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Rewrite NGL wrapper and add interaction with sequences viewer #18

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Rewrite NGL wrapper and add interaction with sequences viewer #18

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277 changes: 141 additions & 136 deletions www/views/public/js/ngl.js
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Original file line number Diff line number Diff line change
@@ -1,17 +1,20 @@
require_js(["/js-find/ngl/ngl.min.js"], function() {y:
$.widget('rbbt.ngl_tool', {
/**
* Viewer: a NGL wrapper
*/
require_js(["/js-find/ngl/ngl.min.js"], function() {
$.widget('rbbt.ngl_viewer', {
options: {
pdb_url: null,
pdb_url_download: null,
pdb: url,
pdb: null,
component_promise: null,
stage: null,
colorScheme: null,
colorScheme: [],
seq2pdb: null,
pdb2seq: null,
appris_features: null,
default_colors: null,
marks: {},
default_colors: {'mark': 'red', 'original_alignment': 'darkslategray', 'align': 'blue', 'feature': 'purple', 'default': 'lightgray'}
layers_sequence: []
},

_create: function() {
Expand All @@ -28,10 +31,10 @@ require_js(["/js-find/ngl/ngl.min.js"], function() {y:
fontFamily: "sans-serif"
});

this._init()
this._init();

// For use this inside mouse hooks
var ths = this
var ths = this;

this.options.stage.viewer.container.appendChild(tooltip);
// remove default hoverPick mouse action
Expand All @@ -42,17 +45,17 @@ require_js(["/js-find/ngl/ngl.min.js"], function() {y:
if(pickingProxy && (pickingProxy.atom || pickingProxy.bond)){
var atom = pickingProxy.atom || pickingProxy.closestBondAtom;
var cp = pickingProxy.canvasPosition;
group = atom.qualifiedName().match(/\[(\w+)\](\d+)(.+)/)
aa = group[1]
pos_pdb = group[2]
first_pos_chain = Object.keys(ths.options.pdb2seq)[0]
chain_letters = new Set(Object.keys(ths.options.pdb2seq).map((pdb_pos) => pdb_pos[0]))
var group = atom.qualifiedName().match(/\[(\w+)\](\d+)(.+)/);
var aa = group[1];
var pos_pdb = group[2];
var first_pos_chain = Object.keys(ths.options.pdb2seq)[0];
var chain_letters = new Set(Object.keys(ths.options.pdb2seq).map(pdb_pos => pdb_pos[0]));
for (let chain_letter of chain_letters) {
pos_seq = ths.options.pdb2seq[chain_letter+':'+ pos_pdb]
if (pos_seq) break
var pos_seq = ths.options.pdb2seq[chain_letter+':'+ pos_pdb];
if (pos_seq) break;
}
rest = group[3]
tooltip.innerText = "AA: " + "[" + aa + "]" + (pos_seq === undefined ? ' not alignment here! ' : pos_seq + 'seq/'+ pos_pdb + 'pdb') + rest
var rest = group[3];
tooltip.innerText = "AA: " + "[" + aa + "] " + (pos_seq === undefined ? ' not alignment here! ' : pos_seq + ' seq / '+ pos_pdb + ' pdb') + rest;
tooltip.style.bottom = (cp.y + 18) + "px";
tooltip.style.left = (cp.x + 15) + "px";
tooltip.style.display = "block";
Expand All @@ -64,203 +67,205 @@ require_js(["/js-find/ngl/ngl.min.js"], function() {y:
this.options.stage.mouseControls.remove("clickPick");
this.options.stage.signals.clicked.add(function(pickingProxy){
if(pickingProxy && (pickingProxy.atom || pickingProxy.bond)){
var buttons = ths.options.stage.mouseControls.mouse.buttons;
// right click
if (buttons == 2) {
// implement here the context menu when right button is pressed
} else {
var atom = pickingProxy.atom || pickingProxy.closestBondAtom;
var cp = pickingProxy.canvasPosition;
group = atom.qualifiedName().match(/\[(\w+)\](\d+)(.+)/)
aa = group[1]
pos_pdb = group[2]
first_pos_chain = Object.keys(ths.options.pdb2seq)[0]
chain_letters = new Set(Object.keys(ths.options.pdb2seq).map((pdb_pos) => pdb_pos[0]))
var group = atom.qualifiedName().match(/\[(\w+)\](\d+)(.+)/);
var aa = group[1];
var pos_pdb = group[2];
var first_pos_chain = Object.keys(ths.options.pdb2seq)[0];
var chain_letters = new Set(Object.keys(ths.options.pdb2seq).map(pdb_pos => pdb_pos[0]));
for (let chain_letter of chain_letters) {
pos_seq = ths.options.pdb2seq[chain_letter+':'+ pos_pdb]
if (pos_seq) break
var pos_seq = ths.options.pdb2seq[chain_letter+':'+ pos_pdb];
if (pos_seq) break;
}
rest = group[3]
tooltip.innerText = "AA: " + "[" + aa + "]" + (pos_seq === undefined ? ' not alignment here! ' : pos_seq + 'seq/'+ pos_pdb + 'pdb') + rest
var rest = group[3]
tooltip.innerText = "AA: " + "[" + aa + "] " + (pos_seq === undefined ? ' not alignment here! ' : pos_seq + ' seq / '+ pos_pdb + ' pdb') + rest;
tooltip.style.bottom = (cp.y + 18) + "px";
tooltip.style.left = (cp.x + 15) + "px";
tooltip.style.display = "block";
ths.mark_position(pos_pdb, 'pdb')
if (pos_seq === undefined) return
ths.mark_positions_by_colors('click', [pos_pdb], 'pdb', 'red')
}
}
});
},

