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