0;e<this.neighbouringElements.length;e++)if(t[e]!==this.neighbouringElements[e])return!1;return!0}getAtomicNumber(){return n.atomicNumbers[this.element]}getMaxBonds(){return n.maxBonds[this.element]}static get maxBonds(){return{H:1,C:4,N:3,O:2,P:3,S:2,B:3,F:1,I:1,Cl:1,Br:1}}static get atomicNumbers(){return{H:1,He:2,Li:3,Be:4,B:5,b:5,C:6,c:6,N:7,n:7,O:8,o:8,F:9,Ne:10,Na:11,Mg:12,Al:13,Si:14,P:15,p:15,S:16,s:16,Cl:17,Ar:18,K:19,Ca:20,Sc:21,Ti:22,V:23,Cr:24,Mn:25,Fe:26,Co:27,Ni:28,Cu:29,Zn:30,Ga:31,Ge:32,As:33,Se:34,Br:35,Kr:36,Rb:37,Sr:38,Y:39,Zr:40,Nb:41,Mo:42,Tc:43,Ru:44,Rh:45,Pd:46,Ag:47,Cd:48,In:49,Sn:50,Sb:51,Te:52,I:53,Xe:54,Cs:55,Ba:56,La:57,Ce:58,Pr:59,Nd:60,Pm:61,Sm:62,Eu:63,Gd:64,Tb:65,Dy:66,Ho:67,Er:68,Tm:69,Yb:70,Lu:71,Hf:72,Ta:73,W:74,Re:75,Os:76,Ir:77,Pt:78,Au:79,Hg:80,Tl:81,Pb:82,Bi:83,Po:84,At:85,Rn:86,Fr:87,Ra:88,Ac:89,Th:90,Pa:91,U:92,Np:93,Pu:94,Am:95,Cm:96,Bk:97,Cf:98,Es:99,Fm:100,Md:101,No:102,Lr:103,Rf:104,Db:105,Sg:106,Bh:107,Hs:108,Mt:109,Ds:110,Rg:111,Cn:112,Uut:113,Uuq:114,Uup:115,Uuh:116,Uus:117,Uuo:118}}static get mass(){return{H:1,He:2,Li:3,Be:4,B:5,b:5,C:6,c:6,N:7,n:7,O:8,o:8,F:9,Ne:10,Na:11,Mg:12,Al:13,Si:14,P:15,p:15,S:16,s:16,Cl:17,Ar:18,K:19,Ca:20,Sc:21,Ti:22,V:23,Cr:24,Mn:25,Fe:26,Co:27,Ni:28,Cu:29,Zn:30,Ga:31,Ge:32,As:33,Se:34,Br:35,Kr:36,Rb:37,Sr:38,Y:39,Zr:40,Nb:41,Mo:42,Tc:43,Ru:44,Rh:45,Pd:46,Ag:47,Cd:48,In:49,Sn:50,Sb:51,Te:52,I:53,Xe:54,Cs:55,Ba:56,La:57,Ce:58,Pr:59,Nd:60,Pm:61,Sm:62,Eu:63,Gd:64,Tb:65,Dy:66,Ho:67,Er:68,Tm:69,Yb:70,Lu:71,Hf:72,Ta:73,W:74,Re:75,Os:76,Ir:77,Pt:78,Au:79,Hg:80,Tl:81,Pb:82,Bi:83,Po:84,At:85,Rn:86,Fr:87,Ra:88,Ac:89,Th:90,Pa:91,U:92,Np:93,Pu:94,Am:95,Cm:96,Bk:97,Cf:98,Es:99,Fm:100,Md:101,No:102,Lr:103,Rf:104,Db:105,Sg:106,Bh:107,Hs:108,Mt:109,Ds:110,Rg:111,Cn:112,Uut:113,Uuq:114,Uup:115,Uuh:116,Uus:117,Uuo:118}}}t.exports=n},841:(t,e,i)=>{const r=i(474),n=i(614),{getChargeText:s}=(i(929),i(843),i(421),i(537));t.exports=class{constructor(t,e,i){this.canvas="string"==typeof t||t instanceof 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r=this.ctx,n=this.offsetX,s=this.offsetY,o=t.clone().shorten(4),h=o.getLeftVector().clone(),a=o.getRightVector().clone();h.x+=n,h.y+=s,a.x+=n,a.y+=s,e||(r.save(),r.globalCompositeOperation="destination-out",r.beginPath(),r.moveTo(h.x,h.y),r.lineTo(a.x,a.y),r.lineCap="round",r.lineWidth=this.opts.bondThickness+1.2,r.strokeStyle=this.themeManager.getColor("BACKGROUND"),r.stroke(),r.globalCompositeOperation="source-over",r.restore()),h=t.getLeftVector().clone(),a=t.getRightVector().clone(),h.x+=n,h.y+=s,a.x+=n,a.y+=s,r.save(),r.beginPath(),r.moveTo(h.x,h.y),r.lineTo(a.x,a.y),r.lineCap="round",r.lineWidth=this.opts.bondThickness;let 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u=n.add(g,n.multiplyScalar(l[0],this.halfBondThickness)),c=n.add(d,n.multiplyScalar(l[0],1.5+this.halfBondThickness)),p=n.add(d,n.multiplyScalar(l[1],1.5+this.halfBondThickness)),f=n.add(g,n.multiplyScalar(l[1],this.halfBondThickness));i.beginPath(),i.moveTo(u.x,u.y),i.lineTo(c.x,c.y),i.lineTo(p.x,p.y),i.lineTo(f.x,f.y);let v=this.ctx.createRadialGradient(a.x,a.y,this.opts.bondLength,a.x,a.y,0);v.addColorStop(.4,this.themeManager.getColor(t.getLeftElement())||this.themeManager.getColor("C")),v.addColorStop(.6,this.themeManager.getColor(t.getRightElement())||this.themeManager.getColor("C")),i.fillStyle=v,i.fill(),i.restore()}drawDashedWedge(t){if(isNaN(t.from.x)||isNaN(t.from.y)||isNaN(t.to.x)||isNaN(t.to.y))return;let e=this.ctx,i=this.offsetX,r=this.offsetY,s=t.getLeftVector().clone(),o=t.getRightVector().clone();s.x+=i,s.y+=r,o.x+=i,o.y+=r,e.save();let h=n.normals(s,o);h[0].normalize(),h[1].normalize();let a,l,g,d,u=t.getRightChiral(),c=t.clone();u?(a=o,l=s,c.shortenRight(1),g=c.getRightVector().clone(),d=c.getLeftVector().clone()):(a=s,l=o,c.shortenLeft(1),g=c.getLeftVector().clone(),d=c.getRightVector().clone()),g.x+=i,g.y+=r,d.x+=i,d.y+=r;let p=n.subtract(l,a).normalize();e.strokeStyle=this.themeManager.getColor("C"),e.lineCap="round",e.lineWidth=this.opts.bondThickness,e.beginPath();let f=t.getLength(),v=1.25/(f/(3*this.opts.bondThickness)),m=!1;for(var b=0;b<1;b+=v){let i=n.multiplyScalar(p,b*f),r=n.add(a,i),s=1.5*b,o=n.multiplyScalar(h[0],s);!m&&b>.5&&(e.stroke(),e.beginPath(),e.strokeStyle=this.themeManager.getColor(t.getRightElement())||this.themeManager.getColor("C"),m=!0),r.subtract(o),e.moveTo(r.x,r.y),r.add(n.multiplyScalar(o,2)),e.lineTo(r.x,r.y)}e.stroke(),e.restore()}drawDebugText(t,e,i){let r=this.ctx;r.save(),r.font="5px Droid Sans, 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m="0",b=0;l>0&&(m=l.toString(),u.font=this.fontSmall,b=u.measureText(m).width),1===a&&"N"===i&&d.hasOwnProperty("0O")&&d.hasOwnProperty("0O-1")&&(d={"0O":{element:"O",count:2,hydrogenCount:0,previousElement:"C",charge:""}},a=0),u.font=this.fontLarge,u.fillStyle=this.themeManager.getColor("BACKGROUND");let y=u.measureText(i);y.totalWidth=y.width+v,y.height=parseInt(this.fontLarge,10);let x=y.width>this.opts.fontSizeLarge?y.width:this.opts.fontSizeLarge;x/=1.5,u.globalCompositeOperation="destination-out",u.beginPath(),u.arc(t+c,e+p,x,0,r.twoPI,!0),u.closePath(),u.fill(),u.globalCompositeOperation="source-over";let S=-y.width/2,A=-y.width/2;u.fillStyle=this.themeManager.getColor(i),u.fillText(i,t+c+S,e+this.opts.halfFontSizeLarge+p),S+=y.width,a&&(u.font=this.fontSmall,u.fillText(f,t+c+S,e-this.opts.fifthFontSizeSmall+p),S+=v),l>0&&(u.font=this.fontSmall,u.fillText(m,t+c+A-b,e-this.opts.fifthFontSizeSmall+p),A-=b),u.font=this.fontLarge;let C=0,R=0;if(1===n){let i=t+c,r=e+p+this.opts.halfFontSizeLarge;C=this.hydrogenWidth,A-=C,"left"===o?i+=A:"right"===o||"up"===o&&h||"down"===o&&h?i+=S:"up"!==o||h?"down"!==o||h||(r+=this.opts.fontSizeLarge+this.opts.quarterFontSizeLarge,i-=this.halfHydrogenWidth):(r-=this.opts.fontSizeLarge+this.opts.quarterFontSizeLarge,i-=this.halfHydrogenWidth),u.fillText("H",i,r),S+=C}else if(n>1){let i=t+c,r=e+p+this.opts.halfFontSizeLarge;C=this.hydrogenWidth,u.font=this.fontSmall,R=u.measureText(n).width,A-=C+R,"left"===o?i+=A:"right"===o||"up"===o&&h||"down"===o&&h?i+=S:"up"!==o||h?"down"!==o||h||(r+=this.opts.fontSizeLarge+this.opts.quarterFontSizeLarge,i-=this.halfHydrogenWidth):(r-=this.opts.fontSizeLarge+this.opts.quarterFontSizeLarge,i-=this.halfHydrogenWidth),u.font=this.fontLarge,u.fillText("H",i,r),u.font=this.fontSmall,u.fillText(n,i+this.halfHydrogenWidth+R,r+this.opts.fifthFontSizeSmall),S+=C+this.halfHydrogenWidth+R}for(let i in d){if(!d.hasOwnProperty(i))continue;let r=0,n=0,h=d[i].element,a=d[i].count,l=d[i].hydrogenCount,g=d[i].charge;u.font=this.fontLarge,a>1&&l>0&&(r=u.measureText("(").width,n=u.measureText(")").width);let f=u.measureText(h).width,v=0,m="",b=0;C=0,l>0&&(C=this.hydrogenWidth),u.font=this.fontSmall,a>1&&(v=u.measureText(a).width),0!==g&&(m=s(g),b=u.measureText(m).width),R=0,l>1&&(R=u.measureText(l).width),u.font=this.fontLarge;let y=t+c,x=e+p+this.opts.halfFontSizeLarge;u.fillStyle=this.themeManager.getColor(h),a>0&&(A-=v),a>1&&l>0&&("left"===o?(A-=n,u.fillText(")",y+A,x)):(u.fillText("(",y+S,x),S+=r)),"left"===o?(A-=f,u.fillText(h,y+A,x)):(u.fillText(h,y+S,x),S+=f),l>0&&("left"===o?(A-=C+R,u.fillText("H",y+A,x),l>1&&(u.font=this.fontSmall,u.fillText(l,y+A+C,x+this.opts.fifthFontSizeSmall))):(u.fillText("H",y+S,x),S+=C,l>1&&(u.font=this.fontSmall,u.fillText(l,y+S,x+this.opts.fifthFontSizeSmall),S+=R))),u.font=this.fontLarge,a>1&&l>0&&("left"===o?(A-=r,u.fillText("(",y+A,x)):(u.fillText(")",y+S,x),S+=n)),u.font=this.fontSmall,a>1&&("left"===o?u.fillText(a,y+A+r+n+C+R+f,x+this.opts.fifthFontSizeSmall):(u.fillText(a,y+S,x+this.opts.fifthFontSizeSmall),S+=v)),0!==g&&("left"===o?u.fillText(m,y+A+r+n+C+R+f,e-this.opts.fifthFontSizeSmall+p):(u.fillText(m,y+S,e-this.opts.fifthFontSizeSmall+p),S+=b))}u.restore()}getChargeText(t){return 1===t?"+":2===t?"2+":-1===t?"