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Dynamic Molecules Generator
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1!=n.getDate()}],["%B",function(n){return n.getMonth()}],["%Y",we]]),Fs={range:function(n,t,e){return Zo.range(Math.ceil(n/e)*e,+t,e).map(Oo)},floor:wt,ceil:wt};js.year=Qa.year,Qa.scale=function(){return Fo(Zo.scale.linear(),js,Hs)};var Os=js.map(function(n){return[n[0].utc,n[1]]}),Ys=Ds.multi([[".%L",function(n){return n.getUTCMilliseconds()}],[":%S",function(n){return n.getUTCSeconds()}],["%I:%M",function(n){return n.getUTCMinutes()}],["%I %p",function(n){return n.getUTCHours()}],["%a %d",function(n){return n.getUTCDay()&&1!=n.getUTCDate()}],["%b %d",function(n){return 1!=n.getUTCDate()}],["%B",function(n){return n.getUTCMonth()}],["%Y",we]]);Os.year=Qa.year.utc,Qa.scale.utc=function(){return Fo(Zo.scale.linear(),Os,Ys)},Zo.text=St(function(n){return n.responseText}),Zo.json=function(n,t){return kt(n,"application/json",Yo,t)},Zo.html=function(n,t){return kt(n,"text/html",Io,t)},Zo.xml=St(function(n){return n.responseXML}),"function"==typeof define&&define.amd?define(Zo):"object"==typeof module&&module.exports&&(module.exports=Zo),this.d3=Zo}(); |
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<!DOCTYPE html> | |
<meta charset="utf-8"> | |
<style> | |
* { box-sizing:border-box; } | |
.link line { | |
stroke: #000000; | |
stroke-opacity: 0.7; | |
stroke-width: 1; | |
} | |
.link line.separator { | |
stroke: #fff; | |
stroke-width: 3px; | |
} | |
.node circle { | |
stroke: #000; | |
stroke-width: 3px; | |
} | |
.container { | |
font-family:'Lucida Sans Unicode'; | |
width:500px; | |
margin:15px auto auto 30px; | |
display:block; | |
background:#FFF; | |
padding:20px 5px 5px; | |
} | |
.footer { text-align:right; } | |
.footer a { color:#53B2C8; } | |
.group { | |
position:relative; | |
margin-bottom:5px; | |
} | |
.examples { | |
color:#999; | |
font-size:12px; | |
font-weight:normal; | |
font-family:'Lucida Sans Unicode'; | |
} | |
.examples a:link { | |
color: #53B2C8; | |
font-weight:bold; | |
} | |
.examples a:visited { | |
color: #53B2C8; | |
font-weight:bold; | |
} | |
.examples a:hover { | |
color: #53B2C8; | |
font-weight:bold; | |
} | |
.examples a:active { | |
color: #53B2C8; | |
font-weight:bold; | |
} | |
input { | |
font-size:16px; | |
padding:10px 10px 10px 5px; | |
display:block; | |
width:300px; | |
border:none; | |
border-bottom:1px solid #757575; | |
} | |
input:focus { outline:none; } | |
label { | |
color:#999; | |
font-size:16px; | |
font-weight:normal; | |
position:absolute; | |
pointer-events:none; | |
left:5px; | |
top:10px; | |
transition:0.2s ease all; | |
-moz-transition:0.2s ease all; | |
-webkit-transition:0.2s ease all; | |
} | |
input:focus ~ label, input:valid ~ label { | |
top:-15px; | |
font-size:13px; | |
color:#5264AE; | |
} | |
.bar { position:relative; display:block; width:350px; } | |
.bar:before, .bar:after { | |
content:''; | |
height:2px; | |
width:0; | |
bottom:1px; | |
position:absolute; | |
background:#5264AE; | |
transition:0.2s ease all; | |
-moz-transition:0.2s ease all; | |
-webkit-transition:0.2s ease all; | |
} | |
.bar:before { left:50%; } | |
.bar:after { right:50%; } | |
input:focus ~ .bar:before, input:focus ~ .bar:after { | |
width:50%; | |
} | |
.highlight { | |
position:absolute; | |
height:60%; | |
width:100px; | |
top:25%; | |
left:0; | |
pointer-events:none; | |
opacity:0.5; | |
} | |
input:focus ~ .highlight { | |
-webkit-animation:inputHighlighter 0.3s ease; | |
-moz-animation:inputHighlighter 0.3s ease; | |
animation:inputHighlighter 0.3s ease; | |
} | |
@-webkit-keyframes inputHighlighter { | |
from { background:#5264AE; } | |
to { width:0; background:transparent; } | |
} | |
@-moz-keyframes inputHighlighter { | |
