3dmol/build/3Dmol-min.js

JavaScript/TypeScript molecular visualization library

/*! For license information please see 3Dmol-min.js.LICENSE.txt */
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i,r,s,n,a,o,h,c,d,u=[],f=e;for((f=[]).push(e[0]),i=1,r=e.length-1;i<r;i++)if(a=e[i],o=e[i+1],a.smoothen){var p=new l.Vector3((a.x+o.x)/2,(a.y+o.y)/2,(a.z+o.z)/2);p.atom=a.atom,f.push(p)}else f.push(a);for(f.push(e[e.length-1]),i=-1,s=f.length;i<=s-3;i++)if(n=f[-1===i?0:i],a=f[i+1],o=f[i+2],h=f[i===s-3?s-1:i+3],c=(new l.Vector3).subVectors(o,n).multiplyScalar(.5),d=(new l.Vector3).subVectors(h,a).multiplyScalar(.5),!o.skip)for(var m=0;m<t;m++){var g=1/t*m,v=a.x+g*c.x+g*g*(-3*a.x+3*o.x-2*c.x-d.x)+g*g*g*(2*a.x-2*o.x+c.x+d.x),_=a.y+g*c.y+g*g*(-3*a.y+3*o.y-2*c.y-d.y)+g*g*g*(2*a.y-2*o.y+c.y+d.y),y=a.z+g*c.z+g*g*(-3*a.z+3*o.z-2*c.z-d.z)+g*g*g*(2*a.z-2*o.z+c.z+d.z),b=new l.Vector3(v,_,y);b.atom=m<t/2?a.atom:o.atom,u.push(b)}return u.push(f[f.length-1]),u}const f=.5,p=1.3,m=.8,g=.4,v=.4;function _(e,t,i,r){for(var s,n,a,o,l=0,c=t.length;l<c;l++){o=Math.round(l*(r.length-1)/c),a=h.CC.color(r[o]);var d=e.updateGeoGroup(2),u=d.vertexArray,f=d.colorArray,p=d.faceArray;u[n=3*(s=d.vertices)]=t[l].x,u[n+1]=t[l].y,u[n+2]=t[l].z,u[n+3]=i[l].x,u[n+4]=i[l].y,u[n+5]=i[l].z;for(var m=0;m<6;++m)f[n+3*m]=a.r,f[n+1+3*m]=a.g,f[n+2+3*m]=a.b;if(l>0){var g=[s,s+1,s-1,s-2],v=d.faceidx;p[v]=g[0],p[v+1]=g[1],p[v+2]=g[3],p[v+3]=g[1],p[v+4]=g[2],p[v+5]=g[3],d.faceidx+=6}d.vertices+=2}}function y(e,t,i,r,s,n,a){a&&"default"!==a||(a="rectangle"),"edged"===a?function(e,t,i,r,s){if(!(t.length<2)){var n,a;if(n=t[0],a=t[t.length-1],n=u(n,r),a=u(a,r),!s)return _(e,n,a,i);var l,c,d,f,p,m,g,v,y,b,x,w,A,C,S,z,M,T,E,L,F,I,O=[],D=[[0,2,-6,-8],[-4,-2,6,4],[7,-1,-5,3],[-3,5,1,-7]];for(A=0,C=n.length;A<C;A++){if(b=Math.round(A*(i.length-1)/C),y=h.CC.color(i[b]),O.push(c=n[A]),O.push(c),O.push(d=a[A]),O.push(d),A<C-1){var k=n[A+1].clone().sub(n[A]);l=a[A].clone().sub(n[A]).cross(k).normalize().multiplyScalar(s)}for(O.push(f=n[A].clone().add(l)),O.push(f),O.push(p=a[A].clone().add(l)),O.push(p),void 0!==c.atom&&(x=c.atom),L=(E=e.updateGeoGroup(8)).vertexArray,F=E.colorArray,I=E.faceArray,L[g=3*(m=E.vertices)]=c.x,L[g+1]=c.y,L[g+2]=c.z,L[g+3]=c.x,L[g+4]=c.y,L[g+5]=c.z,L[g+6]=d.x,L[g+7]=d.y,L[g+8]=d.z,L[g+9]=d.x,L[g+10]=d.y,L[g+11]=d.z,L[g+12]=f.x,L[g+13]=f.y,L[g+14]=f.z,L[g+15]=f.x,L[g+16]=f.y,L[g+17]=f.z,L[g+18]=p.x,L[g+19]=p.y,L[g+20]=p.z,L[g+21]=p.x,L[g+22]=p.y,L[g+23]=p.z,S=0;S<8;++S)F[g+3*S]=y.r,F[g+1+3*S]=y.g,F[g+2+3*S]=y.b;if(A>0){var R=void 0!