/**
* Viewer constructor
*/
_init: function() {
this.options.component_promise = new Promise((resolve, reject) => {
if (this.options.pdb_url.match(/interactome3d/)) {
this.options.pdb_url_download ='/interactome3d?=pdb'+this.options.pdb_url
this.options.pdb_url_download ='/interactome3d?=pdb'+this.options.pdb_url;
} else {
this.options.pdb_url_download = this.options.pdb_url
this.options.pdb_url_download = this.options.pdb_url;
}
this.options.stage.removeAllComponents()
this._reset()
this.options.stage.removeAllComponents();
this._reset();
this._update_color_scheme();

var ths = this;
// only first model in NMR
this.options.stage.loadFile(this.options.pdb_url_download, {ext: 'pdb', firstModelOnly: true}).then(function(component){
//if(component.type !== "structure") return;
component.addRepresentation("cartoon", {
//color: "sstruc" ,
color: ths.options.colorSchemeNGL,
sele: "protein and .CA",
assembly: 'AU',
multipleBond: true
});
component.autoView();
resolve(component)
})
})
this.clear()
resolve(component);
});
});
this.options.stage.setSpin(false);
this.options.stage.rockAnimation.pause(true)
},

_draw: function(){
this.options.colorScheme_promise = new Promise((resolve, reject) => {
var colorScheme = []
if (this.options.marks['mark'].size > 0) {
colorScheme.push([this.options.default_colors['mark'], Array.from(this.options.marks['mark']).join(' or ')])
}
if (this.options.marks['feature'].size > 0) {
colorScheme.push([this.options.default_colors['feature'], Array.from(this.options.marks['feature']).join(' or ')])
}
if (Object.keys(this.options.marks).length > 4) {
for (let key of Object.keys(this.options.marks)){
if (!Object.keys(this.options.default_colors).includes(key)) {
colorScheme.push([key, Array.from(this.options.marks[key]).join(' or ')])
}
}
}
if (this.options.marks['align'].size > 0) {
colorScheme.push([this.options.default_colors['align'], Array.from(this.options.marks['align']).join(' or ')])
}
if (this.options.marks['original_alignment'].size > 0) {
colorScheme.push([this.options.default_colors['original_alignment'], Array.from(this.options.marks['original_alignment']).join(' or ')])
/**
* For drawing colors in order
*/
_update_layers_sequence: function(layer) {
var i = this.options.layers_sequence.indexOf(layer);
if(i != -1) this.options.layers_sequence.splice(i, 1);
if (layer != this.options.layers_sequence[0]) this.options.layers_sequence.unshift(layer);
},

