class TestMoleculeDrawer(unittest.TestCase):
"""
Contains unit tests of the MoleculeDrawer class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.drawer = MoleculeDrawer()
self.molecule = Molecule(SMILES='CC(=O)CC')
def testDrawPNG(self):
"""
Test we can create PNG files from molecules.
"""
from cairo import ImageSurface
path = 'test_molecule.png'
if os.path.exists(path):
os.unlink(path)
surface, cr, (xoff, yoff, width, height) = self.drawer.draw(self.molecule, format='png', path=path)
self.assertTrue(os.path.exists(path), "File doesn't exist")
os.unlink(path)
self.assertIsInstance(surface, ImageSurface)
def testDrawPDF(self):
"""
Test we can create PDF files from molecules.
"""
from cairo import PDFSurface
path = 'test_molecule.pdf'
if os.path.exists(path):
os.unlink(path)
surface, cr, (xoff, yoff, width, height) = self.drawer.draw(self.molecule, format='pdf', path=path)
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
os.unlink(path)
def testDrawPolycycle(self):
"""
Test we can draw a polycyclic molecule
"""
from cairo import PDFSurface
path = 'test_molecule.pdf'
if os.path.exists(path):
os.unlink(path)
polycycle = Molecule(SMILES="C123CC4CC1COCC2CCC34")
surface, cr, (xoff, yoff, width, height) = self.drawer.draw(self.molecule, format='pdf', path=path)
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
os.unlink(path)
def testDrawPDFwithoutFile(self):
"""
Test we can create PDF surface without a temporary file (newer versions of PyCairo?)
"""
from cairo import PDFSurface
surface, cr, (xoff, yoff, width, height) = self.drawer.draw(self.molecule, format='pdf')
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
def __drawLabel(self, configuration, cr, x0, y0, format='pdf'):
boundingRect = self.__getLabelSize(configuration, format=format)
padding = 2
useStructures = self.__useStructureForLabel(configuration)
y = y0
for i, spec in enumerate(configuration.species):
if i > 0:
rect = self.__getTextSize('+', padding=padding, format=format)
x = x0 - 0.5 * (rect[2] - boundingRect[2]) + 2 * padding
self.__drawText('+', cr, x, y)
y += rect[3]
if useStructures:
moleculeDrawer = MoleculeDrawer()
cr.save()
surf, c, rect = moleculeDrawer.draw(spec.molecule[0], format=format)
cr.restore()
x = x0 - 0.5 * (rect[2] - boundingRect[2])
cr.save()
moleculeDrawer.render(cr, offset=(x, y))
cr.restore()
y += rect[3]
else:
rect = self.__getTextSize(spec.label, padding=padding, format=format)
x = x0 - 0.5 * (rect[2] - boundingRect[2]) + 2 * padding
self.__drawText(spec.label, cr, x, y)
y += rect[3]
return boundingRect
def drawMolecule(request, adjlist, format='png'):
"""
Returns an image of the provided adjacency list `adjlist` for a molecule.
urllib is used to quote/unquote the adjacency list.
"""
from rmgpy.molecule import Molecule
from rmgpy.molecule.draw import MoleculeDrawer
from rmgpy.molecule.adjlist import InvalidAdjacencyListError
from django.templatetags.static import static
adjlist = str(urllib.unquote(adjlist))
try:
molecule = Molecule().fromAdjacencyList(adjlist)
except InvalidAdjacencyListError:
response = HttpResponseRedirect(static('img/invalid_icon.png'))
else:
if format == 'png':
response = HttpResponse(content_type="image/png")
surface, _, _ = MoleculeDrawer().draw(molecule, format='png')
surface.write_to_png(response)
elif format == 'svg':
response = HttpResponse(content_type="image/svg+xml")
MoleculeDrawer().draw(molecule, format='svg', target=response)
else:
response = HttpResponse('Image format not implemented.',
status=501)
return response
def _draw_label(self, configuration, cr, x0, y0, file_format='pdf'):
bounding_rect = self._get_label_size(configuration, file_format=file_format)
padding = 2
use_structures = self._use_structure_for_label(configuration)
y = y0
for i, spec in enumerate(configuration.species_list):
if i > 0:
rect = self._get_text_size('+', padding=padding, file_format=file_format)
x = x0 - 0.5 * (rect[2] - bounding_rect[2]) + 2 * padding
self._draw_text('+', cr, x, y)
y += rect[3]
if use_structures:
molecule_drawer = MoleculeDrawer()
cr.save()
rect = molecule_drawer.draw(spec.molecule[0], file_format=file_format)[2]
cr.restore()
x = x0 - 0.5 * (rect[2] - bounding_rect[2])
cr.save()
molecule_drawer.render(cr, offset=(x, y))
cr.restore()
y += rect[3]
else:
rect = self._get_text_size(spec.label, padding=padding, file_format=file_format)
x = x0 - 0.5 * (rect[2] - bounding_rect[2]) + 2 * padding
self._draw_text(spec.label, cr, x, y)
y += rect[3]
return bounding_rect
def drawMolecule(request, adjlist, format='png'):
"""
Returns an image of the provided adjacency list `adjlist` for a molecule.
urllib is used to quote/unquote the adjacency list.
