def drawMolecule(request, adjlist):
"""
Returns an image of the provided adjacency list `adjlist` for a molecule.
Note that the newline character cannot be represented in a URL;
semicolons should be used instead.
"""
from rmgpy.molecule import Molecule
from rmgpy.molecule_draw import drawMolecule
response = HttpResponse(mimetype="image/png")
adjlist = str(adjlist.replace(";", "\n"))
molecule = Molecule().fromAdjacencyList(adjlist)
surface, cr, rect = drawMolecule(molecule, surface="png")
surface.write_to_png(response)
return response
def saveOutputHTML(path, reactionModel):
"""
Save the current set of core species and reactions of `reactionModel` to
an HTML file `path` on disk. As part of this process, drawings of all core
species are created in the species folder (if they don't already exist)
using the :mod:`rmgpy.chem.ext.molecule_draw` module. The :mod:`jinja`
package is used to generate the HTML; if this package is not found, no
HTML will be generated (but the program will carry on).
"""
from model import PDepReaction
from rmgpy.molecule_draw import drawMolecule
try:
import jinja2
except ImportError:
logging.warning("jinja package not found; HTML output will not be saved.")
return
path = os.path.abspath(path)
dirname = os.path.dirname(path)
# Prepare parameters to pass to jinja template
title = 'RMG Output'
species = reactionModel.core.species[:] + reactionModel.outputSpeciesList
re_index = re.compile(r'\((\d+)\)$')
if not os.path.isdir(os.path.join(dirname,'species')):
os.makedirs(os.path.join(dirname,'species'))
for spec in species:
# if the species dictionary came from an RMG-Java job, make them prettier
# We use the presence of a trailing index on the label to discern this
# (A single open parenthesis is not enough (e.g. when using SMILES strings as labels!)
match = re_index.search(spec.label)
if match:
spec.index = int(match.group(0)[1:-1])
spec.label = spec.label[0:match.start()]
# Draw molecules if necessary
fstr = os.path.join(dirname, 'species', '{0}.png'.format(spec))
if not os.path.exists(fstr):
drawMolecule(spec.molecule[0], fstr)
# We want to keep species sorted in the original order in which they were added to the RMG core.
# Rather than ordered by index
# species.sort(key=lambda x: x.index)
reactions = [rxn for rxn in reactionModel.core.reactions ] + reactionModel.outputReactionList
# We want to keep reactions sorted in original order in which they were added to core
# rather than ordered by index
#reactions.sort(key=lambda x: x.index)
familyCount = {}
for rxn in reactions:
print rxn
if isinstance(rxn, PDepReaction):
family = "PDepNetwork"
else:
family = rxn.getSource().label
if family in familyCount:
familyCount[family] += 1
else:
familyCount[family] = 1
families = familyCount.keys()
families.sort()
## jinja2 filters etc.
to_remove_from_css_names = re.compile('[/.\-+,]')
def csssafe(input):
"Replace unsafe CSS class name characters with an underscore."
return to_remove_from_css_names.sub('_',input)
environment = jinja2.Environment()
environment.filters['csssafe'] = csssafe
# Make HTML file
template = environment.from_string(
"""<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
<html lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" >
<title>{{ title }}</title>
<style type="text/css">
body {
font-family: sans-serif;
}
a {
color: #993333;
text-decoration: none;
}
a:visited {
color: #993333;
}
a:hover {
text-decoration: underline;
}
table.speciesList, table.reactionList {
width: 100%;
border-collapse: collapse;
}
table.speciesList th, table.reactionList th {
text-align: left;
}
tr.reaction td {
border-top: 1px solid #808080;
}
td.reactants {
text-align: right;
}
td.products {
text-align: left;
}
td.reactionArrow {
text-align: center;
font-size: 16px;
}
td.species img, td.reactants img, td.products img {
