// =====================================================
// ZeMol - Visualizador de moléculas 3D
// =====================================================

// --- reset global (permite rerodar sem refresh) ---
try {
  var G = window.__PDB3D__;
  if (G && G.ui && G.ui.remove) G.ui.remove();
  if (G && G.meta && G.meta.remove) G.meta.remove();
} catch(e){}
window.__PDB3D__ = {};

// ======= Estado global =======
var __baseData = [], __hiData = [], __baseLayout = null, __lastParsed = null;
var __ssData = {helix:[], sheet:[]}, __ssSel = {helix:false, sheet:false}; // OFF por padrão
var __polOn = false, __polTrace = null;

// sliders
var __caSize = 6;   // tamanho das esferas (CA/átomos)
// sliders
var __opacity = 1.0;   // opacidade global

// MOL/SDF/XYZ
var __isGenericMol = false;
var __molAtoms = null, __molBonds = null;

(function(){
  if (window.__PDB3D__.init) return; window.__PDB3D__.init = true;

  var host = document.getElementById("grafico");

  // ---------- UI ----------
  var ui = document.createElement("div");
  ui.id = "pdb3d-ui2";
  ui.style.margin = "6px 0";
  ui.style.display = "flex";
  ui.style.flexWrap = "wrap";
  ui.style.gap = "8px";
  ui.style.alignItems = "center";
  host.parentNode.insertBefore(ui, host);
  window.__PDB3D__.ui = ui;

  function mkSpan(t){ var s=document.createElement("span"); s.textContent=t; return s; }

  ui.appendChild(mkSpan("Arquivo PDB/MOL/SDF/XYZ:"));
  var inpFile = document.createElement("input");
  inpFile.type = "file";
  inpFile.accept = ".pdb,.ent,.mol,.sdf,.xyz,.txt,text/plain";
  ui.appendChild(inpFile);

  ui.appendChild(mkSpan(" ou PDB ID:"));
  var inpId = document.createElement("input");
  inpId.type = "text"; inpId.placeholder = "ex.: 1CRN"; inpId.size = 8;
  ui.appendChild(inpId);

  var btnFetch = document.createElement("button");
  btnFetch.textContent = "baixar";
  ui.appendChild(btnFetch);
  
  ui.appendChild(mkSpan("  ou PubChem:"));
var inpPub = document.createElement("input");
inpPub.type = "text";
inpPub.placeholder = "CID ou nome (ex.: 2244 ou caffeine)";
inpPub.size = 18;
ui.appendChild(inpPub);

var btnPub = document.createElement("button");
btnPub.textContent = "PubChem 3D";
ui.appendChild(btnPub);


  var info = document.createElement("span");
  info.style.fontSize = "12px"; info.style.color = "#555";
  info.textContent = " selecione arquivo ou informe ID";
  ui.appendChild(info);

  // seleção
  var selBox = document.createElement("input");
  selBox.type = "text";
  selBox.placeholder = "ex.: Arg15, A:15-30, Asp117  |  em MOL: 1-20, C,N,O";
  selBox.size = 36;
  ui.appendChild(selBox);

  var btnHi = document.createElement("button"); btnHi.textContent = "destacar"; ui.appendChild(btnHi);
  var btnClear = document.createElement("button"); btnClear.textContent = "limpar"; ui.appendChild(btnClear);

  // toggles HELIX/SHEET (desmarcados por padrão)
  var cbHelix = document.createElement("input"); cbHelix.type = "checkbox"; cbHelix.checked = false; ui.appendChild(cbHelix);
  var lbHelix = document.createElement("label"); lbHelix.textContent = "hélice"; lbHelix.style.marginRight = "8px"; ui.appendChild(lbHelix);
  var cbSheet = document.createElement("input"); cbSheet.type = "checkbox"; cbSheet.checked = false; ui.appendChild(cbSheet);
  var lbSheet = document.createElement("label"); lbSheet.textContent = "folha β"; ui.appendChild(lbSheet);
  cbHelix.onchange = function(){ __ssSel.helix = !!cbHelix.checked; updatePlot(); };
  cbSheet.onchange = function(){ __ssSel.sheet = !!cbSheet.checked; updatePlot(); };

  // polaridade (PDB apenas)
  var btnPol = document.createElement("button"); btnPol.textContent = "polaridade"; ui.appendChild(btnPol);
  btnPol.onclick = function(){ if(!__isGenericMol){ __polOn = !__polOn; btnPol.style.fontWeight = __polOn ? "700":"400"; updatePlot(); } };

  // slider CA size
  ui.appendChild(mkSpan(" CA size:"));
  var sliderCA = document.createElement("input");
  sliderCA.type = "range"; sliderCA.min = 1; sliderCA.max = 100; sliderCA.value = __caSize;
  sliderCA.style.width = "120px";
  ui.appendChild(sliderCA);
  sliderCA.oninput = function(){ __caSize = parseInt(sliderCA.value,10); updatePlot(); };

  // slider opacidade
  ui.appendChild(mkSpan(" opacidade:"));
  var sliderOp = document.createElement("input");
  sliderOp.type = "range"; sliderOp.min = 1; sliderOp.max = 100; sliderOp.value = Math.round(__opacity*100);
  sliderOp.style.width = "120px";
  ui.appendChild(sliderOp);
  sliderOp.oninput = function(){
    __opacity = Math.max(0, Math.min(1, parseInt(sliderOp.value,10)/100));
    updatePlot();
  };

  // ---- barra de metadados ----
  var metaBar = document.createElement("div");
  metaBar.id = "pdb3d-meta";
  metaBar.style.margin = "6px 0 10px 0";
  metaBar.style.padding = "8px";
  metaBar.style.border = "1px solid #ddd";
  metaBar.style.borderRadius = "6px";
  metaBar.style.background = "#fafafa";
  metaBar.style.fontSize = "12px";
  metaBar.style.lineHeight = "1.35em";
  host.parentNode.insertBefore(metaBar, host);
  window.__PDB3D__.meta = metaBar;