"""
import io
from rmgpy.molecule import Molecule
from rmgpy.molecule.draw import MoleculeDrawer
from rmgpy.molecule.adjlist import InvalidAdjacencyListError
adjlist = urllib.parse.unquote(adjlist)
try:
molecule = Molecule().from_adjacency_list(adjlist)
except (InvalidAdjacencyListError, ValueError):
response = HttpResponseRedirect(static('img/invalid_icon.png'))
else:
if format == 'png':
response = HttpResponse(content_type="image/png")
surface, _, _ = MoleculeDrawer().draw(molecule, file_format='png')
response.write(surface.write_to_png())
elif format == 'svg':
response = HttpResponse(content_type="image/svg+xml")
svg_data = io.BytesIO()
MoleculeDrawer().draw(molecule, file_format='svg', target=svg_data)
response.write(svg_data.getvalue())
else:
response = HttpResponse('Image format not implemented.',
status=501)
return response
def drawMolecule(request, adjlist, format='png'):
"""
Returns an image of the provided adjacency list `adjlist` for a molecule.
urllib is used to quote/unquote the adjacency list.
"""
from rmgpy.molecule import Molecule
from rmgpy.molecule.draw import MoleculeDrawer
from rmgpy.molecule.adjlist import InvalidAdjacencyListError
adjlist = str(urllib.unquote(adjlist))
try:
molecule = Molecule().fromAdjacencyList(adjlist)
except (InvalidAdjacencyListError, ValueError):
response = HttpResponseRedirect(static('img/invalid_icon.png'))
else:
if format == 'png':
response = HttpResponse(content_type="image/png")
surface, _, _ = MoleculeDrawer().draw(molecule, format='png')
surface.write_to_png(response)
elif format == 'svg':
response = HttpResponse(content_type="image/svg+xml")
MoleculeDrawer().draw(molecule, format='svg', target=response)
else:
response = HttpResponse('Image format not implemented.', status=501)
return response
def drawMolecule(request, adjlist):
"""
Returns an image of the provided adjacency list `adjlist` for a molecule.
urllib is used to quote/unquote the adjacency list.
"""
from rmgpy.molecule import Molecule
from rmgpy.molecule.draw import MoleculeDrawer
adjlist = str(urllib.unquote(adjlist))
molecule = Molecule().fromAdjacencyList(adjlist)
surface, cr, rect = MoleculeDrawer().draw(molecule, format='png')
response = HttpResponse(content_type="image/png")
surface.write_to_png(response)
return response
def drawMolecule(request, adjlist):
"""
Returns an image of the provided adjacency list `adjlist` for a molecule.
urllib is used to quote/unquote the adjacency list.
"""
from rmgpy.molecule import Molecule
from rmgpy.molecule.draw import MoleculeDrawer
adjlist = str(urllib.unquote(adjlist))
molecule = Molecule().fromAdjacencyList(adjlist)
surface, cr, rect = MoleculeDrawer().draw(molecule, format='png')
response = HttpResponse(content_type="image/png")
surface.write_to_png(response)
return response
def __getLabelSize(self, configuration, format='pdf'):
"""
"""
width = 0
height = 0
boundingRects = []
if self.__useStructureForLabel(configuration):
for spec in configuration.species:
surface, cr, rect = MoleculeDrawer().draw(spec.molecule[0],
format=format)
boundingRects.append(list(rect))
else:
for spec in configuration.species:
boundingRects.append(
self.__getTextSize(spec.label, format=format))
plusRect = self.__getTextSize('+', format=format)
for rect in boundingRects:
if width < rect[2]: width = rect[2]
height += rect[3] + plusRect[3]
height -= plusRect[3]
return [0, 0, width, height]
def _get_label_size(self, configuration, file_format='pdf'):
"""
"""
width = 0
height = 0
bounding_rects = []
if self._use_structure_for_label(configuration):
for spec in configuration.species:
surface, cr, rect = MoleculeDrawer().draw(
spec.molecule[0], file_format=file_format)
bounding_rects.append(list(rect))
else:
for spec in configuration.species:
bounding_rects.append(
self._get_text_size(spec.label, file_format=file_format))
plus_rect = self._get_text_size('+', file_format=file_format)
for rect in bounding_rects:
if width < rect[2]:
width = rect[2]
height += rect[3] + plus_rect[3]
height -= plus_rect[3]
return [0, 0, width, height]
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 MoleculeDrawer
adjlist = str(adjlist.replace(';', '\n'))
molecule = Molecule().fromAdjacencyList(adjlist)
surface, cr, rect = MoleculeDrawer().draw(molecule, format='png')
png_string = surface.write_to_png()
response = HttpResponse(png_string, mimetype="image/png")
return response
def molDrawer():
dirs = os.listdir('/mnt/d/reactions')
for i in dirs:
dir_path = os.path.join(os.path.join('/mnt/d/reactions', i),
'ssm_product.xyz')
OBMol = readXYZ(dir_path)
rmg_mol = toRMGmol(OBMol)
_path = '/mnt/d/molecules/{}.png'.format(i)
MoleculeDrawer().draw(rmg_mol, file_format='png', target=_path)
def _repr_png_(self):
"""
Return a png picture of the molecule, useful for ipython-qtconsole.