-":-2===t?"2-":""}drawDebugPoint(t,e,i="",r="#f00"){this.drawCircle(t,e,2,r,!0,!0,i)}drawAromaticityRing(t){let e=this.ctx,i=r.apothemFromSideLength(this.opts.bondLength,t.getSize());e.save(),e.strokeStyle=this.themeManager.getColor("C"),e.lineWidth=this.opts.bondThickness,e.beginPath(),e.arc(t.center.x+this.offsetX,t.center.y+this.offsetY,i-this.opts.bondSpacing,0,2*Math.PI,!0),e.closePath(),e.stroke(),e.restore()}clear(){this.ctx.clearRect(0,0,this.canvas.offsetWidth,this.canvas.offsetHeight)}}},237:(t,e,i)=>{const r=i(474),n=i(348),s=i(614),o=i(929),h=(i(843),i(826)),a=i(427),l=i(421),g=i(333),d=i(841),u=i(707),c=i(473),p=i(654),f=i(207);t.exports=class{constructor(t){this.graph=null,this.doubleBondConfigCount=0,this.doubleBondConfig=null,this.ringIdCounter=0,this.ringConnectionIdCounter=0,this.canvasWrapper=null,this.totalOverlapScore=0,this.defaultOptions={width:500,height:500,scale:0,bondThickness:1,bondLength:30,shortBondLength:.8,bondSpacing:.17*30,atomVisualization:"default",isomeric:!0,debug:!1,terminalCarbons:!1,explicitHydrogens:!0,overlapSensitivity:.42,overlapResolutionIterations:1,compactDrawing:!0,fontFamily:"Arial, Helvetica, sans-serif",fontSizeLarge:11,fontSizeSmall:3,padding:10,experimentalSSSR:!1,kkThreshold:.1,kkInnerThreshold:.1,kkMaxIteration:2e4,kkMaxInnerIteration:50,kkMaxEnergy:1e9,themes:{dark:{C:"#fff",O:"#e74c3c",N:"#3498db",F:"#27ae60",CL:"#16a085",BR:"#d35400",I:"#8e44ad",P:"#d35400",S:"#f1c40f",B:"#e67e22",SI:"#e67e22",H:"#aaa",BACKGROUND:"#141414"},light:{C:"#222",O:"#e74c3c",N:"#3498db",F:"#27ae60",CL:"#16a085",BR:"#d35400",I:"#8e44ad",P:"#d35400",S:"#f1c40f",B:"#e67e22",SI:"#e67e22",H:"#666",BACKGROUND:"#fff"},oldschool:{C:"#000",O:"#000",N:"#000",F:"#000",CL:"#000",BR:"#000",I:"#000",P:"#000",S:"#000",B:"#000",SI:"#000",H:"#000",BACKGROUND:"#fff"},solarized:{C:"#586e75",O:"#dc322f",N:"#268bd2",F:"#859900",CL:"#16a085",BR:"#cb4b16",I:"#6c71c4",P:"#d33682",S:"#b58900",B:"#2aa198",SI:"#2aa198",H:"#657b83",BACKGROUND:"#fff"},"solarized-dark":{C:"#93a1a1",O:"#dc322f",N:"#268bd2",F:"#859900",CL:"#16a085",BR:"#cb4b16",I:"#6c71c4",P:"#d33682",S:"#b58900",B:"#2aa198",SI:"#2aa198",H:"#839496",BACKGROUND:"#fff"},matrix:{C:"#678c61",O:"#2fc079",N:"#4f7e7e",F:"#90d762",CL:"#82d967",BR:"#23755a",I:"#409931",P:"#c1ff8a",S:"#faff00",B:"#50b45a",SI:"#409931",H:"#426644",BACKGROUND:"#fff"},github:{C:"#24292f",O:"#cf222e",N:"#0969da",F:"#2da44e",CL:"#6fdd8b",BR:"#bc4c00",I:"#8250df",P:"#bf3989",S:"#d4a72c",B:"#fb8f44",SI:"#bc4c00",H:"#57606a",BACKGROUND:"#fff"},carbon:{C:"#161616",O:"#da1e28",N:"#0f62fe",F:"#198038",CL:"#007d79",BR:"#fa4d56",I:"#8a3ffc",P:"#ff832b",S:"#f1c21b",B:"#8a3800",SI:"#e67e22",H:"#525252",BACKGROUND:"#fff"},cyberpunk:{C:"#ea00d9",O:"#ff3131",N:"#0abdc6",F:"#00ff9f",CL:"#00fe00",BR:"#fe9f20",I:"#ff00ff",P:"#fe7f00",S:"#fcee0c",B:"#ff00ff",SI:"#ffffff",H:"#913cb1",BACKGROUND:"#fff"},gruvbox:{C:"#665c54",O:"#cc241d",N:"#458588",F:"#98971a",CL:"#79740e",BR:"#d65d0e",I:"#b16286",P:"#af3a03",S:"#d79921",B:"#689d6a",SI:"#427b58",H:"#7c6f64",BACKGROUND:"#fbf1c7"},"gruvbox-dark":{C:"#ebdbb2",O:"#cc241d",N:"#458588",F:"#98971a",CL:"#b8bb26",BR:"#d65d0e",I:"#b16286",P:"#fe8019",S:"#d79921",B:"#8ec07c",SI:"#83a598",H:"#bdae93",BACKGROUND:"#282828"},custom:{C:"#222",O:"#e74c3c",N:"#3498db",F:"#27ae60",CL:"#16a085",BR:"#d35400",I:"#8e44ad",P:"#d35400",S:"#f1c40f",B:"#e67e22",SI:"#e67e22",H:"#666",BACKGROUND:"#fff"}}},this.opts=f.extend(!0,this.defaultOptions,t),this.opts.halfBondSpacing=this.opts.bondSpacing/2,this.opts.bondLengthSq=this.opts.bondLength*this.opts.bondLength,this.opts.halfFontSizeLarge=this.opts.fontSizeLarge/2,this.opts.quarterFontSizeLarge=this.opts.fontSizeLarge/4,this.opts.fifthFontSizeSmall=this.opts.fontSizeSmall/5,this.theme=this.opts.themes.dark}draw(t,e,i="light",r=!1){this.initDraw(t,i,r),this.infoOnly||(this.themeManager=new p(this.opts.themes,i),this.canvasWrapper=new d(e,this.themeManager,this.opts)),r||(this.processGraph(),this.canvasWrapper.scale(this.graph.vertices),this.drawEdges(this.opts.debug),this.drawVertices(this.opts.debug),this.canvasWrapper.reset(),this.opts.debug&&(console.log(this.graph),console.log(this.rings),console.log(this.ringConnections)))}edgeRingCount(t){let e=this.graph.edges[t],i=this.graph.vertices[e.sourceId],r=this.graph.vertices[e.targetId];return Math.min(i.value.rings.length,r.value.rings.length)}getBridgedRings(){let t=Array();for(var e=0;e<this.rings.length;e++)this.rings[e].isBridged&&t.push(this.rings[e]);return t}getFusedRings(){let t=Array();for(var e=0;e<this.rings.length;e++)this.rings[e].isFused&&t.push(this.rings[e]);return t}getSpiros(){let t=Array();for(var e=0;e<this.rings.length;e++)this.rings[e].isSpiro&&t.push(this.rings[e]);return t}printRingInfo(){let t="";for(var e=0;e<this.rings.length;e++){const i=this.rings[e];t+=i.id+";",t+=i.members.length+";",t+=i.neighbours.length+";",t+=i.isSpiro?"true;":"false;",t+=i.isFused?"true;":"false;",t+=i.isBridged?"true;":"false;",t+=i.rings.length+";",t+="\n"}return t}rotateDrawing(){let t=0,e=0,i=0;for(var r=0;r<this.graph.vertices.length;r++){let s=this.graph.vertices[r];if(s.value.isDrawn)for(var n=r+1;n<this.graph.vertices.length;n++){let o=this.graph.vertices[n];if(!o.value.isDrawn)continue;let h=s.position.distanceSq(o.position);h>i&&(i=h,t=r,e=n)}}let o=-s.subtract(this.graph.vertices[t].position,this.graph.vertices[e].position).angle();if(!isNaN(o)){let t=o%.523599;for(t<.2617995?o-=t:o+=.523599-t,r=0;r<this.graph.vertices.length;r++)r!==e&&this.graph.vertices[r].position.rotateAround(o,this.graph.vertices[e].position);for(r=0;r<this.rings.length;r++)this.rings[r].center.rotateAround(o,this.graph.vertices[e].position)}}getTotalOverlapScore(){return this.totalOverlapScore}getRingCount(){return this.rings.length}hasBridgedRing(){return this.bridgedRing}getHeavyAtomCount(){let t=0;for(var e=0;e<this.graph.vertices.length;e++)"H"!==this.graph.vertices[e].value.element&&t++;return t}getMolecularFormula(t=null){let e="",i=new Map,r=null===t?this.graph:new u(t,this.opts.isomeric);for(var n=0;n<r.vertices.length;n++){let t=r.vertices[n].value;if(i.has(t.element)?i.set(t.element,i.get(t.element)+1):i.set(t.element,1),t.bracket&&!t.bracket.chirality&&(i.has("H")?i.set("H",i.get("H")+t.bracket.hcount):i.set("H",t.bracket.hcount)),!t.bracket){let e=a.maxBonds[t.element]-t.bondCount;t.isPartOfAromaticRing&&e--,i.has("H")?i.set("H",i.get("H")+e):i.set("H",e)}}if(i.has("C")){let t=i.get("C");e+="C"+(t>1?t:""),i.delete("C")}if(i.has("H")){let t=i.get("H");e+="H"+(t>1?t:""),i.delete("H")}return Object.keys(a.atomicNumbers).sort().map((t=>{if(i.has(t)){let r=i.get(t);e+=t+(r>1?r:"")}})),e}getRingbondType(t,e){if(t.value.getRingbondCount()<1||e.value.getRingbondCount()<1)return null;for(var i=0;i<t.value.ringbonds.length;i++)for(var r=0;r<e.value.ringbonds.length;r++)if(t.value.ringbonds[i].id===e.value.ringbonds[r].id)return"-"===t.value.ringbonds[i].bondType?e.value.ringbonds[r].bond:t.value.ringbonds[i].bond;return null}initDraw(t,e,i,r){this.data=t,this.infoOnly=i,this.ringIdCounter=0,this.ringConnectionIdCounter=0,this.graph=new u(t,this.opts.isomeric),this.rings=Array(),this.ringConnections=Array(),this.originalRings=Array(),this.originalRingConnections=Array(),this.bridgedRing=!1,this.doubleBondConfigCount=null,this.doubleBondConfig=null,this.highlight_atoms=r,this.initRings(),this.initHydrogens()}processGraph(){this.position(),this.restoreRingInformation(),this.resolvePrimaryOverlaps();let t=this.getOverlapScore();this.totalOverlapScore=this.getOverlapScore().total;for(var e=0;e<this.opts.overlapResolutionIterations;e++)for(var i=0;i<this.graph.edges.length;i++){let e=this.graph.edges[i];if(this.isEdgeRotatable(e)){let i=this.graph.getTreeDepth(e.sourceId,e.targetId),n=this.graph.getTreeDepth(e.targetId,e.sourceId),s=e.targetId,o=e.sourceId;if(i>n&&(s=e.sourceId,o=e.targetId),this.getSubtreeOverlapScore(o,s,t.vertexScores).value>this.opts.overlapSensitivity){let e=this.graph.vertices[s],i=this.graph.vertices[o],n=i.getNeighbours(s);if(1===n.length){let t=this.graph.vertices[n[0]],s=t.position.getRotateAwayFromAngle(e.position,i.position,r.toRad(120));this.rotateSubtree(t.id,i.id,s,i.position);let o=this.getOverlapScore().total;o>this.totalOverlapScore?this.rotateSubtree(t.id,i.id,-s,i.position):this.totalOverlapScore=o}else if(2===n.length){if(0!==i.value.rings.length&&0!==e.value.rings.length)continue;let t=this.graph.vertices[n[0]],s=this.graph.vertices[n[1]];if(1===t.value.rings.length&&1===s.value.rings.length){if(t.value.rings[0]!==s.value.rings[0])continue}else{if(0!==t.value.rings.length||0!==s.value.rings.length)continue;{let n=t.position.getRotateAwayFromAngle(e.position,i.position,r.toRad(120)),o=s.position.getRotateAwayFromAngle(e.position,i.position,r.toRad(120));this.rotateSubtree(t.id,i.id,n,i.position),this.rotateSubtree(s.id,i.id,o,i.position);let h=this.getOverlapScore().total;h>this.totalOverlapScore?(this.rotateSubtree(t.id,i.id,-n,i.position),this.rotateSubtree(s.id,i.id,-o,i.position)):this.totalOverlapScore=h}}}t=this.getOverlapScore()}}}this.resolveSecondaryOverlaps(t.scores),this.opts.isomeric&&this.annotateStereochemistry(),this.opts.compactDrawing&&"default"===this.opts.atomVisualization&&this.initPseudoElements(),this.rotateDrawing()}initRings(){let t=new Map;for(var e=this.graph.vertices.length-1;e>=0;e--){let r=this.graph.vertices[e];if(0!