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r=n(474),i=n(348),a=n(614),o=n(929),s=(n(152),n(826)),l=n(427),c=n(421),u=n(333),h=n(841),d=n(707),g=n(688);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,bondThickness:.6,bondLength:15,shortBondLength:.85,bondSpacing:.18*15,atomVisualization:"default",isomeric:!0,debug:!1,terminalCarbons:!1,explicitHydrogens:!1,overlapSensitivity:.42,overlapResolutionIterations:1,compactDrawing:!0,fontSizeLarge:5,fontSizeSmall:3,padding:20,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:"#fff",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:"#222",BACKGROUND:"#fff"}}},this.opts=this.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}extend(){let t=this,e={},n=!1,r=0,i=arguments.length;"[object Boolean]"===Object.prototype.toString.call(arguments[0])&&(n=arguments[0],r++);let a=function(r){for(var i in r)Object.prototype.hasOwnProperty.call(r,i)&&(n&&"[object Object]"===Object.prototype.toString.call(r[i])?e[i]=t.extend(!0,e[i],r[i]):e[i]=r[i])};for(;ri&&(a=e.sourceId,o=e.targetId),this.getSubtreeOverlapScore(o,a,t.vertexScores).value>this.opts.overlapSensitivity){let e=this.graph.vertices[a],n=this.graph.vertices[o],i=n.getNeighbours(a);if(1===i.length){let t=this.graph.vertices[i[0]],a=t.position.getRotateAwayFromAngle(e.position,n.position,r.toRad(120));this.rotateSubtree(t.id,n.id,a,n.position);let o=this.getOverlapScore().total;o>this.totalOverlapScore?this.rotateSubtree(t.id,n.id,-a,n.position):this.totalOverlapScore=o}else if(2===i.length){if(0!==n.value.rings.length&&0!==e.value.rings.length)continue;let t=this.graph.vertices[i[0]],a=this.graph.vertices[i[1]];if(1===t.value.rings.length&&1===a.value.rings.length){if(t.value.rings[0]!==a.value.rings[0])continue}else{if(0!==t.value.rings.length||0!==a.value.rings.length)continue;{let i=t.position.getRotateAwayFromAngle(e.position,n.position,r.toRad(120)),o=a.position.getRotateAwayFromAngle(e.position,n.position,r.toRad(120));this.rotateSubtree(t.id,n.id,i,n.position),this.rotateSubtree(a.id,n.id,o,n.position);let s=this.getOverlapScore().total;s>this.totalOverlapScore?(this.rotateSubtree(t.id,n.id,-i,n.position),this.rotateSubtree(a.id,n.id,-o,n.position)):this.totalOverlapScore=s}}}t=this.getOverlapScore()}}}this.resolveSecondaryOverlaps(t.scores),this.opts.isomeric&&this.annotateStereochemistry(),this.opts.compactDrawing&&"default"===this.opts.atomVisualization&&this.initPseudoElements(),this.rotateDrawing(),this.canvasWrapper.scale(this.graph.vertices),this.drawEdges(this.opts.debug),this.drawVertices(this.opts.debug),this.canvasWrapper.reset()}}edgeRingCount(t){let e=this.graph.edges[t],n=this.graph.vertices[e.sourceId],r=this.graph.vertices[e.targetId];return Math.min(n.value.rings.length,r.value.rings.length)}getBridgedRings(){let t=Array();for(var e=0;en&&(n=s,t=r,e=i)}}let o=-a.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;r1?n:""),e.delete("C")}if(e.has("H")){let n=e.get("H");t+="H"+(n>1?n:""),e.delete("H")}return Object.keys(l.atomicNumbers).sort().map((n=>{if(e.has(n)){let r=e.get(n);t+=n+(r>1?r:"")}})),t}getRingbondType(t,e){if(t.value.getRingbondCount()<1||e.value.getRingbondCount()<1)return null;for(var n=0;n=0;e--){let r=this.graph.vertices[e];if(0!