/**
* Generate the color scheme to be drawn by the viewer
*/
_update_color_scheme: function(){
this.options.colorScheme = [];

for (let layer of this.options.layers_sequence) {
for(let color of Object.keys(this.options.marks[layer])) {
if (this.options.marks[layer][color].size == 0) continue;
this.options.colorScheme.push([color, Array.from(this.options.marks[layer][color]).join(' or ')]);
}
colorScheme.push([this.options.default_colors['default'], '*'])
resolve(colorScheme)
})
this.options.colorScheme_promise.then((colorScheme) => {
this.options.colorScheme = NGL.ColormakerRegistry.addSelectionScheme(colorScheme, "colorScheme" );
this.options.component_promise.then((component) => {component.addRepresentation("cartoon", {
color: this.options.colorScheme,
sele: "protein and .CA",
assembly: 'AU',
})
component.autoView()
})
})
}

this.options.colorScheme.push([this.options.default_colors['default'], '*']);
this.options.colorSchemeNGL = NGL.ColormakerRegistry.addSelectionScheme(this.options.colorScheme, "colorScheme");
},

draw: function(){
this._update_color_scheme();
var ths = this;
this.options.component_promise.then(component => {component.addRepresentation("cartoon", {
color: ths.options.colorSchemeNGL,
sele: "protein and .CA",
assembly: 'AU',
});
//component.autoView();
});
},

_reset: function(){
this._reset_marks()
this.options.marks = {};
this.options.marks['original_alignment'] = {}
this.options.marks['original_alignment'][this.options.default_colors['original_alignment']] = new Set();
this.options.layers_sequence = [];
for (let pos of Object.keys(this.options.seq2pdb)) {
this.options.marks['original_alignment'][this.options.default_colors['original_alignment']].add(this._get_pos(pos, 'seq'));
}
this._update_layers_sequence('original_alignment');
},

clear: function(){
this._reset()
this._draw()
clear_all: function(){
this._reset();
this.draw();
},

_get_pos: function(pos, seq_or_pdb) {
if (seq_or_pdb == 'seq') {
chains = this.options.seq2pdb[pos]
pos = chains[0].match(/[A-Z]:(\d+)/)[1]
clear_by_layers: function(layers){
for (let layer of layers) {
this.options.marks[layer] = new Set();
}
return pos
this.draw();
},

_reset_marks: function() {
this.options.marks = {}
this.options.marks['mark'] = new Set()
this.options.marks['feature'] = new Set()
this.options.marks['align'] = new Set()
this.options.marks['original_alignment'] = new Set()
for (let pos of Object.keys(this.options.seq2pdb)) {
this.options.marks['original_alignment'].add(this._get_pos(pos, 'seq'))
clear_by_layer: function(layer){
this.clear_by_layers([layer])
},

/**
* Get the PDB position from a seq/pdb position
*/
_get_pos: function(pos, seq_or_pdb) {
if (seq_or_pdb == 'seq') {
chains = this.options.seq2pdb[pos];
pos = chains[0].match(/[A-Z]:(\d+)/)[1];
}
return pos;
},