==r.value.ringbonds.length)for(var i=0;i<r.value.ringbonds.length;i++){let e=r.value.ringbonds[i].id,n=r.value.ringbonds[i].bond;if(t.has(e)){let s=r.id,o=t.get(e)[0],a=t.get(e)[1],l=new h(s,o,1);l.setBondType(a||n||"-");let g=this.graph.addEdge(l),d=this.graph.vertices[o];r.addRingbondChild(o,i),r.value.addNeighbouringElement(d.value.element),d.addRingbondChild(s,i),d.value.addNeighbouringElement(r.value.element),r.edges.push(g),d.edges.push(g),t.delete(e)}else t.set(e,[r.id,n])}}let r=c.getRings(this.graph,this.opts.experimentalSSSR);if(null!==r){for(e=0;e<r.length;e++){let t=[...r[e]],n=this.addRing(new l(t));for(i=0;i<t.length;i++)this.graph.vertices[t[i]].value.rings.push(n)}for(e=0;e<this.rings.length-1;e++)for(i=e+1;i<this.rings.length;i++){let t=this.rings[e],r=this.rings[i],n=new g(t,r);n.vertices.size>0&&this.addRingConnection(n)}for(e=0;e<this.rings.length;e++){let t=this.rings[e];t.neighbours=g.getNeighbours(this.ringConnections,t.id)}for(e=0;e<this.rings.length;e++){let t=this.rings[e];this.graph.vertices[t.members[0]].value.addAnchoredRing(t.id)}for(this.backupRingInformation();this.rings.length>0;){let t=-1;for(e=0;e<this.rings.length;e++){let i=this.rings[e];this.isPartOfBridgedRing(i.id)&&!i.isBridged&&(t=i.id)}if(-1===t)break;let i=this.getRing(t),r=this.getBridgedRingRings(i.id);for(this.bridgedRing=!0,this.createBridgedRing(r,i.members[0]),e=0;e<r.length;e++)this.removeRing(r[e])}}}initHydrogens(){if(!this.opts.explicitHydrogens)for(var t=0;t<this.graph.vertices.length;t++){let e=this.graph.vertices[t];if("H"!==e.value.element)continue;let i=this.graph.vertices[e.neighbours[0]];i.value.hasHydrogen=!0,(!i.value.isStereoCenter||i.value.rings.length<2&&!i.value.bridgedRing||i.value.bridgedRing&&i.value.originalRings.length<2)&&(e.value.isDrawn=!1)}}getBridgedRingRings(t){let e=Array(),i=this,r=function(t){let n=i.getRing(t);e.push(t);for(var s=0;s<n.neighbours.length;s++){let o=n.neighbours[s];-1===e.indexOf(o)&&o!==t&&g.isBridge(i.ringConnections,i.graph.vertices,t,o)&&r(o)}};return r(t),n.unique(e)}isPartOfBridgedRing(t){for(var e=0;e<this.ringConnections.length;e++)if(this.ringConnections[e].containsRing(t)&&this.ringConnections[e].isBridge(this.graph.vertices))return!0;return!1}createBridgedRing(t,e){let i=new Set,r=new Set,s=new Set;for(var o=0;o<t.length;o++){let e=this.getRing(t[o]);e.isPartOfBridged=!0;for(var h=0;h<e.members.length;h++)r.add(e.members[h]);for(h=0;h<e.neighbours.length;h++){let i=e.neighbours[h];-1===t.indexOf(i)&&s.add(e.neighbours[h])}}let a=new Set;for(let e of r){let r=this.graph.vertices[e],s=n.intersection(t,r.value.rings);1===r.value.rings.length||1===s.length?i.add(r.id):a.add(r.id)}Array();let g=Array();for(let t of a){let e=this.graph.vertices[t],r=!1;for(let t=0;t<e.edges.length;t++)1===this.edgeRingCount(e.edges[t])&&(r=!0);r?(e.value.isBridgeNode=!0,i.add(e.id)):(e.value.isBridge=!0,i.add(e.id))}let d=new l([...i]);for(this.addRing(d),d.isBridged=!0,d.neighbours=[...s],o=0;o<t.length;o++)d.rings.push(this.getRing(t[o]).clone());for(o=0;o<d.members.length;o++)this.graph.vertices[d.members[o]].value.bridgedRing=d.id;for(o=0;o<g.length;o++)this.graph.vertices[g[o]].value.rings=Array();for(let e of i){let i=this.graph.vertices[e];i.value.rings=n.removeAll(i.value.rings,t),i.value.rings.push(d.id)}for(o=0;o<t.length;o++)for(h=o+1;h<t.length;h++)this.removeRingConnectionsBetween(t[o],t[h]);for(let e of s){let i=this.getRingConnections(e,t);for(h=0;h<i.length;h++)this.getRingConnection(i[h]).updateOther(d.id,e);this.getRing(e).neighbours.push(d.id)}return d}areVerticesInSameRing(t,e){for(var i=0;i<t.value.rings.length;i++)for(var r=0;r<e.value.rings.length;r++)if(t.value.rings[i]===e.value.rings[r])return!0;return!1}getCommonRings(t,e){let i=Array();for(var r=0;r<t.value.rings.length;r++)for(var n=0;n<e.value.rings.length;n++)t.value.rings[r]==e.value.rings[n]&&i.push(t.value.rings[r]);return i}getLargestOrAromaticCommonRing(t,e){let i=this.getCommonRings(t,e),r=0,n=null;for(var s=0;s<i.length;s++){let t=this.getRing(i[s]),e=t.getSize();if(t.isBenzeneLike(this.graph.vertices))return t;e>r&&(r=e,n=t)}return n}getVerticesAt(t,e,i){let r=Array();for(var n=0;n<this.graph.vertices.length;n++){let s=this.graph.vertices[n];s.id!==i&&s.positioned&&t.distanceSq(s.position)<=e*e&&r.push(s.id)}return r}getClosestVertex(t){let e=99999,i=null;for(var r=0;r<this.graph.vertices.length;r++){let n=this.graph.vertices[r];if(n.id===t.id)continue;let s=t.position.distanceSq(n.position);s<e&&(e=s,i=n)}return i}addRing(t){return t.id=this.ringIdCounter++,this.rings.push(t),t.id}removeRing(t){this.rings=this.rings.filter((function(e){return e.id!==t})),this.ringConnections=this.ringConnections.filter((function(e){return e.firstRingId!==t&&e.secondRingId!==t}));for(var e=0;e<this.rings.length;e++){let i=this.rings[e];i.neighbours=i.neighbours.filter((function(e){return e!==t}))}}getRing(t){for(var e=0;e<this.rings.length;e++)if(this.rings[e].id==t)return this.rings[e]}addRingConnection(t){return t.id=this.ringConnectionIdCounter++,this.ringConnections.push(t),t.id}removeRingConnection(t){this.ringConnections=this.ringConnections.filter((function(e){return e.id!==t}))}removeRingConnectionsBetween(t,e){let i=Array();for(var r=0;r<this.ringConnections.length;r++){let n=this.ringConnections[r];(n.firstRingId===t&&n.secondRingId===e||n.firstRingId===e&&n.secondRingId===t)&&i.push(n.id)}for(r=0;r<i.length;r++)this.removeRingConnection(i[r])}getRingConnection(t){for(var e=0;e<this.ringConnections.length;e++)if(this.ringConnections[e].id==t)return this.ringConnections[e]}getRingConnections(t,e){let i=Array();for(var r=0;r<this.ringConnections.length;r++){let s=this.ringConnections[r];for(var n=0;n<e.length;n++){let r=e[n];(s.firstRingId===t&&s.secondRingId===r||s.firstRingId===r&&s.secondRingId===t)&&i.push(s.id)}}return i}getOverlapScore(){let t=0,e=new Float32Array(this.graph.vertices.length);for(var i=0;i<this.graph.vertices.length;i++)e[i]=0;for(i=0;i<this.graph.vertices.length;i++)for(var r=this.graph.vertices.length;--r>i;){let n=this.graph.vertices[i],o=this.graph.vertices[r];if(!n.value.isDrawn||!o.value.isDrawn)continue;let h=s.subtract(n.position,o.position).lengthSq();if(h<this.opts.bondLengthSq){let n=(this.opts.bondLength-Math.sqrt(h))/this.opts.bondLength;t+=n,e[i]+=n,e[r]+=n}}let n=Array();for(i=0;i<this.graph.vertices.length;i++)n.push({id:i,score:e[i]});return n.sort((function(t,e){return e.score-t.score})),{total:t,scores:n,vertexScores:e}}chooseSide(t,e,i){let r=t.getNeighbours(e.id),s=e.getNeighbours(t.id),o=r.length,h=s.length,a=n.merge(r,s),l=[0,0];for(var g=0;g<a.length;g++)this.graph.vertices[a[g]].position.sameSideAs(t.position,e.position,i[0])?l[0]++:l[1]++;let d=[0,0];for(g=0;g<this.graph.vertices.length;g++)this.graph.vertices[g].position.sameSideAs(t.position,e.position,i[0])?d[0]++:d[1]++;return{totalSideCount:d,totalPosition:d[0]>d[1]?0:1,sideCount:l,position:l[0]>l[1]?0:1,anCount:o,bnCount:h}}setRingCenter(t){let e=t.getSize(),i=new s(0,0);for(var r=0;r<e;r++)i.add(this.graph.vertices[t.members[r]].position);t.center=i.divide(e)}getSubringCenter(t,e){let i=e.value.originalRings,r=t.center,n=Number.MAX_VALUE;for(var s=0;s<i.length;s++)for(var o=0;o<t.rings.length;o++)i[s]===t.rings[o].id&&t.rings[o].getSize()<n&&(r=t.rings[o].center,n=t.rings[o].getSize());return r}drawEdges(t){let e=this,i=Array(this.graph.edges.length);if(i.fill(!1),this.graph.traverseBF(0,(function(r){let n=e.graph.getEdges(r.id);for(var s=0;s<n.length;s++){let r=n[s];i[r]||(i[r]=!0,e.drawEdge(r,t))}})),!this.bridgedRing)for(var r=0;r<this.rings.length;r++){let t=this.rings[r];this.isRingAromatic(t)&&this.canvasWrapper.drawAromaticityRing(t)}}drawEdge(t,e){let i=this,r=this.graph.edges[t],h=this.graph.vertices[r.sourceId],a=this.graph.vertices[r.targetId],l=h.value.element,g=a.value.element;if(!(h.value.isDrawn&&a.value.isDrawn||"default"!