from { background:#5264AE; } | |
to { width:0; background:transparent; } | |
} | |
@keyframes inputHighlighter { | |
from { background:#5264AE; } | |
to { width:0; background:transparent; } | |
} | |
</style> | |
<script src="smiles.js"></script> | |
<script src="d3.v3.min.js"></script> | |
<body> | |
<div class="container"> | |
<form onsubmit="return false"> | |
<div id="user" class="group"> | |
<input type="text" required value="" onpaste="onclick_handler(this.value)" onkeyup="onkey_handler(event)"> | |
<span class="highlight"></span> | |
<span class="bar"></span> | |
<label id="textbox">Input...</label> | |
</div> | |
</form> | |
<label> | |
<div id="molecularWeight" style="position: absolute; top:35px; left:400px; width:200px; height:25px">""</div> | |
</label> | |
<div id="examples" style="position: absolute; top:68px; left:46px; width:400px; height:30px"> | |
<p class="examples"><i>examples: </i> | |
<a href="#" onclick="example_handler('C=O C=O C=O C=O C=O C=O C=O C=O C=O')">formaldehyde</a>, | |
<a href="#" onclick="example_handler('FH ClH BrH IH FH ClH BrH IH FH ClH BrH IH')">halides</a>, | |
<a href="#" onclick="example_handler('C=C(C)C=C')">isoprene,</a> | |
<a href="#" onclick="example_handler('NC(C=O)C=C(O)C(N)C')">default</a> | |
</p> | |
</div> | |
<div id="chart"></div> | |
<div><p class="footer"> | |
<a href="https://github.com/chemplexity/molecules" target="_blank">source</a>, | |
<a href="http://www.opensmiles.org/spec/open-smiles-2-grammar.html" target="_blank">help</a> | |
</p></div> | |
</div> | |
</body> | |
<script> | |
/** | |
* Generate dynamic molecules with HTML/CSS/Javascript | |
* (C) 2014 by James Dillon | |
* http://wwww.github.com/chemplexity | |
*/ | |
// Filter input | |
var onkey_handler = function(event) { | |
// Input: 'enter', 'backspace', '=', '0', '9' | |
if (event.keyCode == 13 || event.keyCode == 8 || event.keyCode == 187 || | |
event.keyCode == 48 || event.keycode == 57) | |
{onclick_handler(document.getElementsByTagName("input")[0].value)} | |
// Input: non-alphabet | |
else if (event.keyCode < 65 || event.keyCode > 90) {return false} | |
// Input: alphabet | |
else {onclick_handler(document.getElementsByTagName("input")[0].value)} | |
} | |
var example_handler = function (input) { | |
document.getElementsByTagName("input")[0].value = input; | |
onclick_handler(input); | |
} | |
// Submit input | |
var onclick_handler = function(input) { data(input) }; | |
// SMILES to JSON | |
var data = function(input) { | |
// Check for empty input | |
if (input.length == 0) {return false} | |
// Use custom SMILES converter | |
var molecule = smiles(input); | |
// Add size property to atoms | |
for (i=0; i < molecule.atoms.length; i++) { | |
if(molecule.atoms[i].element == 1) { molecule.atoms[i].size = 5 } | |
else if(molecule.atoms[i].element == 9) { molecule.atoms[i].size = 6 } | |
else if(molecule.atoms[i].element == 35) { molecule.atoms[i].size = 11 } | |
else if(molecule.atoms[i].element == 53) { molecule.atoms[i].size = 13 } | |
else { molecule.atoms[i].size = 8 } | |
} | |
// Add source/target fields | |
for (i=0; i < molecule.bonds.length; i++) { | |
molecule.bonds[i].source_id = molecule.bonds[i].source; | |
molecule.bonds[i].target_id = molecule.bonds[i].target; | |
} | |
// Update graph | |
update(molecule); | |
}; | |
// General properties | |
var margin = {top: 5, right: -5, bottom: 5, left: -5}; | |
var width = 500 - margin.left - margin.right, | |
height = 375 - margin.top - margin.bottom, | |
padding = 1; | |
r = 15; | |
// Size of atoms | |
var radius = d3.scale.sqrt() | |
.range([0, 6]); | |
// Graphics container | |
var svg = d3.select("body").append("svg") | |
.attr("width", width) | |
.attr("height", height); | |
// Molecules container | |
