diff --git a/src/apps/basic-wrapper/index.html b/src/apps/basic-wrapper/index.html
index 07592b99d310d9376a10be671fa594b4314e01e0..e18b1e38c324e755ea68fdb183646e1f245f4950 100644
--- a/src/apps/basic-wrapper/index.html
+++ b/src/apps/basic-wrapper/index.html
@@ -35,19 +35,39 @@
#controls > hr {
margin: 5px 0;
}
+
+ #controls > input, #controls > select {
+ width: 100%;
+ display: block;
+ }
</style>
<link rel="stylesheet" type="text/css" href="app.css" />
<script type="text/javascript" src="./index.js"></script>
</head>
<body>
<div id='controls'>
-
+ <h3>Source</h3>
+ <input type='text' id='url' placeholder='url' />
+ <input type='text' id='assemblyId' placeholder='assembly id' />
+ <select id='format'>
+ <option value='cif' selected>CIF</option>
+ <option value='pdb'>PDB</option>
+ </select>
</div>
<div id="app"></div>
- <script>
+ <script>
+ function $(id) { return document.getElementById(id); }
+
var pdbId = '1grm', assemblyId= '1';
var url = 'https://www.ebi.ac.uk/pdbe/static/entry/' + pdbId + '_updated.cif';
var format = 'cif';
+
+ $('url').value = url;
+ $('url').onchange = function (e) { url = e.target.value; }
+ $('assemblyId').value = assemblyId;
+ $('assemblyId').onchange = function (e) { assemblyId = e.target.value; }
+ $('format').value = format;
+ $('format').onchange = function (e) { format = e.target.value; }
// var url = 'https://www.ebi.ac.uk/pdbe/entry-files/pdb' + pdbId + '.ent';
// var format = 'pdb';
@@ -58,9 +78,8 @@
BasicMolStarWrapper.load({ url: url, format: format, assemblyId: assemblyId });
BasicMolStarWrapper.toggleSpin();
- addHeader('Source');
addControl('Load Asym Unit', () => BasicMolStarWrapper.load({ url: url, format: format }));
- addControl('Load Assembly 1', () => BasicMolStarWrapper.load({ url: url, format: format, assemblyId: assemblyId }));
+ addControl('Load Assembly', () => BasicMolStarWrapper.load({ url: url, format: format, assemblyId: assemblyId }));
addSeparator();
@@ -73,7 +92,7 @@
// adjust this number to make the animation faster or slower
// requires to "restart" the animation if changed
- BasicMolStarWrapper.animate.modelIndex.maxFPS = 4;
+ BasicMolStarWrapper.animate.modelIndex.maxFPS = 30;
addControl('Play To End', () => BasicMolStarWrapper.animate.modelIndex.onceForward());
addControl('Play To Start', () => BasicMolStarWrapper.animate.modelIndex.onceBackward());
@@ -87,18 +106,18 @@
var btn = document.createElement('button');
btn.onclick = action;
btn.innerText = label;
- document.getElementById('controls').appendChild(btn);
+ $('controls').appendChild(btn);
}
function addSeparator() {
var hr = document.createElement('hr');
- document.getElementById('controls').appendChild(hr);
+ $('controls').appendChild(hr);
}
function addHeader(header) {
var h = document.createElement('h3');
h.innerText = header;
- document.getElementById('controls').appendChild(h);
+ $('controls').appendChild(h);
}
</script>
</body>
diff --git a/src/mol-model/structure/model/properties/utils/secondary-structure.ts b/src/mol-model/structure/model/properties/utils/secondary-structure.ts
index 2ebb150cf6386d583f2f9777f3abddfbe6651c52..659a8f9a8b179023a85898c8c1a256cf7d29676e 100644
--- a/src/mol-model/structure/model/properties/utils/secondary-structure.ts
+++ b/src/mol-model/structure/model/properties/utils/secondary-structure.ts
@@ -48,7 +48,7 @@ export function computeModelDSSP(hierarchy: AtomicHierarchy, conformation: Atomi
for (let i = 0, il = proteinResidues.length; i < il; ++i) {
type[proteinResidues[i]] = assignment[i]
}
-
+
const secondaryStructure: SecondaryStructure = {
type,
key: [], // TODO
@@ -287,7 +287,7 @@ function getDSSPAssignment(flags: Uint32Array, useOriginal = false) {
* Q = -332 * 0.42 * 0.20
*
* f is the dimensional factor
- *
+ *
* q1 and q2 are partial charges which are placed on the C,O
* (+q1,-q1) and N,H (-q2,+q2)
*/
@@ -306,7 +306,7 @@ function calcHbondEnergy(oPos: Vec3, cPos: Vec3, nPos: Vec3, hPos: Vec3) {
const distON = Vec3.distance(oPos, nPos)
const e1 = Q / distOH - Q / distCH
- const e2 = Q / distCN - Q / distON
+ const e2 = Q / distCN - Q / distON
return e1 + e2
}
@@ -314,7 +314,7 @@ function calcHbondEnergy(oPos: Vec3, cPos: Vec3, nPos: Vec3, hPos: Vec3) {
* The basic turn pattern is a single H bond of type (i, i + n).