==this.opts.atomVisualization))return;let d=h.position,u=a.position,c=this.getEdgeNormals(r),p=n.clone(c);if(p[0].multiplyScalar(10).add(d),p[1].multiplyScalar(10).add(d),"="===r.bondType||"="===this.getRingbondType(h,a)||r.isPartOfAromaticRing&&this.bridgedRing){let t=this.areVerticesInSameRing(h,a),e=this.chooseSide(h,a,p);if(t){let t=this.getLargestOrAromaticCommonRing(h,a).center;c[0].multiplyScalar(i.opts.bondSpacing),c[1].multiplyScalar(i.opts.bondSpacing);let e=null;e=t.sameSideAs(h.position,a.position,s.add(d,c[0]))?new o(s.add(d,c[0]),s.add(u,c[0]),l,g):new o(s.add(d,c[1]),s.add(u,c[1]),l,g),e.shorten(this.opts.bondLength-this.opts.shortBondLength*this.opts.bondLength),r.isPartOfAromaticRing?this.canvasWrapper.drawLine(e,!0):this.canvasWrapper.drawLine(e),this.canvasWrapper.drawLine(new o(d,u,l,g))}else if(r.center||h.isTerminal()&&a.isTerminal()){c[0].multiplyScalar(i.opts.halfBondSpacing),c[1].multiplyScalar(i.opts.halfBondSpacing);let t=new o(s.add(d,c[0]),s.add(u,c[0]),l,g),e=new o(s.add(d,c[1]),s.add(u,c[1]),l,g);this.canvasWrapper.drawLine(t),this.canvasWrapper.drawLine(e)}else if(0==e.anCount&&e.bnCount>1||0==e.bnCount&&e.anCount>1){c[0].multiplyScalar(i.opts.halfBondSpacing),c[1].multiplyScalar(i.opts.halfBondSpacing);let t=new o(s.add(d,c[0]),s.add(u,c[0]),l,g),e=new o(s.add(d,c[1]),s.add(u,c[1]),l,g);this.canvasWrapper.drawLine(t),this.canvasWrapper.drawLine(e)}else if(e.sideCount[0]>e.sideCount[1]){c[0].multiplyScalar(i.opts.bondSpacing),c[1].multiplyScalar(i.opts.bondSpacing);let t=new o(s.add(d,c[0]),s.add(u,c[0]),l,g);t.shorten(this.opts.bondLength-this.opts.shortBondLength*this.opts.bondLength),this.canvasWrapper.drawLine(t),this.canvasWrapper.drawLine(new o(d,u,l,g))}else if(e.sideCount[0]<e.sideCount[1]){c[0].multiplyScalar(i.opts.bondSpacing),c[1].multiplyScalar(i.opts.bondSpacing);let t=new o(s.add(d,c[1]),s.add(u,c[1]),l,g);t.shorten(this.opts.bondLength-this.opts.shortBondLength*this.opts.bondLength),this.canvasWrapper.drawLine(t),this.canvasWrapper.drawLine(new o(d,u,l,g))}else if(e.totalSideCount[0]>e.totalSideCount[1]){c[0].multiplyScalar(i.opts.bondSpacing),c[1].multiplyScalar(i.opts.bondSpacing);let t=new o(s.add(d,c[0]),s.add(u,c[0]),l,g);t.shorten(this.opts.bondLength-this.opts.shortBondLength*this.opts.bondLength),this.canvasWrapper.drawLine(t),this.canvasWrapper.drawLine(new o(d,u,l,g))}else if(e.totalSideCount[0]<=e.totalSideCount[1]){c[0].multiplyScalar(i.opts.bondSpacing),c[1].multiplyScalar(i.opts.bondSpacing);let t=new o(s.add(d,c[1]),s.add(u,c[1]),l,g);t.shorten(this.opts.bondLength-this.opts.shortBondLength*this.opts.bondLength),this.canvasWrapper.drawLine(t),this.canvasWrapper.drawLine(new o(d,u,l,g))}}else if("#"===r.bondType){c[0].multiplyScalar(i.opts.bondSpacing/1.5),c[1].multiplyScalar(i.opts.bondSpacing/1.5);let t=new o(s.add(d,c[0]),s.add(u,c[0]),l,g),e=new o(s.add(d,c[1]),s.add(u,c[1]),l,g);this.canvasWrapper.drawLine(t),this.canvasWrapper.drawLine(e),this.canvasWrapper.drawLine(new o(d,u,l,g))}else if("."===r.bondType);else{let t=h.value.isStereoCenter,e=a.value.isStereoCenter;"up"===r.wedge?this.canvasWrapper.drawWedge(new o(d,u,l,g,t,e)):"down"===r.wedge?this.canvasWrapper.drawDashedWedge(new o(d,u,l,g,t,e)):this.canvasWrapper.drawLine(new o(d,u,l,g,t,e))}if(e){let e=s.midpoint(d,u);this.canvasWrapper.drawDebugText(e.x,e.y,"e: "+t)}}drawVertices(t){var e=this.graph.vertices.length;for(e=0;e<this.graph.vertices.length;e++){let i=this.graph.vertices[e],r=i.value,o=0,h=0,l=i.value.bondCount,g=r.element,d=a.maxBonds[g]-l,u=i.getTextDirection(this.graph.vertices),c=!(!this.opts.terminalCarbons&&"C"===g&&!r.hasAttachedPseudoElements)&&i.isTerminal(),p="C"===r.element;if("N"===r.element&&r.isPartOfAromaticRing&&(d=0),r.bracket&&(d=r.bracket.hcount,o=r.bracket.charge,h=r.bracket.isotope),"allballs"===this.opts.atomVisualization)this.canvasWrapper.drawBall(i.position.x,i.position.y,g);else if(r.isDrawn&&(!p||r.drawExplicit||c||r.hasAttachedPseudoElements)||1===this.graph.vertices.length)"default"===this.opts.atomVisualization?this.canvasWrapper.drawText(i.position.x,i.position.y,g,d,u,c,o,h,this.graph.vertices.length,r.getAttachedPseudoElements()):"balls"===this.opts.atomVisualization&&this.canvasWrapper.drawBall(i.position.x,i.position.y,g);else if(2===i.getNeighbourCount()&&1==i.forcePositioned){let t=this.graph.vertices[i.neighbours[0]].position,e=this.graph.vertices[i.neighbours[1]].position,r=s.threePointangle(i.position,t,e);Math.abs(Math.PI-r)<.1&&this.canvasWrapper.drawPoint(i.position.x,i.position.y,g)}if(t){let t="v: "+i.id+" "+n.print(r.ringbonds);this.canvasWrapper.drawDebugText(i.position.x,i.position.y,t)}}if(this.opts.debug)for(e=0;e<this.rings.length;e++){let t=this.rings[e].center;this.canvasWrapper.drawDebugPoint(t.x,t.y,"r: "+this.rings[e].id)}}position(){let t=null;for(var e=0;e<this.graph.vertices.length;e++)if(null!==this.graph.vertices[e].value.bridgedRing){t=this.graph.vertices[e];break}if(null===t)for(e=0;e<this.rings.length;e++)if(this.rings[e].isBridged){t=this.graph.vertices[this.rings[e].members[0]];break}null===t&&this.rings.length>0&&(t=this.graph.vertices[this.rings[0].members[0]]),null===t&&(t=this.graph.vertices[0]),this.createNextBond(t,null,0)}backupRingInformation(){this.originalRings=Array(),this.originalRingConnections=Array();for(var t=0;t<this.rings.length;t++)this.originalRings.push(this.rings[t]);for(t=0;t<this.ringConnections.length;t++)this.originalRingConnections.push(this.ringConnections[t]);for(t=0;t<this.graph.vertices.length;t++)this.graph.vertices[t].value.backupRings()}restoreRingInformation(){let t=this.getBridgedRings();this.rings=Array(),this.ringConnections=Array();for(var e=0;e<t.length;e++){let r=t[e];for(var i=0;i<r.rings.length;i++){let t=r.rings[i];this.originalRings[t.id].center=t.center}}for(e=0;e<this.originalRings.length;e++)this.rings.push(this.originalRings[e]);for(e=0;e<this.originalRingConnections.length;e++)this.ringConnections.push(this.originalRingConnections[e]);for(e=0;e<this.graph.vertices.length;e++)this.graph.vertices[e].value.restoreRings()}createRing(t,e=null,i=null,n=null){if(t.positioned)return;e=e||new s(0,0);let o=t.getOrderedNeighbours(this.ringConnections),h=i?s.subtract(i.position,e).angle():0,a=r.polyCircumradius(this.opts.bondLength,t.getSize()),l=r.centralAngle(t.getSize());t.centralAngle=l;let d=h,u=this,c=i?i.id:null;if(-1===t.members.indexOf(c)&&(i&&(i.positioned=!1),c=t.members[0]),t.isBridged){this.graph.kkLayout(t.members.slice(),e,i.id,t,this.opts.bondLength,this.opts.kkThreshold,this.opts.kkInnerThreshold,this.opts.kkMaxIteration,this.opts.kkMaxInnerIteration,this.opts.kkMaxEnergy),t.positioned=!0,this.setRingCenter(t),e=t.center;for(var p=0;p<t.rings.length;p++)this.setRingCenter(t.rings[p])}else t.eachMember(this.graph.vertices,(function(i){let r=u.graph.vertices[i];r.positioned||r.setPosition(e.x+Math.cos(d)*a,e.y+Math.sin(d)*a),d+=l,(!t.isBridged||t.rings.length<3)&&(r.angle=d,r.positioned=!0)}),c,n?n.id:null);for(t.positioned=!0,t.center=e,p=0;p<o.length;p++){let i=this.getRing(o[p].neighbour);if(i.positioned)continue;let n=g.getVertices(this.ringConnections,t.id,i.id);if(2===n.length){t.isFused=!0,i.isFused=!0;let o=this.graph.vertices[n[0]],h=this.graph.vertices[n[1]],a=s.midpoint(o.position,h.position),l=s.normals(o.position,h.position);l[0].normalize(),l[1].normalize();let g=r.polyCircumradius(this.opts.bondLength,i.getSize()),d=r.apothem(g,i.getSize());l[0].multiplyScalar(d).add(a),l[1].multiplyScalar(d).add(a);let u=l[0];s.subtract(e,l[1]).lengthSq()>s.subtract(e,l[0]).lengthSq()&&(u=l[1]);let c=s.subtract(o.position,u),p=s.subtract(h.position,u);-1===c.clockwise(p)?i.positioned||this.createRing(i,u,o,h):i.positioned||this.createRing(i,u,h,o)}else if(1===n.length){t.isSpiro=!0,i.isSpiro=!0;let o=this.graph.vertices[n[0]],h=s.subtract(e,o.position);h.invert(),h.normalize();let a=r.polyCircumradius(this.opts.bondLength,i.getSize());h.multiplyScalar(a),h.add(o.position),i.positioned||this.createRing(i,h,o)}}for(p=0;p<t.members.length;p++){let e=this.graph.vertices[t.members[p]],i=e.neighbours;for(var f=0;f<i.length;f++){let t=this.graph.vertices[i[f]];t.positioned||(t.value.isConnectedToRing=!0,this.createNextBond(t,e,0))}}}rotateSubtree(t,e,i,r){let n=this;this.graph.traverseTree(t,e,(function(t){t.position.rotateAround(i,r);for(var e=0;e<t.value.anchoredRings.length;e++){let s=n.rings[t.value.anchoredRings[e]];s&&s.center.rotateAround(i,r)}}))}getSubtreeOverlapScore(t,e,i){let r=this,n=0,o=new s(0,0),h=0;return this.graph.traverseTree(t,e,(function(t){if(!t.value.isDrawn)return;let e=i[t.id];e>r.opts.overlapSensitivity&&(n+=e,h++);let s=r.graph.vertices[t.id].position.clone();s.multiplyScalar(e),o.add(s)})),o.divide(n),{value:n/h,center:o}}getCurrentCenterOfMass(){let t=new s(0,0),e=0;for(var i=0;i<this.graph.vertices.length;i++){let r=this.graph.vertices[i];r.positioned&&(t.add(r.position),e++)}return t.divide(e)}getCurrentCenterOfMassInNeigbourhood(t,e=2*this.opts.bondLength){let i=new s(0,0),r=0,n=e*e;for(var o=0;o<this.graph.vertices.length;o++){let e=this.graph.vertices[o];e.positioned&&t.distanceSq(e.position)<n&&(i.add(e.position),r++)}return i.divide(r)}resolvePrimaryOverlaps(){let t=Array(),e=Array(this.graph.vertices.length);for(var i=0;i<this.rings.length;i++){let s=this.rings[i];for(var r=0;r<s.members.length;r++){let i=this.graph.vertices[s.members[r]];if(e[i.id])continue;e[i.id]=!0;let o=this.getNonRingNeighbours(i.id);if(o.length>1){let e=Array();for(var n=0;n<i.value.rings.length;n++)e.push(i.value.rings[n]);t.push({common:i,rings:e,vertices:o})}else if(1===o.length&&2===i.value.rings.length){let