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structures-view.html
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<link rel="import" href="protein-overview.html">
<link rel="import" href="isoform-selector.html">
<link rel="import" href="bioviz-v2-section.html">
<link rel="import" href="triple-viewer.html">
<link rel="import" href="keywords-section.html">
<link rel="import" href="xrefs-section.html">
<link rel="import" href="external-scripts.html">
<link rel="import" href="nextprot-elements-shared-styles.html">
<!--
`structures-view`
View listing sequence annotations.
#### Example
<structures-view nx-config='{"entry": "P52701"}'></structures-view>
@demo demo/structures-view-demo.html
-->
<dom-module id="structures-view">
<template>
<style include="nextprot-elements-shared-styles">
:host {
display: block;
background:#f8f8f8;
overflow-y: auto;
}
</style>
<div class="row">
<div id="nxOverview" class="col-md-12">
<protein-overview nx-config="{{nxConfig}}" nx-entry-data="[[nxEntryData]]" lazy-loading="[[lazyLoading]]"></protein-overview>
</div>
</div>
<div id="noDataWarning" class='alert alert-warning noData' hidden>There is no structure related features available in neXtProt for [[nxConfig.entry]].
Suggestions for updates are welcome! Please <a href='mailto:[email protected]'>contact us</a>.
</div>
<div id="nxPositionalAnnotations" class="row nxSection">
<isoform-selector nx-config="{{nxConfig}}" iso-name="{{isoName}}" nx-entry-data="[[nxEntryData]]"
lazy-loading="[[lazyLoading]]"
feature-viewer-ready="{{featureViewerReady}}"></isoform-selector>
<triple-viewer nx-config="{{nxConfig}}" count="{{positionalAnnotationsCount}}" hide-sequence-viewer iso-name="[[isoName]]" selection="{{selection}}"
feature-list='[
{
"APIRef": "sequence",
"metadata": {"name": "Sequence"}
},
{
"APIRef": "domain",
"metadata": {
"name": "Domain",
"className": "domain",
"color": "#B3C2C2",
"type": "rect",
"filter": "Region"
}
},
{
"APIRef": "repeat",
"metadata": {
"name": "Repeat",
"className": "repeat",
"color": "#98B7D5",
"type": "rect",
"filter": "Region"
}
},
{
"APIRef": "calcium-binding-region",
"metadata": {
"name": "Calcium binding",
"className": "calcium",
"color": "#B3C2E1",
"type": "rect",
"filter": "Region"
}
},
{
"APIRef": "zinc-finger-region",
"metadata": {
"name": "Zinc finger",
"className": "calcium",
"color": "#B3C2E1",
"type": "rect",
"filter": "Region"
}
},
{
"APIRef": "dna-binding-region",
"metadata": {
"name": "DNA binding",
"className": "dnabind",
"color": "#B3C2FF",
"type": "rect",
"filter": "Region"
}
},
{
"APIRef": "nucleotide-phosphate-binding-region",
"metadata": {
"name": "Nucleotide binding",
"className": "nucleobind",
"color": "#B3D1B3",
"type": "rect",
"filter": "Region"
}
},
{
"APIRef": "coiled-coil-region",
"metadata": {
"name": "Coiled-coil",
"className": "coiledcoil",
"color": "#B3D1C2",
"type": "rect",
"filter": "Region"
}
},
{
"APIRef": "short-sequence-motif",
"metadata": {
"name": "Sequence motif",
"className": "motif",
"color": "#B3D1D1",
"type": "rect",
"filter": "Region"
}
},
{
"APIRef": "compositionally-biased-region",
"metadata": {
"name": "Composition bias",
"className": "biased",
"color": "#B3D1E1",
"type": "rect",
"filter": "Region"
}
},
{
"APIRef": "interacting-region",
"metadata": {
"name": "Interacting region",
"className": "intregion",
"color": "#B3C2F0",
"type": "rect",
"filter": "Region"
}
},
{
"APIRef": "miscellaneous-region",
"metadata": {
"name": "Region",
"className": "miscregion",
"color": "#B3C2B3",
"type": "rect",
"filter": "Region"
}
},
{
"APIRef": "topological-domain",
"metadata": {
"name": "Topological domain",
"className": "topodomain",
"color": "#A5DBA5",
"type": "rect",
"filter": "Topology"
}
},
{
"APIRef": "transmembrane-region",
"metadata": {
"name": "Membrane",
"className": "membrane",
"color": "#A5DBB7",