"""
from rmgpy.molecule.draw import MoleculeDrawer
tempFileName = 'temp_molecule.png'
MoleculeDrawer().draw(self, 'png', tempFileName)
png = open(tempFileName, 'rb').read()
os.unlink(tempFileName)
return png
def get(self, request, pk):
structure = Structure.objects.get(pk=pk)
molecule = structure.to_rmg()
(
surface,
_,
_,
) = MoleculeDrawer().draw(molecule, file_format="png")
response = HttpResponse(surface.write_to_png(), content_type="image/png")
return response
def draw(self, path):
"""
Generate a pictorial representation of the chemical graph using the
:mod:`draw` module. Use `path` to specify the file to save
the generated image to; the image type is automatically determined by
extension. Valid extensions are ``.png``, ``.svg``, ``.pdf``, and
``.ps``; of these, the first is a raster format and the remainder are
vector formats.
"""
from rmgpy.molecule.draw import MoleculeDrawer
format = os.path.splitext(path)[-1][1:].lower()
MoleculeDrawer().draw(self, format, target=path)
def drawMolecule(request, adjlist):
"""
Returns an image of the provided adjacency list `adjlist` for a molecule.
urllib is used to quote/unquote the adjacency list.
"""
from rmgpy.molecule import Molecule
from rmgpy.molecule.draw import MoleculeDrawer
adjlist = str(urllib.unquote(adjlist))
molecule = Molecule().fromAdjacencyList(adjlist)
response = HttpResponse(content_type="image/svg+xml")
MoleculeDrawer().draw(molecule, format='svg', target=response)
return response
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.kinetics import Arrhenius, MultiArrhenius, MultiPDepArrhenius
from rmgpy.molecule.draw import MoleculeDrawer
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'
speciesList = [spec1 for spec1, spec2 in commonSpeciesList] + [
spec2 for spec1, spec2 in commonSpeciesList
] + speciesList1 + speciesList2
re_index = re.compile(r'\((\d+)\)$')
if not os.path.isdir(os.path.join(dirname, 'species1')):
os.makedirs(os.path.join(dirname, 'species1'))
if not os.path.isdir(os.path.join(dirname, 'species2')):
os.makedirs(os.path.join(dirname, 'species2'))
for spec1, spec2 in commonSpeciesList:
# 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!)
match1 = re_index.search(spec1.label)
if match1:
spec1.index = int(match1.group(0)[1:-1])
spec1.label = spec1.label[0:match1.start()]
match2 = re_index.search(spec2.label)
if match2:
spec2.index = int(match2.group(0)[1:-1])
spec2.label = spec2.label[0:match2.start()]
# Draw molecules if necessary
fstr = os.path.join(dirname, 'species1', '{0}.png'.format(spec1))
if not os.path.exists(fstr):
try:
MoleculeDrawer().draw(spec1.molecule[0], 'png', fstr)
except IndexError:
raise OutputError(
'{0} species could not be drawn because it did not contain a molecular structure. Please recheck your files.'
.format(getSpeciesIdentifier(spec1)))
fstr = os.path.join(dirname, 'species2', '{0}.png'.format(spec2))
if not os.path.exists(fstr):
try:
MoleculeDrawer().draw(spec2.molecule[0], 'png', fstr)
except IndexError:
raise OutputError(
'{0} species could not be drawn because it did not contain a molecular structure. Please recheck your files.'
.format(getSpeciesIdentifier(spec2)))
for spec in speciesList1:
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, 'species1', '{0}.png'.format(spec))
if not os.path.exists(fstr):
try:
MoleculeDrawer().draw(spec.molecule[0], 'png', fstr)
except IndexError:
raise OutputError(
'{0} species could not be drawn because it did not contain a molecular structure. Please recheck your files.'
.format(getSpeciesIdentifier(spec)))
for spec in speciesList2:
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, 'species2', '{0}.png'.format(spec))
if not os.path.exists(fstr):
try:
MoleculeDrawer().draw(spec.molecule[0], 'png', fstr)
except IndexError:
raise OutputError(
'{0} species could not be drawn because it did not contain a molecular structure. Please recheck your files.'
