| Option name | Type | Description |
|---|---|---|
| data | Object | Data used to create the cluster. See example below |
| display | Object | Display options passed to SVPath |
| meta | Object | User-defined key:value pairs to add to the Cluster. |
Clusters are made up of a group of Peaks. Typically a cluster for an NMR spectrum would correspond to a multiplet of peaks.
data = {
peaks: [
{ center: 2.22, amplitude: 0.6, width: 0.005 },
{ center: 2.34, amplitude: 0.6, width: 0.005 }
]
}
// The data may also contain upper_bound and lower attributes.
// The bounds can shown on the Viewer when a cluster is selected,
// if the SVSelection.show_bounds is true.
data = {
peaks: [...],
lower_bound: 2.0,
upper_bound: 2.4
}
Cluster inherits methods and properties from SVPath.
function Cluster(data, display, meta) {
var self = this;
data = data || { };
display_defaults = { visible: false };
display = JSV.merge(display_defaults, data.display, display);
meta = JSV.merge(data.meta, meta);
JSV.SVPath.call(this, display, meta);
this._peaks = new JSV.SVSet();
this._atoms = new JSV.SVSet();
this.lower_bound = JSV.number(data.lower_bound);
this.upper_bound = JSV.number(data.upper_bound);
this.weight = JSV.number(data.weight);
this.protons = JSV.number(data.protons);
if (data.peaks) {
data.peaks.forEach(function(peak_data) {
self.add_peak(new JSV.Peak(peak_data))
});
}
}
JSV.inherits(Cluster, JSV.SVPath);
Cluster.prototype.toString = function() { return 'Cluster'; }
| Option name | Type | Description |
|---|---|---|
| peak | Peak | Peak to add |
Add a Peak to the cluster
Cluster.prototype.add_peak = function(peak) {
this._peaks.push(peak);
this.multiplet_type = undefined;
peak._cluster = this;
}
Reorder all the peaks in the Cluster by their center property.
Cluster.prototype.update = function() {
this._peaks.order_by('center');
}
| Option name | Type | Description |
|---|---|---|
| term | Integer,String,Array | See SVSet.get for details. |
Returns an SVSet of peaks or a single Peak from the Cluster.
Cluster.prototype.peaks = function(term) {
return this._peaks.get(term);
}
Returns the parent Compound.
Cluster.prototype.compound = function() {
return this._compound;
}
Returns the parent Spectrum.
Cluster.prototype.spectrum = function() {
return this.compound().spectrum();
}
Return the center of the cluster: an average of center value for all the peaks in the cluster.
Cluster.prototype.center = function() {
var center;
if (this.peaks().present()) {
center = d3.mean(this.peaks(), function(p) { return p.center });
}
return center;
}
| Option name | Type | Description |
|---|---|---|
| term | Integer,String,Array | See SVSet.get for details. |
Returns an SVSet of atoms or a single Atom from the Cluster.
Cluster.prototype.atoms = function(term) {
return this._atoms.get(term);
}
// http://pubs.acs.org/paragonplus/submission/acs_nmr_guidelines.pdf
// http://www.chem.uci.edu/~jsnowick/groupweb/files/MultipletGuideV4.pdf
Cluster.prototype.determine_multiplet_type = function() {
var self = this;
var peaks = self.peaks();
var type = 'm';
if (peaks.length == 1) {
type = 's';
} else if (peaks.length == 2) {
type = 'd';
} else if (peaks.length == 3) {
type = 't';
} else if (peaks.length == 4) {
if (double_of_doublets(peaks)) {
type = 'dd';
} else {
type = 'q';
}
} else if (peaks.length == 5) {
type = 'quint';
} else if (peaks.length == 6) {
if (triplet_of_doublets(peaks)) {
type = 'td';
} else {
type = 'dt';
}
}
return type
}
// All the peaks should be close to the same height
var double_of_doublets = function(peaks) {
var within = 0.1; // amount all heights must be within of the max height
var heights = peaks.map(function(p) { return p.amplitude });
var max_height = d3.max(heights);
var range_min = max_height * (1 - within);
var range_max = max_height * (1 + within);
return heights.every(function(h) { return h >= range_min && h <= range_max })
}
// The middle 2 peaks should be higher than all the other peaks
var triplet_of_doublets = function(peaks) {
var heights = peaks.map(function(p) { return p.amplitude });
var middle_height = d3.min(heights.slice(2,3));
var check_heights = heights.slice(0,1).concat(heights.slice(4,5));
return check_heights.every(function(h) { return h <= middle_height })
}
// Return the json required to create the multiplet nmrml
Cluster.prototype.nmrml_multiplet_json = function() {
var json;
switch (this.multiplet_type) {
case 's':
json = {_cvRef: 'NMRCV', _accession: 'NMR:1000194', _name: 'singlet feature'};
break;
case 'd':
json = {_cvRef: 'NMRCV', _accession: 'NMR:1000184', _name: 'doublet feature'};
break;
case 't':
json = {_cvRef: 'NMRCV', _accession: 'NMR:1000185', _name: 'triplet feature'};
break;
case 'q':
json = {_cvRef: 'NMRCV', _accession: 'NMR:1000186', _name: 'quatruplet feature'};
break;
case 'dd':
json = {_cvRef: 'NMRCV', _accession: 'NMR:1000192', _name: 'doublet of doublets feature'};
break;
case 'quint':
json = {_cvRef: 'NMRCV', _accession: 'NMR:1000195', _name: 'quintet feature'};
break;
case 'dt':
json = {_cvRef: 'NMRCV', _accession: 'NMR:1000196', _name: 'doublet of triplets feature'};
break;
case 'td':
json = {_cvRef: 'NMRCV', _accession: 'NMR:1000197', _name: 'triplet of doublets feature'};
break;
case 'm':
json = {_cvRef: 'NMRCV', _accession: 'NMR:1400305', _name: 'multiplet feature'};
break;
default:
json = {_cvRef: 'NMRCV', _accession: 'NMR:1400305', _name: 'multiplet feature'};
}
return json
}
/////////////////////////////////////////////////////////////////////////////
// Cluster Properties (setters/getters)
/////////////////////////////////////////////////////////////////////////////
Object.defineProperties(Cluster.prototype, {
'multiplet_type': {
get: function() {
if (!this._multiplet_type) {
this._multiplet_type = this.determine_multiplet_type();
}
return this._multiplet_type
},
set: function(type) {
this._multiplet_type = type;
}
},
'atom_refs': {
get: function() {
if (this.atoms().length > 0) {
return this.atoms().map(function(a) { return a.id });
} else {
return this._atom_refs || []
}
},
set: function(refs) {
this._atom_refs = refs;
}
}
});
JSV.Cluster = Cluster;
})(JSpectraViewer);