  // wrapper
  var root = host.parentNode, wrap = document.getElementById("pdb3d-wrap");
  if (!wrap) {
    wrap = document.createElement("div");
    wrap.id = "pdb3d-wrap";
    wrap.style.display = "grid";
    wrap.style.gridTemplateRows = "auto auto 1fr";
    wrap.style.gap = "8px";
    wrap.style.width = "100%";
    wrap.style.boxSizing = "border-box";
    root.insertBefore(wrap, host);
  }
  if (ui.parentNode !== wrap) wrap.appendChild(ui);
  if (metaBar.parentNode !== wrap) wrap.appendChild(metaBar);
  if (host.parentNode !== wrap) wrap.appendChild(host);
  ui.style.width = "100%"; metaBar.style.width = "100%"; host.style.width = "100%";
  host.style.display = "block"; host.style.clear = "both"; host.style.minHeight = "820px";

  function updateMetaBar(meta, counts, extra){
    var t = meta && meta.title ? meta.title : "";
    var h = meta && meta.header? meta.header: "";
    var txt = (__isGenericMol
      ? ("MOL/SDF/XYZ — átomos: "+(counts.atoms||0)+"  ligações: "+(counts.bonds||0))
      : (h+"--"+t+"  cadeias: "+(counts.chains||0)+"   ligantes: "+(counts.lig||0)+"   ions: "+(counts.ions||0)+"   S-S: "+(counts.ss||0))
    );
    metaBar.textContent = txt + (extra ? ("  "+extra) : "");
  }

  // ===== Cores e utils =====
  var chainPalette = ["#1f77b4","#ff7f0e","#2ca02c","#d62728","#9467bd","#8c564b","#e377c2","#7f7f7f","#bcbd22","#17becf"];
  var ionColors = {"NA":"#1f77b4","K":"#9467bd","CA":"#2ca02c","MG":"#8c564b","ZN":"#7f7f7f","FE":"#d62728","MN":"#bcbd22","CU":"#ff7f0e","NI":"#17becf","CO":"#e377c2"};
  var ionSet={}; for (var k in ionColors) ionSet[k]=true;

  // CPK (compacto)
  var CPK = {
    H:"#FFFFFF", C:"#909090", N:"#3050F8", O:"#FF0D0D", F:"#90E050", CL:"#1FF01F",
    BR:"#A62929", I:"#940094", P:"#FF8000", S:"#FFFF30",
    NA:"#AB5CF2", K:"#8F40D4", MG:"#8AFF00", CA:"#3DFF00",
    FE:"#E06633", ZN:"#7D80B0", CU:"#C88033", NI:"#50D050",
    SI:"#F0C8A0", SE:"#FFA100", AU:"#FFD123", AG:"#C0C0C0"
  };
  function cpk(el){ if(!el) return "#CCCCCC"; el=String(el).toUpperCase().trim(); return CPK[el] || CPK[el.replace(/[^A-Z]/g,"")] || "#CCCCCC"; }

  var NL=String.fromCharCode(10), CR=String.fromCharCode(13);
  function splitLines(t){ var s=String(t||""); s=s.split(CR+NL).join(NL); s=s.split(CR).join(NL); return s.split(NL); }
  function dist2(a,b){ var dx=a.x-b.x,dy=a.y-b.y,dz=a.z-b.z; return dx*dx+dy*dy+dz*dz; }
  function splitSpaces(s){ var a=[],cur=""; for (var i=0;i<s.length;i++){ var ch=s.charAt(i); if(ch===" "||ch==="	"){ if(cur){a.push(cur);cur="";} } else { cur+=ch; } } if(cur){a.push(cur);} return a; }

  // AA / NA
  var AA3 = {ALA:"ALA",ARG:"ARG",ASN:"ASN",ASP:"ASP",CYS:"CYS",GLN:"GLN",GLU:"GLU",GLY:"GLY",HIS:"HIS",ILE:"ILE",LEU:"LEU",LYS:"LYS",MET:"MET",PHE:"PHE",PRO:"PRO",SER:"SER",THR:"THR",TRP:"TRP",TYR:"TYR",VAL:"VAL"};
  var AA1 = {A:"ALA",R:"ARG",N:"ASN",D:"ASP",C:"CYS",Q:"GLN",E:"GLU",G:"GLY",H:"HIS",I:"ILE",L:"LEU",K:"LYS",M:"MET",F:"PHE",P:"PRO",S:"SER",T:"THR",W:"TRP",Y:"TYR",V:"VAL"};
  
  // --- grupos e helpers de AA ---
var AA_GROUPS = {
  basico:       ["ARG","LYS","HIS"],
  acido:      ["ASP","GLU"],
  aromatico:    ["PHE","TYR","TRP"],
  polar:       ["SER","THR","ASN","GLN","TYR","CYS","HIS"],
  apolar: ["ILE","VAL","LEU","PHE","CYS","MET","ALA","TRP","TYR"],
  small:       ["GLY","ALA","SER"],
  carga:     ["ASP","GLU","ARG","LYS","HIS"]
};

function normalizeAA(tok){ // 1 letra -> 3 letras; já-3-letras permanece
  if (!tok) return null;
  tok = tok.toUpperCase().trim();
  if (tok.length===1 && AA1[tok]) return AA1[tok];
  if (AA3[tok]) return tok;
  return null;
}
function aaListFromToken(s){ // aceita “ARG”, “R”, “ARG/LYS”, “arg+lys”, “aromatic”, etc.
  if (!s) return null;
  s = s.trim();
  var key = s.toLowerCase();

  // grupo?
  if (AA_GROUPS[key]) return AA_GROUPS[key].slice();

  // lista explícita (separada por , ; / +)
  var parts = s.split(/[,+/;s]+/).filter(Boolean);
  if (parts.length){
    var out = [];
    for (var i=0;i<parts.length;i++){
      var aa = normalizeAA(parts[i]);
      if (aa) out.push(aa);
    }
    if (out.length) return out;
  }
  // 1 item simples
  var aa1 = normalizeAA(s);
  return aa1? [aa1] : null;
}

  
  var KD  = {ILE:4.5,VAL:4.2,LEU:3.8,PHE:2.8,CYS:2.5,MET:1.9,ALA:1.8,GLY:-0.4,THR:-0.7,SER:-0.8,TRP:-0.9,TYR:-1.3,PRO:-1.6,HIS:-3.2,GLU:-3.5,GLN:-3.5,ASP:-3.5,ASN:-3.5,LYS:-3.9,ARG:-4.5};
  function aaPolarity(res){ var kd = KD[(res||"").toUpperCase()]; return (typeof kd==="number")? -kd : 0; }

  var NA_RES = {DA:1,DC:1,DG:1,DT:1, A:1,C:1,G:1,U:1, ADE:1,CYT:1,GUA:1,THY:1,URA:1};
  function isNA(r){ return !!NA_RES[String(r||"").toUpperCase()]; }
  function isNABackboneAtom(n){ n=String(n||"").toUpperCase(); return (n==="P" || n==="C4'" || n==="C4*"); }
  function isAA3(x){ return !!AA3[String(x||"").toUpperCase()]; }