.format(getSpeciesIdentifier(spec)))
familyCount1 = {}
familyCount2 = {}
for rxn1, rxn2 in commonReactions:
if isinstance(rxn2.kinetics, (MultiArrhenius, MultiPDepArrhenius)):
rxn2.duplicate = True
if isinstance(rxn1, PDepReaction):
family = "PDepNetwork"
else:
family = rxn1.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="100%">
{% for spec1, spec2 in commonSpecies %}
<tr>
<td width="100%" colspan="4">
<table align="center">
<tr class="species">
<td>{{ spec1.label }}</td>
<td class="structure" align="center"><a href="{{spec1.molecule[0].getURL()}}"><img src="species1/{{ spec1|replace('#','%23') }}.png" alt="{{ spec1 }}" title="{{ spec1 }}"></a></td>
<td>{{ "%.2f"|format(spec1.molecule[0].getMolecularWeight() * 1000) }}</td>
</tr>
</table>
</td>
</tr>
{% if spec1.thermo and spec2.thermo %}
{% if spec1.thermo.isIdenticalTo(spec2.thermo) %}
<tr width=100%>
<td colspan="4" valign="top" width=50%><div align="center"><font color="blue">IDENTICAL THERMO WAS FOUND FOR THIS SPECIES.</font></div>
</tr>
{% elif spec1.thermo.isSimilarTo(spec2.thermo) %}
<tr width=100%>
<td colspan="4" valign="top" width=50%><div align="center"><font color="green">SIMILAR THERMO WAS FOUND FOR THIS SPECIES.</font></div>
</tr>
{% else %}
<tr width=100%>
<td colspan="4" valign="top" width=50%><div align="center"><font color="red">DIFFERENT THERMO WAS FOUND FOR THIS SPECIES.</font></div>
</tr>
{% endif%}
<tr>
<td width="10%">{{ spec1.index }}. </td>
<td width="40%">
<table width="100%">
<tr>
<th>H300</th>
<th>S300</th>
<th>Cp300</th>
<th>Cp500</th>
<th>Cp1000</th>
<th>Cp1500</th>
</tr>
<tr>
<td>{% if spec1.thermo.Tmin.value_si <= 300 %}
{{ "%.2f"|format(spec1.thermo.getEnthalpy(300) / 4184) }}
{% endif %}</td>
<td>
{% if spec1.thermo.Tmin.value_si <= 300 %}
{{ "%.2f"|format(spec1.thermo.getEntropy(300) / 4.184) }}
{% endif %}</td>
<td>{{ "%.2f"|format(spec1.thermo.getHeatCapacity(300) / 4.184) }}</td>
<td>{{ "%.2f"|format(spec1.thermo.getHeatCapacity(500) / 4.184) }}</td>
<td>{{ "%.2f"|format(spec1.thermo.getHeatCapacity(1000) / 4.184) }}</td>
<td>{{ "%.2f"|format(spec1.thermo.getHeatCapacity(1500) / 4.184) }}</td>
</tr>
</table>
</td>
<td width="10%">{{ spec2.index }}.</td>
<td width="40%">
<table width="100%">
<tr>
<th>H300</th>
<th>S300</th>
<th>Cp300</th>
<th>Cp500</th>
<th>Cp1000</th>
<th>Cp1500</th>
</tr>
<tr>
<td>{% if spec2.thermo.Tmin.value_si <= 300 %}
{{ "%.2f"|format(spec2.thermo.getEnthalpy(300) / 4184) }}
{% endif %}</td>
<td>{% if spec2.thermo.Tmin.value_si <= 300 %}
{{ "%.2f"|format(spec2.thermo.getEntropy(300) / 4.184) }}
{% endif %}</td>
<td>{{ "%.2f"|format(spec2.thermo.getHeatCapacity(300) / 4.184) }}</td>
<td>{{ "%.2f"|format(spec2.thermo.getHeatCapacity(500) / 4.184) }}</td>
<td>{{ "%.2f"|format(spec2.thermo.getHeatCapacity(1000) / 4.184) }}</td>
<td>{{ "%.2f"|format(spec2.thermo.getHeatCapacity(1500) / 4.184) }}</td>
</tr>
</table>
</td>
</tr>
{% endif %}
<tr>
<td width="100%" colspan="4"><hr/></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="species1/{{ 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="species2/{{ 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 %}
<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="species1/{{ 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="species1/{{ 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 colspan="4" valign="top" width=50%><div align="center"><font color="blue">IDENTICAL KINETICS WERE FOUND FOR THIS REACTION.</font></div>
</tr>
{% elif rxn1.kinetics.isSimilarTo(rxn2.kinetics) %}
<tr width=100%>
<td colspan="4" valign="top" width=50%><div align="center"><font color="green">SIMILAR KINETICS WERE FOUND FOR THIS REACTION.</font></div>
</tr>
{% else %}
<tr width=100%>
<td colspan="4" valign="top" width=50%><div align="center"><font color="red">DIFFERENT KINETICS WERE FOUND FOR THIS REACTION.</font></div>
</tr>
{% endif%}
<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%>{% if not rxn1.isIsomorphic(rxn2, eitherDirection=False) %}
<td colspan="2" width=50%></td>
<td colspan="2" width=50%>* Reaction was found in reverse
{% if not rxn2.duplicate %}
<P><b>Fitted Reverse Kinetics:</b>
{% if not rxn2.kinetics.isPressureDependent() %}
{{rxn2.generateReverseRateCoefficient().toHTML() }}
{% else %} Pressure dependent
{% endif %}
{% endif %}
<P><b>Original Kinetics:</b>
{% 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(speciesList) }}</font></td>
<td colspan="2" valign="top" width=50%><font size="1pt" face="courier">{{ rxn2.toChemkin(speciesList) }}</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>