==r.value.ringbonds.length)for(var n=0;n0&&this.addRingConnection(i)}for(e=0;e0;){let t=-1;for(e=0;er&&(r=e,i=t)}return i}getVerticesAt(t,e,n){let r=Array();for(var i=0;in;){let i=this.graph.vertices[n],o=this.graph.vertices[r];if(!i.value.isDrawn||!o.value.isDrawn)continue;let s=a.subtract(i.position,o.position).lengthSq();if(sh[1]?0:1,sideCount:c,position:c[0]>c[1]?0:1,anCount:o,bnCount:s}}setRingCenter(t){let e=t.getSize(),n=new a(0,0);for(var r=0;r1||0==e.bnCount&&e.anCount>1){g[0].multiplyScalar(n.opts.halfBondSpacing),g[1].multiplyScalar(n.opts.halfBondSpacing);let t=new o(a.add(h,g[0]),a.add(d,g[0]),c,u),e=new o(a.add(h,g[1]),a.add(d,g[1]),c,u);this.canvasWrapper.drawLine(t),this.canvasWrapper.drawLine(e)}else if(e.sideCount[0]>e.sideCount[1]){g[0].multiplyScalar(n.opts.bondSpacing),g[1].multiplyScalar(n.opts.bondSpacing);let t=new o(a.add(h,g[0]),a.add(d,g[0]),c,u);t.shorten(this.opts.bondLength-this.opts.shortBondLength*this.opts.bondLength),this.canvasWrapper.drawLine(t),this.canvasWrapper.drawLine(new o(h,d,c,u))}else if(e.sideCount[0]e.totalSideCount[1]){g[0].multiplyScalar(n.opts.bondSpacing),g[1].multiplyScalar(n.opts.bondSpacing);let t=new o(a.add(h,g[0]),a.add(d,g[0]),c,u);t.shorten(this.opts.bondLength-this.opts.shortBondLength*this.opts.bondLength),this.canvasWrapper.drawLine(t),this.canvasWrapper.drawLine(new o(h,d,c,u))}else if(e.totalSideCount[0]<=e.totalSideCount[1]){g[0].multiplyScalar(n.opts.bondSpacing),g[1].multiplyScalar(n.opts.bondSpacing);let t=new o(a.add(h,g[1]),a.add(d,g[1]),c,u);t.shorten(this.opts.bondLength-this.opts.shortBondLength*this.opts.bondLength),this.canvasWrapper.drawLine(t),this.canvasWrapper.drawLine(new o(h,d,c,u))}}else if("#"===r.bondType){g[0].multiplyScalar(n.opts.bondSpacing/1.5),g[1].multiplyScalar(n.opts.bondSpacing/1.5);let t=new o(a.add(h,g[0]),a.add(d,g[0]),c,u),e=new o(a.add(h,g[1]),a.add(d,g[1]),c,u);this.canvasWrapper.drawLine(t),this.canvasWrapper.drawLine(e),this.canvasWrapper.drawLine(new o(h,d,c,u))}else if("."===r.bondType);else{let t=s.value.isStereoCenter,e=l.value.isStereoCenter;"up"===r.wedge?this.canvasWrapper.drawWedge(new o(h,d,c,u,t,e)):"down"===r.wedge?this.canvasWrapper.drawDashedWedge(new o(h,d,c,u,t,e)):this.canvasWrapper.drawLine(new o(h,d,c,u,t,e))}if(e){let e=a.midpoint(h,d);this.canvasWrapper.drawDebugText(e.x,e.y,"e: "+t)}}drawVertices(t){var e=this.graph.vertices.length;for(e=0;e0&&null===t&&(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;ta.subtract(e,c[0]).lengthSq()&&(d=c[1]);let g=a.subtract(o.position,d),f=a.subtract(s.position,d);-1===g.clockwise(f)?n.positioned||this.createRing(n,d,o,s):n.positioned||this.createRing(n,d,s,o)}else if(1===i.length){t.isSpiro=!0,n.isSpiro=!0;let o=this.graph.vertices[i[0]],s=a.subtract(e,o.position);s.invert(),s.normalize();let l=r.polyCircumradius(this.opts.bondLength,n.getSize());s.multiplyScalar(l),s.add(o.position),n.positioned||this.createRing(n,s,o)}}for(f=0;fr.opts.overlapSensitivity&&(i+=e,s++);let