Merge branch 'local_3dmol'

package.json

@@ -1,6 +1,6 @@
 {
   "name": "3dmol",
-  "version": "2.1.0",
+  "version": "2.2.1post1",
   "description": "JavaScript/TypeScript molecular visualization library",
   "repository": {
     "type": "git",

py3Dmol/py3Dmol/__init__.py

@@ -54,7 +54,7 @@ class view(object):
        the exception that the functions all return None.
        http://3dmol.org/doc/GLViewer.html
     '''
-    def __init__(self,query='',width=640,height=480,viewergrid=None,data=None,style=None,linked=True,options=dict(),format=None,js='https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.1.0/3Dmol-min.js'):
+    def __init__(self,query='',width=640,height=480,viewergrid=None,data=None,style=None,linked=True,options=dict(),format=None,js='https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.2.1-post1/3Dmol-min.js'):
         '''Create a 3Dmol.js view.
             width -- width in pixels of container
             height -- height in pixels of container

py3Dmol/setup.py

@@ -24,7 +24,7 @@
     # the version across setup.py and the project code, see
     # https://packaging.python.org/en/latest/single_source_version.html
     # Keep version in synce with 3Dmol.js version.  Use "postX" suffix if needed
-    version='2.1.0',
+    version='2.2.1',
 
     description='An IPython interface for embedding 3Dmol.js views in Jupyter notebooks',
     long_description=long_description,

src/GLModel.ts

@@ -2836,7 +2836,7 @@ export class GLModel {
                 console.log("Unknown format: " + format);
                 // try to guess correct format from data contents
                 if (data instanceof Uint8Array) {
-                    format = "mmtf"; //currently only supported binary format?
+                    format = "bcif"; //mmtf deprecated so go with bcif
                 } else if ((data as string).match(/^@<TRIPOS>MOLECULE/gm)) {
                     format = "mol2";
                 } else if ((data as string).match(/^data_/gm) && (data as string).match(/^loop_/gm)) {

src/GLViewer.ts

@@ -110,6 +110,7 @@ export class GLViewer {
     private longTouchTimeout: any;
 
     private divwatcher: any;
+    private intwatcher: any;
     private spinInterval: any;
 
 
@@ -651,6 +652,19 @@ export class GLViewer {
             this.divwatcher.observe(this.container);
         }
 
+        if (typeof (window.IntersectionObserver) !== "undefined") {
+            //make sure a viewer that is becoming visible is alive
+            let intcallback = (entries, observer) => {
+                entries.forEach((entry) => {
+                    if(entry.isIntersecting) {
+                        this.resize();
+                    }
+                });
+            };
+            this.intwatcher = new window.IntersectionObserver(intcallback);
+            this.intwatcher.observe(this.container);
+        }
+
         try {
             if (typeof (this.callback) === "function")
                 this.callback(this);
@@ -1373,7 +1387,6 @@ export class GLViewer {
         } else if (this.animated) {
             this._viewer.resumeAnimate();
         }
-
         this.updateSize();
 
         if (regen) { //restored rendere, need to regenerate scene

src/autoload.ts

@@ -64,7 +64,7 @@ export function autoload(viewer?: any, callback?: (arg0: any) => void) {
                 viewerdiv.dataset[datatypes[datatypes.length - 1]] = molName;
             }
 
-            var divdata = viewerdiv.dataset;
+            let divdata = viewerdiv.dataset;
             for (i in divdata) {
                 if ((i.substring(0, 3) === "pdb" && (i !== "pdb"))) {
                     datauri.push("https://files.rcsb.org/view/" + divdata[i] + ".pdb");
@@ -187,7 +187,7 @@ export function autoload(viewer?: any, callback?: (arg0: any) => void) {
                 }
             };
 