{% 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="species1/{{ 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="species1/{{ 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="species2/{{ 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="species2/{{ 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,
speciesList=speciesList))
f.close()
def saveOutputHTML(path, reactionModel, partCoreEdge='core'):
"""
Save the current set of species and reactions of `reactionModel` to
an HTML file `path` on disk. As part of this process, drawings of all
species are created in the species folder (if they don't already exist)
using the :mod:`rmgpy.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 MoleculeDrawer
from rmgpy.chemkin import getSpeciesIdentifier
try:
import jinja2
except ImportError:
logging.warning(
"jinja2 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'
if partCoreEdge == 'core':
species = reactionModel.core.species[:] + reactionModel.outputSpeciesList
if not os.path.isdir(os.path.join(dirname, 'species')):
os.makedirs(os.path.join(dirname, 'species'))
elif partCoreEdge == 'edge':
species = reactionModel.edge.species[:] + reactionModel.outputSpeciesList
if not os.path.isdir(os.path.join(dirname, 'species_edge')):
os.makedirs(os.path.join(dirname, 'species_edge'))
re_index_search = re.compile(r'\((\d+)\)$').search
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
if partCoreEdge == 'core':
fstr = os.path.join(dirname, 'species', '{0}.png'.format(spec))
elif partCoreEdge == 'edge':
fstr = os.path.join(dirname, 'species_edge',
'{0}.png'.format(spec))
if not os.path.exists(fstr):
try:
MoleculeDrawer().draw(spec.molecule[0], 'png', fstr)
except IndexError:
raise OutputError(
"{0} species could not be drawn because it did not contain a molecular structure. Please recheck your files."
.format(getSpeciesIdentifier(spec)))
# 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)
if partCoreEdge == 'core':
reactions = [rxn for rxn in reactionModel.core.reactions
] + reactionModel.outputReactionList
elif partCoreEdge == 'edge':
reactions = [rxn for rxn in reactionModel.edge.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:
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
if partCoreEdge == 'core':
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>
{% if spec.thermo %}
<tr>
<td>
<table align="center">
<tr>
<th>H298</th>
<th>S298</th>
<th>Cp300</th>
<th>Cp500</th>
<th>Cp1000</th>
<th>Cp1500</th>
</tr>
<tr>
<td>
{% if spec.thermo.Tmin.value_si <= 298 %}
{{ "%.2f"|format(spec.thermo.getEnthalpy(298) / 4184) }}
{% endif %} </td>
<td>{% if spec.thermo.Tmin.value_si <= 298 %}
{{ "%.2f"|format(spec.thermo.getEntropy(298) / 4.184) }}
{% endif %}</td>
<td>{{ "%.2f"|format(spec.thermo.getHeatCapacity(300) / 4.184) }}</td>
<td>{{ "%.2f"|format(spec.thermo.getHeatCapacity(500) / 4.184) }}</td>
<td>{{ "%.2f"|format(spec.thermo.getHeatCapacity(1000) / 4.184) }}</td>
<td>{{ "%.2f"|format(spec.thermo.getHeatCapacity(1500) / 4.184) }}</td>
</tr>
</table>
</td></tr>
{% endif %}
{% 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>
""")
elif partCoreEdge == 'edge':
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_edge/{{ 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>
{% if spec.thermo %}
<tr>
<td>
<table align="center">
<tr>
<th>H298</th>
<th>S298</th>
<th>Cp300</th>
<th>Cp500</th>
<th>Cp1000</th>
<th>Cp1500</th>
</tr>
<tr>
<td>
{% if spec.thermo.Tmin.value_si <= 298 %}
{{ "%.2f"|format(spec.thermo.getEnthalpy(298) / 4184) }}
{% endif %} </td>
<td>{% if spec.thermo.Tmin.value_si <= 298 %}
{{ "%.2f"|format(spec.thermo.getEntropy(298) / 4.184) }}
{% endif %}</td>
<td>{{ "%.2f"|format(spec.thermo.getHeatCapacity(300) / 4.184) }}</td>
<td>{{ "%.2f"|format(spec.thermo.getHeatCapacity(500) / 4.184) }}</td>
<td>{{ "%.2f"|format(spec.thermo.getHeatCapacity(1000) / 4.184) }}</td>
<td>{{ "%.2f"|format(spec.thermo.getHeatCapacity(1500) / 4.184) }}</td>
</tr>
</table>
</td></tr>
{% endif %}
{% 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_edge/{{ 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_edge/{{ 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()
class TestMoleculeDrawer(unittest.TestCase):
"""
Contains unit tests of the MoleculeDrawer class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.drawer = MoleculeDrawer()
self.molecule = Molecule(smiles='CC(=O)CC')
def test_draw_png(self):
"""
Test we can create PNG files from molecules.