vertical-align: middle;
}
tr.comment {
font-size: small;
}
tr.kinetics {
font-size: small;
}
.KineticsData {
# border: 1px solid gray;
}
.KineticsData th {
width: 15em;
word-wrap: none;
}
.KineticsData td {
width: 3em;
}
.chemkin, .KineticsData_repr {
white-space: pre-wrap;
font-size: x-small;
font-family: "Andale Mono", monospace;
}
.hide_comment .comment{
display: none !important;
}
.hide_kinetics .kinetics{
display: none !important;
}
.hide_chemkin .chemkin{
display: none !important;
}
</style>
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.1/jquery.min.js"></script>
<script type="text/javascript" src="../../../external/jquery.min.js"></script>
<script type="text/javascript">
function updateFamily(family) {
if (family.checked) {
$("."+family.value).show();
} else {
$("."+family.value).hide();
}
}
function updateDetails(type) {
if (type.checked) {
$(".reactionList").removeClass("hide_"+type.value);
} else {
$(".reactionList").addClass("hide_"+type.value);
}
}
function checkAllFamilies() {
$("#familySelector").find("[name='family']").each(function() { this.checked = true; updateFamily(this); });
return false;
}
function uncheckAllFamilies() {
$("#familySelector").find("[name='family']").each(function() { this.checked = false; updateFamily(this); });
return false;
}
function checkAllDetails() {
$("#familySelector").find("[name='detail']").each(function() { this.checked = true; updateDetails(this); });
return false;
}
function uncheckAllDetails() {
$("#familySelector").find("[name='detail']").each(function() { this.checked = false; updateDetails(this); });
return false;
}
$(document).ready(function() {
checkAllFamilies();
uncheckAllDetails();
});
</script>
</head>
<body>
<h1>{{ title }}</h1>
<h2>Species ({{ species|length }})</h2>
<table class="speciesList">
<tr><th>Index</th><th>Structure</th><th>Label</th><th>Mol. Wt. (g/mol)</th></tr>
{% for spec in species %}
<tr class="species">
<td class="index">
{{ spec.index }}.</td>
<td class="structure"><a href={{ spec.molecule[0].getURL() }}><img src="species/{{ spec|replace('#','%23') }}.png" alt="{{ spec }}" title="{{ spec }}"></a></td>
<td class="label">{{ spec.label }}</td>
<td>{{ "%.2f"|format(spec.molecule[0].getMolecularWeight() * 1000) }}</td>
</tr>
{% endfor %}
</table>
<h2>Reactions ({{ reactions|length }})</h2>
<form id='familySelector' action="">
<h4>Reaction families:</h4>
{% for family in families %} <input type="checkbox" id="{{ family|csssafe }}" name="family" value="{{ family|csssafe }}" checked="checked" onclick="updateFamily(this);"><label for="{{ family|csssafe }}">{{ family }} ({{ familyCount[family] }} rxn{{ 's' if familyCount[family] != 1 }})</label><br>
{% endfor %}
<a href="javascript:checkAllFamilies();" onclick="checkAllFamilies()">check all</a> <a href="javascript:uncheckAllFamilies();" onclick="uncheckAllFamilies();">uncheck all</a><br>
<h4>Reaction Details:</h4>
<input type="checkbox" id="kinetics" name="detail" value="kinetics" onclick="updateDetails(this);"><label for="kinetics">Kinetics</label><br>
<input type="checkbox" id="comment" name="detail" value="comment" onclick="updateDetails(this);"><label for="comment">Comments</label><br>
<input type="checkbox" id="chemkin" name="detail" value="chemkin" onclick="updateDetails(this);"><label for="chemkin">Chemkin strings</label><br>
<a href="javascript:checkAllDetails();" onclick="checkAllDetails()">check all</a> <a href="javascript:uncheckAllDetails();" onclick="uncheckAllDetails();">uncheck all</a>
</form>
<h4>Reaction List:</h4>
<table class="reactionList hide_comment hide_kinetics hide_chemkin">
<tr><th>Index</th><th colspan="3" style="text-align: center;">Reaction</th><th>Family</th></tr>
{% for rxn in reactions %}
<tr class="reaction {{ rxn.getSource().label|csssafe }}">
