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xray.html
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xray.html
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<!DOCTYPE html>
<html lang="en">
<head>
<title>PDB statistics: X-ray data processing</title>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<link rel="stylesheet" type="text/css" href="css/dc.css"/>
<style>
html { margin: 0 auto; max-width: 980px; overflow-y: scroll; }
body { font: 14px sans-serif; line-height: 20px; }
.clearfix:before, .clearfix:after {
display: table; line-height: 0; content: ""; }
.clearfix:after { clear: both; }
h2 { text-align: center; margin-bottom: 10px; color: #444; }
h1#loading { text-align: center; color: #aaa; font-size: 40px; }
strong { color: #333; }
a.reset, #rel_switch { text-decoration: none; padding: 0 3px;
color: white; background: teal; }
a.reset:hover, #rel_switch:hover { text-decoration: underline; }
#chart-time, #chart-coltime { float: none; display: table; width: 100%; }
.time-comment { position:absolute; color:#555; z-index:-1; font-size: 13px;
line-height: 140%; }
@media only screen and (max-width: 750px) {
.time-comment { display: none; }
}
#top-row, #bottom-row { display: table; margin: 0 auto; }
#chart-facility, #chart-detec, #chart-reduc { margin-right: 20px; }
#chart-facility select { min-width: 180px; min-height: 200px; }
#chart-sg { margin-right: 5px; }
#chart-sg select { min-width: 140px; min-height: 182px; }
.x-axis-label { font-size: 13px; }
div.dc-chart g.row text.row { fill: black; font-size: 12px; }
div.dc-chart rect.deselected + text.row { fill: #555; }
#data-table { font: 13px sans-serif; min-width: 460px; }
#data-table { border-collapse: collapse; }
#data-table td, #data-table th { border: 3px solid white; }
.dc-table-label { background: #bdd; font-weight:bold; }
#data-table thead { background: #acc; }
#data-table tbody { background: #dee; }
#data-table tbody tr:hover { background: #f2fff8; }
#data-table tbody td { padding:0 5px 0 5px; }
#data-table a { text-decoration: none; }
@media only screen and (max-width: 700px) {
#data-table { font-size: 12px; }
}
#footnote { font-size: 12px; text-align: center; color:#444; padding: 8px 0; }
#subh { text-align:center; font-size:14px; color:#444;
margin:-2px 0 14px 100px; }
@media only screen and (max-width: 600px) {
#subh { margin-left: 0; display: table; }
}
#tcontainer {
width:100%; clear:both;
min-height: 450px;
position:relative;
background-repeat: no-repeat space; background-position: right;
}
#info-box {
background: white;
border-top: 1px solid #aaa;
padding-left: 20px;
position:absolute; top:45px; left:460px;
}
@media only screen and (max-width: 700px) {
#info-box { display: none; }
}
#info-box span { color:#888; font-size:14px; }
#info-box img { position: absolute; top:-250px; left:0; z-index:-1; }
</style>
</head>
<body>
<h2>PDB entries deposited since 2008</h2>
<p id="subh"><b>Each</b> chart can be used to filter data in other charts!