e=Array();for(n=0;n<i.value.rings.length;n++)e.push(i.value.rings[n]);t.push({common:i,rings:e,vertices:o})}}}for(i=0;i<t.length;i++){let e=t[i];if(2===e.vertices.length){let t=e.vertices[0],i=e.vertices[1];if(!t.value.isDrawn||!i.value.isDrawn)continue;let r=(2*Math.PI-this.getRing(e.rings[0]).getAngle())/6;this.rotateSubtree(t.id,e.common.id,r,e.common.position),this.rotateSubtree(i.id,e.common.id,-r,e.common.position);let n=this.getOverlapScore(),s=this.getSubtreeOverlapScore(t.id,e.common.id,n.vertexScores),o=this.getSubtreeOverlapScore(i.id,e.common.id,n.vertexScores),h=s.value+o.value;this.rotateSubtree(t.id,e.common.id,-2*r,e.common.position),this.rotateSubtree(i.id,e.common.id,2*r,e.common.position),n=this.getOverlapScore(),s=this.getSubtreeOverlapScore(t.id,e.common.id,n.vertexScores),o=this.getSubtreeOverlapScore(i.id,e.common.id,n.vertexScores),s.value+o.value>h&&(this.rotateSubtree(t.id,e.common.id,2*r,e.common.position),this.rotateSubtree(i.id,e.common.id,-2*r,e.common.position))}else 1===e.vertices.length&&e.rings.length}}resolveSecondaryOverlaps(t){for(var e=0;e<t.length;e++)if(t[e].score>this.opts.overlapSensitivity){let i=this.graph.vertices[t[e].id];if(i.isTerminal()){let t=this.getClosestVertex(i);if(t){let e=null;e=t.isTerminal()?0===t.id?this.graph.vertices[1].position:t.previousPosition:0===t.id?this.graph.vertices[1].position:t.position;let n=0===i.id?this.graph.vertices[1].position:i.previousPosition;i.position.rotateAwayFrom(e,n,r.toRad(20))}}}}getLastVertexWithAngle(t){let e=0,i=null;for(;!e&&t;)i=this.graph.vertices[t],e=i.angle,t=i.parentVertexId;return i}createNextBond(t,e=null,i=0,o=!1,h=!1){if(t.positioned&&!h)return;let a=!1;if(e){let i=this.graph.getEdge(t.id,e.id);"/"!==i.bondType&&"\\"!==i.bondType||++this.doubleBondConfigCount%2!=1||null===this.doubleBondConfig&&(this.doubleBondConfig=i.bondType,a=!0,null===e.parentVertexId&&t.value.branchBond&&("/"===this.doubleBondConfig?this.doubleBondConfig="\\":"\\"===this.doubleBondConfig&&(this.doubleBondConfig="/")))}if(!h)if(e)if(e.value.rings.length>0){let i=e.neighbours,r=null,o=new s(0,0);if(null===e.value.bridgedRing&&e.value.rings.length>1)for(var l=0;l<i.length;l++){let t=this.graph.vertices[i[l]];if(n.containsAll(t.value.rings,e.value.rings)){r=t;break}}if(null===r){for(l=0;l<i.length;l++){let t=this.graph.vertices[i[l]];t.positioned&&this.areVerticesInSameRing(t,e)&&o.add(s.subtract(t.position,e.position))}o.invert().normalize().multiplyScalar(this.opts.bondLength).add(e.position)}else o=r.position.clone().rotateAround(Math.PI,e.position);t.previousPosition=e.position,t.setPositionFromVector(o),t.positioned=!0}else{let r=new s(this.opts.bondLength,0);r.rotate(i),r.add(e.position),t.setPositionFromVector(r),t.previousPosition=e.position,t.positioned=!0}else{let e=new s(this.opts.bondLength,0);e.rotate(r.toRad(-60)),t.previousPosition=e,t.setPosition(this.opts.bondLength,0),t.angle=r.toRad(-60),null===t.value.bridgedRing&&(t.positioned=!0)}if(null!==t.value.bridgedRing){let e=this.getRing(t.value.bridgedRing);if(!e.positioned){let i=s.subtract(t.previousPosition,t.position);i.invert(),i.normalize();let n=r.polyCircumradius(this.opts.bondLength,e.members.length);i.multiplyScalar(n),i.add(t.position),this.createRing(e,i,t)}}else if(t.value.rings.length>0){let e=this.getRing(t.value.rings[0]);if(!e.positioned){let i=s.subtract(t.previousPosition,t.position);i.invert(),i.normalize();let n=r.polyCircumradius(this.opts.bondLength,e.getSize());i.multiplyScalar(n),i.add(t.position),this.createRing(e,i,t)}}else{t.value.isStereoCenter;let i=t.getNeighbours(),h=Array();for(l=0;l<i.length;l++)this.graph.vertices[i[l]].value.isDrawn&&h.push(i[l]);e&&(h=n.remove(h,e.id));let g=t.getAngle();if(1===h.length){let i=this.graph.vertices[h[0]];if("#"===t.value.bondType||e&&"#"===e.value.bondType||"="===t.value.bondType&&e&&0===e.value.rings.length&&"="===e.value.bondType&&"-"!==t.value.branchBond)t.value.drawExplicit=!1,e&&(this.graph.getEdge(t.id,e.id).center=!0),this.graph.getEdge(t.id,i.id).center=!0,("#"===t.value.bondType||e&&"#"===e.value.bondType)&&(i.angle=0),i.drawExplicit=!0,this.createNextBond(i,t,g+i.angle);else if(e&&e.value.rings.length>0){let e=r.toRad(60),n=-e,o=new s(this.opts.bondLength,0),h=new s(this.opts.bondLength,0);o.rotate(e).add(t.position),h.rotate(n).add(t.position);let a=this.getCurrentCenterOfMass(),l=o.distanceSq(a),d=h.distanceSq(a);i.angle=l<d?n:e,this.createNextBond(i,t,g+i.angle)}else{let r=t.angle;if(e&&e.neighbours.length>3?r=r>0?Math.min(1.0472,r):r<0?Math.max(-1.0472,r):1.0472:r||(r=this.getLastVertexWithAngle(t.id).angle,r||(r=1.0472)),e&&!a){let e=this.graph.getEdge(t.id,i.id).bondType;"/"===e?("/"===this.doubleBondConfig||"\\"===this.doubleBondConfig&&(r=-r),this.doubleBondConfig=null):"\\"===e&&("/"===this.doubleBondConfig?r=-r:this.doubleBondConfig,this.doubleBondConfig=null)}i.angle=o?r:-r,this.createNextBond(i,t,g+i.angle)}}else if(2===h.length){let i=t.angle;i||(i=1.0472);let r=this.graph.getTreeDepth(h[0],t.id),n=this.graph.getTreeDepth(h[1],t.id),s=this.graph.vertices[h[0]],o=this.graph.vertices[h[1]];s.value.subtreeDepth=r,o.value.subtreeDepth=n;let a=this.graph.getTreeDepth(e?e.id:null,t.id);e&&(e.value.subtreeDepth=a);let l=0,d=1;"C"===o.value.element&&"C"!==s.value.element&&n>1&&r<5?(l=1,d=0):"C"!==o.value.element&&"C"===s.value.element&&r>1&&n<5?(l=0,d=1):n>r&&(l=1,d=0);let u=this.graph.vertices[h[l]],c=this.graph.vertices[h[d]],p=(this.graph.getEdge(t.id,u.id),this.graph.getEdge(t.id,c.id),!1);a<r&&a<n&&(p=!0),c.angle=i,u.angle=-i,"\\"===this.doubleBondConfig?"\\"===c.value.branchBond&&(c.angle=-i,u.angle=i):"/"===this.doubleBondConfig&&"/"===c.value.branchBond&&(c.angle=-i,u.angle=i),this.createNextBond(c,t,g+c.angle,p),this.createNextBond(u,t,g+u.angle,p)}else if(3===h.length){let i=this.graph.getTreeDepth(h[0],t.id),n=this.graph.getTreeDepth(h[1],t.id),s=this.graph.getTreeDepth(h[2],t.id),o=this.graph.vertices[h[0]],a=this.graph.vertices[h[1]],l=this.graph.vertices[h[2]];o.value.subtreeDepth=i,a.value.subtreeDepth=n,l.value.subtreeDepth=s,n>i&&n>s?(o=this.graph.vertices[h[1]],a=this.graph.vertices[h[0]],l=this.graph.vertices[h[2]]):s>i&&s>n&&(o=this.graph.vertices[h[2]],a=this.graph.vertices[h[0]],l=this.graph.vertices[h[1]]),e&&e.value.rings.length<1&&o.value.rings.length<1&&a.value.rings.length<1&&l.value.rings.length<1&&1===this.graph.getTreeDepth(a.id,t.id)&&1===this.graph.getTreeDepth(l.id,t.id)&&this.graph.getTreeDepth(o.id,t.id)>1?(o.angle=-t.angle,t.angle>=0?(a.angle=r.toRad(30),l.angle=r.toRad(90)):(a.angle=-r.toRad(30),l.angle=-r.toRad(90)),this.createNextBond(o,t,g+o.angle),this.createNextBond(a,t,g+a.angle),this.createNextBond(l,t,g+l.angle)):(o.angle=0,a.angle=r.toRad(90),l.angle=-r.toRad(90),this.createNextBond(o,t,g+o.angle),this.createNextBond(a,t,g+a.angle),this.createNextBond(l,t,g+l.angle))}else if(4===h.length){let e=this.graph.getTreeDepth(h[0],t.id),i=this.graph.getTreeDepth(h[1],t.id),n=this.graph.getTreeDepth(h[2],t.id),s=this.graph.getTreeDepth(h[3],t.id),o=this.graph.vertices[h[0]],a=this.graph.vertices[h[1]],l=this.graph.vertices[h[2]],d=this.graph.vertices[h[3]];o.value.subtreeDepth=e,a.value.subtreeDepth=i,l.value.subtreeDepth=n,d.value.subtreeDepth=s,i>e&&i>n&&i>s?(o=this.graph.vertices[h[1]],a=this.graph.vertices[h[0]],l=this.graph.vertices[h[2]],d=this.graph.vertices[h[3]]):n>e&&n>i&&n>s?(o=this.graph.vertices[h[2]],a=this.graph.vertices[h[0]],l=this.graph.vertices[h[1]],d=this.graph.vertices[h[3]]):s>e&&s>i&&s>n&&(o=this.graph.vertices[h[3]],a=this.graph.vertices[h[0]],l=this.graph.vertices[h[1]],d=this.graph.vertices[h[2]]),o.angle=-r.toRad(36),a.angle=r.toRad(36),l.angle=-r.toRad(108),d.angle=r.toRad(108),this.createNextBond(o,t,g+o.angle),this.createNextBond(a,t,g+a.angle),this.createNextBond(l,t,g+l.angle),this.createNextBond(d,t,g+d.angle)}}}getCommonRingbondNeighbour(t){let e=t.neighbours;for(var i=0;i<e.length;i++){let r=this.graph.vertices[e[i]];if(n.containsAll(r.value.rings,t.value.rings))return r}return null}isPointInRing(t){for(var e=0;e<this.rings.length;e++){let i=this.rings[e];if(!i.positioned)continue;let n=r.polyCircumradius(this.opts.bondLength,i.getSize()),s=n*n;if(t.distanceSq(i.center)<s)return!0}return!1}isEdgeInRing(t){let e=this.graph.vertices[t.sourceId],i=this.graph.vertices[t.targetId];return this.areVerticesInSameRing(e,i)}isEdgeRotatable(t){let e=this.graph.vertices[t.sourceId],i=this.graph.vertices[t.targetId];return!("-"!