a=r.graph.vertices[t.id].position.clone();a.multiplyScalar(e),o.add(a)})),o.divide(i),{value:i/s,center:o}}getCurrentCenterOfMass(){let t=new a(0,0),e=0;for(var n=0;n1){let e=Array();for(var i=0;is&&(this.rotateSubtree(t.id,e.common.id,2*r,e.common.position),this.rotateSubtree(n.id,e.common.id,-2*r,e.common.position))}else 1===e.vertices.length&&e.rings.length}}resolveSecondaryOverlaps(t){for(var e=0;ethis.opts.overlapSensitivity){let n=this.graph.vertices[t[e].id];if(n.isTerminal()){let t=this.getClosestVertex(n);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 i=0===n.id?this.graph.vertices[1].position:n.previousPosition;n.position.rotateAwayFrom(e,i,r.toRad(20))}}}}getLastVertexWithAngle(t){let e=0,n=null;for(;!e&&t;)n=this.graph.vertices[t],e=n.angle,t=n.parentVertexId;return n}createNextBond(t,e=null,n=0,o=!1,s=!1){if(t.positioned&&!s)return;let l=!1;if(e){let n=this.graph.getEdge(t.id,e.id);"/"!==n.bondType&&"\\"!==n.bondType||++this.doubleBondConfigCount%2!=1||null===this.doubleBondConfig&&(this.doubleBondConfig=n.bondType,l=!0,null===e.parentVertexId&&t.value.branchBond&&("/"===this.doubleBondConfig?this.doubleBondConfig="\\":"\\"===this.doubleBondConfig&&(this.doubleBondConfig="/")))}if(!s)if(e)if(e.value.rings.length>0){let n=e.neighbours,r=null,o=new a(0,0);if(null===e.value.bridgedRing&&e.value.rings.length>1)for(var c=0;c0){let e=this.getRing(t.value.rings[0]);if(!e.positioned){let n=a.subtract(t.previousPosition,t.position);n.invert(),n.normalize();let i=r.polyCircumradius(this.opts.bondLength,e.getSize());n.multiplyScalar(i),n.add(t.position),this.createRing(e,n,t)}}else{t.value.isStereoCenter;let n=t.getNeighbours(),s=Array();for(c=0;c0){let e=r.toRad(60),i=-e,o=new a(this.opts.bondLength,0),s=new a(this.opts.bondLength,0);o.rotate(e).add(t.position),s.rotate(i).add(t.position);let l=this.getCurrentCenterOfMass(),c=o.distanceSq(l),h=s.distanceSq(l);n.angle=c3?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&&!l){let e=this.graph.getEdge(t.id,n.id).bondType;"/"===e?("/"===this.doubleBondConfig||"\\"===this.doubleBondConfig&&(r=-r),this.doubleBondConfig=null):"\\"===e&&("/"===this.doubleBondConfig?r=-r:this.doubleBondConfig,this.doubleBondConfig=null)}n.angle=o?r:-r,this.createNextBond(n,t,u+n.angle)}}else if(2===s.length){let n=t.angle;n||(n=1.0472);let r=this.graph.getTreeDepth(s[0],t.id),i=this.graph.getTreeDepth(s[1],t.id),a=this.graph.vertices[s[0]],o=this.graph.vertices[s[1]];a.value.subtreeDepth=r,o.value.subtreeDepth=i;let l=this.graph.getTreeDepth(e?e.id:null,t.id);e&&(e.value.subtreeDepth=l);let c=0,h=1;"C"===o.value.element&&"C"!==a.value.element&&i>1&&r<5?(c=1,h=0):"C"!==o.value.element&&"C"===a.value.element&&r>1&&i<5?(c=0,h=1):i>r&&(c=1,h=0);let d=this.graph.vertices[s[c]],g=this.graph.vertices[s[h]],f=(this.graph.getEdge(t.id,d.id),this.graph.getEdge(t.id,g.id),!1);ln&&i>a?