var vis = d3.select("#chart") | |
.append("svg:svg") | |
.attr("width", width) | |
.attr("height", height) | |
.append("g") | |
// Start d3.js | |
var force = d3.layout.force() | |
.size([width + margin.left + margin.right, height + margin.top + margin.bottom]) | |
.charge(-300) | |
.gravity(0.8) | |
.linkDistance(-40) | |
.theta(0.1) | |
// Update graph with new molecule | |
function update(molecule) { | |
// Prevent bonds from overlapping | |
var bonding = []; | |
// Create invisible nodes between atoms | |
molecule.bonds.forEach(function(link) { | |
bonding.push({ | |
source: molecule.atoms[link.source], | |
target: molecule.atoms[link.target] | |
}); | |
}); | |
// Concatenate invisible nodes with atoms | |
force.nodes(molecule.atoms.concat(bonding)) | |
force.links(molecule.bonds) | |
vis.selectAll(".node").remove() | |
// Initialize bonds | |
var link = vis.selectAll(".link") | |
.data(force.links(), function(d) { return d.source +"-"+ d.target; }) | |
// Update bonds | |
link.enter().append("g") | |
.attr("class", "link") | |
.on('mouseover', function (d) {return update_fragment(molecule, d.source, d.target)}) | |
//.on('mouseout', bondType) | |
link.append("line") | |
.style("stroke-width", function(d) { return (d.order * 3 - 1) * 2 + "px"; }) | |
link.filter(function(d) { return d.order > 1; }).append("line") | |
.attr("class", "separator"); | |
// Remove bonds from last molecule | |
link.exit().remove() | |
// Set rigid bonds | |
var bonding = vis.selectAll(".link-node") | |
.data(bonding) | |
bonding.enter().append("circle") | |
.attr("class", "link-node") | |
.attr("visibility", "hidden"); | |
bonding.exit().remove() | |
// Initialize atoms | |
var node = vis.selectAll(".node") | |
.data(molecule.atoms, function(d) {return d.atom_id}) | |
// Update atoms | |
node.enter().append("circle") | |
.attr("class", "node") | |
.call(force.drag) | |
.style("fill", function(d) { return d.color; }) | |
.attr("r", function(d) { return d.size+2 }) | |
.style("stroke", "black") | |
.style("stroke-width", 3) | |
.style("stroke-opacity", 0.9); | |
// Remove atoms from last molecule | |
node.exit() | |
.attr('x', 0) | |
.transition() | |
.duration(100) | |
.attr('x', 60) | |
.style('fill-opacity', 0) | |
.remove() | |
// Dynamic movement | |
force.on("tick", function () { | |
link.selectAll("line") | |
.attr("x1", function(d) { return d.source.x; }) | |
.attr("y1", function(d) { return d.source.y; }) | |
.attr("x2", function(d) { return d.target.x; }) | |
.attr("y2", function(d) { return d.target.y; }) | |
node.attr("cx", function(d) { return d.x = Math.max(r, Math.min(width - r, d.x)); }) | |
.attr("cy", function(d) { return d.y = Math.max(r, Math.min(height - r, d.y)); }) | |
bonding.attr("cx", function(d) { return d.x = (d.source.x + d.target.x) * 0.5; }) | |
.attr("cy", function(d) { return d.y = (d.source.y + d.target.y) * 0.5; }); | |
}); | |
force.start() | |
// Update molecular weight values | |
update_text(molecule) | |
} | |
// Display molecular weight | |
function update_text(molecule) { | |
document.getElementById("molecularWeight").innerHTML = molecule.molecule_weight + " g/mol"; | |
} | |
// Display fragmentation molecular weight | |
function update_fragment(molecule, source, target) { | |
// Selected bond data | |
var bondSelected = d3.select(this).node() | |
// Calculate molecular weight of fragments | |
var sourceFragment = 0; | |
var targetFragment = 0; | |
var totalFragment = []; | |
//console.log(findObjects(molecule.bonds, "source_id", source.index)); | |
//var x = findObjects(molecule.bonds, "source_id"; | |
//console.log(source.index) | |
} | |
// Default molecule | |
data("NC(C=O)C=C(O)C(N)C"); | |
// | |
// Utility | |
// | |
// Find object key/value | |
function findObjects(array, key, value) { | |
