//pbd file is attached for now, can pull from the web.
pdbText = REM2_PDB.text()
schemeId = {
return NGL.ColormakerRegistry.addScheme(function (params) {
this.atomColor = function (atom) {
if(selected_sites[atom.residue.resno]) {
console.log("# Site: " + atom.residue.resno)
let site_color = "gray"; // gray for Neutral
console.log("Class: " + selected_sites[atom.residue.resno].class)
if (selected_sites[atom.residue.resno].class == "Purifying") {
site_color = "red";
}
if (selected_sites[atom.residue.resno].class == "Diversifying") {
site_color = "blue";
}
if (selected_sites[atom.residue.resno].class == "Invariable") {
site_color = "yellow";
}
return color_hash[site_color];
//return color_hash[selected_sites[atom.residue.resno].color];
}
else {
// gray
//return 0x808080;
return color_hash["gray"]
}
}
})
}
html`<div id='alignment_div'>`
d3=require("d3")
bioseq = require("bioseq")
React = r('react')
r = require.alias({
react: "react@16/umd/react.production.min.js",
"react-dom": "react-dom@16/umd/react-dom.production.min.js"
})
// component.defaultParameters
selected_sites = {
let site_table = ResultsTable;
let site_hash = {};
site_table.forEach(site_datum => site_hash[+site_datum.PDBSite] = site_datum);
return site_hash;
}
import {textcolor} from "@observablehq/text-color-annotations-in-markdown"
color_hash = {
return {
blue: 0x00FFFF,
red: 0xcf5b5b,
yellow: 0xFFFF00,
green: 0x5fcf5b,
pink: 0xFFC0CB,
gray: 0x808080
};
}
selection_string = _.map (
Object.keys(selected_sites), (i, s) => ['A'].map(chain => i + ':' + chain).join(" OR ")
).join (" OR ")
REM2_PDB = FileAttachment("3cbq.pdb")
ResultsTable = FileAttachment("mammalian_REM2_StructureView@9.csv").csv()
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