(o=this.graph.vertices[s[1]],l=this.graph.vertices[s[0]],c=this.graph.vertices[s[2]]):a>n&&a>i&&(o=this.graph.vertices[s[2]],l=this.graph.vertices[s[0]],c=this.graph.vertices[s[1]]),e&&e.value.rings.length<1&&o.value.rings.length<1&&l.value.rings.length<1&&c.value.rings.length<1&&1===this.graph.getTreeDepth(l.id,t.id)&&1===this.graph.getTreeDepth(c.id,t.id)&&this.graph.getTreeDepth(o.id,t.id)>1?(o.angle=-t.angle,t.angle>=0?(l.angle=r.toRad(30),c.angle=r.toRad(90)):(l.angle=-r.toRad(30),c.angle=-r.toRad(90)),this.createNextBond(o,t,u+o.angle),this.createNextBond(l,t,u+l.angle),this.createNextBond(c,t,u+c.angle)):(o.angle=0,l.angle=r.toRad(90),c.angle=-r.toRad(90),this.createNextBond(o,t,u+o.angle),this.createNextBond(l,t,u+l.angle),this.createNextBond(c,t,u+c.angle))}else if(4===s.length){let e=this.graph.getTreeDepth(s[0],t.id),n=this.graph.getTreeDepth(s[1],t.id),i=this.graph.getTreeDepth(s[2],t.id),a=this.graph.getTreeDepth(s[3],t.id),o=this.graph.vertices[s[0]],l=this.graph.vertices[s[1]],c=this.graph.vertices[s[2]],h=this.graph.vertices[s[3]];o.value.subtreeDepth=e,l.value.subtreeDepth=n,c.value.subtreeDepth=i,h.value.subtreeDepth=a,n>e&&n>i&&n>a?(o=this.graph.vertices[s[1]],l=this.graph.vertices[s[0]],c=this.graph.vertices[s[2]],h=this.graph.vertices[s[3]]):i>e&&i>n&&i>a?(o=this.graph.vertices[s[2]],l=this.graph.vertices[s[0]],c=this.graph.vertices[s[1]],h=this.graph.vertices[s[3]]):a>e&&a>n&&a>i&&(o=this.graph.vertices[s[3]],l=this.graph.vertices[s[0]],c=this.graph.vertices[s[1]],h=this.graph.vertices[s[2]]),o.angle=-r.toRad(36),l.angle=r.toRad(36),c.angle=-r.toRad(108),h.angle=r.toRad(108),this.createNextBond(o,t,u+o.angle),this.createNextBond(l,t,u+l.angle),this.createNextBond(c,t,u+c.angle),this.createNextBond(h,t,u+h.angle)}}}getCommonRingbondNeighbour(t){let e=t.neighbours;for(var n=0;n0&&n.value.rings.length>0&&this.areVerticesInSameRing(e,n))}isRingAromatic(t){for(var e=0;ec&&(c=l[e][1].length),n=0;nu&&(u=l[e][1][n].length);for(e=0;ee[1][n][r])return-1;if(t[1][n][r]1&&a.value.hasHydrogen,A=a.value.hasHydrogen?1:0;for(e=0;ee[0]?-1:t[0]=0&&(n=n===b?x:b,o[h[e]]!==t);e--);this.graph.getEdge(a.id,t).wedge=n}}a.value.chirality=y}}visitStereochemistry(t,e,n,r,i,a,o=0){n[t]=1;let s=this.graph.vertices[t],l=s.value.getAtomicNumber();r.length<=a&&r.push(Array());for(var c=0;c0)continue;if("P"===n.value.element)continue;if("C"===n.value.element&&3===i.length&&"N"===i[0].value.element&&"N"===i[1].value.element&&"N"===i[2].value.element)continue;let a=0,o=0;for(e=0;e1&&o++}if(o>1||a<2)continue;let s=null;for(e=0;e1&&(s=t)}for(e=0;e1)continue;t.value.isDrawn=!1;let r=l.maxBonds[t.value.element]-t.value.bondCount,a="";t.value.bracket&&(r=t.value.bracket.hcount,a=t.value.bracket.charge||0),n.value.attachPseudoElement(t.value.element,s?s.value.element:null,r,a)}}for(t=0;t{class e{constructor(t,e,n=1){this.id=null,this.sourceId=t,this.targetId=e,this.weight=n,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,$:4}}}t.exports=e},707:(t,e,n)=>{const r=n(474),i=(n(614),n(152)),a=n(826),o=(n(421),n(427));class s{constructor(t,e=!1){this.vertices=Array(),this.edges=Array(),this.vertexIdsToEdgeId={},this.isomeric=e,this._time=0,this._init(t)}_init(t,e=0,n=null,r=!1){let s=new o(t.atom.element?t.atom.element:t.atom,t.bond);s.branchBond=t.branchBond,s.ringbonds=t.ringbonds,s.bracket=t.atom.element?t.atom:null;let l=new i(s),c=this.vertices[n];if(this.addVertex(l),null!