c) Other -> Display Mode +
API Documents of the advanced UI library iCn3DUI
Change Log:
+The production version icn3d-1.2.3 was release on September 13, 2016. The MMTF format started to support https.
+
The production version icn3d-1.2.2 was release on August 18, 2016. Added a switch button to switch between all atoms and selected atoms. When the mode is "selected atoms", the switch and the text "selection" next to it are colored in orange. The menu "Style", "Color", and "Surface" are colored in orange and only apply to selected atoms.
diff --git a/package.json b/package.json
index 1d672d83..79202ceb 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
{
"name": "icn3d",
- "version": "1.2.2",
+ "version": "1.2.3",
"description": "iCn3D Structure Viewer",
"main": "index.html",
"scripts": {
diff --git a/src/icn3dui/full_ui.js b/src/icn3dui/full_ui.js
index 23f0d05e..7c7df595 100644
--- a/src/icn3dui/full_ui.js
+++ b/src/icn3dui/full_ui.js
@@ -3513,6 +3513,14 @@ iCn3DUI.prototype = {
html += " ";
html += " - Reset
";
html += " - Reset Orien.
";
+
+ html += " - Display Mode";
+ html += "
";
+ html += " - Apply style, color,
surface to all atoms ";
+ html += " - Apply style, color,
surface only to selection ";
+ html += "
";
+ html += " ";
+
html += " - Center
";
html += " - Backward
";
html += " - Forward
";
@@ -3836,8 +3844,8 @@ iCn3DUI.prototype = {
html += " ";
html += " ";
- html += " AllSelection";
- html += " ";
+ html += " All atomsSelection";
+ html += " ";
if(me.cfg.cid === undefined) {
html += " Structure:
";
@@ -5368,6 +5376,14 @@ iCn3DUI.prototype = {
me.setModeAndDisplay('all');
}
});
+
+ $("#" + me.pre + "menu6_modeall").click(function (e) {
+ me.setModeAndDisplay('all');
+ });
+
+ $("#" + me.pre + "menu6_modeselection").click(function (e) {
+ me.setModeAndDisplay('selection');
+ });
},
clickSeqOrAlignSeq: function() { var me = this;
diff --git a/src/icn3dui/parsers/mmtf_parser.js b/src/icn3dui/parsers/mmtf_parser.js
index a59d45d3..849cbcf2 100644
--- a/src/icn3dui/parsers/mmtf_parser.js
+++ b/src/icn3dui/parsers/mmtf_parser.js
@@ -2,18 +2,6 @@
// Contributors: Jiyao Wang, Alexander Rose, Peter Rose
// requires the library mmtf.js
iCn3DUI.prototype.downloadMmtf = function (mmtfid) { var me = this;
- // The MMTF service doesn't support https, use http instead
- var uri, dataType;
- if(document.location.protocol === "https:") {
- var url = document.location.href;
- url = url.replace('https', 'http');
- //window.open(url, '_self');
-
- alert("For now, MMTF files can ONLY be retrieved by http protocol, not https. Thus MMTF format can NOT work in NCBI pages, which are https only now. Please check back later.");
-
- return;
- }
-
MMTF.fetch(
mmtfid,
// onLoad callback
@@ -50,6 +38,7 @@
var prevSS = 'coil';
var prevChain = '';
+ var prevResi = 0;
var serial = 0;
@@ -90,7 +79,7 @@
}
// no residue can be both ssbegin and ssend in DSSP calculated secondary structures
- var bSetPrevResidue = 0; // 0: no need to reset, 1: reset previous residue to "ssbegin = true", 2: reset previous residue to "ssend = true"
+ var bSetPrevSsend = false;
if(chain !== prevChain) {
// new chain
@@ -102,6 +91,16 @@
ssbegin = false;
ssend = false;
}
+