<td class="index"><a href="{{ rxn.getURL() }}" title="Search on RMG website" class="searchlink">{{ rxn.index }}.</a></td>
<td class="reactants">{% for reactant in rxn.reactants %}<a href="{{ reactant.molecule[0].getURL() }}"><img src="species/{{ reactant|replace('#','%23') }}.png" alt="{{ reactant }}" title="{{ reactant }}, MW = {{ "%.2f g/mol"|format(reactant.molecule[0].getMolecularWeight() * 1000) }}"></a>{% if not loop.last %} + {% endif %}{% endfor %}</td>
<td class="reactionArrow">{% if rxn.reversible %}⇔{% else %}→{% endif %}</td>
<td class="products">{% for product in rxn.products %}<a href="{{ product.molecule[0].getURL() }}"><img src="species/{{ product|replace('#','%23') }}.png" alt="{{ product }}" title="{{ product }}, MW = {{ "%.2f g/mol"|format(product.molecule[0].getMolecularWeight() * 1000) }}"></a>{% if not loop.last %} + {% endif %}{% endfor %}</td>
<td class="family">{{ rxn.getSource().label }}</td>
</tr>
<tr class="kinetics {{ rxn.getSource().label|csssafe }}">
<td></td>
<td colspan="4">{{ rxn.kinetics.toHTML() }}</td>
</tr>
<tr class="chemkin {{ rxn.getSource().label|csssafe }}">
<td></td>
<td colspan="4">{{ rxn.toChemkin(species) }}</td>
</tr>
<tr class="comment {{ rxn.getSource().label|csssafe }}">
<td></td>
<td colspan="4">{{ rxn.kinetics.comment }}</td>
</tr>
{% endfor %}
</table>
</body>
</html>
""")
f = open(path, 'w')
f.write(template.render(title=title, species=species, reactions=reactions, families=families, familyCount=familyCount))
f.close()
def saveDiffHTML(path, commonSpeciesList, speciesList1, speciesList2, commonReactions, uniqueReactions1, uniqueReactions2):
"""
This function outputs the species and reactions on an HTML page
for the comparison of two RMG models.
"""
from model import PDepReaction
from rmgpy.molecule_draw import drawMolecule
try:
import jinja2
except ImportError:
logging.warning("jinja package not found; HTML output will not be saved.")
return
path = os.path.abspath(path)
dirname = os.path.dirname(path)
# Prepare parameters to pass to jinja template
title = 'RMG Model Comparison'
species = commonSpeciesList + speciesList1 + speciesList2
re_index = re.compile(r'\((\d+)\)$')
if not os.path.isdir(os.path.join(dirname,'species')):
os.makedirs(os.path.join(dirname,'species'))
for spec in species:
# if the species dictionary came from an RMG-Java job, make them prettier
# We use the presence of a trailing index on the label to discern this
# (A single open parenthesis is not enough (e.g. when using SMILES strings as labels!)
match = re_index.search(spec.label)
if match:
spec.index = int(match.group(0)[1:-1])
spec.label = spec.label[0:match.start()]
# Draw molecules if necessary
fstr = os.path.join(dirname, 'species', '{0}.png'.format(spec))
if not os.path.exists(fstr):
drawMolecule(spec.molecule[0], fstr)
familyCount1 = {}
familyCount2 = {}
for rxn in commonReactions:
if isinstance(rxn, PDepReaction):
family = "PDepNetwork"
else:
family = rxn.getSource().label
if family in familyCount1:
familyCount1[family] += 1
familyCount2[family] += 1
else:
familyCount1[family] = 1
familyCount2[family] = 1
for rxn in uniqueReactions1:
if isinstance(rxn, PDepReaction):
family = "PDepNetwork"
else:
family = rxn.getSource().label
if family in familyCount1:
familyCount1[family] += 1
else:
familyCount1[family] = 1
for rxn in uniqueReactions2:
if isinstance(rxn, PDepReaction):
family = "PDepNetwork"
else:
family = rxn.getSource().label
if family in familyCount2:
familyCount2[family] += 1
else:
familyCount2[family] = 1
families1 = familyCount1.keys()
families2 = familyCount2.keys()
families1.sort()
families2.sort()
## jinja2 filters etc.
to_remove_from_css_names = re.compile('[/.\-+,]')
def csssafe(input):
"Replace unsafe CSS class name characters with an underscore."