==n){l.setParentVertexId(n),l.value.addNeighbouringElement(c.value.element),c.addChild(l.id),c.value.addNeighbouringElement(s.element),c.spanningTreeChildren.push(l.id);let t=new a(n,l.id,1),e=null;r?(t.setBondType(l.value.branchBond||"-"),e=l.id,t.setBondType(l.value.branchBond||"-"),e=l.id):(t.setBondType(c.value.bondType||"-"),e=c.id),this.addEdge(t)}let u=t.ringbondCount+1;s.bracket&&(u+=s.bracket.hcount);let h=0;if(s.bracket&&s.bracket.chirality){s.isStereoCenter=!0,h=s.bracket.hcount;for(var d=0;dn[r][a]+n[a][i]&&(n[r][i]=n[r][a]+n[a][i]);return n}getSubgraphDistanceMatrix(t){let e=t.length,n=this.getSubgraphAdjacencyMatrix(t),r=Array(e);for(var i=0;ir[i][o]+r[o][a]&&(r[i][a]=r[i][o]+r[o][a]);return r}getAdjacencyList(){let t=this.vertices.length,e=Array(t);for(var n=0;n0;){let t=i.shift(),n=this.vertices[t];e(n);for(var a=0;ar&&(r=a)}return r+1}traverseTree(t,e,n,r=Number.MAX_SAFE_INTEGER,i=!1,a=1,o=null){if(null===o&&(o=new Uint8Array(this.vertices.length)),a>r+1||1===o[t])return;o[t]=1;let s=this.vertices[t],l=s.getNeighbours(e);(!i||a>1)&&n(s);for(var c=0;ct&&!1===m[s]&&(t=i,e=s,n=a,r=o)}return[e,t,n,r]},N=function(t,e,n){let r=0,i=0,a=0,o=f[t],l=p[t],c=v[t],h=y[t];for(s=u;s--;){if(s===t)continue;let e=f[s],n=p[s],u=c[s],d=h[s],g=(o-e)*(o-e),m=1/Math.pow(g+(l-n)*(l-n),1.5);r+=d*(1-u*(l-n)*(l-n)*m),i+=d*(1-u*g*m),a+=d*(u*(o-e)*(l-n)*m)}0===r&&(r=.1),0===i&&(i=.1),0===a&&(a=.1);let d=e/r+n/a;d/=a/r-i/a;let g=-(a*d+e)/r;f[t]+=g,p[t]+=d;let m,b,x,w,$,A=S[t];for(e=0,n=0,o=f[t],l=p[t],s=u;s--;)t!==s&&(m=f[s],b=p[s],x=A[s][0],w=A[s][1],$=1/Math.sqrt((o-m)*(o-m)+(l-b)*(l-b)),g=h[s]*(o-m-c[s]*(o-m)*$),d=h[s]*(l-b-c[s]*(l-b)*$),A[s]=[g,d],e+=g,n+=d,M[s]+=g-x,T[s]+=d-w);M[t]=e,T[t]=n},L=1e9,P=0,D=0,I=0,E=0,B=0,O=0;for(;L>.1&&2e3>B;)for(B++,[P,L,D,I]=R(),E=L,O=0;E>.1&&50>O;)O++,N(P,D,I),[E,D,I]=k(P);for(s=u;s--;){let e=t[s],n=this.vertices[e];n.position.x=f[s],n.position.y=p[s],n.positioned=!0,n.forcePositioned=!0}}_bridgeDfs(t,e,n,r,i,a,o){e[t]=!0,n[t]=r[t]=++this._time;for(var s=0;sn[t]&&o.push([t,l]))}}static getConnectedComponents(t){let e=t.length,n=new Array(e),r=new Array;n.fill(!1);for(var i=0;i1&&r.push(e)}return r}static getConnectedComponentCount(t){let e=t.length,n=new Array(e),r=0;n.fill(!1);for(var i=0;i{const r=n(614);class i{constructor(t=new r(0,0),e=new r(0,0),n=null,i=null,a=!1,o=!1){this.from=t,this.to=e,this.elementFrom=n,this.elementTo=i,this.chiralFrom=a,this.chiralTo=o}clone(){return new i(this.from.clone(),this.to.clone(),this.elementFrom,this.elementTo)}getLength(){return Math.sqrt(Math.pow(this.to.x-this.from.x,2)+Math.pow(this.to.y-this.from.y,2))}getAngle(){return r.subtract(this.getRightVector(),this.getLeftVector()).angle()}getRightVector(){return this.from.x{class e{static round(t,e){return e=e||1,Number(Math.round(t+"e"+e)+"e-"+e)}static meanAngle(t){let 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