<a id="reset-all" class="reset" style="visibility: hidden;"
href="#" onclick="dc.filterAll();dc.redrawAll();return false;">reset
all filters</a>
</p>
<h1 id="loading">LOADING DATA...</h1>
<div id="all-data" style="visibility: hidden;">
<div id="top-row">
<div id="chart-facility">
<strong>Facility</strong>
<a class="reset" href="#">reset</a>
<div class="clearfix"></div>
</div>
<div id="chart-detec">
<strong>Detector</strong>
<a class="reset" href="#";>reset</a>
<div class="clearfix"></div>
</div>
<div id="chart-reduc">
<strong>Reduction</strong>
<a class="reset" href="#">reset</a>
<div class="clearfix"></div>
</div>
<div id="chart-scale">
<strong>Scaling</strong>
<a class="reset" href="#">reset</a>
<div class="clearfix"></div>
</div>
</div>
<div id="chart-coltime" style="position:relative">
<strong>Data collections</strong> per month
<span class="time-comment" style="left:40px; top:25px;">
old data was deposited mostly<br>before 2008 and is not shown</span>
<span class="time-comment" style="right:5px; top:25px;">
recent data is <br>mostly unreleased</span>
<a class="reset" href="#">reset</a>
<div class="clearfix"></div>
</div>
<div id="chart-time" style="position:relative"><strong>Depositions</strong>
(not <a href="#" id="rel_switch">releases</a>) per week
<a class="reset" href="#">reset</a>
<span class="time-comment" style="left:55px; top:30px;"
>select a time range to see<br>how things were changing</span>
<span class="time-comment" style="right:77%; top:80px;"
>arbitrary cut-off →</span>
<div class="clearfix"></div>
</div>
<div id="bottom-row">
<div id="chart-resol">
<strong>Resolution</strong>
<a class="reset" href="#">reset</a>
<div class="clearfix"></div>
</div>
<div id="chart-sg">
<strong>Spacegroup</strong>
<a class="reset" href="#">reset</a>
<div class="clearfix"></div>
</div>
<div id="chart-sol">
<strong>Solution</strong>
<a class="reset" href="#">reset</a>
<div class="clearfix"></div>
</div>
<div id="chart-ref">
<strong>Refinement</strong>
<a class="reset" href="#">reset</a>
<div class="clearfix"></div>
</div>
</div>
<div id="data-count">
<b class="filter-count"></b> selected out of
<span class="total-count"></span> records (max.
<select onchange="set_table_size(+this.value);" autocomplete=off>
<option value="0">0</option>
<option value="30" selected>30</option>
<option value="100">100</option>
<option value="300">300</option>
<option value="1000">1000</option>
</select>
rows are shown below).
</div>
<div id="tcontainer">
<table id="data-table">
<thead>
<tr class="header">
<th>Code</th>
<th>Res.</th>
<th>Collected</th>
<th>Deposited</th>
<th>Links</th>
</tr>
</thead>
</table>
<div id="info-box"><span>← move mouse over a row to see pic</span
><img src=""></div>
</div>
</div>
<div id="footnote" style="clear:both;">
This is part of the
<a href="https://project-gemmi.github.io/">project GEMMI</a>.
Uses <a href="https://dc-js.github.io/dc.js/">dc.js</a>,
<a href="https://d3js.org/">d3</a> and
<a href="http://crossfilter.github.io/crossfilter/">crossfilter</a>.
Last update: 2021-01-21.
Images are from <a href="http://www.pdbj.org/">PDBj</a>.
<b><a href="https://github.com/project-gemmi/pdb-stats">
Source code and info...</a></b>
</div>
<!--
<script type="text/javascript" src="js/d3.js"></script>