==w&&void 0!==x&&w.serial!==x.serial;for(S=0;S<4;S++){var P=[m+D[S][0],m+D[S][1],m+D[S][2],m+D[S][3]];if(I[v=E.faceidx]=P[0],I[v+1]=P[1],I[v+2]=P[3],I[v+3]=P[1],I[v+4]=P[2],I[v+5]=P[3],E.faceidx+=6,x.clickable||w.clickable||x.hoverable||w.hoverable){var U=O[P[3]].clone(),B=O[P[0]].clone(),N=O[P[2]].clone(),G=O[P[1]].clone();if(U.atom=O[P[3]].atom||null,N.atom=O[P[2]].atom||null,B.atom=O[P[0]].atom||null,G.atom=O[P[1]].atom||null,R){var V=U.clone().add(B).multiplyScalar(.5),j=N.clone().add(G).multiplyScalar(.5),H=U.clone().add(G).multiplyScalar(.5);S%2==0?((w.clickable||w.hoverable)&&(z=new o.Triangle(V,H,U),M=new o.Triangle(j,N,H),T=new o.Triangle(H,N,U),w.intersectionShape.triangle.push(z),w.intersectionShape.triangle.push(M),w.intersectionShape.triangle.push(T)),(x.clickable||x.hoverable)&&(z=new o.Triangle(B,G,H),M=new o.Triangle(G,j,H),T=new o.Triangle(B,H,V),x.intersectionShape.triangle.push(z),x.intersectionShape.triangle.push(M),x.intersectionShape.triangle.push(T))):((x.clickable||x.hoverable)&&(z=new o.Triangle(V,H,U),M=new o.Triangle(j,N,H),T=new o.Triangle(H,N,U),x.intersectionShape.triangle.push(z),x.intersectionShape.triangle.push(M),x.intersectionShape.triangle.push(T)),(w.clickable||w.hoverable)&&(z=new o.Triangle(B,G,H),M=new o.Triangle(G,j,H),T=new o.Triangle(B,H,V),w.intersectionShape.triangle.push(z),w.intersectionShape.triangle.push(M),w.intersectionShape.triangle.push(T)))}else(x.clickable||x.hoverable)&&(z=new o.Triangle(B,G,U),M=new o.Triangle(G,N,U),x.intersectionShape.triangle.push(z),x.intersectionShape.triangle.push(M))}}}E.vertices+=8,w=x}var W=O.length-8;for(L=(E=e.updateGeoGroup(8)).vertexArray,F=E.colorArray,I=E.faceArray,g=3*(m=E.vertices),v=E.faceidx,A=0;A<4;A++){O.push(O[2*A]),O.push(O[W+2*A]);var q=O[2*A],Y=O[W+2*A];L[g+6*A]=q.x,L[g+1+6*A]=q.y,L[g+2+6*A]=q.z,L[g+3+6*A]=Y.x,L[g+4+6*A]=Y.y,L[g+5+6*A]=Y.z,F[g+6*A]=y.r,F[g+1+6*A]=y.g,F[g+2+6*A]=y.b,F[g+3+6*A]=y.r,F[g+4+6*A]=y.g,F[g+5+6*A]=y.b}W+=8,z=[m,m+2,m+6,m+4],M=[m+1,m+5,m+7,m+3],I[v]=z[0],I[v+1]=z[1],I[v+2]=z[3],I[v+3]=z[1],I[v+4]=z[2],I[v+5]=z[3],I[v+6]=M[0],I[v+7]=M[1],I[v+8]=M[3],I[v+9]=M[1],I[v+10]=M[2],I[v+11]=M[3],E.faceidx+=12,E.vertices+=8}}(e,t,i,r,s):"rectangle"!==a&&"oval"!==a&&"parabola"!