==t.bondType||e.isTerminal()||i.isTerminal()||e.value.rings.length>0&&i.value.rings.length>0&&this.areVerticesInSameRing(e,i))}isRingAromatic(t){for(var e=0;e<t.members.length;e++)if(!this.graph.vertices[t.members[e]].value.isPartOfAromaticRing)return!1;return!0}getEdgeNormals(t){let e=this.graph.vertices[t.sourceId].position,i=this.graph.vertices[t.targetId].position;return s.units(e,i)}getNonRingNeighbours(t){let e=Array(),i=this.graph.vertices[t],r=i.neighbours;for(var s=0;s<r.length;s++){let t=this.graph.vertices[r[s]];0===n.intersection(i.value.rings,t.value.rings).length&&0==t.value.isBridge&&e.push(t)}return e}annotateStereochemistry(){for(var t=0;t<this.graph.vertices.length;t++){let s=this.graph.vertices[t];if(!s.value.isStereoCenter)continue;let o=s.getNeighbours(),h=o.length,a=Array(h);for(var e=0;e<h;e++){let t=new Uint8Array(this.graph.vertices.length),r=Array(Array());t[s.id]=1,this.visitStereochemistry(o[e],s.id,t,r,10,0);for(var i=0;i<r.length;i++)r[i].sort((function(t,e){return e-t}));a[e]=[e,r]}let l=0,g=0;for(e=0;e<a.length;e++)for(a[e][1].length>l&&(l=a[e][1].length),i=0;i<a[e][1].length;i++)a[e][1][i].length>g&&(g=a[e][1][i].length);for(e=0;e<a.length;e++){let t=l-a[e][1].length;for(i=0;i<t;i++)a[e][1].push([]);for(a[e][1].push([o[e]]),i=0;i<a[e][1].length;i++){let t=g-a[e][1][i].length;for(var n=0;n<t;n++)a[e][1][i].push(0)}}a.sort((function(t,e){for(var i=0;i<t[1].length;i++)for(var r=0;r<t[1][i].length;r++){if(t[1][i][r]>e[1][i][r])return-1;if(t[1][i][r]<e[1][i][r])return 1}return 0}));let d=new Uint8Array(h);for(e=0;e<h;e++)d[e]=a[e][0],s.value.priority=e;let u=this.graph.vertices[o[d[0]]].position,c=this.graph.vertices[o[d[1]]].position,p=this.graph.vertices[o[d[2]]].position,f=u.relativeClockwise(c,s.position),v=(u.relativeClockwise(p,s.position),-1===f),m="@"===s.value.bracket.chirality?-1:1,b=r.parityOfPermutation(d)*m==1?"R":"S",y="down",x="up";(v&&"R"!==b||!v&&"S"!==b)&&(s.value.hydrogenDirection="up",y="up",x="down"),s.value.hasHydrogen&&(this.graph.getEdge(s.id,o[d[d.length-1]]).wedge=y);let S=new Array(o.length-1),A=s.value.rings.length>1&&s.value.hasHydrogen,C=s.value.hasHydrogen?1:0;for(e=0;e<d.length-C;e++){S[e]=new Uint32Array(2);let t=this.graph.vertices[o[d[e]]];S[e][0]+=t.value.isStereoCenter?0:1e5,S[e][0]+=this.areVerticesInSameRing(t,s)?0:1e4,S[e][0]+=t.value.isHeteroAtom()?1e3:0,S[e][0]-=0===t.value.subtreeDepth?1e3:0,S[e][0]+=1e3-t.value.subtreeDepth,S[e][1]=o[d[e]]}if(S.sort((function(t,e){return t[0]>e[0]?-1:t[0]<e[0]?1:0})),!A){let t=S[0][1];if(s.value.hasHydrogen)this.graph.getEdge(s.id,t).wedge=x;else{let i=x;for(e=d.length-1;e>=0&&(i=i===y?x:y,o[d[e]]!==t);e--);this.graph.getEdge(s.id,t).wedge=i}}s.value.chirality=b}}visitStereochemistry(t,e,i,r,n,s,o=0){i[t]=1;let h=this.graph.vertices[t],a=h.value.getAtomicNumber();r.length<=s&&r.push(Array());for(var l=0;l<this.graph.getEdge(t,e).weight;l++)r[s].push(1e3*o+a);let g=this.graph.vertices[t].neighbours;for(l=0;l<g.length;l++)1!==i[g[l]]&&s<n-1&&this.visitStereochemistry(g[l],t,i.slice(),r,n,s+1,a);if(s<n-1){let e=0;for(l=0;l<g.length;l++)e+=this.graph.getEdge(t,g[l]).weight;for(l=0;l<h.value.getMaxBonds()-e;l++)r.length<=s+1&&r.push(Array()),r[s+1].push(1e3*a+1)}}initPseudoElements(){for(var t=0;t<this.graph.vertices.length;t++){const i=this.graph.vertices[t],r=i.neighbours;let n=Array(r.length);for(var e=0;e<r.length;e++)n[e]=this.graph.vertices[r[e]];if(i.getNeighbourCount()<3||i.value.rings.length>0)continue;if("P"===i.value.element)continue;if("C"===i.value.element&&3===n.length&&"N"===n[0].value.element&&"N"===n[1].value.element&&"N"===n[2].value.element)continue;let s=0,o=0;for(e=0;e<n.length;e++){let t=n[e],i=t.value.element,r=t.getNeighbourCount();"C"!==i&&"H"!==i&&1===r&&s++,r>1&&o++}if(o>1||s<2)continue;let h=null;for(e=0;e<n.length;e++){let t=n[e];t.getNeighbourCount()>1&&(h=t)}for(e=0;e<n.length;e++){let t=n[e];if(t.getNeighbourCount()>1)continue;t.value.isDrawn=!1;let r=a.maxBonds[t.value.element]-t.value.bondCount,s="";t.value.bracket&&(r=t.value.bracket.hcount,s=t.value.bracket.charge||0),i.value.attachPseudoElement(t.value.element,h?h.value.element:null,r,s)}}for(t=0;t<this.graph.vertices.length;t++){const i=this.graph.vertices[t],r=i.value,n=r.element;if("C"===n||"H"===n||!r.isDrawn)continue;const s=i.neighbours;let o=Array(s.length);for(e=0;e<s.length;e++)o[e]=this.graph.vertices[s[e]];for(e=0;e<o.length;e++){let t=o[e].value;if(!t.hasAttachedPseudoElements||2!==t.getAttachedPseudoElementsCount())continue;const r=t.getAttachedPseudoElements();r.hasOwnProperty("0O")&&r.hasOwnProperty("3C")&&(t.isDrawn=!1,i.value.attachPseudoElement("Ac","",0))}}}}},826:t=>{class e{constructor(t,e,i=1){this.id=null,this.sourceId=t,this.targetId=e,this.weight=i,this.bondType="-",this.isPartOfAromaticRing=!1,this.center=!1,this.wedge=""}setBondType(t){this.bondType=t,this.weight=e.bonds[t]}static get bonds(){return{"-":1,"/":1,"\\":1,"=":2,"#":3,$:4}}}t.exports=e},707:(t,e,i)=>{const r=i(474),n=(i(614),i(843)),s=i(826),o=(i(421),i(427));class h{constructor(t,e=!1){this.vertices=Array(),this.edges=Array(),this.vertexIdsToEdgeId={},this.isomeric=e,this._time=0,this._init(t)}_init(t,e=0,i=null,r=!1){let h=new o(t.atom.element?t.atom.element:t.atom,t.bond);h.branchBond=t.branchBond,h.ringbonds=t.ringbonds,h.bracket=t.atom.element?t.atom:null,h.class=t.atom.class;let a=new n(h),l=this.vertices[i];if(this.addVertex(a),null!==i){a.setParentVertexId(i),a.value.addNeighbouringElement(l.value.element),l.addChild(a.id),l.value.addNeighbouringElement(h.element),l.spanningTreeChildren.push(a.id);let t=new s(i,a.id,1),e=null;r?(t.setBondType(a.value.branchBond||"-"),e=a.id,t.setBondType(a.value.branchBond||"-"),e=a.id):(t.setBondType(l.value.bondType||"-"),e=l.id),this.addEdge(t)}let g=t.ringbondCount+1;h.bracket&&(g+=h.bracket.hcount);let d=0;if(h.bracket&&h.bracket.chirality){h.isStereoCenter=!0,d=h.bracket.hcount;for(var u=0;u<d;u++)this._init({atom:"H",isBracket:"false",branches:Array(),branchCount:0,ringbonds:Array(),ringbondCount:!1,next:null,hasNext:!1,bond:"-"},u,a.id,!0)}for(u=0;u<t.branchCount;u++)this._init(t.branches[u],u+g,a.id,!0);t.hasNext&&this._init(t.next,t.branchCount+g,a.id)}clear(){this.vertices=Array(),this.edges=Array(),this.vertexIdsToEdgeId={}}addVertex(t){return t.id=this.vertices.length,this.vertices.push(t),t.id}addEdge(t){let e=this.vertices[t.sourceId],i=this.vertices[t.targetId];return t.id=this.edges.length,this.edges.push(t),this.vertexIdsToEdgeId[t.sourceId+"_"+t.targetId]=t.id,this.vertexIdsToEdgeId[t.targetId+"_"+t.sourceId]=t.id,t.isPartOfAromaticRing=e.value.isPartOfAromaticRing&&i.value.isPartOfAromaticRing,e.value.bondCount+=t.weight,i.value.bondCount+=t.weight,e.edges.push(t.id),i.edges.push(t.id),t.id}getEdge(t,e){let i=this.vertexIdsToEdgeId[t+"_"+e];return void 0===i?null:this.edges[i]}getEdges(t){let e=Array(),i=this.vertices[t];for(var r=0;r<i.neighbours.length;r++)e.push(this.vertexIdsToEdgeId[t+"_"+i.neighbours[r]]);return e}hasEdge(t,e){return void 0!==this.vertexIdsToEdgeId[t+"_"+e]}getVertexList(){let t=[this.vertices.length];for(var e=0;e<this.vertices.length;e++)t[e]=this.vertices[e].id;return t}getEdgeList(){let t=Array(this.edges.length);for(var e=0;e<this.edges.length;e++)t[e]=[this.edges[e].sourceId,this.edges[e].targetId];return t}getAdjacencyMatrix(){let t=this.vertices.length,e=Array(t);for(var i=0;i<t;i++)e[i]=new Array(t),e[i].fill(0);for(i=0;i<this.edges.length;i++){let t=this.edges[i];e[t.sourceId][t.targetId]=1,e[t.targetId][t.sourceId]=1}return e}getComponentsAdjacencyMatrix(){let t=this.vertices.length,e=Array(t),i=this.getBridges();for(var r=0;r<t;r++)e[r]=new Array(t),e[r].fill(0);for(r=0;r<this.edges.length;r++){let t=this.edges[r];e[t.sourceId][t.targetId]=1,e[t.targetId][t.sourceId]=1}for(r=0;r<i.length;r++)e[i[r][0]][i[r][1]]=0,e[i[r][1]][i[r][0]]=0;return e}getSubgraphAdjacencyMatrix(t){let e=t.length,i=Array(e);for(var r=0;r<e;r++){i[r]=new Array(e),i[r].fill(0);for(var n=0;n<e;n++)r!==n&&this.hasEdge(t[r],t[n])&&(i[r][n]=1)}return i}getDistanceMatrix(){let t=this.vertices.length,e=this.getAdjacencyMatrix(),i=Array(t);for(var r=0;r<t;r++)i[r]=Array(t),i[r].fill(1/0);for(r=0;r<t;r++)for(var n=0;n<t;n++)1===e[r][n]&&(i[r][n]=1);for(var s=0;s<t;s++)for(r=0;r<t;r++)for(n=0;n<t;n++)i[r][n]>i[r][s]+i[s][n]&&(i[r][n]=i[r][s]+i[s][n]);return i}getSubgraphDistanceMatrix(t){let e=t.length,i=this.getSubgraphAdjacencyMatrix(t),r=Array(e);for(var n=0;n<e;n++)r[n]=Array(e),r[n].fill(1/0);for(n=0;n<e;n++)for(var s=0;s<e;s++)1===i[n][s]&&(r[n][s]=1);for(var o=0;o<e;o++)for(n=0;n<e;n++)for(s=0;s<e;s++)r[n][s]>r[n][o]+r[o][s]&&(r[n][s]=r[n][o]+r[o][s]);return r}getAdjacencyList(){let t=this.vertices.length,e=Array(t);for(var i=0;i<t;i++){e[i]=[];for(var r=0;r<t;r++)i!==r&&this.hasEdge(this.vertices[i].id,this.vertices[r].id)&&e[i].push(r)}return e}getSubgraphAdjacencyList(t){let e=t.length,i=Array(e);for(var r=0;r<e;r++){i[r]=Array();for(var n=0;n<e;n++)r!