for (var i = 0; i < array.length; i++) { if (array[i][key] == value) { return array[i]; }} | |
return null | |
} | |
/** | |
function bondType() { | |
// Selected bond data | |
var bondSelected = d3.select(this).node().__data__ | |
// Calculate molecular weight of fragments | |
var sourceFragment = 0; | |
var targetFragment = 0; | |
var totalFragment = []; | |
// Traverse nodes | |
for (i = 0; i < molecule.atoms.length; i++) { | |
// Current target | |
var targetAtom = bondSelected.target; | |
if (findObjects(totalFragment, "id", targetAtom) == null) { | |
totalFragment.push({id: bondSelected.target}) | |
} | |
// for (i = 0; i < molecule.nodes.length; i++) { linkIndex[i + "," + i] = 1; } | |
// molecule.links.forEach(function(d) { linkIndex[d.source.index + "," + d.target.index] = 1; }); | |
// function neighboring(a, b) { return linkIndex[a.index + "," + b.index]; } | |
console.log(d3.select(this).node().__data__) | |
} | |
*/ | |
</script> |
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/** | |
* Convert SMILES to JSON | |
* (C) 2014 by James Dillon | |
* http://wwww.chemplexity.com | |
* | |
*/ | |
function smiles(input) { | |
// Parse input using SMILES grammar | |
var grammar = definitions(); | |
// Filter input | |
var input = input.split("") | |
if (input.length == 0 || input.length > 100) return false; | |
if (findObjects(grammar.atoms, 'symbol', input[0]) == null) return false; | |
if (findObjects(grammar.atoms, 'symbol', input[input.length-1]) == null) return false; | |
// Create a new molecule | |
var molecule = { | |
molecule_id: input, | |
molecule_weight: 0, | |
atoms: [], | |
bonds: [] | |
}; | |
// Molecules are composed of atoms | |
function atom(id, weight, symbol, element, valence, color) { | |
this.atom_id = id; | |
this.atom_weight = weight; | |
this.symbol = symbol; | |
this.element = element; | |
this.valence = valence; | |
this.color = color; | |
} | |
// Atoms are connected by bonds | |
function bond(id, source, target, type, value) { | |
this.bond_id = id; | |
this.source = source; | |
this.target = target; | |
this.type = type; | |
this.order = value; | |
} | |
// Begin parsing input string | |
var index = {atoms: [], non_atoms: [], branches: [], bonds: [], rings: []}; | |
var counter = {branches: -1, empty: -1, last: "start"}; | |
// | |
// Atoms | |
// | |
// Find atoms | |
for (i = 0; i < input.length; i++) { | |
// Compare input with SMILES grammar | |
var match = findObjects(grammar.atoms, 'symbol', input[i]); | |
// Check match | |
if (match != null) { | |
// Check for two letter elements | |
var exceptions = ["H", "B", "C", "S", "A"]; | |
if (exceptions.indexOf(match.symbol)) { | |
// Compare concatenated string with SMILES grammar | |
var matchSpecial = findObjects(grammar.atoms, 'symbol', match.symbol + input[i+1]); | |
// Check special match | |
if (matchSpecial != null) { | |
// Replace current element in array with two letter element | |
input[i] = matchSpecial.symbol; | |
match = matchSpecial; | |
// Remove extra element | |
input.splice(i+1, 1); | |
} | |
} | |
// Set atom properties | |
var properties = { | |
atom_id: match.symbol + i, | |
atom_weight: match.weight, | |
symbol: match.symbol, | |
element: match.element, | |
valence: match.valence, | |
color: match.color | |
}; | |
// Update molecule with new atom | |
addAtom(properties); | |
// Update index of atom locations | |
updateIndex(index.atoms, i, molecule.atoms.length-1, 0, properties.valence[0]) | |
} | |
// Update index of non-atoms | |
else {updateIndex(index.non_atoms, i)} | |
} | |
// | |
// Branches | |
// | |
// Find branches | |
for (i = 0; i < index.non_atoms.length; i++) { | |
// Retrieve input value | |
var value = input[index.non_atoms[i].input], | |
position = index.non_atoms[i].input; | |