==a||function(e,t,i,r,s,n,a){var l,c,d,f,p,m,g,v,y,b;if((d=t.length)<2||t[0].length<2)return;for(l=0;l<d;l++)t[l]=u(t[l],r);if(f=t[0].length,!s)return _(e,t[0],t[d-1],i);var x=[],w=[],A=[];for(c=0;c<d;c++)x.push(.25+1.5*Math.sqrt((d-1)*c-Math.pow(c,2))/(d-1)),w.push(.5),A.push(2*(Math.pow(c/d,2)-c/d)+.6);var C,S,z,M,T,E,L,F,I,O,D=[];for(c=0;c<2*d-1;c++)D[c]=[c,c+1,c+1-2*d,c-2*d];D[2*d-1]=[c,c+1-2*d,c+1-4*d,c-2*d];let k=e.updateGeoGroup();for(l=0;l<f;l++){let r=e.groups,n=!1;var R,P;for(k=e.updateGeoGroup(2*d),r!=e.groups&&l>0&&(l-=1,n=!0),E=Math.round(l*(i.length-1)/f),T=h.CC.color(i[E]),y=g,b=v,g=[],v=[],p=[],void 0!==t[0][l].atom&&(M=t[0][l].atom,"oval"===a?m=x:"rectangle"===a?m=w:"parabola"===a&&(m=A)),m||(m=w),c=0;c<d;c++)R=l<f-1?t[c][l+1].clone().sub(t[c][l]):t[c][l-1].clone().sub(t[c][l]).negate(),P=c<d-1?t[c+1][l].clone().sub(t[c][l]):t[c-1][l].clone().sub(t[c][l]).negate(),p[c]=P.cross(R).normalize().multiplyScalar(s*m[c]);for(c=0;c<d;c++)g[c]=t[c][l].clone().add(p[c].clone().negate());for(c=0;c<d;c++)v[c]=t[c][l].clone().add(p[c]);for(L=k.vertexArray,F=k.colorArray,I=k.faceArray,S=3*(C=k.vertices),c=0;c<d;c++)L[S+3*c+0]=g[c].x,L[S+3*c+1]=g[c].y,L[S+3*c+2]=g[c].z;for(c=0;c<d;c++)L[S+3*c+0+3*d]=v[d-1-c].x,L[S+3*c+1+3*d]=v[d-1-c].y,L[S+3*c+2+3*d]=v[d-1-c].z;for(c=0;c<2*d;++c)F[S+3*c+0]=T.r,F[S+3*c+1]=T.g,F[S+3*c+2]=T.b;if(l>0&&!n){for(c=0;c<2*d;c++)O=[C+D[c][0],C+D[c][1],C+D[c][2],C+D[c][3]],I[z=k.faceidx]=O[0],I[z+1]=O[1],I[z+2]=O[3],I[z+3]=O[1],I[z+4]=O[2],I[z+5]=O[3],k.faceidx+=6;if(M.clickable||M.hoverable){var U=[];for(c in U.push(new o.Triangle(y[0],g[0],g[d-1])),U.push(new o.Triangle(y[0],g[d-1],y[d-1])),U.push(new o.Triangle(y[d-1],g[d-1],v[d-1])),U.push(new o.Triangle(y[d-1],v[d-1],b[d-1])),U.push(new o.Triangle(v[0],b[0],b[d-1])),U.push(new o.Triangle(v[d-1],v[0],b[d-1])),U.push(new o.Triangle(g[0],y[0],b[0])),U.push(new o.Triangle(v[0],g[0],b[0])),U)M.intersectionShape.triangle.push(U[c])}}k.vertices+=2*d}for(L=k.vertexArray,F=k.colorArray,I=k.faceArray,S=3*(C=k.vertices),z=k.faceidx,l=0;l<d-1;l++)O=[l,l+1,2*d-2-l,2*d-1-l],I[z=k.faceidx]=O[0],I[z+1]=O[1],I[z+2]=O[3],I[z+3]=O[1],I[z+4]=O[2],I[z+5]=O[3],k.faceidx+=6;for(l=0;l<d-1;l++)O=[C-1-l,C-2-l,C-2*d+l+1,C-2*d+l],I[z=k.faceidx]=O[0],I[z+1]=O[1],I[z+2]=O[3],I[z+3]=O[1],I[z+4]=O[2],I[z+5]=O[3],k.faceidx+=6}(e,t,i,r,s,0,a)}function b(e){return e&&"C"===e.elem&&"CA"===e.atom}function x(e,t){if(e&&t&&e.chain===t.chain){if(!(e.hetflag||t.hetflag||e.reschain!==t.reschain||e.resi!==t.resi&&e.resi!==t.resi-1))return!0;if(e.resi<t.resi){var i=e.x-t.x,r=e.y-t.y,s=e.z-t.z,n=i*i+r*r+s*s;if("CA"==e.atom&&"CA"==t.atom&&n<16)return!0;if(("P"==e.atom||"P"==t.atom)&&n<64)return!0}}return!1}function w(e,t,i,r,s){if(null!