-            var glviewer = viewer;
+            let glviewer = viewer;
             try {
                 var config: any = specStringToObject(viewerdiv.dataset.config) || {};
                 if (config.backgroundColor === undefined) config.backgroundColor = bgcolor;
@@ -213,7 +213,7 @@ export function autoload(viewer?: any, callback?: (arg0: any) => void) {
             if (datauri.length != 0) {
                 //load multiple data elements in serial
                 let i = 0;
-                var process = function (moldata: any) {
+                let process = ((viewerdiv, glviewer) => function (moldata: any) {
                     //add moldata to viewer and load next model
                     uri = datauri[i]; //this is where the moldata came from
                     var type = viewerdiv.dataset.type || viewerdiv.dataset.datatype || datatypes[i];
@@ -240,7 +240,7 @@ export function autoload(viewer?: any, callback?: (arg0: any) => void) {
                         processing_autoinit = false;
                         if (callback) callback(glviewer);
                     }
-                };
+                })(viewerdiv,glviewer);
                 get(datauri[0]).then(process);
 
             }

src/parsers/BCIF.ts

@@ -13,6 +13,145 @@ import { isEmpty } from "./utils/isEmpty";
 declare var MMTF: MMTFobj;
 
 
+class Connectivity {
+  C: Record<string, Record<string, Record<string, number>>> = {};
+
+  constructor(comp_bond) {
+    if (comp_bond) {
+      let ids = comp_bond.getField('comp_id');
+      let a1s = comp_bond.getField('atom_id_1');
+      let a2s = comp_bond.getField('atom_id_2');
+      let orders = comp_bond.getField('value_order');
+
+      for (let i = 0; i < ids.length; i++) {
+        let resn = ids[i];
+        let a1 = a1s[i];
+        let a2 = a2s[i];
+        let oname = orders[i];
+        let o = 1;
+        if (oname == 'doub') o = 2;
+        else if (oname == 'trip') o = 3;
+
+        if (this.C[resn] == undefined) {
+          this.C[resn] = {};
+        }
+        if (this.C[resn][a1] == undefined) {
+          this.C[resn][a1] = {};
+        }
+        if (this.C[resn][a2] == undefined) {
+          this.C[resn][a2] = {};
+        }
+        this.C[resn][a1][a2] = o;
+        this.C[resn][a2][a1] = o;
+      }
+    }
+  }
+
+  //returns bond order, zero if not connected
+  order(resn: string, atom1: string, atom2: string): number {
+    if (this.C[resn] !== undefined) {
+      if (this.C[resn][atom1] !== undefined) {
+        if (this.C[resn][atom1][atom2] !== undefined) {
+          return this.C[resn][atom1][atom2];
+        }
+      }
+    }
+    return 0;
+  }
+}
+
+/* Class for recording inter-component connectivity */
+class StructConn {
+  public C: [[string,number,string,string],[string,number,string,string],number][] = []; //chain,resi,resn,atomn
+
+  constructor(struct_conn) {
+    if(struct_conn) {
+      //have no idea what the deal with with ptnr3..
+      let types = struct_conn.getField('conn_type_id');
+      let chain1 = struct_conn.getField('ptnr1_label_asym_id');
+      let resi1 = struct_conn.getField('ptnr1_label_seq_id');
+      let resn1 = struct_conn.getField('ptnr1_label_comp_id');
+      let a1 = struct_conn.getField('ptnr1_label_atom_id');
+      let chain2 = struct_conn.getField('ptnr2_label_asym_id');
+      let resi2 = struct_conn.getField('ptnr2_label_seq_id');
+      let resn2 = struct_conn.getField('ptnr2_label_comp_id');
+      let a2 = struct_conn.getField('ptnr2_label_atom_id');
+      let bo = struct_conn.getField('pdbx_value_order');
+
+      for(let i = 0; i < types.length; i++) {
+        if(types[i] == 'disulf' || types[i] == 'covale') { //metal too?
+          let o = bo ? (bo[i] == "" ? 1: parseInt(bo[i])) : 1;
+          this.C.push([[chain1[i],resi1[i],resn1[i],a1[i]],[chain2[i],resi2[i],resn2[i],a2[i]],o]);
+        }
+      }
+
+    }
+  }
+}
+
+/* group atoms by chain/resid */
+class Residues {
+  R: Record<string, Record<number, Record<string, Array<AtomSpec>>>> = {}; //chain, resid, resn (redundant), atom list
+  constructor() {
+
+  }
+
+  add(a: AtomSpec) {
+    if (this.R[a.lchain] == undefined) this.R[a.lchain] = {};
+    if (this.R[a.lchain][a.lresi] == undefined) this.R[a.lchain][a.lresi] = {};
+    if (this.R[a.lchain][a.lresi][a.lresn] == undefined) this.R[a.lchain][a.lresi][a.lresn] = [];
+    this.R[a.lchain][a.lresi][a.lresn].push(a);
+    this.R[a.lchain][a.lresi][a.lresn][a.atom] = a; //look up by atom name
+  }
+
+  private geta([ch,resi,resn,aname]: [string,number,string,string]) {
+    if(this.R[ch] !== undefined &&
+      this.R[ch][resi] !== undefined &&
+      this.R[ch][resi][resn] !== undefined) {
+        return this.R[ch][resi][resn][aname];
+      }
+    return undefined;
+  }
+
+  setBonds(C: Connectivity, SC: StructConn) {
+    for(let ch in this.R) {
+      for(let resi in this.R[ch]) {
+        for(let resn in this.R[ch][resi]) {
+          let atoms = this.R[ch][resi][resn];
+          for(let i = 0; i < atoms.length; i++) {
+            for(let j = i+1; j < atoms.length; j++) {
+              let a1 = atoms[i];
+              let a2 = atoms[j];
+              let bo = C.order(resn,a1.atom,a2.atom);
+              if(bo > 0) {
+                a1.bonds.push(a2.index);
+                a2.bonds.push(a1.index);
+                a1.bondOrder.push(bo);
+                a2.bondOrder.push(bo);
+              }
+            }
+          }
+        }
+      }
+    }
+
+    for(let conn of SC.C) {
+      let a1 = conn[0];
+      let a2 = conn[1];
+      let bo = conn[2];
+      let atom1 = this.geta(a1);
+      let atom2 = this.geta(a2);
+      if(atom1 != undefined && atom2 != undefined) {
+        atom1.bonds.push(atom2.index);
+        atom2.bonds.push(atom1.index);
+        atom1.bondOrder.push(bo);
+        atom2.bondOrder.push(bo);      
+      }
+    }
+
+  }
+}
+
 