return to_remove_from_css_names.sub('_',input)
environment = jinja2.Environment()
environment.filters['csssafe'] = csssafe
# Make HTML file
template = environment.from_string(
"""<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
<html lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" >
<title>{{ title }}</title>
<style type="text/css">
body {
font-family: sans-serif;
}
a {
color: #993333;
text-decoration: none;
}
a:visited {
color: #993333;
}
a:hover {
text-decoration: underline;
}
table.speciesList, table.reactionList {
width: 100%;
border-collapse: collapse;
}
table.speciesList th, table.reactionList th {
text-align: left;
}
tr.reaction td {
border-top: 1px solid #808080;
}
td.reactants {
text-align: right;
}
td.products {
text-align: left;
}
td.reactionArrow {
text-align: center;
font-size: 16px;
}
td.species img, td.reactants img, td.products img {
vertical-align: middle;
}
tr.comment {
font-size: small;
}
tr.kinetics {
font-size: small;
}
.KineticsData {
# border: 1px solid gray;
}
.KineticsData th {
width: 15em;
word-wrap: none;
}
.KineticsData td {
width: 3em;
}
.chemkin, .KineticsData_repr {
white-space: pre-wrap;
font-size: x-small;
font-family: "Andale Mono", monospace;
}
.hide_comment .comment{
display: none !important;
}
.hide_kinetics .kinetics{
display: none !important;
}
.hide_chemkin .chemkin{
display: none !important;
}
</style>
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.1/jquery.min.js"></script>
<script type="text/javascript" src="../../../external/jquery.min.js"></script>
<script type="text/javascript">
function updateFamily(family) {
if (family.checked) {
$("."+family.value).show();
} else {
$("."+family.value).hide();
}
}
function updateDetails(type) {
if (type.checked) {
$(".reactionList").removeClass("hide_"+type.value);
} else {
$(".reactionList").addClass("hide_"+type.value);
}
}
function checkAllFamilies() {
$("#familySelector").find("[name='family']").each(function() { this.checked = true; updateFamily(this); });
return false;
}
function uncheckAllFamilies() {
$("#familySelector").find("[name='family']").each(function() { this.checked = false; updateFamily(this); });
return false;
}
function checkAllDetails() {
$("#familySelector").find("[name='detail']").each(function() { this.checked = true; updateDetails(this); });
return false;
}
function uncheckAllDetails() {
$("#familySelector").find("[name='detail']").each(function() { this.checked = false; updateDetails(this); });
return false;
}
$(document).ready(function() {
checkAllFamilies();
uncheckAllDetails();
});
</script>
</head>
<body>
<h1>{{ title }}</h1>
<h2 align="center">Common Species ({{ commonSpecies|length }})</h2>
<table width="50%" align="center">
<tr><th>Index</th><th>Structure</th><th>Label</th><th>Mol. Wt. (g/mol)</th></tr>
{% for spec in commonSpecies %}
<tr class="species">
<td class="index" align="center">
{{ spec.index }}.</td>
<td class="structure" align="center"><a href="{{spec.molecule[0].getURL()}}"><img src="species/{{ spec|replace('#','%23') }}.png" alt="{{ spec }}" title="{{ spec }}"></a></td>
<td class="label" align="center">{{ spec.label }}</td>
<td>{{ "%.2f"|format(spec.molecule[0].getMolecularWeight() * 1000) }}</td>
</tr>
{% endfor %}
</table>
<table width=100%>
<tr colspan="2">
<td width=50% valign="top">
<h2>Model 1: Unique Species ({{ speciesList1|length }})</h2>
<table class="speciesList">
<tr><th>Index</th><th>Structure</th><th>Label</th><th>Mol. Wt. (g/mol)</th></tr>
{% for spec in speciesList1 %}
<tr class="species">
<td class="index">
{{ spec.index }}.</td>