=t&&0!=t.vertices){s&&(t.initTypedArrays(),t.setUpNormals());var n=new a.MeshDoubleLambertMaterial;n.vertexColors=a.Coloring.FaceColors,"number"==typeof i&&i>=0&&i<1&&(n.transparent=!0,n.opacity=i),n.outline=r;var o=new a.Mesh(t,n);e.add(o)}}function A(e,t,i,r,s,n,a,o,h){var c,d,u,v,_,y;if(r&&s&&a){var b=s.sub(r);b.normalize();var x=o[h];for(d=h+1;d<o.length&&(x=o[d]).atom!=a.atom;d++);if((x=x?new l.Vector3(x.x,x.y,x.z):new l.Vector3(0,0,0)).sub(r),"arrow start"===a.ss){var w=x.clone().multiplyScalar(.3).cross(s);r.add(w);var A=x.clone().cross(b).normalize();b.rotateAboutVector(A,.43)}for(a.style.cartoon.ribbon?c=a.style.cartoon.thickness||g:a.style.cartoon.width?c=a.style.cartoon.width:"c"===a.ss?c="P"===a.atom?m:f:"arrow start"===a.ss?(c=p,_=!0):c="arrow end"===a.ss||"h"===a.ss&&a.style.cartoon.tubes||"tube start"===a.ss?f:p,null!=n&&b.dot(n)<0&&b.negate(),b.multiplyScalar(c),d=0;d<t;d++)u=2*d/(t-1)-1,(v=new l.Vector3(r.x+u*b.x,r.y+u*b.y,r.z+u*b.z)).atom=a,i&&"s"===a.ss&&(v.smoothen=!0),e[d].push(v);if(_)for(b.multiplyScalar(2),d=0;d<t;d++)u=2*d/(t-1)-1,(v=new l.Vector3(r.x+u*b.x,r.y+u*b.y,r.z+u*b.z)).atom=a,v.smoothen=!1,v.skip=!0,e[d].push(v);return y=a.style.cartoon.style||"default",e.style?e.style!=y&&(console.log("Warning: a cartoon chain's strand-style is ambiguous"),e.style="default"):e.style=y,"arrow start"!==a.ss&&"arrow end"!==a.ss||(a.ss="s"),_}}const C={C:!0,CA:!0,O:!0,P:!0,OP2:!0,O2P:!0,"O5'":!0,"O3'":!0,"C5'":!0,"C2'":!0,"O5*":!0,"O3*":!0,"C5*":!0,"C2*":!0,N1:!0,N3:!0},S={DA:!0,DG:!0,A:!0,G:!0},z={DT:!0,DC:!0,U:!0,C:!0,T:!0},M={DA:!0,DG:!0,A:!0,G:!0,DT:!0,DC:!0,U:!0,C:!0,T:!0};function T(e,t,i,n=10){let u=n,f=n;var p,m,_,T,E,L,F,I,O,D,k,R,P,U,B,N,G,V,j=new a.Geometry(!0),H=new a.Geometry(!0),W=[],q=[],Y=1,Z=!1,X={};for(var K in 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P=0;for(p=0;p<T;p++){var U=g.chainsPerModel[p],B=v[v.length-1],N=[];for(_.push({symmetries:E,cryst:I}),h=0;h<U;++h){var G=g.groupsPerChain[y],V=K(g.chainIdList.subarray(4*y,4*y+4));g.chainNameList&&(V=K(g.chainNameList.subarray(4*y,4*y+4)));var j=b,H="";for(c=0;c<G;++c){var W=g.groupList[g.groupTypeList[b]],q=W.atomNameList.length,Y=0,Z=!1,J=!1;if(w){Y=w[b];var ee=Q(Y);0!=b&&ee==H||(Z=!0),H=ee;var te=b+1;(te>=w.length||Q(w[te]!=ee))&&(J=!0)}var ie=g.groupIdList[b],re=W.groupName;let e=W.chemCompType;var se=x;let t=$.has(e)||!D[y];for(u=0