  // HEADER/TITLE
  function extractHeaderTitle(pdbText){
    var lines=splitLines(pdbText),header="",title="";
    for (var i=0;i<lines.length;i++){
      var L=lines[i]; if (L.length<5) continue; var rec=L.substr(0,6);
      if (rec==="HEADER"&&header===""){ header=L.substr(10).trim(); }
      if (L.substr(0,5)==="TITLE"){ var part=L.substr(10).trim(); if(part) title+=(title?" ":"")+part; }
      if (rec==="ATOM  "||rec==="HETATM") break;
    } return {header:header,title:title};
  }

  // seleção AA
  function buildCAIndex(CA){
    var idx={}; for (var ch in CA){ var arr=CA[ch]||[]; idx[ch]={}; for (var i=0;i<arr.length;i++){ idx[ch][arr[i].resSeq]=arr[i]; } }
    return idx;
  }
  function parseResidLabel(lbl){
  lbl = String(lbl||"").trim();
  if (!lbl) return null;

  var chain = null;
  var parts = lbl.split(":");
  if (parts.length===2){
    chain = (parts[0]||"").trim().toUpperCase() || null;
    lbl   = (parts[1]||"").trim();
  }

  // caso 1: só-letras (ex.: ARG | arg/lys | aromatic)
  if (/^[A-Za-z+-_,;/s]+$/.test(lbl) && !/[0-9]/.test(lbl)){
    var list = aaListFromToken(lbl);
    if (list && list.length){
      return { chain: chain, aaList: list }; // << nova via
    }
    return { chain: chain, raw: lbl };
  }

  // caso 2: faixa tipo "15-30"
  var range = lbl.split("-");
  if (range.length===2){
    return { chain: chain, range: [range[0].trim(), range[1].trim()] };
  }

  // caso 3: AA + número (ARG117, A117, etc.)
  var m = /^([A-Za-z]{1,3})?([0-9]+)$/.exec(lbl);
  if (!m) return { chain: chain, raw: lbl };

  var aa = m[1] ? m[1].toUpperCase() : null;
  var n  = parseInt(m[2],10);
  if (aa && aa.length===1 && AA1[aa]) aa = AA1[aa];
  if (aa && AA3[aa]!==aa) aa = AA3[aa] || aa;

  return { chain: chain, aa: aa, n: n };
}

  function expandEntry(entry){
    function numFrom(s){ var m=/^([A-Za-z]{0,3})?([0-9]+)$/.exec(String(s||"").trim()); return m?parseInt(m[2],10):null; }
    var out=[]; if(entry.range){ var n1=numFrom(entry.range[0]), n2=numFrom(entry.range[1]); if(n1!=null&&n2!=null){ if(n1>n2){var t=n1;n1=n2;n2=t;} for(var n=n1;n<=n2;n++) out.push({chain:entry.chain,n:n}); } return out; }
    if(entry.n!=null) out.push({chain:entry.chain,n:entry.n,aa:entry.aa}); return out;
  }
  function parseSelectionQuery(q, CA){
  if (__isGenericMol) return parseSelectionForMol(q); // modo MOL/XYZ

  var idx = buildCAIndex(CA);
  var items = String(q||"").split(",");
  var sel = [];

  for (var i=0;i<items.length;i++){
    var tok = parseResidLabel(items[i]);
    if (!tok) continue;

    // (A) lista de AAs (ex.: ARG, ARG/LYS, aromatic...)
    if (tok.aaList && tok.aaList.length){
      var want = {}; tok.aaList.forEach(function(a){ want[a]=1; });
      if (tok.chain){
        var arr = CA[tok.chain]||[];
        for (var u=0; u<arr.length; u++){
          var r = arr[u];
          if (want[(r.resName||"").toUpperCase()]) sel.push(r);
        }
      } else {
        for (var ch in CA){
          var arr2 = CA[ch]||[];
          for (var v=0; v<arr2.length; v++){
            var r2 = arr2[v];
            if (want[(r2.resName||"").toUpperCase()]) sel.push(r2);
          }
        }
      }
      continue;
    }

    // (B) faixas/índices já existentes
    var expanded = expandEntry(tok, CA);
    for (var k=0;k<expanded.length;k++){
      var c = expanded[k].chain, n = expanded[k].n;
      if (!c){
        for (var ch in idx){
          var obj = idx[ch][n]; if (!obj) continue;
          if (tok.aa && obj.resName.toUpperCase() !== tok.aa) continue;
          sel.push(obj);
        }
      } else {
        var obj2 = (idx[c]||{})[n];
        if (obj2){
          if (tok.aa && obj2.resName.toUpperCase() !== tok.aa) continue;
          sel.push(obj2);
        }
      }
    }
  }

  // unique por chain:resSeq
  var seen={}, uniq=[];
  for (var j=0;j<sel.length;j++){
    var key=(sel[j].chain||"_")+":"+sel[j].resSeq;
    if (!seen[key]){ seen[key]=1; uniq.push(sel[j]); }
  }
  return uniq;
}


  function makeHighlightTraces(selected){
    if(!selected||!selected.length) return [];
    var xs=[],ys=[],zs=[],txt=[];
    for(var i=0;i<selected.length;i++){
      var r=selected[i]; xs.push(r.x); ys.push(r.y); zs.push(r.z);
      txt.push("Cadeia "+(r.chain||" ")+(r.resName?" "+r.resName:"")+" "+(r.resSeq||""));
    }
    return [{
      type:"scatter3d", mode:"markers",
      x:xs, y:ys, z:zs, text:txt, hoverinfo:"text",
      name:"selecionados",
      marker:{ size:8, opacity:__opacity, color:"#e31a1c" }
    }];
  }

  function fadeBaseData(enable){
    if(!__baseData) return;
    for(var i=0;i<__baseData.length;i++){
      var tr=__baseData[i];
      if(tr.type==="scatter3d"){
        if(tr.line)   tr.line.opacity   = enable? 0.25 : __opacity;
        if(tr.marker) tr.marker.opacity = enable? 0.25 : __opacity;
      }
    }
  }