* We assign an n-turn at residue i if there is an H bond from CO(i) to NH(i + n),
* i.e., “n-turn(i)=: Hbond(i, i + n), n = 3, 4, 5.”
- *
+ *
* Type: T
*/
function assignTurns(ctx: DSSPContext) {
@@ -322,7 +322,7 @@ function assignTurns(ctx: DSSPContext) {
const { chains, residueAtomSegments, chainAtomSegments } = hierarchy
const { label_asym_id } = chains
- const turnFlag = [ 0, 0, 0, DSSPType.Flag.T3, DSSPType.Flag.T4, DSSPType.Flag.T5 ]
+ const turnFlag = [0, 0, 0, DSSPType.Flag.T3, DSSPType.Flag.T4, DSSPType.Flag.T5]
for (let i = 0, il = proteinResidues.length; i < il; ++i) {
const rI = proteinResidues[i]
@@ -347,18 +347,18 @@ function assignTurns(ctx: DSSPContext) {
/**
* Two nonoverlapping stretches of three residues each, i - 1, i, i + 1 and j - 1, j, j + 1,
- * form either a parallel or antiparallel bridge, depending on which of
+ * form either a parallel or antiparallel bridge, depending on which of
* two basic patterns is matched. We assign a bridge between residues i and j
* if there are two H bonds characteristic of P-structure; in particular,
- *
+ *
* Parallel Bridge(i, j) =:
* [Hbond(i - 1, j) and Hbond(j, i + 1)] or
* [Hbond(j - 1, i) and Hbond(i, j + 1)]
- *
+ *
* Antiparallel Bridge(i, j) =:
* [Hbond(i, j) and Hbond(j, i)] or
* [Hbond(i - 1, j + 1) and Hbond(j - 1, i + l)]
- *
+ *
* Type: B
*/
function assignBridges(ctx: DSSPContext) {
@@ -371,7 +371,7 @@ function assignBridges(ctx: DSSPContext) {
for (let t = offset[k], _t = offset[k + 1]; t < _t; t++) {
const l = b[t]
if (k > l) continue
-
+
// Parallel Bridge(i, j) =: [Hbond(i - 1, j) and Hbond(j, i + 1)]
i = k + 1 // k is i - 1
j = l
@@ -411,18 +411,18 @@ function assignBridges(ctx: DSSPContext) {
* A minimal helix is defined by two consecutive n-turns.
* For example, a 4-helix, of minimal length 4 from residues i to i + 3,
* requires 4-turns at residues i - 1 and i,
- *
+ *
* 3-helix(i,i + 2)=: [3-turn(i - 1) and 3-turn(i)]
* 4-helix(i,i + 3)=: [4-turn(i - 1) and 4-turn(i)]
* 5-helix(i,i + 4)=: [5-turn(i - 1) and 5-turn(i)]
- *
+ *
* Type: G (n=3), H (n=4), I (n=5)
*/
function assignHelices(ctx: DSSPContext) {
const { proteinResidues, flags } = ctx
-
- const turnFlag = [ 0, 0, 0, DSSPType.Flag.T3, DSSPType.Flag.T4, DSSPType.Flag.T5 ]
- const helixFlag = [ 0, 0, 0, DSSPType.Flag.G, DSSPType.Flag.H, DSSPType.Flag.I ]
+
+ const turnFlag = [0, 0, 0, DSSPType.Flag.T3, DSSPType.Flag.T4, DSSPType.Flag.T5]
+ const helixFlag = [0, 0, 0, DSSPType.Flag.G, DSSPType.Flag.H, DSSPType.Flag.I]
for (let i = 1, il = proteinResidues.length; i < il; ++i) {
const fI = DSSPType.create(flags[i])
@@ -440,7 +440,7 @@ function assignHelices(ctx: DSSPContext) {
/**
* ladder=: set of one or more consecutive bridges of identical type
- *
+ *
* Type: E
*/
function assignLadders(ctx: DSSPContext) {
@@ -449,7 +449,7 @@ function assignLadders(ctx: DSSPContext) {
/**
* sheet=: set of one or more ladders connected by shared residues
- *
+ *
* Type: E
*/
function assignSheets(ctx: DSSPContext) {
@@ -458,7 +458,7 @@ function assignSheets(ctx: DSSPContext) {
/**
* Bend(i) =: [angle ((CW - Ca(i - 2)),(C"(i + 2) - C"(i))) > 70"]
- *
+ *
* Type: S
*/
function assignBends(ctx: DSSPContext) {