// Compare input with SMILES grammar | |
var match = findObjects(grammar.branches, 'symbol', value); | |
// Check match | |
if (match != null) { | |
switch (match.type) { | |
// Branch starts | |
case "start": | |
counter.branches += 1; | |
index.branches[counter.branches] = {start: position, end: -1}; | |
// Update counters | |
if (counter.last == "start") {counter.empty = counter.branches-1} | |
counter.last = "start"; | |
break; | |
// Branch ends | |
case "end": | |
// Last occurring start branch | |
if (counter.last == "start") { | |
index.branches[counter.branches].end = position | |
} | |
// Last empty start branch | |
else { | |
index.branches[counter.empty].end = position; | |
counter.empty += -1; | |
} | |
// Update counter | |
counter.last = "end"; | |
break; | |
} | |
} | |
} | |
// Find nearest atoms to branches | |
for (i = 0; i < index.branches.length; i++) { | |
index.branches[i].left = -1; | |
index.branches[i].node = -1; | |
index.branches[i].right = -1; | |
// Increment distance from branch index to nearest atom | |
for (j = 1; j <= index.atoms.length; j++) { | |
var left = findObjects(index.atoms, "input", index.branches[i].start - j); | |
var node = findObjects(index.atoms, "input", index.branches[i].start + j); | |
var right = findObjects(index.atoms, "input", index.branches[i].end + j); | |
// Check match | |
if (left != null && index.branches[i].left == -1) {index.branches[i].left = left.output;} | |
if (node != null && index.branches[i].node == -1) {index.branches[i].node = node.output;} | |
if (right != null && index.branches[i].right == -1) {index.branches[i].right = right.output;} | |
} | |
// Special Case: double bond at branch start | |
if (i > 0 && input[index.branches[i].start] == "=") { | |
var bondType = "double"; | |
var bondValue = 2; } | |
else { | |
var bondType = "single"; | |
var bondValue = 1; } | |
// Set bond properties for left to center atom | |
var bondProperties = { | |
bond_id: molecule.bonds.length, | |
source: index.branches[i].left, | |
target: index.branches[i].node, | |
type: bondType, | |
value: bondValue | |
}; | |
// Update molecule with new bond | |
addBond(bondProperties); | |
// Update bond count for atom | |
index.atoms[index.branches[i].left].bonds += bondValue; | |
index.atoms[index.branches[i].node].bonds += bondValue; | |
// Set bond properties for left to right atom | |
var bondProperties = { | |
bond_id: molecule.bonds.length, | |
source: index.branches[i].left, | |
target: index.branches[i].right, | |
type: "single", | |
value: 1 | |
}; | |
// Update molecule with new bond | |
addBond(bondProperties); | |
// Update bond count for atom | |
index.atoms[index.branches[i].left].bonds += 1; | |
index.atoms[index.branches[i].right].bonds += 1; | |
} | |
// | |
// Single Bonds | |
// | |
// Find implicit bonds | |
for (i = 1; i < index.atoms.length; i++) { | |
// Determine distance between atoms | |
if (index.atoms[i].input - index.atoms[i - 1].input == 1) { | |
// Set bond properties for right to node atom | |
var bondProperties = { | |
bond_id: molecule.bonds.length, | |
source: index.atoms[i-1].output, | |
target: index.atoms[i].output, | |
type: "single", | |
value: 1 | |
}; | |
// Update molecule with new bond | |
addBond(bondProperties); | |
// Update bond count for atom | |
index.atoms[i].bonds += 1; | |
index.atoms[i-1].bonds += 1; | |
} | |
} | |
// | |
// Double/Triple Bonds | |
// | |
// Find explicit bonds | |
for (i = 0; i < index.non_atoms.length; i++) { | |
// Retrieve input value | |
var value = input[index.non_atoms[i].input], | |
position = index.non_atoms[i].input; | |
// Compare input with SMILES grammar | |
var match = findObjects(grammar.bonds, 'symbol', value); | |
// Check match | |
if (match != null) { | |