  // ---------- Parser PDB ----------
  function parsePDB(txt){
    var lines=splitLines(txt);
    var CA={},CYS_CA={},CYS_SG=[],ssBonds=[],ions=[],ligResidues={},helices=[],sheets=[];
    var modelStarted=false,firstModelOnly=true;

    for(var i=0;i<lines.length;i++){
      var line=lines[i]; if(line.length<6) continue; var rec=line.substr(0,6);

      if(rec==="HELIX "){
        var ch1=(line.length>20? line.substr(19,1):" ").trim()||" ";
        var s1 =parseInt((line.length>25? line.substr(21,4):"").trim(),10);
        var ch2=(line.length>33? line.substr(31,1):" ").trim()||" ";
        var s2 =parseInt((line.length>38? line.substr(33,4):"").trim(),10);
        if(isFinite(s1)&&isFinite(s2)) helices.push({chain:ch1,start:s1,end:s2});
        continue;
      }
      if(rec==="SHEET "){
        var chS=(line.length>22? line.substr(21,1):" ").trim()||" ";
        var sS =parseInt((line.length>27? line.substr(22,4):"").trim(),10);
        var chE=(line.length>34? line.substr(32,1):" ").trim()||" ";
        var eS =parseInt((line.length>39? line.substr(33,4):"").trim(),10);
        if(isFinite(sS)&&isFinite(eS)) sheets.push({chain:chS,start:sS,end:eS});
      }

      if(rec==="MODEL "){ if(firstModelOnly){ if(modelStarted) break; modelStarted=true; } }
      if(rec==="ENDMDL"){ if(firstModelOnly) break; }

      if(rec==="SSBOND"){
        var c1=line.substr(15,1),s1b=parseInt(line.substr(17,4),10);
        var c2=line.substr(29,1),s2b=parseInt(line.substr(31,4),10);
        if(isFinite(s1b)&&isFinite(s2b)) ssBonds.push({c1:c1,r1:s1b,c2:c2,r2:s2b});
        continue;
      }
      if(rec!=="ATOM  "&&rec!=="HETATM") continue;
      if(line.length<54) continue;

      var name=line.substr(12,4).trim();
      var resName=line.substr(17,3).trim();
      var chain=line.substr(21,1)||" ";
      var resSeq=parseInt(line.substr(22,4),10);
      var iCode=line.substr(26,1).trim();
      var x=parseFloat(line.substr(30,8)), y=parseFloat(line.substr(38,8)), z=parseFloat(line.substr(46,8));
      var alt=line.substr(16,1);
      if(!isFinite(x)||!isFinite(y)||!isFinite(z)) continue;
      if(alt&&alt!==" "&&alt!=="A") continue;

      if(rec==="ATOM  "){
        // Proteína: CA; Nucleotídeo: P/C4' como pseudo-CA
        var takeAsBackbone = false;
        if (name==="CA") takeAsBackbone = true;
        else if (isNA(resName) && isNABackboneAtom(name)) takeAsBackbone = true;

        if (takeAsBackbone){
          if(!CA[chain]) CA[chain]=[];
          var obj={x:x,y:y,z:z,resName:resName,resSeq:resSeq,iCode:iCode,chain:chain};

          // tenta ler valor ao fim; senão: aa→KD, NA→0
          var pol=null;
          if (line.length>66){
            var tail=line.substr(66).trim();
            if (tail){
              var toks=splitSpaces(tail);
              var last=toks.length? toks[toks.length-1] : "";
              var v=parseFloat(last);
              if (!isNaN(v)) pol=v;
            }
          }
          if (pol===null) pol = isNA(resName) ? 0 : aaPolarity(resName);
          obj.pol=pol;

          CA[chain].push(obj);

          if(resName==="CYS" && name==="CA"){
            CYS_CA[chain+":"+resSeq]={x:x,y:y,z:z};
          }
        }

        if(resName==="CYS" && name==="SG"){ CYS_SG.push({chain:chain,resSeq:resSeq,x:x,y:y,z:z}); }
      } else {
        var isWater=(resName==="HOH"||resName==="WAT"||resName==="DOD"||resName==="SOL");
        if (isWater) continue;

        var el=""; if (line.length>=78) el=line.substr(76,2).trim().toUpperCase();
        if (!el) el=line.substr(12,2).trim().toUpperCase();

        if (ionSet[el]){
          ions.push({x:x,y:y,z:z,el:el,name:name,resName:resName,chain:chain,resSeq:resSeq});
        } else {
          var key=chain+":"+resSeq+":"+resName;
          if (!ligResidues[key]) ligResidues[key]={ chain:chain, resSeq:resSeq, resName:resName, atoms:[] };
          ligResidues[key].atoms.push({x:x,y:y,z:z, el:el, atom:name});
          if (!ligResidues.__names) ligResidues.__names={};
          ligResidues.__names[resName]=true;
        }
      }
    }

    var sPairs=[];
    for(var p=0;p<ssBonds.length;p++){
      var ssp=ssBonds[p];
      var ca1=CYS_CA[ssp.c1+":"+ssp.r1], ca2=CYS_CA[ssp.c2+":"+ssp.r2];
      if(ca1&&ca2) sPairs.push({a:ca1,b:ca2});
    }
    if(sPairs.length===0){
      var thr2=2.2*2.2;
      for(var i1=0;i1<CYS_SG.length;i1++){
        for(var j=i1+1;j<CYS_SG.length;j++){
          if(dist2(CYS_SG[i1],CYS_SG[j])<=thr2){
            var ca1=CYS_CA[CYS_SG[i1].chain+":"+CYS_SG[i1].resSeq];
            var ca2=CYS_CA[CYS_SG[j].chain+":"+CYS_SG[j].resSeq];
            if(ca1&&ca2) sPairs.push({a:ca1,b:ca2});
          }
        }
      }
    }

    var ligNames=[]; if (ligResidues.__names){ for (var nm in ligResidues.__names) ligNames.push(nm); ligNames.sort(); }
    return { CA:CA, sPairs:sPairs, ions:ions, ligResidues:ligResidues, ligNames:ligNames, helices:helices, sheets:sheets };
  }