"type": "rect",
"filter": "Topology"
}
},
{
"APIRef": "intramembrane-region",
"metadata": {
"name": "Membrane",
"className": "intramembrane",
"color": "#A5DBB7",
"type": "rect",
"filter": "Topology"
}
},
{
"APIRef": "miscellaneous-site",
"metadata": {
"name": "Site",
"className": "site",
"color": "#B3F0E1",
"type": "unique",
"filter": "Site"
}
},
{
"APIRef": "active-site",
"metadata": {
"name": "Active site",
"className": "actSite",
"color": "#B3F0F0",
"type": "unique",
"filter": "Site"
}
},
{
"APIRef": "binding-site",
"metadata": {
"name": "Binding site",
"className": "bindsite",
"color": "#82E6FF",
"type": "unique",
"filter": "Site"
}
},
{
"APIRef": "cleavage-site",
"metadata": {
"name": "Cleavage site",
"className": "cleavsite",
"color": "#B3FFB3",
"type": "unique",
"filter": "Site"
}
},
{
"APIRef": "metal-binding-site",
"metadata": {
"name": "Metal binding",
"className": "metal",
"color": "#B3FFC2",
"type": "unique",
"filter": "Site"
}
},
{
"APIRef": "variant",
"metadata": {
"name": "Variant",
"className": "variant",
"color": "rgba(0,255,154,0.3)",
"type": "unique",
"filter": "Variant"
}
},
{
"APIRef": "mutagenesis",
"metadata": {
"name": "Mutagenesis",
"className": "mutagenesis",
"color": "#73FFE3",
"type": "unique",
"filter": "Variant"
}
},
{
"APIRef": "sequence-conflict",
"metadata": {
"name": "Conflict",
"className": "seqconflict",
"color": "#6FFFFF",
"type": "unique",
"filter": "Conflict"
}
},
{
"APIRef": "beta-strand",
"metadata": {
"name": "Beta strand",
"className": "betastrand",
"color": "#B3F0C2",
"type": "rect",
"filter": "Secondary structure"
}
},
{
"APIRef": "helix",
"metadata": {
"name": "Helix",
"className": "helix",
"color": "#B3F0D1",
"type": "rect",
"filter": "Secondary structure"
}
},
{
"APIRef": "turn",
"metadata": {
"name": "Turn",
"className": "turn",
"color": "#B3F0E1",
"type": "rect",
"filter": "Secondary structure"
}
},
{
"APIRef": "isoform-mapping",
"metadata": {}
}]' nx-entry-data="[[nxEntryData]]"
feature-viewer-ready="{{featureViewerReady}}">
</triple-viewer>
<bioviz-v2-section nx-config="{{nxConfig}}" isoform="[[isoName]]" selection="[[selection]]"></bioviz-v2-section>
</div>
<div class="row">
<div id="nxKeywords" class="col-md-12">
<keywords-section categories='["Technical term"]'
exceptions='["KW-0021", "KW-0181", "KW-0903", "KW-0895", "KW-0374", "KW-0511", "KW-0582", "KW-0814"]'
nx-config="{{nxConfig}}" count="{{keywordsCount}}"
nx-entry-data="[[nxEntryData]]" lazy-loading="[[lazyLoading]]">
</keywords-section>
</div>
</div>
<div class="row">
<div id="nxXrefs" class="col-md-12">
<xrefs-section
categories='["SAM", "SASBDB", "BMRB", "PCDDB", "AlphaFoldDB", "DisProt", "Proteopedia", "SMR", "UniLectin", "IDEAL"]'
nx-config="{{nxConfig}}"
view="structures"
count="{{xrefsCount}}"></xrefs-section>
</div>
</div>
</template>
<script>
Polymer({
is: 'structures-view',
properties: {
nxConfig: {
type: Object,
value: {}
},
goldOnly: {
type: Boolean,
value: false
},
positionalAnnotationsCount: {
type: Number,
value: -1,
observer: "_checkAnnotations"
},
keywordsCount: {
type: Number,
observer: "_checkKeywords"
},
xrefsCount: {
type: Number,
observer: "_checkXrefs"
},
nxEntryData: {
type: String,
value: ""
},
lazyLoading: {
type: Boolean,
value: false,
},
featureViewerReady: {
type: Boolean,
value: false,
notify: true
}
},
_checkAnnotations: function() {
if (this.positionalAnnotationsCount==0) {
this.$.nxPositionalAnnotations.hidden=true;
this.$.noDataWarning.hidden=false;
} else {
this.$.nxPositionalAnnotations.hidden=false;
this.$.noDataWarning.hidden=true;
}
},
_checkKeywords: function(){
this.keywordsCount===0 ? this.$.nxKeywords.hidden=true : this.$.nxKeywords.hidden=false;
},
_checkXrefs: function(){
this.xrefsCount===0 ? this.$.nxXrefs.hidden=true : this.$.nxXrefs.hidden=false;
}
});
</script>
</dom-module>