// Update index | |
index.bonds.push({input: position, type: match.type, value: match.value}); | |
} | |
} | |
// Find nearest atoms to bonds | |
for (i = 0; i < index.bonds.length; i++) { | |
index.bonds[i].left = -1; | |
index.bonds[i].right = -1; | |
// Increment distance from bond index to nearest atom | |
for (j = 1; j <= index.atoms.length; j++) { | |
var left = findObjects(index.atoms, "input", index.bonds[i].input - j); | |
var right = findObjects(index.atoms, "input", index.bonds[i].input + j); | |
// Check match | |
if (left != null && index.bonds[i].left == -1) {index.bonds[i].left = left.output} | |
if (right != null && index.bonds[i].right == -1) {index.bonds[i].right = right.output} | |
} | |
// Set bond properties for left to node atom | |
var bondProperties = { | |
bond_id: molecule.bonds.length, | |
source: index.bonds[i].left, | |
target: index.bonds[i].right, | |
type: index.bonds[i].type, | |
value: index.bonds[i].value | |
}; | |
// Update molecule with new bond | |
addBond(bondProperties); | |
// Update bond count for atom | |
index.atoms[index.bonds[i].left].bonds += index.bonds[i].value; | |
index.atoms[index.bonds[i].right].bonds += index.bonds[i].value; | |
} | |
// | |
// Rings | |
// | |
// Find explicit rings | |
for (i = 0; i < index.non_atoms.length; i++) { | |
// Retrieve input value | |
var value = input[index.non_atoms[i].input], | |
position = index.non_atoms[i].input; | |
// Compare input with SMILES grammar | |
var match = findObjects(grammar.rings, 'symbol', value); | |
// Check match | |
if (match != null) { | |
index.rings.push({output: findObjects(index.atoms, "input", position-1), value: value}); | |
} | |
} | |
// Find nearest atoms to rings | |
var x = index.rings.length / 2 | |
for (i = 0; i < x; i++) { | |
// Ring starting position | |
var left = index.rings[i]; | |
// Remove item from array | |
index.rings.splice(i, 1); | |
// Ring ending position | |
var right = findObjects(index.rings, 'value', index.rings[i].value); | |
// Set bond properties for ring atoms | |
var bondProperties = { | |
bond_id: molecule.bonds.length, | |
source: left.output.output, | |
target: right.output.output, | |
type: "single", | |
value: 1 | |
} | |
} | |
// | |
// Hydrogens | |
// | |
// Add hydrogen to available atoms | |
for (i = 0; i < index.atoms.length; i++) { | |
// Determine number of hydrogen to add | |
var hydrogen = index.atoms[i].valence - index.atoms[i].bonds; | |
// Create new atom | |
for (j = 1; j <= hydrogen; j++) { | |
// Set atom properties | |
var properties = { | |
atom_id: "H" + molecule.atoms.length, | |
atom_weight: 1.008, | |
symbol: "H", | |
element: 1, | |
valence: 1, | |
color: "#E9E9E9" | |
}; | |
// Update molecule with new atom | |
addAtom(properties); | |
// Set bond properties for left to node atom | |
var bondProperties = { | |
bond_id: molecule.bonds.length, | |
source: index.atoms[i].output, | |
target: molecule.atoms.length-1, | |
type: "single", | |
value: 1 | |
}; | |
// Update molecule with new bond | |
addBond(bondProperties); | |
} | |
} | |
// | |
// Update Molecule | |
// | |
//Add atom to molecule | |
function addAtom(a) { | |
var newAtom = new atom(a.atom_id, a.atom_weight, a.symbol, a.element, a.valence, a.color); | |
molecule.atoms.push(newAtom); | |
} | |
// Add bond to molecule | |
function addBond(b) { | |
var newBond = new bond(b.bond_id, b.source, b.target, b.type, b.value); | |
molecule.bonds.push(newBond); | |
} | |
// | |
// Molecular Weight | |
// | |
// Determine molecular weight | |
for (i = 0; i < molecule.atoms.length; i++) { | |
molecule.molecule_weight += molecule.atoms[i].atom_weight; | |
} | |
// Round value to two decimal places | |
molecule.molecule_weight = Math.round(molecule.molecule_weight*100)/100 | |
// | |