-->
<script type="text/javascript" src="https://d3js.org/d3.v3.min.js"></script>
<script type="text/javascript" src="js/crossfilter.js"></script>
<script type="text/javascript" src="js/dc.min.js"></script>
<script type="text/javascript">
"use strict";
var data;
var facility_chart = dc.selectMenu('#chart-facility');
var detec_chart = dc.pieChart('#chart-detec');
var reduc_chart = dc.pieChart('#chart-reduc');
var scale_chart = dc.pieChart('#chart-scale');
var time_chart = dc.barChart('#chart-time');
var coltime_chart = dc.barChart('#chart-coltime');
var sg_chart = dc.selectMenu('#chart-sg');
var resol_chart = dc.barChart('#chart-resol');
var sol_chart = dc.rowChart('#chart-sol');
var ref_chart = dc.pieChart('#chart-ref');
var table = dc.dataTable('#data-table');
var plot_rel_date = false;
var rel_switch = document.getElementById('rel_switch');
rel_switch.onclick = function() {
plot_rel_date = !plot_rel_date;
rel_switch.parentNode.firstChild.textContent =
plot_rel_date ? "Releases" : "Depositions";
rel_switch.textContent = plot_rel_date ? "depositions" : "releases";
time_chart.filterAll();
time_chart.dimension().dispose();
var time_dim = data.dimension(plot_rel_date
? (function(d) { return d3.time.week(d[9]); })
: (function(d) { return d3.time.week(d[8]); }));
time_chart.dimension(time_dim)
time_chart.group(time_dim.group())
dc.redrawAll();
return false;
};
d3.json('data.json', function(json) {
var SOURCES = {
'H': 'home source',
'F': 'XFEL (any)',
'?': 'synchrotron',
'-': 'unspecified',
'a': 'APS (US, IL)',
'e': 'ESRF (FR)',
'd': 'Diamond LS (UK)',
's': 'Swiss LS (CH)',
'A': 'ALS (US, Cal)',
'S': 'Stanford SRL (US)',
'n': 'NSLS (US, NY)',
'h': 'Shanghai SRF (CN)',
'p': 'Photon Factory (JP)',
'8': 'SPring-8 (JP)',
'b': 'BESSY (DE)',
'u': 'Australian S (AU)',
'f': 'SOLEIL (FR)',
'k': 'PAL/PLS (KR)',
'c': 'CLSI (CA)',
't': 'NSRRC (TW)',
'C': 'CHESS (US, NY)',
'm': 'MAX (SE)',
'D': 'DESY (DE)',
'L': 'LNLS (BR)',
'Z': 'ALBA (ES)',
'E': 'Elettra (IT)',
'B': 'Beijing SRF (CN)',
'U': 'SRS (UK)',
'I': 'Indus (IN)',
'y': 'SLAC (US, Cal)',
'K': 'KSRS (RU, Moscow)',
'z': 'CAMD (US, LA)',
'i': 'AichiSR (JP)',
'g': 'SAGA-LS (JP)',
'T': 'Siam Photon P. (TH)',
};
var SPACEGROUPS = [
"P 1", "P -1", "P 1 2 1", "P 1 21 1", "C 1 2 1", "P 1 m 1", "P 1 c 1",
"C 1 m 1", "C 1 c 1", "P 1 2/m 1", "P 1 21/m 1", "C 1 2/m 1", "P 1 2/c 1",
"P 1 21/c 1", "C 1 2/c 1", "P 2 2 2", "P 2 2 21", "P 21 21 2", "P 21 21 21",
"C 2 2 21", "C 2 2 2", "F 2 2 2", "I 2 2 2", "I 21 21 21", "P m m 2",
"P m c 21", "P c c 2", "P m a 2", "P c a 21", "P n c 2", "P m n 21",
"P b a 2", "P n a 21", "P n n 2", "C m m 2", "C m c 21", "C c c 2",
"A m m 2", "A b m 2", "A m a 2", "A b a 2", "F m m 2", "F d d 2", "I m m 2",
"I b a 2", "I m a 2", "P m m m", "P n n n", "P c c m", "P b a n", "P m m a",
"P n n a", "P m n a", "P c c a", "P b a m", "P c c n", "P b c m", "P n n m",
"P m m n", "P b c n", "P b c a", "P n m a", "C m c m", "C m c a", "C m m m",
"C c c m", "C m m a", "C c c a", "F m m m", "F d d d", "I m m m", "I b a m",
"I b c a", "I m m a", "P 4", "P 41", "P 42", "P 43", "I 4", "I 41", "P -4",
"I -4", "P 4/m", "P 42/m", "P 4/n", "P 42/n", "I 4/m", "I 41/a", "P 4 2 2",
"P 4 21 2", "P 41 2 2", "P 41 21 2", "P 42 2 2", "P 42 21 2", "P 43 2 2",