==n&&this.hasEdge(t[r],t[n])&&i[r].push(n)}return i}getBridges(){let t=this.vertices.length,e=new Array(t),i=new Array(t),r=new Array(t),n=new Array(t),s=this.getAdjacencyList(),o=Array();e.fill(!1),n.fill(null),this._time=0;for(var h=0;h<t;h++)e[h]||this._bridgeDfs(h,e,i,r,n,s,o);return o}traverseBF(t,e){let i=this.vertices.length,r=new Array(i);r.fill(!1);for(var n=[t];n.length>0;){let t=n.shift(),i=this.vertices[t];e(i);for(var s=0;s<i.neighbours.length;s++){let t=i.neighbours[s];r[t]||(r[t]=!0,n.push(t))}}}getTreeDepth(t,e){if(null===t||null===e)return 0;let i=this.vertices[t].getSpanningTreeNeighbours(e),r=0;for(var n=0;n<i.length;n++){let e=i[n],s=this.getTreeDepth(e,t);s>r&&(r=s)}return r+1}traverseTree(t,e,i,r=999999,n=!1,s=1,o=null){if(null===o&&(o=new Uint8Array(this.vertices.length)),s>r+1||1===o[t])return;o[t]=1;let h=this.vertices[t],a=h.getNeighbours(e);(!n||s>1)&&i(h);for(var l=0;l<a.length;l++)this.traverseTree(a[l],t,i,r,n,s+1,o)}kkLayout(t,e,i,n,s,o=.1,h=.1,a=2e3,l=50,g=1e9){let d=s;for(var u=t.length;u--;)var c=this.vertices[t[u]].neighbours.length;let p=this.getSubgraphDistanceMatrix(t),f=t.length,v=r.polyCircumradius(500,f),m=r.centralAngle(f),b=0,y=new Float32Array(f),x=new Float32Array(f),S=Array(f);for(u=f;u--;){let i=this.vertices[t[u]];i.positioned?(y[u]=i.position.x,x[u]=i.position.y):(y[u]=e.x+Math.cos(b)*v,x[u]=e.y+Math.sin(b)*v),S[u]=i.positioned,b+=m}let A=Array(f);for(u=f;u--;)for(A[u]=new Array(f),c=f;c--;)A[u][c]=s*p[u][c];let C=Array(f);for(u=f;u--;)for(C[u]=Array(f),c=f;c--;)C[u][c]=d*Math.pow(p[u][c],-2);let R,w,T,B,I,P,L,N=Array(f),O=new Float32Array(f),M=new 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t.id=this.id,t.insiders=r.clone(this.insiders),t.neighbours=r.clone(this.neighbours),t.positioned=this.positioned,t.center=this.center.clone(),t.rings=r.clone(this.rings),t.isBridged=this.isBridged,t.isPartOfBridged=this.isPartOfBridged,t.isSpiro=this.isSpiro,t.isFused=this.isFused,t.centralAngle=this.centralAngle,t.canFlip=this.canFlip,t}getSize(){return this.members.length}getPolygon(t){let e=[];for(let i=0;i<this.members.length;i++)e.push(t[this.members[i]].position);return e}getAngle(){return Math.PI-this.centralAngle}eachMember(t,e,i,r){let n=i=i||0===i?i:this.members[0],s=0;for(;null!=n&&s<100;){let o=n;e(o),n=t[n].getNextInRing(t,this.id,r),r=o,n==i&&(n=null),s++}}getOrderedNeighbours(t){let e=Array(this.neighbours.length);for(let i=0;i<this.neighbours.length;i++){let r=s.getVertices(t,this.id,this.neighbours[i]);e[i]={n:r.length,neighbour:this.neighbours[i]}}return e.sort((function(t,e){return e.n-t.n})),e}isBenzeneLike(t){let e=this.getDoubleBondCount(t),i=this.members.length;return 3===e&&6===i||2===e&&5===i}getDoubleBondCount(t){let e=0;for(let i=0;i<this.members.length;i++){let r=t[this.members[i]].value;"="!==r.bondType&&"="!==r.branchBond||e++}return e}contains(t){for(let e=0;e<this.members.length;e++)if(this.members[e]==t)return!0;return!1}}t.exports=o},333:(t,e,i)=>{i(843),i(421),t.exports=class{constructor(t,e){this.id=null,this.firstRingId=t.id,this.secondRingId=e.id,this.vertices=new Set;for(var i=0;i<t.members.length;i++){let r=t.members[i];for(let t=0;t<e.members.length;t++)r===e.members[t]&&this.addVertex(r)}}addVertex(t){this.vertices.add(t)}updateOther(t,e){this.firstRingId===e?this.secondRingId=t:this.firstRingId=t}containsRing(t){return this.firstRingId===t||this.secondRingId===t}isBridge(t){if(this.vertices.size>2)return!0;for(let e of this.vertices)if(t[e].value.rings.length>2)return!0;return!1}static isBridge(t,e,i,r){let n=null;for(let s=0;s<t.length;s++)if(n=t[s],n.firstRingId===i&&n.secondRingId===r||n.firstRingId===r&&n.secondRingId===i)return n.isBridge(e);return!1}static getNeighbours(t,e){let i=[];for(let r=0;r<t.length;r++){let n=t[r];n.firstRingId===e?i.push(n.secondRingId):n.secondRingId===e&&i.push(n.firstRingId)}return i}static getVertices(t,e,i){for(let r=0;r<t.length;r++){let n=t[r];if(n.firstRingId===e&&n.secondRingId===i||n.firstRingId===i&&n.secondRingId===e)return[...n.vertices]}}}},473:(t,e,i)=>{const r=i(707);class n{static getRings(t,e=!1){let i=t.getComponentsAdjacencyMatrix();if(0===i.length)return null;let s=r.getConnectedComponents(i),o=Array();for(var h=0;h<s.length;h++){let i=s[h],r=t.getSubgraphAdjacencyMatrix([...i]),g=new Uint16Array(r.length),d=new Uint16Array(r.length);for(var a=0;a<r.length;a++){d[a]=0,g[a]=0;for(var l=0;l<r[a].length;l++)g[a]+=r[a][l]}let u=0;for(a=0;a<r.length;a++)for(l=a+1;l<r.length;l++)u+=r[a][l];let c=u-r.length+1,p=!0;for(a=0;a<g.length;a++)3!==g[a]&&(p=!1);if(p&&(c=2+u-r.length),1===c){o.push([...i]);continue}e&&(c=999);let{d:f,pe:v,pe_prime:m}=n.getPathIncludedDistanceMatrices(r),b=n.getRingCandidates(f,v,m),y=n.getSSSR(b,f,r,v,m,g,d,c);for(a=0;a<y.length;a++){let t=Array(y[a].size),e=0;for(let r of y[a])t[e++]=i[r];o.push(t)}}return o}static matrixToString(t){let e="";for(var i=0;i<t.length;i++){for(var r=0;r<t[i].length;r++)e+=t[i][r]+" ";e+="\n"}return e}static getPathIncludedDistanceMatrices(t){let e=t.length,i=Array(e),r=Array(e),n=Array(e);for(var s=0,o=0,h=0,a=e;a--;){i[a]=Array(e),r[a]=Array(e),n[a]=Array(e);for(var l=e;l--;)i[a][l]=a===l||1===t[a][l]?t[a][l]:Number.POSITIVE_INFINITY,1===i[a][l]?r[a][l]=[[[a,l]]]:r[a][l]=Array(),n[a][l]=Array()}for(var g=e;g--;)for(a=e;a--;)for(l=e;l--;){const t=i[a][l],e=i[a][g]+i[g][l];if(t>e){if(t===e+1)for(n[a][l]=[r[a][l].length],s=r[a][l].length;s--;)for(n[a][l][s]=[r[a][l][s].length],o=r[a][l][s].length;o--;)for(n[a][l][s][o]=[r[a][l][s][o].length],h=r[a][l][s][o].length;h--;)n[a][l][s][o][h]=[r[a][l][s][o][0],r[a][l][s][o][1]];else n[a][l]=Array();for(i[a][l]=e,r[a][l]=[[]],s=r[a][g][0].length;s--;)r[a][l][0].push(r[a][g][0][s]);for(s=r[g][l][0].length;s--;)r[a][l][0].push(r[g][l][0][s])}else if(t===e){if(r[a][g].length&&r[g][l].length)if(r[a][l].length){let t=Array();for(s=r[a][g][0].length;s--;)t.push(r[a][g][0][s]);for(s=r[g][l][0].length;s--;)t.push(r[g][l][0][s]);r[a][l].push(t)}else{let t=Array();for(s=r[a][g][0].length;s--;)t.push(r[a][g][0][s]);for(s=r[g][l][0].length;s--;)t.push(r[g][l][0][s]);r[a][l][0]=t}}else if(t===e-1)if(n[a][l].length){let t=Array();for(s=r[a][g][0].length;s--;)t.push(r[a][g][0][s]);for(s=r[g][l][0].length;s--;)t.push(r[g][l][0][s]);n[a][l].push(t)}else{let t=Array();for(s=r[a][g][0].length;s--;)t.push(r[a][g][0][s]);for(s=r[g][l][0].length;s--;)t.push(r[g][l][0][s]);n[a][l][0]=t}}return{d:i,pe:r,pe_prime:n}}static getRingCandidates(t,e,i){let r=t.length,n=Array(),s=0;for(let o=0;o<r;o++)for(let h=0;h<r;h++)0===t[o][h]||1===e[o][h].length&&0===i[o][h]||(s=0!==i[o][h].length?2*(t[o][h]+.5):2*t[o][h],s!==1/0&&n.push([s,e[o][h],i[o][h]]));return n.sort((function(t,e){return t[0]-e[0]})),n}static getSSSR(t,e,i,r,s,o,h,a){let l=Array(),g=Array();for(let e=0;e<t.length;e++)if(t[e][0]%2!=0)for(let r=0;r<t[e][2].length;r++){let s=t[e][1][0].concat(t[e][2][r]);for(var d=0;d<s.length;d++)s[d][0].constructor===Array&&(s[d]=s[d][0]);let u=n.bondsToAtoms(s);if(n.getBondCount(u,i)!==u.size||n.pathSetsContain(l,u,s,g,o,h)||(l.push(u),g=g.concat(s)),l.length>a)return l}else for(let r=0;r<t[e][1].length-1;r++){let s=t[e][1][r].concat(t[e][1][r+1]);for(d=0;d<s.length;d++)s[d][0].constructor===Array&&(s[d]=s[d][0]);let u=n.bondsToAtoms(s);if(n.getBondCount(u,i)!==u.size||n.pathSetsContain(l,u,s,g,o,h)||(l.push(u),g=g.concat(s)),l.length>a)return l}return l}static getEdgeCount(t){let e=0,i=t.length;for(var r=i-1;r--;)for(var n=i;n--;)1===t[r][n]&&e++;return e}static getEdgeList(t){let e=t.length,i=Array();for(var r=e-1;r--;)for(var n=e;n--;)1===t[r][n]&&i.push([r,n]);return i}static bondsToAtoms(t){let e=new Set;for(var i=t.length;i--;)e.add(t[i][0]),e.add(t[i][1]);return e}static getBondCount(t,e){let i=0;for(let r of t)for(let n of t)r!==n&&(i+=e[r][n]);return i/2}static pathSetsContain(t,e,i,r,s,o){for(var h=t.length;h--;){if(n.isSupersetOf(e,t[h]))return!0;if(t[h].size===e.size&&n.areSetsEqual(t[h],e))return!0}let a=0,l=!1;for(h=i.length;h--;)for(var g=r.length;g--;)(i[h][0]===r[g][0]&&i[h][1]===r[g][1]||i[h][1]===r[g][0]&&i[h][0]===r[g][1])&&a++,a===i.length&&(l=!0);let d=!1;if(l)for(let t of e)if(o[t]<s[t]){d=!0;break}if(l&&!d)return!0;for(let t of e)o[t]++;return!1}static areSetsEqual(t,e){if(t.size!==e.size)return!1;for(let i of t)if(!e.has(i))return!1;return!0}static isSupersetOf(t,e){for(var i of e)if(!t.has(i))return!1;return!0}}t.exports=n},654:t=>{t.exports=class{constructor(t,e){this.colors=t,this.theme=this.colors[e]}getColor(t){return t&&(t=t.toUpperCase())in this.theme?this.theme[t]:this.theme.C}setTheme(t){this.colors.hasOwnProperty(t)&&(this.theme=this.colors[t])}}},537:t=>{t.exports={getChargeText:function(t){return 1===t?"