<td class="structure"><a href="{{ spec.molecule[0].getURL() }}"><img src="species/{{ spec|replace('#','%23') }}.png" alt="{{ spec }}" title="{{ spec }}"></a></td>
<td class="label">{{ spec.label }}</td>
<td>{{ "%.2f"|format(spec.molecule[0].getMolecularWeight() * 1000) }}</td>
</tr>
{% endfor %}
</table>
</td>
<td width=50% valign="top">
<h2>Model 2: Unique Species ({{ speciesList2|length }})</h2>
<table class="speciesList">
<tr><th>Index</th><th>Structure</th><th>Label</th><th>Mol. Wt. (g/mol)</th></tr>
{% for spec in speciesList2 %}
<tr class="species">
<td class="index">
{{ spec.index }}.</td>
<td class="structure"><a href="{{ spec.molecule[0].getURL() }}"><img src="species/{{ spec|replace('#','%23') }}.png" alt="{{ spec }}" title="{{ spec }}"></a></td>
<td class="label">{{ spec.label }}</td>
<td>{{ "%.2f"|format(spec.molecule[0].getMolecularWeight() * 1000) }}</td>
</tr>
{% endfor %}
</table>
</td></tr>
<tr colspan="2">
<td width=50% valign="top">
<h2>Model 1 Reactions ({{ commonReactions|length + uniqueReactions1|length}})</h2>
<form id='familySelector' action="">
<h4>Reaction families:</h4>
{% for family in families1 %} <input type="checkbox" id="{{ family|csssafe }}" name="family" value="{{ family|csssafe }}" checked="checked" onclick="updateFamily(this);"><label for="{{ family|csssafe }}">{{ family }} ({{ familyCount1[family] }} rxn{{ 's' if familyCount1[family] != 1 }})</label><br>
{% endfor %}
<a href="javascript:checkAllFamilies();" onclick="checkAllFamilies()">check all</a> <a href="javascript:uncheckAllFamilies();" onclick="uncheckAllFamilies();">uncheck all</a><br>
<h4>Reaction Details:</h4>
<input type="checkbox" id="kinetics" name="detail" value="kinetics" onclick="updateDetails(this);"><label for="kinetics">Kinetics</label><br>
<input type="checkbox" id="comment" name="detail" value="comment" onclick="updateDetails(this);"><label for="comment">Comments</label><br>
<input type="checkbox" id="chemkin" name="detail" value="chemkin" onclick="updateDetails(this);"><label for="chemkin">Chemkin strings</label><br>
<a href="javascript:checkAllDetails();" onclick="checkAllDetails()">check all</a> <a href="javascript:uncheckAllDetails();" onclick="uncheckAllDetails();">uncheck all</a>
</form>
</td>
<td width=50% valign="top">
<h2>Model 2 Reactions ({{ commonReactions|length +uniqueReactions2|length}})</h2>
<form id='familySelector' action="">
<h4>Reaction families:</h4>
{% for family in families2 %} <input type="checkbox" id="{{ family|csssafe }}" name="family" value="{{ family|csssafe }}" checked="checked" onclick="updateFamily(this);"><label for="{{ family|csssafe }}">{{ family }} ({{ familyCount2[family] }} rxn{{ 's' if familyCount2[family] != 1 }})</label><br>
{% endfor %}
<a href="javascript:checkAllFamilies();" onclick="checkAllFamilies()">check all</a> <a href="javascript:uncheckAllFamilies();" onclick="uncheckAllFamilies();">uncheck all</a><br>
<h4>Reaction Details:</h4>
<input type="checkbox" id="kinetics" name="detail" value="kinetics" onclick="updateDetails(this);"><label for="kinetics">Kinetics</label><br>
<input type="checkbox" id="comment" name="detail" value="comment" onclick="updateDetails(this);"><label for="comment">Comments</label><br>
<input type="checkbox" id="chemkin" name="detail" value="chemkin" onclick="updateDetails(this);"><label for="chemkin">Chemkin strings</label><br>
<a href="javascript:checkAllDetails();" onclick="checkAllDetails()">check all</a> <a href="javascript:uncheckAllDetails();" onclick="uncheckAllDetails();">uncheck all</a>
</form>
</td>
</tr>
</table>
<table width=100%>
<tr><td width=100% align="center">
<h2>Common Reactions ({{ commonReactions|length}})</h2></td></tr>