"P 43 21 2", "I 4 2 2", "I 41 2 2", "P 4 m m", "P 4 b m", "P 42 c m",
"P 42 n m", "P 4 c c", "P 4 n c", "P 42 m c", "P 42 b c", "I 4 m m",
"I 4 c m", "I 41 m d", "I 41 c d", "P -4 2 m", "P -4 2 c", "P -4 21 m",
"P -4 21 c", "P -4 m 2", "P -4 c 2", "P -4 b 2", "P -4 n 2", "I -4 m 2",
"I -4 c 2", "I -4 2 m", "I -4 2 d", "P 4/m m m", "P 4/m c c", "P 4/n b m",
"P 4/n n c", "P 4/m b m", "P 4/m n c", "P 4/n m m", "P 4/n c c",
"P 42/m m c", "P 42/m c m", "P 42/n b c", "P 42/n n m", "P 42/m b c",
"P 42/m n m", "P 42/n m c", "P 42/n c m", "I 4/m m m", "I 4/m c m",
"I 41/a m d", "I 41/a c d", "P 3", "P 31", "P 32", "R 3", "P -3", "R -3",
"P 3 1 2", "P 3 2 1", "P 31 1 2", "P 31 2 1", "P 32 1 2", "P 32 2 1",
"R 3 2", "P 3 m 1", "P 3 1 m", "P 3 c 1", "P 3 1 c", "R 3 m", "R 3 c",
"P -3 1 m", "P -3 1 c", "P -3 m 1", "P -3 c 1", "R -3 m", "R -3 c", "P 6",
"P 61", "P 65", "P 62", "P 64", "P 63", "P -6", "P 6/m", "P 63/m",
"P 6 2 2", "P 61 2 2", "P 65 2 2", "P 62 2 2", "P 64 2 2", "P 63 2 2",
"P 6 m m", "P 6 c c", "P 63 c m", "P 63 m c", "P -6 m 2", "P -6 c 2",
"P -6 2 m", "P -6 2 c", "P 6/m m m", "P 6/m c c", "P 63/m c m",
"P 63/m m c", "P 2 3", "F 2 3", "I 2 3", "P 21 3", "I 21 3", "P m -3",
"P n -3", "F m -3", "F d -3", "I m -3", "P a -3", "I a -3", "P 4 3 2",
"P 42 3 2", "F 4 3 2", "F 41 3 2", "I 4 3 2", "P 43 3 2", "P 41 3 2",
"I 41 3 2", "P -4 3 m", "F -4 3 m", "I -4 3 m", "P -4 3 n", "F -4 3 c",
"I -4 3 d", "P m -3 m", "P n -3 n", "P m -3 n", "P n -3 m", "F m -3 m",
"F m -3 c", "F d -3 m", "F d -3 c", "I m -3 m", "I a -3 d"];
var DETECT = ['?', 'CCD', 'PAD', 'IP'];
var DETECT_FULL = ['Not specified', 'CCD', 'Pixel Array Detector',
'Image Plate'];
var REDUC_SOFT = { 'X':'XDS', 'H':'HKL', 'M':'Mosflm', 'd':'d*TREK',
'D':'DIALS', 'O': 'Other', '-':'?' };
var SCALE_SOFT = { 'A':'Aimless', 'S':'SCALA', 'H':'HKL', 'X':'XSCALE',
'd':'d*TREK', 'O': 'Other', '-':'?' };
var REF_SOFT = { 'R':'Refmac', 'P':'Phenix', 'B':'BUSTER', 'C':'CNS',
'-':'other/mix' };
var STRUCT_SOL = ['known structure', 'MR', 'SAD', 'MAD', 'MIR/SIR',
'SIRAS', 'MIRAS', 'unspecified / other'];
function format_month(n) {
var y = (n / 12) | 0;
n -= 12 * y - 1;
return (1989 + y) + (n < 10 ? '-0' : '-') + n;
}
function format_date(date) { return date.toISOString().substr(0, 10); }
function parse_date(n) {
return new Date(Date.UTC(1989, (n >> 5), (n & 31)));
}
var code_map = {}
json.forEach(function (d) {
d[8] = parse_date(d[8]);
d[9] = parse_date(d[9]);
code_map[d[0]] = d;
});
data = crossfilter(json);
var all = data.groupAll();
var table_dim = data.dimension(function(d) { return d[9]; });
var facil_dim = data.dimension(function(d) { return d[1]; });
var detec_dim = data.dimension(function(d) { return d[2]; });
var reduc_dim = data.dimension(function(d) { return d[3][0]; });
var scale_dim = data.dimension(function(d) { return d[3][1]; });
var time_dim = data.dimension(function(d) { return d3.time.week(d[8]); });
var coltime_dim = data.dimension(function(d) {
return new Date(1989, d[7] || 0, 15);
});
var sg_dim = data.dimension(function(d) { return d[4]; });
var resol_dim = data.dimension(function(d) { return d[5] || -1; });
var sol_dim = data.dimension(function(d) { return d[6]; });
var ref_dim = data.dimension(function(d) { return d[3][2]; });
function make_title(dict) {