 /** 
  * @param bindata - binary UInt8Array buffer or a base64 encoded string
@@ -22,7 +161,7 @@ declare var MMTF: MMTFobj;
 export function BCIF(bindata: any, options: ParserOptionsSpec) {
 
   var noH = !options.keepH; // suppress hydrogens by default
-  //var selAltLoc = options.altLoc ? options.altLoc : 'A'; //default alternate location to select if present
+  var selAltLoc = options.altLoc ? options.altLoc : 'A'; //default alternate location to select if present
   var computeStruct = !options.noComputeSecondaryStructure;
   //var assemblyIndex = options.assemblyIndex ? options.assemblyIndex : 0;
   const noAssembly = !options.doAssembly; // don't assemble by default
@@ -59,10 +198,10 @@ export function BCIF(bindata: any, options: ParserOptionsSpec) {
 
 
 
-  //loop over models, 
+  //loop over models
   for (let m = 0; m < numModels; m++) {
-
-    const serialToIndex: number[] = []; // map from pdb serial to index in atoms
+    let startm = atoms.length;
+    const serialToIndex: [number, number][] = []; // map from pdb serial to index in atoms
     modelData.push({ symmetries: [] });
     atoms.push([]);
 
@@ -158,8 +297,13 @@ export function BCIF(bindata: any, options: ParserOptionsSpec) {
         modelData[modelData.length - 1].symmetries.push(matrix);
       }
     }
-    //atom info
 