"""
try:
from cairocffi import ImageSurface
except ImportError:
from cairo import ImageSurface
path = 'test_molecule.png'
if os.path.exists(path):
os.unlink(path)
surface, _cr, (_xoff, _yoff, width, height) = self.drawer.draw(self.molecule, file_format='png', target=path)
self.assertTrue(os.path.exists(path), "File doesn't exist")
self.assertGreater(width, height)
os.unlink(path)
self.assertIsInstance(surface, ImageSurface)
def test_draw_pdf(self):
"""
Test we can create PDF files from molecules.
"""
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
path = 'test_molecule.pdf'
if os.path.exists(path):
os.unlink(path)
surface, _cr, (_xoff, _yoff, width, height) = self.drawer.draw(self.molecule, file_format='pdf', target=path)
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
os.unlink(path)
def test_draw_polycycle(self):
"""
Test we can draw a polycyclic molecule
"""
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
path = 'test_molecule.pdf'
if os.path.exists(path):
os.unlink(path)
polycycle = Molecule(smiles="C123CC4CC1COCC2CCC34")
surface, _cr, (_xoff, _yoff, width, height) = self.drawer.draw(polycycle, file_format='pdf', target=path)
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
os.unlink(path)
def test_draw_pdf_without_file(self):
"""
Test we can create PDF surface without a temporary file (newer versions of PyCairo?)
"""
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
surface, _cr, (_xoff, _yoff, width, height) = self.drawer.draw(self.molecule, file_format='pdf')
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
def test_draw_non_standard_bonds(self):
spec = Species().from_smiles('[CH2]C=C[CH2]')
hybrid = spec.get_resonance_hybrid()
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
surface, _cr, (_xoff, _yoff, width, height) = self.drawer.draw(hybrid, file_format='pdf')
self.assertGreater(width, height)
self.assertIsInstance(surface, PDFSurface)
def test_draw_hydrogen_bond_adsorbate(self):
molecule = Molecule().from_adjacency_list("""
1 O u0 p3 c-1 {2,S} {10,H}
2 N u0 p0 c+1 {1,S} {3,D} {4,S}
3 O u0 p2 c0 {2,D}
4 O u0 p2 c0 {2,S} {7,S}
5 N u0 p1 c0 {6,S} {8,S} {9,S} {7,H}
6 O u0 p2 c0 {5,S} {10,S}
7 H u0 p0 c0 {4,S} {5,H}
8 H u0 p0 c0 {5,S}
9 H u0 p0 c0 {5,S}
10 H u0 p0 c0 {6,S} {1,H}
11 X u0 p0 c0
"""
)
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
surface, _cr, (_xoff, _yoff, _width, _height) = self.drawer.draw(molecule, file_format='pdf')
self.assertIsInstance(surface, PDFSurface)
class TestMoleculeDrawer(unittest.TestCase):
"""
Contains unit tests of the MoleculeDrawer class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.drawer = MoleculeDrawer()
self.molecule = Molecule(SMILES='CC(=O)CC')
def testDrawPNG(self):
"""
Test we can create PNG files from molecules.
"""
try:
from cairocffi import ImageSurface
except ImportError:
from cairo import ImageSurface
path = 'test_molecule.png'
if os.path.exists(path):
os.unlink(path)
surface, cr, (xoff, yoff, width,
height) = self.drawer.draw(self.molecule,
format='png',
target=path)
self.assertTrue(os.path.exists(path), "File doesn't exist")
os.unlink(path)
self.assertIsInstance(surface, ImageSurface)
def testDrawPDF(self):
"""
Test we can create PDF files from molecules.