  // ---------- Traces ----------
  function tracesCA(CA){
  var out=[],idx=0;
  for (var ch in CA){
    var arr=CA[ch];
    arr.sort(function(a,b){ return (a.resSeq-b.resSeq) || (a.iCode||"").localeCompare(b.iCode||""); });
    var xs=[],ys=[],zs=[],txt=[];
    for (var k=0;k<arr.length;k++){
      var r=arr[k]; xs.push(r.x); ys.push(r.y); zs.push(r.z);
      txt.push("Chain "+ch+" "+r.resName+" "+r.resSeq);
    }
    var chainLooksNA = arr.every(function(r){ return !isAA3(r.resName); });
    var col = chainLooksNA ? "#444444" : chainPalette[idx%chainPalette.length];

    out.push({
      type:"scatter3d",
      mode:"lines+markers",
      x:xs,y:ys,z:zs,text:txt,hoverinfo:"text",
      name:"Chain "+ch,
      line:{width:3,color:col,opacity:__opacity},
      marker:{size:__caSize,color:col,opacity:__opacity},
      _isCA:true // <<< flag pra sabermos que este trace é de CA
    });
    idx++;
  }
  return out;
}


  function tracesSS(sPairs){
    var out=[];
    for(var i=0;i<sPairs.length;i++){
      var p=sPairs[i];
      out.push({
        type:"scatter3d", mode:"lines",
        x:[p.a.x,p.b.x], y:[p.a.y,p.b.y], z:[p.a.z,p.b.z],
        name:"S-S", hoverinfo:"none",
        line:{width:4,color:"#ffd11a",opacity:__opacity},
        showlegend:(i===0)
      });
    }
    return out;
  }

function tracesLig(ligResidues){
  var out = [];
  var firstLegend = true;              // só o primeiro par (linhas+marcadores) aparece na legenda
  var thr = 1.9, thr2 = thr*thr;

  function ensure(dict,key){
    if(!dict[key]) dict[key] = {x:[],y:[],z:[], lx:[],ly:[],lz:[]};
    return dict[key];
  }

  for (var key in ligResidues){
    if (key === "__names") continue;
    var g = ligResidues[key], A = g.atoms;
    if (!A || !A.length) continue;

    var byEl = {};

    // pontos por elemento
    for (var k=0;k<A.length;k++){
      var el = (A[k].el||"").toUpperCase();
      var b  = ensure(byEl, el);
      b.x.push(A[k].x); b.y.push(A[k].y); b.z.push(A[k].z);
    }

    // ligações por distância (stick simples; usa a cor do 1º átomo do par)
    for (var i=0;i<A.length;i++){
      for (var j=i+1;j<A.length;j++){
        var dx=A[i].x-A[j].x, dy=A[i].y-A[j].y, dz=A[i].z-A[j].z;
        var d2=dx*dx+dy*dy+dz*dz;
        if (d2<=thr2){
          var elLine=(A[i].el||"").toUpperCase();
          var bb=ensure(byEl, elLine);
          bb.lx.push(A[i].x, A[j].x, null);
          bb.ly.push(A[i].y, A[j].y, null);
          bb.lz.push(A[i].z, A[j].z, null);
        }
      }
    }

    // emite para cada elemento um par (lines + markers) no mesmo grupo "lig"
    for (var el in byEl){
      var b = byEl[el];

      if (b.lx.length){
        out.push({
          type: "scatter3d",
          mode: "lines",
          x: b.lx, y: b.ly, z: b.lz,
          hoverinfo: "none",
          name: firstLegend ? "Ligantes (ligações)" : "Lig (ligações)",
          line: { width: 3, color: cpk(el), opacity: __opacity },
          showlegend: firstLegend,
          legendgroup: "lig"
        });
      }

      out.push({
        type: "scatter3d",
        mode: "markers",
        x: b.x, y: b.y, z: b.z,
        text: Array(b.x.length).fill("Ligante "+g.resName+" • "+el),
        hoverinfo: "text",
        name: firstLegend ? "Ligantes (átomos)" : "Lig (átomos)",
        marker: { size: 2, color: cpk(el), opacity: __opacity },
        showlegend: firstLegend,
        legendgroup: "lig"
      });

      firstLegend = false; // só o primeiro par entra na legenda
    }
  }

  return out;
}


  function tracesIons(ions){
    if(!ions.length) return [];
    var byEl={}, out=[];
    ions.forEach(function(a){ (byEl[a.el]=byEl[a.el]||[]).push(a); });
    for (var el in byEl){
      var arr=byEl[el], xs=[],ys=[],zs=[],txt=[];
      arr.forEach(function(a){ xs.push(a.x); ys.push(a.y); zs.push(a.z); txt.push(el+" ("+a.resName+")"); });
      out.push({
        type:"scatter3d", mode:"markers",
        x:xs,y:ys,z:zs, text:txt, hoverinfo:"text",
        name:"ion "+el,
        marker:{ size:7, color:(ionColors[el]||"#f0f"), opacity:__opacity }
      });
    }
    return out;
  }

  // HELIX/SHEET helpers
  function _sliceCA(CA, chain, start, end){
    var arr=(CA[chain]||[]).slice().sort(function(a,b){ if(a.resSeq!==b.resSeq) return a.resSeq-b.resSeq; return (a.iCode||"").localeCompare(b.iCode||""); });
    var xs=[],ys=[],zs=[],txt=[];
    for (var i=0;i<arr.length;i++){
      var r=arr[i]; if (r.resSeq>=start && r.resSeq<=end){
        xs.push(r.x); ys.push(r.y); zs.push(r.z);
        txt.push("Chain "+(r.chain||" ")+" "+r.resName+" "+r.resSeq);
      }
    }
    return {x:xs,y:ys,z:zs,txt:txt};
  }
  function tracesSecStruct(CA,segs,color,label){
    var out=[], first=true;
    for (var k=0;k<segs.length;k++){
      var s=segs[k];
      var poly=_sliceCA(CA,(s.chain||" ").toUpperCase(),s.start,s.end);
      if (poly.x.length<2) continue;
      out.push({
        type:"scatter3d", mode:"lines",
        x:poly.x,y:poly.y,z:poly.z, text:poly.txt, hoverinfo:"text",
        name:label,
        line:{width:8,color:color,opacity:__opacity},
        showlegend:first
      });
      out.push({
        type:"scatter3d", mode:"markers",
        x:poly.x,y:poly.y,z:poly.z, hoverinfo:"skip",
        name:label+" (pontos)",
        marker:{size:2,color:color,opacity:__opacity},
        showlegend:false
      });
      first=false;
    }
    return out;
  }