// Output | |
// | |
// Output molecule in JSON format | |
return molecule; | |
} | |
// | |
// Definitions | |
// | |
// SMILES grammar definitions | |
function definitions() { | |
// TODO: Add more atom types | |
var atomDefinitions = [ | |
{symbol: "H", element: 1, weight: 1.008, valence: [1], color: "#E9E9E9"}, | |
{symbol: "He", element: 2, weight: 4.002, valence: [1], color: "#2A79AF"}, | |
{symbol: "B", element: 5, weight: 10.81, valence: [3], color: "#B37831"}, | |
{symbol: "C", element: 6, weight: 12.01, valence: [4], color: "#272727"}, | |
{symbol: "N", element: 7, weight: 14.01, valence: [3,5], color: "#0033CC"}, | |
{symbol: "O", element: 8, weight: 16.00, valence: [2], color: "#FF1919"}, | |
{symbol: "F", element: 9, weight: 19.00, valence: [1], color: "#8536AF"}, | |
{symbol: "Si", element: 14, weight: 28.09, valence: [4], color: "#797979"}, | |
{symbol: "P", element: 15, weight: 30.97, valence: [3,5], color: "#00AE78"}, | |
{symbol: "S", element: 16, weight: 32.06, valence: [2,4,6], color: "#FFD700"}, | |
{symbol: "Cl", element: 17, weight: 35.45, valence: [1], color: "#00FF6C"}, | |
{symbol: "As", element: 33, weight: 74.92, valence: [1], color: "#272727"}, | |
{symbol: "Se", element: 34, weight: 78.96, valence: [1], color: "#BC0000"}, | |
{symbol: "Br", element: 35, weight: 79.90, valence: [1], color: "#FFA669"}, | |
{symbol: "I", element: 53, weight: 126.90, valence: [1], color: "#1A306D"}, | |
{symbol: "c", element: 6, weight: 12.01, valence: [1], color: "#272727"}, | |
{symbol: "n", element: 7, weight: 14.01, valence: [1], color: "#0033CC"}, | |
{symbol: "o", element: 8, weight: 16.00, valence: [1], color: "#FF1919"}, | |
{symbol: "p", element: 15, weight: 30.97, valence: [1], color: "#00AE78"}, | |
{symbol: "s", element: 16, weight: 32.06, valence: [1], color: "#FFD700"}, | |
{symbol: "as", element: 33, weight: 74.92, valence: [1], color: "#272727"}, | |
{symbol: "se", element: 34, weight: 78.96, valence: [1], color: "#BC0000"} | |
]; | |
var bondDefinitions = [ | |
{symbol: "-", type: "single", value: 1}, | |
{symbol: "=", type: "double", value: 2}, | |
{symbol: "#", type: "triple", value: 3}, | |
{symbol: "$", type: "triple", value: 3}, | |
{symbol: ":", type: "aromatic", value: 1.5}, | |
{symbol: "//", type: "double", value: "cis"}, | |
{symbol: "\\\\", type: "double", value: "cis"}, | |
{symbol: "/\\", type: "double", value: "trans"}, | |
{symbol: "\\/", type: "double", value: "trans"}, | |
{symbol: ".", type: "ionic", value: 0} | |
]; | |
var branchDefinitions = [ | |
{symbol: "(", type: "start"}, | |
{symbol: ")", type: "end"} | |
]; | |
var ringDefinitions = [ | |
{symbol: "1"}, | |
{symbol: "2"}, | |
{symbol: "3"}, | |
{symbol: "4"}, | |
{symbol: "5"}, | |
{symbol: "6"}, | |
{symbol: "7"}, | |
{symbol: "8"}, | |
{symbol: "9"} | |
]; | |
var chargeDefinitions = [ | |
{symbol: "+", value: 1}, | |
{symbol: "-", value: -1}, | |
{symbol: "++", value: 2}, | |
{symbol: "--", value: -2} | |
]; | |
// TODO: Add more chirality types | |
var chiralityDefinitions = [ | |
{symbol: "@", value: "R"}, | |
{symbol: "@@", value: "S"} | |
]; | |
return { | |
atoms: atomDefinitions, | |
bonds: bondDefinitions, | |
branches: branchDefinitions, | |
rings: ringDefinitions, | |
charges: chargeDefinitions, | |
chirality: chiralityDefinitions | |
} | |
} | |
// | |
// Utility | |
// | |
// Find object key/value | |
function findObjects(array, key, value) { | |
for (var i = 0; i < array.length; i++) { if (array[i][key] == value) { return array[i]; }} | |
return null | |
} | |
// Index values for atoms | |
function updateIndex(array, input, output, bonds, valence) { | |
array.push({input: input, output: output, bonds: bonds, valence: valence}) | |
} |
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