+":2===t?"2+":-1===t?"-":-2===t?"2-":""}}},614:t=>{class e{constructor(t,e){0==arguments.length?(this.x=0,this.y=0):1==arguments.length?(this.x=t.x,this.y=t.y):(this.x=t,this.y=e)}clone(){return new e(this.x,this.y)}toString(){return"("+this.x+","+this.y+")"}add(t){return this.x+=t.x,this.y+=t.y,this}subtract(t){return this.x-=t.x,this.y-=t.y,this}divide(t){return this.x/=t,this.y/=t,this}multiply(t){return this.x*=t.x,this.y*=t.y,this}multiplyScalar(t){return this.x*=t,this.y*=t,this}invert(){return 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e(0,0);for(var r=0;r<t.length;r++){let e=t[r];i.add(e)}return i.normalize()}}t.exports=e},843:(t,e,i)=>{const r=i(474),n=i(348),s=i(614);i(427);class o{constructor(t,e=0,i=0){this.id=null,this.value=t,this.position=new s(e||0,i||0),this.previousPosition=new s(0,0),this.parentVertexId=null,this.children=Array(),this.spanningTreeChildren=Array(),this.edges=Array(),this.positioned=!1,this.angle=null,this.dir=1,this.neighbourCount=0,this.neighbours=Array(),this.neighbouringElements=Array(),this.forcePositioned=!1}setPosition(t,e){this.position.x=t,this.position.y=e}setPositionFromVector(t){this.position.x=t.x,this.position.y=t.y}addChild(t){this.children.push(t),this.neighbours.push(t),this.neighbourCount++}addRingbondChild(t,e){if(this.children.push(t),this.value.bracket){let 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chython/algorithms/calculate2d/molecule.py

@@ -0,0 +1,149 @@
+# -*- coding: utf-8 -*-
+#
+#  Copyright 2019-2025 Ramil Nugmanov <nougmanoff@protonmail.com>
+#  Copyright 2019, 2020 Dinar Batyrshin <batyrshin-dinar@mail.ru>
+#  This file is part of chython.
+#
+#  chython is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU Lesser General Public License as published by
+#  the Free Software Foundation; either version 3 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+#  GNU Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public License
+#  along with this program; if not, see <https://www.gnu.org/licenses/>.
+#
+from math import sqrt
+from random import random
+from typing import TYPE_CHECKING, Union, Dict
+from ...exceptions import ImplementationError
+from ...periodictable.base.vector import Vector
+
+
+try:
+    from importlib.resources import files
+except ImportError:  # python3.8
+    from importlib_resources import files
+
+
+if TYPE_CHECKING:
+    from chython import MoleculeContainer
+
+try:
+    from py_mini_racer import MiniRacer, JSEvalException
+
+    ctx = MiniRacer()
+    ctx.eval('const self = this')
+    ctx.eval(files(__package__).joinpath('clean2d.js').read_text())
+except RuntimeError:
+    ctx = None
+
+
+class Calculate2DMolecule:
+    __slots__ = ()
+    _atoms: Dict[int, 'Element']
+    _bonds: Dict[int, Dict[int, 'Bond']]
+
+    def clean2d(self: Union['MoleculeContainer', 'Calculate2DMolecule']):
+        """
+        Calculate 2d layout of graph. https://pubs.acs.org/doi/10.1021/acs.jcim.7b00425 JS implementation used.
+        """
+        if ctx is None:
+            raise ImportError('py_mini_racer is not installed or broken')
+        plane = {}
+        entry = iter(sorted(self, key=lambda n: len(self._bonds[n])))
+        for _ in range(min(5, len(self))):
+            smiles, order = self.__clean2d_prepare(next(entry))
+            try:
+                xy = ctx.call('$.clean2d', smiles)
+            except JSEvalException:
+                continue
+            break
+        else:
+            raise ImplementationError
+
+        shift_x, shift_y = xy[0]
+        for n, (x, y) in zip(order, xy):
+            plane[n] = (x - shift_x, shift_y - y)
+
+        bonds = []
+        for n, m, _ in self.bonds():
+            xn, yn = plane[n]
+            xm, ym = plane[m]
+            bonds.append(sqrt((xm - xn) ** 2 + (ym - yn) ** 2))
+        if bonds:
+            bond_reduce = sum(bonds) / len(bonds) / .825
+        else:
+            bond_reduce = 1.
+
+        atoms = self._atoms
+        for n, (x, y) in plane.items():
+            atoms[n].xy = (x / bond_reduce,  y / bond_reduce)
+
+        if self.connected_components_count > 1:
+            shift_x = 0.
+            for c in self.connected_components:
+                shift_x = self._fix_plane_mean(shift_x, component=c) + .9
+        self.__dict__.pop('__cached_method__repr_svg_', None)
+
+    def _fix_plane_mean(self, shift_x: float, shift_y=0., component=None) -> float:
+        atoms = self._atoms
+        if component is None:
+            component = atoms
+
+        left_atom = atoms[min(component, key=lambda x: atoms[x].x)]
+        right_atom = atoms[max(component, key=lambda x: atoms[x].x)]
+
+        min_x = left_atom.x - shift_x
+        if len(left_atom.atomic_symbol) == 2:
+            min_x -= .2
+
+        max_x = right_atom.x - min_x
+        min_y = min(atoms[x].y for x in component)
+        max_y = max(atoms[x].y for x in component)
+        mean_y = (max_y + min_y) / 2 - shift_y
+        delta = Vector(min_x, mean_y)
+        for n in component:
+            atoms[n].xy -= delta
+
+        if -.18 <= right_atom.y <= .18:
+            factor = right_atom.implicit_hydrogens
+            if factor == 1:
+                max_x += .15
+            elif factor:
+                max_x += .25
+        return max_x
+
+    def _fix_plane_min(self, shift_x: float, shift_y=0., component=None) -> float:
+        atoms = self._atoms
+        if component is None:
+            component = atoms
+
+        right_atom = atoms[max(component, key=lambda x: atoms[x].x)]
+        min_x = min(atoms[x].x for x in component) - shift_x
+        max_x = right_atom.x - min_x
+        min_y = min(atoms[x].y for x in component) - shift_y
+        delta = Vector(min_x, min_y)
+        for n in component:
+            atoms[n].xy -= delta
+
+        if shift_y - .18 <= right_atom.y <= shift_y + .18:
+            factor = right_atom.implicit_hydrogens
+            if factor == 1:
+                max_x += .15
+            elif factor:
+                max_x += .25
+        return max_x
+
+    def __clean2d_prepare(self: 'MoleculeContainer', entry):
+        w = {n: random() for n in self._atoms}
+        w[entry] = -1
+        smiles, order = self._smiles(w.__getitem__, random=True, charges=False, stereo=False, _return_order=True)
+        return ''.join(smiles).replace('~', '-'), order
+
+
+__all__ = ['Calculate2DMolecule']

chython/algorithms/calculate2d/reaction.py

@@ -0,0 +1,80 @@
+# -*- coding: utf-8 -*-
+#
+#  Copyright 2019-2025 Ramil Nugmanov <nougmanoff@protonmail.com>
+#  This file is part of chython.
+#
+#  chython is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU Lesser General Public License as published by
+#  the Free Software Foundation; either version 3 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+#  GNU Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public License
+#  along with this program; if not, see <https://www.gnu.org/licenses/>.
+#
+from typing import TYPE_CHECKING
+
+
+if TYPE_CHECKING:
+    from chython import ReactionContainer
+
+
+class Calculate2DReaction:
+    __slots__ = ()
+
+    def clean2d(self: 'ReactionContainer'):
+        """
+        Recalculate 2d coordinates
+        """
+        for m in self.molecules():
+            m.clean2d()
+        self.fix_positions()
+
+    def fix_positions(self: 'ReactionContainer'):
+        """
+        Fix coordinates of molecules in reaction
+        """
+        shift_x = 0
+        reactants = self.reactants
+        amount = len(reactants) - 1
+        signs = []
+        for m in reactants:
+            max_x = m._fix_plane_mean(shift_x)
+            if amount:
+                max_x += .2
+                signs.append(max_x)
+                amount -= 1
+            shift_x = max_x + 1
+        arrow_min = shift_x
+
+        if self.reagents:
+            shift_x += .4
+            for m in self.reagents:
+                max_x = m._fix_plane_min(shift_x, .5)
+                shift_x = max_x + 1
+            shift_x += .4
+            if shift_x - arrow_min < 3:
+                shift_x = arrow_min + 3
+        else:
+            shift_x += 3
+        arrow_max = shift_x - 1
+
+        products = self.products
+        amount = len(products) - 1
+        for m in products:
+            max_x = m._fix_plane_mean(shift_x)
+            if amount:
+                max_x += .2
+                signs.append(max_x)
+                amount -= 1
+            shift_x = max_x + 1
+        self._arrow = (arrow_min, arrow_max)
+        self._signs = tuple(signs)
+        self.flush_cache(keep_molecule_cache=True)
+
+
+__all__ = ['Calculate2DReaction']