  // Polaridade
  function makePolarityTrace(CA){
    var xs=[],ys=[],zs=[],cv=[],txt=[],cmin=1e9,cmax=-1e9;
    for (var ch in CA){
      var arr=CA[ch]||[];
      for (var i=0;i<arr.length;i++){
        var r=arr[i];
        var pol=(typeof r.pol==="number")? r.pol : (isNA(r.resName)? 0 : aaPolarity(r.resName));
        xs.push(r.x); ys.push(r.y); zs.push(r.z); cv.push(pol);
        if (pol<cmin) cmin=pol; if (pol>cmax) cmax=pol;
        txt.push("Chain "+r.chain+" "+r.resName+" "+r.resSeq+" | pol "+(pol.toFixed?pol.toFixed(2):pol));
      }
    }
    if (!xs.length) return null;
    return {
      type:"scatter3d", mode:"markers",
      x:xs,y:ys,z:zs,text:txt,hoverinfo:"text",
      name:"polaridade (CA)",
      marker:{ size:5, color:cv, opacity:__opacity,
        colorscale:[[0,'#2166ac'],[0.5,'#f7f7f7'],[1,'#b2182b']], cmin:cmin, cmax:cmax,
        colorbar:{title:"polaridade"} },
      showlegend:true
    };
  }

function layout3D(title){
  return {
    title: title,
    scene:{ xaxis:{visible:false}, yaxis:{visible:false}, zaxis:{visible:false}, aspectmode:"data" },
    margin:{l:0,r:0,t:40,b:0},
    showlegend:true,
    legend: {
      // permite clicar uma única entrada "Ligantes" para esconder/mostrar todos
      groupclick: "togglegroup",
      itemclick: "toggle"
    }
  };
}


  // ======== MOL/SDF/XYZ parsers ========
  function parseMOLorSDF(text){
    var lines=splitLines(text), atoms=[], bonds=[];
    var i=0, v3000=false;
    for(; i<lines.length; i++){
      if(/^s*Ms+V30s+BEGINs+CTAB/i.test(lines[i])){ v3000=true; break; }
      if(/V2000/.test(lines[i])){ break; }
    }
    if(i>=lines.length) i=3; // fallback

    if(v3000){
      var inAtoms=false,inBonds=false;
      for(var k=0;k<lines.length;k++){
        var L=lines[k];
        if(/Ms+V30s+BEGINs+ATOM/i.test(L)){ inAtoms=true; continue; }
        if(/Ms+V30s+ENDs+ATOM/i.test(L)){ inAtoms=false; continue; }
        if(/Ms+V30s+BEGINs+BOND/i.test(L)){ inBonds=true; continue; }
        if(/Ms+V30s+ENDs+BOND/i.test(L)){ inBonds=false; continue; }
        if(inAtoms && /Ms+V30s+/i.test(L)){
          var t=splitSpaces(L.replace(/^.*Ms+V30s+/i,""));
          if(t.length>=6){ atoms.push({el:t[1], x:parseFloat(t[2]), y:parseFloat(t[3]), z:parseFloat(t[4])}); }
        }
        if(inBonds && /Ms+V30s+/i.test(L)){
          var b=splitSpaces(L.replace(/^.*Ms+V30s+/i,""));
          if(b.length>=5){ bonds.push({a1:parseInt(b[2],10)-1, a2:parseInt(b[3],10)-1, order:parseInt(b[1],10)||1}); }
        }
      }
    } else {
      var counts = lines[i]||"";
      var na = parseInt((counts.substr(0,3)||"0"),10);
      var nb = parseInt((counts.substr(3,3)||"0"),10);
      var aStart=i+1, bStart=aStart+na;
      for(var ia=0; ia<na; ia++){
        var L=lines[aStart+ia]||"";
        var x=parseFloat(L.substr(0,10)), y=parseFloat(L.substr(10,10)), z=parseFloat(L.substr(20,10));
        var el=(L.substr(31,3)||"").trim();
        atoms.push({el:el,x:x,y:y,z:z});
      }
      for(var ib=0; ib<nb; ib++){
        var B=lines[bStart+ib]||"";
        var a1=parseInt(B.substr(0,3),10)-1, a2=parseInt(B.substr(3,3),10)-1, order=parseInt(B.substr(6,3),10)||1;
        bonds.push({a1:a1,a2:a2,order:order});
      }
    }
    return {atoms:atoms,bonds:bonds};
  }

  function parseXYZ(text){
    var lines=splitLines(text).filter(Boolean);
    var n=parseInt(lines[0],10);
    var atoms=[];
    for(var i=2;i<2+n && i<lines.length;i++){
      var t=splitSpaces(lines[i]);
      if(t.length>=4){ atoms.push({el:t[0],x:parseFloat(t[1]),y:parseFloat(t[2]),z:parseFloat(t[3])}); }
    }
    return {atoms:atoms,bonds:inferBonds(atoms)};
  }

  // infer bonds por distância
  var RC={H:0.31,C:0.76,N:0.71,O:0.66,F:0.57,P:1.07,S:1.05,CL:1.02,BR:1.20,I:1.39};
  function rc(el){el=(el||"").toUpperCase(); return (RC[el]!=null?RC[el]:0.77);}
  function inferBonds(at){ var b=[], n=at.length; for(var i=0;i<n;i++) for(var j=i+1;j<n;j++){
    var rcut=1.2*(rc(at[i].el)+rc(at[j].el)); var d2=dist2(at[i],at[j]); if(d2<=rcut*rcut) b.push({a1:i,a2:j,order:1});
  } return b; }