"""
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
path = 'test_molecule.pdf'
if os.path.exists(path):
os.unlink(path)
surface, cr, (xoff, yoff, width,
height) = self.drawer.draw(self.molecule,
format='pdf',
target=path)
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
os.unlink(path)
def testDrawPolycycle(self):
"""
Test we can draw a polycyclic molecule
"""
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
path = 'test_molecule.pdf'
if os.path.exists(path):
os.unlink(path)
polycycle = Molecule(SMILES="C123CC4CC1COCC2CCC34")
surface, cr, (xoff, yoff, width,
height) = self.drawer.draw(self.molecule,
format='pdf',
target=path)
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
os.unlink(path)
def testDrawPDFwithoutFile(self):
"""
Test we can create PDF surface without a temporary file (newer versions of PyCairo?)
"""
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
surface, cr, (xoff, yoff, width,
height) = self.drawer.draw(self.molecule, format='pdf')
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
def testDrawNonStandardBonds(self):
spec = Species().fromSMILES('[CH2]C=C[CH2]')
hybrid = spec.getResonanceHybrid()
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
surface, cr, (xoff, yoff, width,
height) = self.drawer.draw(hybrid, format='pdf')
self.assertIsInstance(surface, PDFSurface)
class TestMoleculeDrawer(unittest.TestCase):
"""
Contains unit tests of the MoleculeDrawer class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.drawer = MoleculeDrawer()
self.molecule = Molecule(SMILES='CC(=O)CC')
def testDrawPNG(self):
"""
Test we can create PNG files from molecules.
"""
try:
from cairocffi import ImageSurface
except ImportError:
from cairo import ImageSurface
path = 'test_molecule.png'
if os.path.exists(path):
os.unlink(path)
surface, cr, (xoff, yoff, width, height) = self.drawer.draw(self.molecule, format='png', target=path)
self.assertTrue(os.path.exists(path), "File doesn't exist")
os.unlink(path)
self.assertIsInstance(surface, ImageSurface)
def testDrawPDF(self):
"""
Test we can create PDF files from molecules.
"""
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
path = 'test_molecule.pdf'
if os.path.exists(path):
os.unlink(path)
surface, cr, (xoff, yoff, width, height) = self.drawer.draw(self.molecule, format='pdf', target=path)
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
os.unlink(path)
def testDrawPolycycle(self):
"""
Test we can draw a polycyclic molecule
"""
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
path = 'test_molecule.pdf'
if os.path.exists(path):
os.unlink(path)
polycycle = Molecule(SMILES="C123CC4CC1COCC2CCC34")
surface, cr, (xoff, yoff, width, height) = self.drawer.draw(self.molecule, format='pdf', target=path)
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
os.unlink(path)
def testDrawPDFwithoutFile(self):
"""
Test we can create PDF surface without a temporary file (newer versions of PyCairo?)
"""
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
surface, cr, (xoff, yoff, width, height) = self.drawer.draw(self.molecule, format='pdf')
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
def testDrawNonStandardBonds(self):
spec = Species().fromSMILES('[CH2]C=C[CH2]')
hybrid = spec.getResonanceHybrid()
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
surface, cr, (xoff, yoff, width, height) = self.drawer.draw(hybrid, format='pdf')
self.assertIsInstance(surface, PDFSurface)
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.drawer = MoleculeDrawer()
self.molecule = Molecule(SMILES='CC(=O)CC')
def saveFluxAnalysisHTML(path,
idx,
speciesROP,
negativeROPList=[],
positiveROPList=[],
speciesList=[]):
"""
Save the flux analysis for a given species to HTML.
"""
import os
from rmgpy.molecule.draw import MoleculeDrawer
from rmgpy.chemkin import getSpeciesIdentifier
from .html import renderSpecies, renderReactionROP, STYLE_HEADER
try:
import jinja2
except ImportError:
print "jinja2 package not found; HTML output will not be saved."
return
path = os.path.abspath(path)
dirname = os.path.dirname(path)
if not os.path.isdir(os.path.join(dirname, 'species')):
os.makedirs(os.path.join(dirname, 'species'))
for spec in speciesList:
# Draw molecules
speciesLabel = getSpeciesIdentifier(spec)
fstr = os.path.join(dirname, 'species', '{0}.png'.format(speciesLabel))
if not os.path.exists(fstr):
try:
MoleculeDrawer().draw(spec.molecule[0], 'png', fstr)
except IndexError:
raise Exception(
"{0} species could not be drawn because it did not contain a molecular structure. Please recheck your files."