<tr colspan="1"><td width=100%>
<table class="reactionList hide_comment hide_kinetics hide_chemkin" width=100% cellpadding="10">
<tr colspan="4" width=100%><th>Index.</th><th>Family</th><th>Index.</th><th>Family</th></tr>
{% for rxn1, rxn2 in commonReactions.iteritems() %}
<tr>
<td width=100% colspan="4"><hr>
<table align="center">
<tr>
<td class="reactants" align="right">{% for reactant in rxn1.reactants %}<a href="{{reactant.molecule[0].getURL() }}"><img src="species/{{ reactant|replace('#','%23') }}.png" alt="{{ reactant }}" title="{{ reactant }}, MW = {{ "%.2f"|format(reactant.molecule[0].getMolecularWeight() * 1000) }}"></a>{% if not loop.last %} + {% endif %}{% endfor %}</td>
<td class="reactionArrow" align="center">{% if rxn1.reversible %}⇔{% else %}→{% endif %}</td>
<td class="products" align="left">{% for product in rxn1.products %}<a href="{{product.molecule[0].getURL()}}"><img src="species/{{ product|replace('#','%23') }}.png" alt="{{ product }}" title="{{ product }}, MW = {{ "%.2f"|format(product.molecule[0].getMolecularWeight() * 1000) }}"></a>{% if not loop.last %} + {% endif %}{% endfor %}</td>
</tr>
</table>
</td>
</tr>
{% if rxn1.kinetics.isIdenticalTo(rxn2.kinetics) %}
<tr width=100%>
<td class="index" width=10%><a href="{{ rxn1.getURL() }}" title="Search on RMG website" class="searchlink">{{ rxn1.index }}.</a></td>
<td class="family" width=40%>{{ rxn1.getSource().label }}</td>
<td class="index" width=10%><a href="{{ rxn2.getURL() }}" title="Search on RMG website" class="searchlink">{{ rxn2.index }}.</a></td>
<td class="family" width=40%>{{ rxn2.getSource().label }}</td>
</tr>
<tr width=100%>
<td colspan="4" valign="top" width=50%><div align="center"><font color="red">IDENTICAL KINETICS WERE FOUND FOR THIS REACTION.</font></div>
<P>{{ rxn1.kinetics.toHTML() }}</td>
</tr>
<tr width=100%>
<td colspan="4" valign="top" width=50%><font size="1pt" face="courier">{{ rxn1.toChemkin(commonSpecies) }}</font></td>
</tr>
<tr width=100%>
<td colspan="2" valign="top" width=50%><font size="1pt">Model 1 Comments:
<br>{{ rxn1.kinetics.comment }}</font></td>
<td colspan="2" valign="top" width=50%><font size="1pt">Model 2 Comments:
<br>{{ rxn2.kinetics.comment }}</font></td>
</tr>
{% else %}
<tr width=100%>
<td class="index" width=10%><a href="{{ rxn1.getURL() }}" title="Search on RMG website" class="searchlink">{{ rxn1.index }}.</a></td>
<td class="family" width=40%>{{ rxn1.getSource().label }}</td>
<td class="index" width=10%><a href="{{ rxn2.getURL() }}" title="Search on RMG website" class="searchlink">{{ rxn2.index }}.</a></td>
<td class="family" width=40%>{{ rxn2.getSource().label }}</td>
</tr>
<tr width=100%>
<td colspan="2" width=50%></td>
<td colspan="2" width=50%>{% if not rxn1.isIsomorphic(rxn2, eitherDirection=False) %} * Reaction was found in reverse {% endif %}</td>
</tr>
<tr width=100%>
<td colspan="2" valign="top" width=50%>{{ rxn1.kinetics.toHTML() }}</td>
<td colspan="2" valign="top" width=50%>{{ rxn2.kinetics.toHTML() }}</td>
</tr>
<tr width=100%>
<td colspan="2" valign="top" width=50%><font size="1pt" face="courier">{{ rxn1.toChemkin(commonSpecies) }}</font></td>
<td colspan="2" valign="top" width=50%><font size="1pt" face="courier">{{ rxn2.toChemkin(commonSpecies) }}</font></td>
</tr>
<tr width=100%>
<td colspan="2" valign="top" width=50%><font size="1pt">{{ rxn1.kinetics.comment }}</font></td>
<td colspan="2" valign="top" width=50%><font size="1pt">{{ rxn2.kinetics.comment }}</font></td>
</tr>
{% endif %}
{% endfor %}
</table>
</td></tr></table>
<table>
<tr>
<td width=50% valign="top">
<h2>Model 1: Unique Reactions ({{ uniqueReactions1|length}})</h2>