+ // set up the end of previous chain
+ if(prevSS !== 'coil') {
+ var prevResid = structure + '_' + prevChain + '_' + prevResi.toString();
+
+ for(var i in me.icn3d.residues[prevResid]) {
+ me.icn3d.atoms[i].ssbegin = false;
+ me.icn3d.atoms[i].ssend = true;
+ }
+ }
}
else if(ss !== prevSS) {
if(prevSS === 'coil') {
@@ -109,12 +108,12 @@
ssend = false;
}
else if(ss === 'coil') {
- bSetPrevResidue = 2;
+ bSetPrevSsend = true;
ssbegin = false;
ssend = false;
}
else if( (prevSS === 'sheet' && ss === 'helix') || (prevSS === 'helix' && ss === 'sheet')) {
- bSetPrevResidue = 1;
+ bSetPrevSsend = true;
ssbegin = true;
ssend = false;
}
@@ -124,14 +123,7 @@
ssend = false;
}
- if(bSetPrevResidue == 1) { //1: reset previous residue to "ssbegin = true"
- var prevResid = structure + '_' + chain + '_' + (resi - 1).toString();
- for(var i in me.icn3d.residues[prevResid]) {
- me.icn3d.atoms[i].ssbegin = true;
- me.icn3d.atoms[i].ssend = false;
- }
- }
- else if(bSetPrevResidue == 2) { //2: reset previous residue to "ssend = true"
+ if(bSetPrevSsend) {
var prevResid = structure + '_' + chain + '_' + (resi - 1).toString();
for(var i in me.icn3d.residues[prevResid]) {
me.icn3d.atoms[i].ssbegin = false;
@@ -141,6 +133,7 @@
prevSS = ss;
prevChain = chain;
+ prevResi = resi;
het = false;
bProtein = false;
diff --git a/src/mmtf.js b/src/mmtf.js
index 6bca5a85..99e09eab 100644
--- a/src/mmtf.js
+++ b/src/mmtf.js
@@ -1 +1 @@
-!function(r,t){"object"==typeof exports&&"undefined"!=typeof module?t(exports):"function"==typeof define&&define.amd?define(["exports"],t):t(r.MMTF=r.MMTF||{})}(this,function(r){"use strict";function t(r,t,n){for(var e=(r.byteLength,0),i=n.length;i>e;e++){var o=n.charCodeAt(e);if(128>o)r.setUint8(t++,o>>>0&127|0);else if(2048>o)r.setUint8(t++,o>>>6&31|192),r.setUint8(t++,o>>>0&63|128);else if(65536>o)r.setUint8(t++,o>>>12&15|224),r.setUint8(t++,o>>>6&63|128),r.setUint8(t++,o>>>0&63|128);else{if(!(1114112>o))throw new Error("bad codepoint "+o);r.setUint8(t++,o>>>18&7|240),r.setUint8(t++,o>>>12&63|128),r.setUint8(t++,o>>>6&63|128),r.setUint8(t++,o>>>0&63|128)}}}function n(r){for(var t=0,n=0,e=r.length;e>n;n++){var i=r.charCodeAt(n);if(128>i)t+=1;else if(2048>i)t+=2;else if(65536>i)t+=3;else{if(!(1114112>i))throw new Error("bad codepoint "+i);t+=4}}return t}function e(r,i,o){var a=typeof r;if("string"===a){var u=n(r);if(32>u)return i.setUint8(o,160|u),t(i,o+1,r),1+u;if(256>u)return i.setUint8(o,217),i.setUint8(o+1,u),t(i,o+2,r),2+u;if(65536>u)return i.setUint8(o,218),i.setUint16(o+1,u),t(i,o+3,r),3+u;if(4294967296>u)return i.setUint8(o,219),i.setUint32(o+1,u),t(i,o+5,r),5+u}if(r instanceof Uint8Array){var u=r.byteLength,s=new Uint8Array(i.buffer);if(256>u)return i.setUint8(o,196),i.setUint8(o+1,u),s.set(r,o+2),2+u;if(65536>u)return i.setUint8(o,197),i.setUint16(o+1,u),s.set(r,o+3),3+u;if(4294967296>u)return i.setUint8(o,198),i.setUint32(o+1,u),s.set(r,o+5),5+u}if("number"===a){if(!isFinite(r))throw new Error("Number not finite: "+r);if(Math.floor(r)!