return (function(p) {
var v = dict[p.key];
return (v == '?' ? 'not specified' : v ) + ': ' + p.value;
});
}
d3.select('#loading').remove();
d3.select('#all-data').style('visibility', null);
function setup_chart(chart) {
var root_el = chart.root()[0][0];
var reset_el = root_el.getElementsByClassName('reset')[0];
reset_el.style.visibility = 'hidden';
reset_el.onclick = function() {
chart.filterAll();
dc.redrawAll();
return false;
};
return chart;
}
function setup_circle(chart, dim) {
return setup_chart(chart).width(200).height(200).innerRadius(55)
.controlsUseVisibility(true)
.dimension(dim)
.group(dim.group());
}
setup_chart(facility_chart)
.dimension(facil_dim)
.group(facil_dim.group())
.title(function(p) { return SOURCES[p.key] + ': ' + p.value; })
.order(function(a, b){ return b.value - a.value; })
.controlsUseVisibility(true)
.multiple(true).numberVisible(10);
setup_circle(detec_chart, detec_dim)
.ordering(function(p){ return [3,1,2,0].indexOf(p.key); })
.minAngleForLabel(0.0)
.label(function(p) { return DETECT[p.key]; })
.title(function(p) { return DETECT_FULL[p.key] + ': ' + p.value; })
.colors(d3.scale.ordinal().range(
['#a6761d', '#66a61e', '#7570b3', '#e6ab02']));
setup_circle(reduc_chart, reduc_dim)
.ordering(function(p){ return 'MHdXO-D'.indexOf(p.key); })
.minAngleForLabel(0.1)
.label(function(p) { return REDUC_SOFT[p.key]; })
.title(make_title(REDUC_SOFT))
.colors(d3.scale.category10());
setup_circle(scale_chart, scale_dim)
.ordering(function(p){ return 'ASHdXO-'.indexOf(p.key); })
.minAngleForLabel(0.05)
.label(function(p) { return SCALE_SOFT[p.key]; })
.title(make_title(SCALE_SOFT))
.colors(d3.scale.ordinal().range(['#1f77b4', '#8899cc',
'#ff7f0e', '#2ca02c', '#d62728', '#9467bd', '#8c564b']));
var date_range = [new Date(2005, 0), new Date(2021, 0)];
setup_chart(coltime_chart)
.width(null).height(100)
.margins({top: 5, right: 5, bottom: 20, left: 36})
.dimension(coltime_dim)
.group(coltime_dim.group())
.xUnits(function() { return 13 * 12; })
.gap(1)
.x(d3.time.scale().domain(date_range))
.elasticY(true)
.controlsUseVisibility(true)
.renderHorizontalGridLines(true);
coltime_chart.yAxis().ticks(3);
setup_chart(time_chart)
.width(null).height(100)
.margins({top: 5, right: 5, bottom: 20, left: 36})
.dimension(time_dim)
.group(time_dim.group())
.centerBar(true)
.alwaysUseRounding(true)
.x(d3.time.scale().domain(date_range))
.elasticY(true)
.controlsUseVisibility(true)
.renderHorizontalGridLines(true);
time_chart.yAxis().ticks(3);
setup_chart(sg_chart)
.dimension(sg_dim)
.group(sg_dim.group())
.title(function(p) { return SPACEGROUPS[p.key-1] + ': ' + p.value; })
.order(function(a, b){ return b.value - a.value; })
.controlsUseVisibility(true)
.multiple(true).numberVisible(10);
setup_chart(resol_chart)
.width(250).height(200)
.margins({top: 5, right: 10, bottom: 20, left: 35})
.dimension(resol_dim)
.group(resol_dim.group())
.centerBar(true)
.gap(1)
.x(d3.scale.linear().domain([0, 5]))
.xUnits(function() { return 50; })
.colors(d3.scale.ordinal().range(['#41ab5d']))
.controlsUseVisibility(true)
.elasticY(true);
resol_chart.yAxis().ticks(4).tickFormat(d3.format('d'));
resol_chart.xAxis().ticks(12);
setup_chart(sol_chart)
.width(180).height(200)
.dimension(sol_dim)
.group(sol_dim.group())