.format(speciesLabel))
#title = 'Flux Analysis for Species {label} at x = {x}'.format(label=getSpeciesIdentifier(species), x=speciesROP.xvarData[idx])
#self.totalNegativeRate[idx]
#print '{num}. {rxnString}\t Actual flux = {flux}\t % of Total Positive ROP = {fluxpercent}'.format(num=i+1, rxnString=rxnRop.rxnString, flux=rxnRop.data[idx], fluxpercent=rxnRop.fluxPercentage[idx])
environment = jinja2.Environment()
environment.filters['renderSpecies'] = renderSpecies
environment.filters['renderReactionROP'] = renderReactionROP
environment.filters['getSpeciesIdentifier'] = getSpeciesIdentifier
# 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>Flux Analysis for Species {{speciesROP.speciesObject|getSpeciesIdentifier}} at x = {{speciesROP.xvarData[idx]}}</title>
{{style}}
</head>
<body>
<h1>Flux Analysis for Species {{speciesROP.speciesObject|getSpeciesIdentifier}} at x = {{speciesROP.xvarData[idx]}}</h1>
<h2>Species</h2>
<table class="speciesList">
<tr><th>Label</th><th>Structure</th><th>SMILES</th><th>Thermo</th>
{{speciesROP.speciesObject|renderSpecies(thermo=True)}}
</table>
<hr>
<h3>Net ROP = {{speciesROP.totalRopData[idx]}}</h3>
<hr size=3>
<h2>Top Negative Flux Reactions Depleting Species {{speciesROP.speciesObject|getSpeciesIdentifier}}</h2>
<h3>Total Negative ROP = {{speciesROP.totalNegativeRate[idx]}}</h3>
<table class="reactionList" hide_comment hide_kinetics hide_chemkin">
{% for rxnROP in negativeROPList %}
{{rxnROP|renderReactionROP(speciesList, showROP=True, idx=idx)}}
{% endfor %}
</table>
<hr size=3>
<h2>Top Positive Flux Reactions Accumulating Species {{speciesROP.speciesObject|getSpeciesIdentifier}}</h2>
<h3>Total Positive ROP = {{speciesROP.totalPositiveRate[idx]}}</h3>
<table class="reactionList" hide_comment hide_kinetics hide_chemkin">
{% for rxnROP in positiveROPList %}
{{rxnROP|renderReactionROP(speciesList, showROP=True, idx=idx)}}
{% endfor %}
</table>
</body>
</html>
""")
f = open(path, 'w')
f.write(
template.render(style=STYLE_HEADER,
idx=idx,
speciesROP=speciesROP,
negativeROPList=negativeROPList,
positiveROPList=positiveROPList,
speciesList=speciesList))
f.close()
class TestMoleculeDrawer(unittest.TestCase):
"""
Contains unit tests of the MoleculeDrawer class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.drawer = MoleculeDrawer()
self.molecule = Molecule(SMILES='CC(=O)CC')
def testDrawPNG(self):
"""
Test we can create PNG files from molecules.
"""
from cairo import ImageSurface
path = 'test_molecule.png'
if os.path.exists(path):
os.unlink(path)
surface, cr, (xoff, yoff, width,
height) = self.drawer.draw(self.molecule,
format='png',
path=path)
self.assertTrue(os.path.exists(path), "File doesn't exist")
os.unlink(path)
self.assertIsInstance(surface, ImageSurface)
def testDrawPDF(self):
"""
Test we can create PDF files from molecules.
"""
from cairo import PDFSurface
path = 'test_molecule.pdf'
if os.path.exists(path):
os.unlink(path)
surface, cr, (xoff, yoff, width,
height) = self.drawer.draw(self.molecule,
format='pdf',
path=path)
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
os.unlink(path)
def testDrawPolycycle(self):
"""
Test we can draw a polycyclic molecule
"""
from cairo import PDFSurface
path = 'test_molecule.pdf'
if os.path.exists(path):
os.unlink(path)
polycycle = Molecule(SMILES="C123CC4CC1COCC2CCC34")
surface, cr, (xoff, yoff, width,
height) = self.drawer.draw(self.molecule,
format='pdf',
path=path)
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
os.unlink(path)
def testDrawPDFwithoutFile(self):
"""
Test we can create PDF surface without a temporary file (newer versions of PyCairo?)
"""
from cairo import PDFSurface
surface, cr, (xoff, yoff, width,
height) = self.drawer.draw(self.molecule, format='pdf')
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.drawer = MoleculeDrawer()
self.molecule = Molecule(SMILES='CC(=O)CC')
#generate species images
mech_path = path + '/data/' + mech
speciesPath = mech_path + '/species/'
if not os.path.isdir(speciesPath):
os.makedirs(speciesPath)
species = species_list[:]
re_index_search = re.compile(r'\((\d+)\)$').search
for spec in species:
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(mech_path, 'species', '{0}.png'.format(spec))
if not os.path.exists(fstr):
try:
MoleculeDrawer().draw(spec.molecule[0], 'png', fstr)
except IndexError:
raise OutputError("{0} species could not be drawn!".format(
getSpeciesIdentifier(spec)))
species_target = 'C=CC[CH]CCCCCCC'
# search the target species in model
mol_tgt = Molecule().fromSMILES(species_target)
for spc in species_list:
if spc.isIsomorphic(mol_tgt):
print '{} is found in model with spc name {}'.format(
mol_tgt, getSpeciesIdentifier(spc))
break