==r)return i.setUint8(o,203),i.setFloat64(o+1,r),9;if(r>=0){if(128>r)return i.setUint8(o,r),1;if(256>r)return i.setUint8(o,204),i.setUint8(o+1,r),2;if(65536>r)return i.setUint8(o,205),i.setUint16(o+1,r),3;if(4294967296>r)return i.setUint8(o,206),i.setUint32(o+1,r),5;throw new Error("Number too big 0x"+r.toString(16))}if(r>=-32)return i.setInt8(o,r),1;if(r>=-128)return i.setUint8(o,208),i.setInt8(o+1,r),2;if(r>=-32768)return i.setUint8(o,209),i.setInt16(o+1,r),3;if(r>=-2147483648)return i.setUint8(o,210),i.setInt32(o+1,r),5;throw new Error("Number too small -0x"+(-r).toString(16).substr(1))}if(null===r)return i.setUint8(o,192),1;if("boolean"===a)return i.setUint8(o,r?195:194),1;if("object"===a){var u,f=0,c=Array.isArray(r);if(c)u=r.length;else{var d=Object.keys(r);u=d.length}var f;if(16>u?(i.setUint8(o,u|(c?144:128)),f=1):65536>u?(i.setUint8(o,c?220:222),i.setUint16(o+1,u),f=3):4294967296>u&&(i.setUint8(o,c?221:223),i.setUint32(o+1,u),f=5),c)for(var l=0;u>l;l++)f+=e(r[l],i,o+f);else for(var l=0;u>l;l++){var g=d[l];f+=e(g,i,o+f),f+=e(r[g],i,o+f)}return f}throw new Error("Unknown type "+a)}function i(r){var t=typeof r;if("string"===t){var e=n(r);if(32>e)return 1+e;if(256>e)return 2+e;if(65536>e)return 3+e;if(4294967296>e)return 5+e}if(r instanceof Uint8Array){var e=r.byteLength;if(256>e)return 2+e;if(65536>e)return 3+e;if(4294967296>e)return 5+e}if("number"===t){if(Math.floor(r)!==r)return 9;if(r>=0){if(128>r)return 1;if(256>r)return 2;if(65536>r)return 3;if(4294967296>r)return 5;throw new Error("Number too big 0x"+r.toString(16))}if(r>=-32)return 1;if(r>=-128)return 2;if(r>=-32768)return 3;if(r>=-2147483648)return 5;throw new Error("Number too small -0x"+r.toString(16).substr(1))}if("boolean"===t||null===r)return 1;if("object"===t){var e,o=0;if(Array.isArray(r)){e=r.length;for(var a=0;e>a;a++)o+=i(r[a])}else{var u=Object.keys(r);e=u.length;for(var a=0;e>a;a++){var s=u[a];o+=i(s)+i(r[s])}}if(16>e)return 1+o;if(65536>e)return 3+o;if(4294967296>e)return 5+o;throw new Error("Array or object too long 0x"+e.toString(16))}throw new Error("Unknown type "+t)}function o(r){var t=new ArrayBuffer(i(r)),n=new DataView(t);return e(r,n,0),new Uint8Array(t)}function a(r,t,n){return t?new r(t.buffer,t.byteOffset,t.byteLength/(n||1)):void 0}function u(r){return a(DataView,r)}function s(r){return a(Uint8Array,r)}function f(r){return 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+ html += " | ";
if(me.cfg.cid === undefined) {
html += " Structure: "; @@ -5368,6 +5376,14 @@ iCn3DUI.prototype = { me.setModeAndDisplay('all'); } }); + + $("#" + me.pre + "menu6_modeall").click(function (e) { + me.setModeAndDisplay('all'); + }); + + $("#" + me.pre + "menu6_modeselection").click(function (e) { + me.setModeAndDisplay('selection'); + }); }, clickSeqOrAlignSeq: function() { var me = this; diff --git a/src/icn3dui/parsers/mmtf_parser.js b/src/icn3dui/parsers/mmtf_parser.js index a59d45d3..849cbcf2 100644 --- a/src/icn3dui/parsers/mmtf_parser.js +++ b/src/icn3dui/parsers/mmtf_parser.js @@ -2,18 +2,6 @@ // Contributors: Jiyao Wang, Alexander Rose, Peter Rose // requires the library mmtf.js iCn3DUI.prototype.downloadMmtf = function (mmtfid) { var me = this; - // The MMTF service doesn't support https, use http instead - var uri, dataType; - if(document.location.protocol === "https:") { - var url = document.location.href; - url = url.replace('https', 