+    //extract connectivity information
+    let connect = new Connectivity(cats.chem_comp_bond);
+    let residues = new Residues();
+    let sconnect = new StructConn(cats.struct_conn);
+
+    //atom info
     let asites = cats.atom_site;
     let atomCount = asites.rowCount;
     let group_pdb = asites.getField('group_PDB')
@@ -192,7 +336,10 @@ export function BCIF(bindata: any, options: ParserOptionsSpec) {
         if (options.multimodel) {
           if (!options.onemol) {
             atoms.push([]);
-            modelData.push(modelData[modelData.length-1]);
+            modelData.push(modelData[modelData.length - 1]);
+            curmodel = modelnums[i];
+            residues.setBonds(connect, sconnect);
+            residues = new Residues();
           }
         } else {
           break; //first model only
@@ -225,13 +372,15 @@ export function BCIF(bindata: any, options: ParserOptionsSpec) {
         : label_comp_id
           ? label_comp_id[i].trim()
           : undefined;
+      atom.lresn = label_comp_id ? label_comp_id[i].trim() : undefined;
       atom.atom = auth_atom_id
         ? auth_atom_id[i].replace(/"/gm, "")
         : label_atom_id
           ? label_atom_id[i].replace(/"/gm, "")
           : undefined; //"primed" names are in quotes
 
       atom.icode = icodes ? icodes[i] : undefined;
+      atom.altLoc = atom.icode;
       atom.hetflag =
         !group_pdb ||
         group_pdb[i] === "HETA" ||
@@ -244,32 +393,41 @@ export function BCIF(bindata: any, options: ParserOptionsSpec) {
       atom.elem = elem[0].toUpperCase() + elem.substring(1, 2).toLowerCase();
       if (bfactors) atom.b = bfactors[i];
 
-      if(noH && atom.elem == 'H') {
+      if (noH && atom.elem == 'H') {
+        continue;
+      }
+      if (atom.altLoc != '' && atom.altLoc != selAltLoc && selAltLoc != '*') {
         continue;
       }
 
       atom.bonds = [];
       atom.ss = "c";
       atom.serial = serials[i];
-      serialToIndex[atom.serial] = i;
+      atom.model = curmodel;
       atom.bondOrder = [];
       atom.properties = {};
+      atom.index = atoms[atoms.length - 1].length;
+      serialToIndex[atom.serial] = [atoms.length, atom.index];
       atoms[atoms.length - 1].push(atom);
-    }
+      residues.add(atom);
 
+    }
 
+    residues.setBonds(connect, sconnect);
     // Assign secondary structures from pdb file
     if (!isEmpty(sslookup)) {
-      let matoms = atoms[atoms.length - 1];
-      for (let i = 0; i < matoms.length; i++) {
-        const atom = matoms[i];
-        if (atom === undefined) continue;
-        if (atom.lchain in sslookup && atom.lresi in sslookup[atom.lchain]) {
-          const code = sslookup[atom.lchain][atom.lresi];
-          atom.ss = code[0];
-          if (code.length > 1) {
-            if (code[1] == "1") atom.ssbegin = true;
-            else if (code[1] == "2") atom.ssend = true;
+      for (let mi = startm; mi < atoms.length; mi++) {
+        let matoms = atoms[mi];
+        for (let i = 0; i < matoms.length; i++) {
+          const atom = matoms[i];
+          if (atom === undefined) continue;
+          if (atom.lchain in sslookup && atom.lresi in sslookup[atom.lchain]) {
+            const code = sslookup[atom.lchain][atom.lresi];
+            atom.ss = code[0];
+            if (code.length > 1) {
+              if (code[1] == "1") atom.ssbegin = true;
+              else if (code[1] == "2") atom.ssend = true;
+            }
           }
         }
       }

src/parsers/CIF.ts

@@ -279,6 +279,9 @@ export function CIF(str: string, options: ParserOptionsSpec = {}) {
         !mmCIF._atom_site_group_pdb ||
         mmCIF._atom_site_group_pdb[i] === "HETA" ||
         mmCIF._atom_site_group_pdb[i] === "HETATM";
+      if(mmCIF._atom_site_b_iso_or_equiv ) {
+        atom.b = parseFloat(mmCIF._atom_site_b_iso_or_equiv[i]);
+      }
       let elem = "X";
       if (mmCIF._atom_site_type_symbol) {
         elem = mmCIF._atom_site_type_symbol[i].replace(/\(?\+?\d+.*/, "");