// mark, align, original_alignment, feature, color
_mark_position: function(pos, seq_or_pdb, color) {
color in this.options.marks || (this.options.marks[color] = new Set());
this.options.marks[color].add(this._get_pos(pos, seq_or_pdb))
_mark_position: function(layer, pos, seq_or_pdb, color) {
this.options.marks[layer][color].add(this._get_pos(pos, seq_or_pdb));
},

mark_positions_by_colors: function(pos_list, seq_or_pdb, color_or_list) {
/*
* Default colors: mark, align, original_alignment, feature, color
*/
mark_positions_by_colors: function(layer, pos_list, seq_or_pdb, color_or_list, draw = true) {
this._update_layers_sequence(layer);
layer in this.options.marks || (this.options.marks[layer] = new Set());;
if (Array.isArray(color_or_list)) {
for (i = 0; i < pos_list.length; i++){
this._mark_position(pos_list[i], 'seq', color_or_list[i])
var color = color_or_list[i];
color in this.options.marks[layer] || (this.options.marks[layer][color] = new Set());;
this._mark_position(layer, pos_list[i], seq_or_pdb, color);
}
} else {
var color = color_or_list
color in this.options.marks[layer] || (this.options.marks[layer][color] = new Set());;
for (let pos of pos_list) {
this._mark_position(pos, 'seq', color_or_list)
this._mark_position(layer, pos, seq_or_pdb, color);
}
}
this._draw()
},

mark_position: function(pos, seq_or_pdb){
this._mark_position(pos, seq_or_pdb, 'mark')
this._draw()
},

mark_positions: function(pos_list, seq_or_pdb) {
this.mark_positions_by_colors(pos_list, 'seq', 'mark')
},

mark_appris_features: function() {
pos_seq_features = []
for (let feature of this.options.appris_features) {
pos_seq = feature['start']
pos_pdb = this.options.seq2pdb[pos_seq]
if (feature['type'] == 'firestar' && pos_pdb) {
pos_seq_features.push(pos_seq)
}
}
this.mark_positions_by_colors(pos_seq_features, 'seq', 'feature')
},

align: function(){
this._reset()
this.mark_positions_by_colors(Object.keys(this.options.seq2pdb), 'seq', 'align')
if (draw) this.draw();
},

color_mutation_density_subset: function(residues, residue_incidence) {
pos_list = []
var pos_list = [];
var log10_counts = [];
for (let pos of residues) {
if (this.options.seq2pdb[pos]){
var count = parseInt(residue_incidence[pos]) + 1;
var log_count = Math.log(count) / Math.log(10);
log10_counts.push(log_count)
pos_list.push(pos)
log10_counts.push(log_count);
pos_list.push(pos);
}
}

log10_counts.push(0)
log10_counts.push(0);

colors = get_gradient(log10_counts, '#00FF00', '#FF0000');
var colors = get_gradient(log10_counts, '#00FF00', '#FF0000');

return {'pos_list': pos_list, 'colors': colors }
return {'pos_list': pos_list, 'colors': colors };
},

color_mutation_density: function(residue_incidence) {
console.log('color_mutation_density')
this._reset()
pos_colors = this.color_mutation_density_subset(Object.keys(residue_incidence), residue_incidence)
this.mark_positions_by_colors(pos_colors['pos_list'], 'seq', pos_colors['colors'])
pos_colors = this.color_mutation_density_subset(Object.keys(residue_incidence), residue_incidence);
this.mark_positions_by_colors('cosmic_mutation_density', pos_colors['pos_list'], 'seq', pos_colors['colors']);
},

screenshot: function() {
this.options.stage.makeImage({factor: 1, antialias: true}).then((blob) => NGL.download(blob, this.options.pdb + ".png"))
this.options.stage.makeImage({factor: 1, antialias: true}).then(blob => NGL.download(blob, this.options.pdb + ".png"));
},

resize: function() {
this.options.stage.autoView()
this.options.stage.autoView();
},

spin: function() {
this.options.stage.toggleSpin()
this.options.stage.toggleSpin();
},

fullscreen: function() {
this.options.stage.toggleFullscreen()
this.options.stage.toggleFullscreen();
}
})
})
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