  // Traces MOL/SDF/XYZ
  function tracesMol(atoms,bonds){
    if(!atoms||!atoms.length) return [];
    var xs=[],ys=[],zs=[];
    for (var i=0;i<bonds.length;i++){
      var a1=atoms[bonds[i].a1], a2=atoms[bonds[i].a2];
      if(!a1||!a2) continue;
      xs.push(a1.x,a2.x,null); ys.push(a1.y,a2.y,null); zs.push(a1.z,a2.z,null);
    }
    var out=[];
    if(xs.length){
      out.push({type:"scatter3d",mode:"lines",x:xs,y:ys,z:zs,hoverinfo:"none",name:"ligações",
                line:{width:3,color:"#888",opacity:__opacity},showlegend:true});
    }
    var ax=[],ay=[],az=[],col=[],txt=[];
    for (var k=0;k<atoms.length;k++){
      var a=atoms[k]; ax.push(a.x); ay.push(a.y); az.push(a.z); col.push(cpk(a.el)); txt.push((a.el||"?")+" #"+(k+1));
    }
    out.push({type:"scatter3d",mode:"markers",x:ax,y:ay,z:az,text:txt,hoverinfo:"text",name:"átomos",
              marker:{size:4,color:col,opacity:__opacity},showlegend:true});
    return out;
  }

  // seleção em MOL
  function parseSelectionForMol(q){
    if(!__molAtoms) return [];
    var parts=String(q||"").split(",").map(function(s){return s.trim();}).filter(Boolean);
    var idxSel={}, ret=[];
    function add(i){ if(i>=0 && i<__molAtoms.length && !idxSel[i]){ idxSel[i]=1; ret.push(__molAtoms[i]); } }
    for(var i=0;i<parts.length;i++){
      var p=parts[i];
      if(/^[0-9]+-[0-9]+$/.test(p)){ var t=p.split("-"); var a=parseInt(t[0],10)-1, b=parseInt(t[1],10)-1; if(a>b){var tt=a;a=b;b=tt;} for(var k=a;k<=b;k++) add(k); continue; }
      if(/^[0-9]+$/.test(p)){ add(parseInt(p,10)-1); continue; }
      var list=p.replace(/s+/g,"").split(/[,;]+/).filter(Boolean);
      if(list.length){
        var set={}; list.forEach(function(e){ set[e.toUpperCase()]=1; });
        for(var j=0;j<__molAtoms.length;j++){ if(set[(__molAtoms[j].el||"").toUpperCase()]) add(j); }
      }
    }
    return ret;
  }

  // ---------- Render ----------
  function renderFromPDB(txt,title){
    __isGenericMol=false;
    var meta=extractHeaderTitle(txt), parsed=parsePDB(txt), ligList=parsed.ligNames||[];

    var base=[]
      .concat(tracesCA(parsed.CA))
      .concat(tracesSS(parsed.sPairs))
      .concat(tracesLig(parsed.ligResidues))
      .concat(tracesIons(parsed.ions));

    if(!base.length){
      info.textContent=" nenhum dado plotavel";
      Plotly.react("grafico",[ {type:"scatter",x:[0],y:[0],mode:"text",text:["PDB sem dados"]} ],{title:"Sem dados"});
      updateMetaBar(meta,{chains:0,lig:0,ions:0,ss:0});
      return;
    }

    __baseData=base; __baseLayout=layout3D(title); __hiData=[]; __lastParsed=parsed;
    __ssData.helix=tracesSecStruct(parsed.CA,parsed.helices,"#ff0000","hélice α");
    __ssData.sheet=tracesSecStruct(parsed.CA,parsed.sheets, "#ffa500","folha β");
    __polTrace = makePolarityTrace(parsed.CA);

    var nChains=Object.keys(parsed.CA).length;
    var nLig=Object.keys(parsed.ligResidues).length; if(parsed.ligResidues.__names) nLig--;
    updateMetaBar(meta,{chains:nChains,lig:nLig,ions:parsed.ions.length,ss:parsed.sPairs.length},
                  (ligList.length?("lig: ["+ligList.join(", ")+"]"):""));
    fadeBaseData(false);
    __baseData.forEach(function(tr){ tr.__isBase = true; });

    updatePlot();
    info.textContent=" pronto: "+title.replace(/^PDB:s*/,"");
  }

  function renderFromMol(text, title){
    __isGenericMol=true; __polOn=false; __polTrace=null; __hiData=[];
    var mol=parseMOLorSDF(text);
    if(!mol.atoms.length){
      info.textContent=" arquivo sem átomos reconhecíveis";
      Plotly.react("grafico",[ {type:"scatter",x:[0],y:[0],mode:"text",text:["Sem dados"]} ],{title:"Sem dados"});
      return;
    }
    __molAtoms=mol.atoms; __molBonds=mol.bonds||inferBonds(mol.atoms);
    __baseData=tracesMol(__molAtoms,__molBonds);
    __baseLayout=layout3D(title); __lastParsed=null; __ssData.helix=[]; __ssData.sheet=[];
    updateMetaBar(null,{atoms:__molAtoms.length,bonds:__molBonds.length});
    Plotly.react("grafico", __baseData, __baseLayout);
    info.textContent=" pronto: "+title;
  }

  function renderFromXYZ(text, title){
    __isGenericMol=true; __polOn=false; __polTrace=null; __hiData=[];
    var mol=parseXYZ(text); __molAtoms=mol.atoms; __molBonds=mol.bonds;
    __baseData=tracesMol(__molAtoms,__molBonds);
    __baseLayout=layout3D(title); __lastParsed=null; __ssData.helix=[]; __ssData.sheet=[];
    updateMetaBar(null,{atoms:__molAtoms.length,bonds:__molBonds.length});
    Plotly.react("grafico", __baseData, __baseLayout);
    info.textContent=" pronto: "+title;
  }
  
  // depois de montar __baseData:
__baseData.forEach(function(tr){ tr.__isBase = true; });

  
  function __applySlidersToTraces(allTraces, fadeOn){
  // fadeOn = true quando polaridade/destaque estiverem ativos (deixa base mais clarinha)
  var baseOpacity = __opacity;
  var fadedOpacity = Math.min(0.25, baseOpacity);

  for (var i=0;i<allTraces.length;i++){
    var tr = allTraces[i];
    if (tr.type !== "scatter3d") continue;

    // Opacidade padrão
    var targetOpacity = baseOpacity;