.label(make_title(STRUCT_SOL))
.title(make_title(STRUCT_SOL))
.ordering(function(d){ return d.key; })
.margins({top: 5, right: 15, bottom: 20, left: 5})
.controlsUseVisibility(true)
.elasticX(true)
.colors(d3.scale.ordinal().domain('kosmSiM-')
.range(['#74a9cf', '#ffffb3', '#c2e699', '#78c679',
'#31a354','#78c679', '#006d2c', '#f46d43']));
sol_chart.xAxis().ticks(2);
setup_circle(ref_chart, ref_dim)
.ordering(function(p){ return 'BCR-P'.indexOf(p.key); })
.minAngleForLabel(0.1)
.label(function(p) { return REF_SOFT[p.key]; })
.title(make_title(REF_SOFT))
.colors(d3.scale.ordinal().range(
['#d62728', '#8c564b', '#8899cc', '#9467bd', '#e6ab02']));
dc.dataCount('#data-count').dimension(data).group(all)
.on('renderlet', function(chart) {
var all = chart.dimension().size() == chart.group().value();
d3.select('#reset-all').style('visibility', all ? 'hidden' : 'visible');
});
function select_row(e) {
var tr = this;
var code = tr.firstChild.innerHTML;
var y = tr.offsetTop + 10;
var d = code_map[code];
var box = document.getElementById('info-box');
box.style.top = y + 'px';
box.firstChild.style.color = '#444';
box.firstChild.innerHTML = '<b>'+code+'</b><br>solved by: ' +
STRUCT_SOL[d[6]] + '<br>software: ' + REDUC_SOFT[d[3][0]] + ' / ' +
SCALE_SOFT[d[3][1]] + ' / ' + REF_SOFT[d[3][2]];
var src = 'https://pdbj.org/rest/molmil-renderer?type=mine&id=' + code.toLowerCase();
if (box.lastChild.src === src) {
box.style.visibility = 'visible';
return;
}
box.lastChild.src = ''
box.lastChild.style.top = (y > 200 ? -250 : 50) + 'px';
box.style.visibility = 'visible';
timer = setTimeout(function() {
box.lastChild.src = src;
}, 500);
return false;
}
var timer;
table
.width(null).height(540)
.size(30)
.dimension(table_dim)
.group(function(d) { return 'Released ' + format_date(d[9]); })
.columns([
function(d) { return d[0]; },
function(d) { return d[5] ? d[5].toFixed(1) : ''; },
function(d) {
return (d[7] ? format_month(d[7]) : '?') +
' @' + SOURCES[d[1]].split(' ')[0];
},
function(d) { return format_date(d[8]); },
function(d) {
return '<a href="http://www.rcsb.org/pdb/explore.do?structureId=' +
d[0] + '">RCSB</a> <a href="https://www.ebi.ac.uk/pdbe/entry/pdb/' +
d[0] + '/">PDBe</a> <a href="http://pdbj.org/mine/summary/' +
d[0] + '">PDBj</a>';
},
])
.order(d3.descending)
.on('preRedraw', function(chart, filter){
document.getElementById('info-box').style.visibility = 'hidden';
})
.on('renderlet', function(chart) {
var nodes = document.getElementById('data-table')
.getElementsByClassName('dc-table-row');
for (var i=0; i < nodes.length; i++) {
nodes[i].onmouseover = select_row;
nodes[i].onmouseout = function() { clearTimeout(timer); }
}
});
var on_resize = function() {
var body_w = d3.select('body').node().getBoundingClientRect().width;
resol_chart.width(body_w > 980 ? 400 : body_w > 360 ? 340 : body_w-20);
var time_tics = body_w > 700 ? 15 : 5;
coltime_chart.xAxis().ticks(time_tics);
time_chart.xAxis().ticks(time_tics);
// maybe .brushOn(off) for mobile?
dc.renderAll();
};
on_resize();
d3.select(window).on('resize', on_resize);
});
var set_table_size = function(n) {
d3.select('#data-table').style('visibility', n === 0 ? 'hidden' : 'visible');
table.size(n);
table.redraw();
}
</script>
</body>
</html>
<!-- vim: set et ts=2 sw=2: -->