'http'); - //window.open(url, '_self'); - - alert("For now, MMTF files can ONLY be retrieved by http protocol, not https. Thus MMTF format can NOT work in NCBI pages, which are https only now. Please check back later."); - - return; - } - MMTF.fetch( mmtfid, // onLoad callback @@ -50,6 +38,7 @@ var prevSS = 'coil'; var prevChain = ''; + var prevResi = 0; var serial = 0; @@ -90,7 +79,7 @@ } // no residue can be both ssbegin and ssend in DSSP calculated secondary structures - var bSetPrevResidue = 0; // 0: no need to reset, 1: reset previous residue to "ssbegin = true", 2: reset previous residue to "ssend = true" + var bSetPrevSsend = false; if(chain !== prevChain) { // new chain @@ -102,6 +91,16 @@ ssbegin = false; ssend = false; } + + // set up the end of previous chain + if(prevSS !== 'coil') { + var prevResid = structure + '_' + prevChain + '_' + prevResi.toString(); + + for(var i in me.icn3d.residues[prevResid]) { + me.icn3d.atoms[i].ssbegin = false; + me.icn3d.atoms[i].ssend = true; + } + } } else if(ss !== prevSS) { if(prevSS === 'coil') { @@ -109,12 +108,12 @@ ssend = false; } else if(ss === 'coil') { - bSetPrevResidue = 2; + bSetPrevSsend = true; ssbegin = false; ssend = false; } else if( (prevSS === 'sheet' && ss === 'helix') || (prevSS === 'helix' && ss === 'sheet')) { - bSetPrevResidue = 1; + bSetPrevSsend = true; ssbegin = true; ssend = false; } @@ -124,14 +123,7 @@ ssend = false; } - if(bSetPrevResidue == 1) { //1: reset previous residue to "ssbegin = true" - var prevResid = structure + '_' + chain + '_' + (resi - 1).toString(); - for(var i in me.icn3d.residues[prevResid]) { - me.icn3d.atoms[i].ssbegin = true; - me.icn3d.atoms[i].ssend = false; - } - } - else if(bSetPrevResidue == 2) { //2: reset previous residue to "ssend = true" + if(bSetPrevSsend) { var prevResid = structure + '_' + chain + '_' + (resi - 1).toString(); for(var i in me.icn3d.residues[prevResid]) { me.icn3d.atoms[i].ssbegin = false; @@ -141,6 +133,7 @@ prevSS = ss; prevChain = chain; + prevResi = resi; het = false; bProtein = false; diff --git a/src/mmtf.js b/src/mmtf.js index 6bca5a85..99e09eab 100644 --- a/src/mmtf.js +++ b/src/mmtf.js @@ -1 +1 @@ -!function(r,t){"object"==typeof exports&&"undefined"!=typeof module?t(exports):"function"==typeof define&&define.amd?define(["exports"],t):t(r.MMTF=r.MMTF||{})}(this,function(r){"use strict";function t(r,t,n){for(var e=(r.byteLength,0),i=n.length;i>e;e++){var o=n.charCodeAt(e);if(128>o)r.setUint8(t++,o>>>0&127|0);else if(2048>o)r.setUint8(t++,o>>>6&31|192),r.setUint8(t++,o>>>0&63|128);else if(65536>o)r.setUint8(t++,o>>>12&15|224),r.setUint8(t++,o>>>6&63|128),r.setUint8(t++,o>>>0&63|128);else{if(!(1114112>o))throw new Error("bad codepoint "+o);r.setUint8(t++,o>>>18&7|240),r.setUint8(t++,o>>>12&63|128),r.setUint8(t++,o>>>6&63|128),r.setUint8(t++,o>>>0&63|128)}}}function n(r){for(var t=0,n=0,e=r.length;e>n;n++){var i=r.charCodeAt(n);if(128>i)t+=1;else if(2048>i)t+=2;else if(65536>i)t+=3;else{if(!(1114112>i))throw new Error("bad codepoint "+i);t+=4}}return t}function e(r,i,o){var a=typeof r;if("string"===a){var u=n(r);if(32>u)return i.setUint8(o,160|u),t(i,o+1,r),1+u;if(256>u)return 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