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Commit fc470293 authored by David Sehnal's avatar David Sehnal
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basic wrapper tweaks

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src/apps/basic-wrapper/index.html
+ 27
− 8
View file @ fc470293
......@@ -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>
......
src/mol-model/structure/model/properties/utils/secondary-structure.ts
+ 18
− 18
View file @ fc470293
......@@ -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) {
......
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