    // Se for um trace que está nos "dados base" e o fade estiver ligado, clareia:
    // (marcamos o fade na própria chamada de updatePlot; aqui só aplicamos)
    if (tr.__isBase && fadeOn){
      targetOpacity = fadedOpacity;
    }

    if (tr.line){
      tr.line.opacity = targetOpacity;
    }
    if (tr.marker){
      tr.marker.opacity = targetOpacity;

      // PDB: só CA; Moléculas pequenas (PubChem/MOL/XYZ): todos os markers
      if (__isGenericMol || tr._isCA){
        tr.marker.size = __caSize;
      }
    }
  }
}


  function updatePlot(){
  if(!__baseData||!__baseLayout) return;

  var fade = (!__isGenericMol && (__polOn || (__hiData && __hiData.length)));

  var all = [].concat(__baseData);
  if(!__isGenericMol){
    if(__ssSel.helix && __ssData.helix.length) all = all.concat(__ssData.helix);
    if(__ssSel.sheet && __ssData.sheet.length) all = all.concat(__ssData.sheet);
    if(__polOn && __polTrace) all = all.concat([__polTrace]);
  }
  if(__hiData && __hiData.length) all = all.concat(__hiData);

  // <<< aplica sliders (tamanho CA + opacidade) antes de renderizar
  __applySlidersToTraces(all, fade);

  Plotly.react("grafico", all, __baseLayout);
}


  // ======== Handlers ========
  btnHi.onclick=function(){
    if(__isGenericMol){
      var sel = parseSelectionForMol(selBox.value);
      if(!sel.length){ info.textContent=" nenhum átomo encontrado"; __hiData=[]; updatePlot(); return; }
      __hiData = makeHighlightTraces(sel); updatePlot(); info.textContent=" selecionados: "+sel.length; return;
    }
    if(!__lastParsed || !__lastParsed.CA){ info.textContent=" carregue um PDB antes"; return; }
    var q=selBox.value, sel=parseSelectionQuery(q, __lastParsed.CA);
    if(!sel.length){ info.textContent=" nenhum residuo correspondente a: "+q; __hiData=[]; updatePlot(); return; }
    __hiData = makeHighlightTraces(sel); updatePlot(); info.textContent=" selecionados: "+sel.length;
  };

  btnClear.onclick=function(){ __hiData=[]; fadeBaseData(false); updatePlot(); info.textContent=" destaque limpo"; };

  inpFile.onchange=function(){
    var f=inpFile.files&&inpFile.files[0]; if(!f) return;
    info.textContent=" carregando "+f.name+" ..."; var r=new FileReader();
    r.onload=function(ev){
      var txt=ev.target.result||"", name=(f.name||"").toLowerCase();
      if(/.(mol|sdf)$/.test(name)) return renderFromMol(txt,"MOL/SDF: "+f.name);
      if(/.(xyz)$/.test(name))     return renderFromXYZ(txt,"XYZ: "+f.name);
      return renderFromPDB(txt,"PDB: "+f.name);
    };
    r.readAsText(f);
  };
  
  btnPub.onclick = function(){
  var q = (inpPub.value||"").trim();
  if (!q){ info.textContent=" informe CID ou nome (PubChem)"; return; }

  var isCID = /^[0-9]+$/.test(q);
  var baseCID  = "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/";
  var baseNAME = "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/";
  var url3D    = (isCID? (baseCID+q) : (baseNAME+encodeURIComponent(q))) + "/SDF?record_type=3d";
  var url2D    = (isCID? (baseCID+q) : (baseNAME+encodeURIComponent(q))) + "/SDF"; // fallback sem 3D

  info.textContent = " baixando (PubChem) " + q + " ...";

  fetch(url3D)
    .then(function(r){ if(!r.ok) throw 0; return r.text(); })
    .then(function(sdf){ renderFromMol(sdf, "PubChem: "+q); })
    .catch(function(){
      // tenta sem record_type=3d (às vezes não há conformação 3D salva)
      fetch(url2D)
        .then(function(r2){ if(!r2.ok) throw 0; return r2.text(); })
        .then(function(sdf2){ renderFromMol(sdf2, "PubChem: "+q+" (2D->3D flat)"); })
        .catch(function(){
          info.textContent = " erro ao baixar do PubChem: "+q;
          Plotly.react("grafico",
            [{type:"scatter",x:[0],y:[0],mode:"text",text:["Nao foi possivel baixar do PubChem"]}],
            {title:"Erro PubChem"}
          );
        });
    });
};


  btnFetch.onclick=function(){
    var raw=(inpId.value||"").trim(); if(!raw){ info.textContent=" informe um ID"; return; }
    var idU=raw.toUpperCase(), idL=raw.toLowerCase();
    info.textContent=" baixando "+idU+" ...";
    var url1="https://files.rcsb.org/download/"+idU+".pdb";
    var url1b="https://files.rcsb.org/view/"+idU+".pdb";
    var url2="https://www.ebi.ac.uk/pdbe/entry-files/download/pdb"+idL+".ent";
    fetch(url1).then(function(r){ if(!r.ok) throw 0; return r.text(); })
      .then(function(txt){ return renderFromPDB(txt,"PDB: "+idU+".pdb"); })
      .catch(function(){
        return fetch(url1b).then(function(r1b){ if(!r1b.ok) throw 0; return r1b.text(); })
          .then(function(txt1b){ return renderFromPDB(txt1b,"PDB: "+idU+".pdb"); })
          .catch(function(){
            return fetch(url2).then(function(r2){ if(!r2.ok) throw 0; return r2.text(); })
              .then(function(txt2){ return renderFromPDB(txt2,"PDB: "+idU); })
              .catch(function(){
                info.textContent = " erro ao baixar "+idU;
                Plotly.react("grafico",
                  [{type:"scatter",x:[0],y:[0],mode:"text",text:["Nao foi possivel baixar "+idU]}],
                  {title:"Erro download"});
              });
          });
      });
  };

  // retorno inicial
  var data0=[{type:"scatter",mode:"text",x:[0],y:[0],text:["Use upload (PDB/MOL/SDF/XYZ) ou informe um ID e clique em baixar."],hoverinfo:"none",showlegend:false}];
  var layout0={title:"PDB/MOL 3D viewer",margin:{l:0,r:0,t:40,b:0}};
  Plotly.react("grafico", data0, layout0);

})(); // fim IIFE