<table class="reactionList hide_comment hide_kinetics hide_chemkin">
<tr><th>Index</th><th colspan="3" style="text-align: center;">Reaction</th><th>Family</th></tr>
{% for rxn in uniqueReactions1 %}
<tr class="reaction {{ rxn.getSource().label|csssafe }}">
<td class="index"><a href="{{ rxn.getURL() }}" title="Search on RMG website" class="searchlink">{{ rxn.index }}.</a></td>
<td class="reactants">{% for reactant in rxn.reactants %}<a href="{{ reactant.molecule[0].getURL() }}"><img src="species/{{ reactant|replace('#','%23') }}.png" alt="{{ reactant }}" title="{{ reactant }}, MW = {{ "%.2f"|format(reactant.molecule[0].getMolecularWeight() * 1000) }}"></a>{% if not loop.last %} + {% endif %}{% endfor %}</td>
<td class="reactionArrow">{% if rxn.reversible %}⇔{% else %}→{% endif %}</td>
<td class="products">{% for product in rxn.products %}<a href="{{ product.molecule[0].getURL() }}"><img src="species/{{ product|replace('#','%23') }}.png" alt="{{ product }}" title="{{ product }}, MW = {{ "%.2f"|format(product.molecule[0].getMolecularWeight() * 1000) }}"></a>{% if not loop.last %} + {% endif %}{% endfor %}</td>
<td class="family">{{ rxn.getSource().label }}</td>
</tr>
<tr class="kinetics {{ rxn.getSource().label|csssafe }}">
<td></td>
<td colspan="4">{{ rxn.kinetics.toHTML() }}</td>
</tr>
<tr class="chemkin {{ rxn.getSource().label|csssafe }}">
<td></td>
<td colspan="4">{{ rxn.toChemkin(species) }}</td>
</tr>
<tr class="comment {{ rxn.getSource().label|csssafe }}">
<td></td>
<td colspan="4">{{ rxn.kinetics.comment }}</td>
</tr>
{% endfor %}
</table>
</td>
<td width=50% valign="top">
<h2>Model 2: Unique Reactions ({{ uniqueReactions2|length}})</h2>
<table class="reactionList hide_comment hide_kinetics hide_chemkin">
<tr><th>Index</th><th colspan="3" style="text-align: center;">Reaction</th><th>Family</th></tr>
{% for rxn in uniqueReactions2 %}
<tr class="reaction {{ rxn.getSource().label|csssafe }}">
<td class="index"><a href="{{ rxn.getURL() }}" title="Search on RMG website" class="searchlink">{{ rxn.index }}.</a></td>
<td class="reactants">{% for reactant in rxn.reactants %}<a href="{{ reactant.molecule[0].getURL() }}"><img src="species/{{ reactant|replace('#','%23') }}.png" alt="{{ reactant }}" title="{{ reactant }}, MW = {{ "%.2f"|format(reactant.molecule[0].getMolecularWeight() * 1000) }}"></a>{% if not loop.last %} + {% endif %}{% endfor %}</td>
<td class="reactionArrow">{% if rxn.reversible %}⇔{% else %}→{% endif %}</td>
<td class="products">{% for product in rxn.products %}<a href="{{ product.molecule[0].getURL() }}"><img src="species/{{ product|replace('#','%23') }}.png" alt="{{ product }}" title="{{ product }}, MW = {{ "%.2f"|format(product.molecule[0].getMolecularWeight() * 1000) }}"></a>{% if not loop.last %} + {% endif %}{% endfor %}</td>
<td class="family">{{ rxn.getSource().label }}</td>
</tr>
<tr class="kinetics {{ rxn.getSource().label|csssafe }}">
<td></td>
<td colspan="4">{{ rxn.kinetics.toHTML() }}</td>
</tr>
<tr class="chemkin {{ rxn.getSource().label|csssafe }}">
<td></td>
<td colspan="4">{{ rxn.toChemkin(species) }}</td>
</tr>
<tr class="comment {{ rxn.getSource().label|csssafe }}">
<td></td>
<td colspan="4">{{ rxn.kinetics.comment }}</td>
</tr>
{% endfor %}
</table>
</td>
</table>
</body>
</html>
""")
f = open(path, 'w')
f.write(template.render(title=title, commonSpecies=commonSpeciesList, speciesList1=speciesList1, speciesList2 = speciesList2, commonReactions=commonReactions, uniqueReactions1=uniqueReactions1, uniqueReactions2=uniqueReactions2, families1=families1, families2=families2, familyCount1=familyCount1,familyCount2=familyCount2))
f.close()
