def EniSearch(request):
"""
Creates webpage form to display detergent and deposit structures upon entering smiles as well as returns binding constants
between the detergent and deposit
"""
from tools import getAbrahamAB
if request.method == "POST":
form = EniSearchForm(request.POST, error_class=DivErrorList)
if form.is_valid():
detergent_adjlist = form.cleaned_data["detergent"]
deposit_adjlist = form.cleaned_data["deposit"]
detergent = Molecule()
detergent.fromAdjacencyList(detergent_adjlist)
detergent_smiles = detergent.toSMILES()
detergent_structure = getStructureMarkup(detergent)
deposit = Molecule()
deposit.fromAdjacencyList(deposit_adjlist)
deposit_smiles = deposit.toSMILES()
deposit_structure = getStructureMarkup(deposit)
detergentA, detergentB = getAbrahamAB(detergent_smiles)
depositA, depositB = getAbrahamAB(deposit_smiles)
# Estimating the binding strength assuming the the detergent to be the donor and dirt to be acceptor
logK_AB = 7.354 * detergentA * depositB
# Estimating the binding strength assuming the the detergent to be the acceptor and dirt to be donor
logK_BA = 7.354 * detergentB * depositA
else:
detergentA = 0
detergentB = 0
depositA = 0
depositB = 0
logK_AB = 0
logK_BA = 0
form = EniSearchForm()
return render_to_response(
"EniSearch.html",
{
"detergentA": detergentA,
"detergentB": detergentB,
"depositA": depositA,
"depositB": depositB,
"logKAB": logK_AB,
"logKBA": logK_BA,
"form": form,
},
context_instance=RequestContext(request),
)
def example():
"""Create a set of sample tables"""
# In practice, you'd most likely be embedding your HTML tables in
# a web page template. For demonstration purposes, we'll create a
# simple page with a few default styles.
htmlheader = """\
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01//EN">
<html>
<head>
<title>Sample table</title>
<style type="text/css">
body { font-family: Helvetica,Arial,FreeSans; }
table.reporttable { border-style: solid; border-width: 1px; }
table.reporttable tr.tr_odd { background-color: #eee; }
table.reporttable tr.tr_even { background-color: #bbb; }
table.reporttable th { background-color: blue; color: white; }
table.reporttable td.cell_bold { font-weight: bold; }
table.reporttable td.cell_money { text-align: right; font-family: monospace; }
</style>
</head>
<body>
"""
htmlfooter = """\
</body>
</html>"""
exampletypes = ((PDFTable, 'pdf'), (HTMLTable, 'html'), (SpreadsheetTable, 'xls'))
#### Example with several row types
# mainrs = RowSpec(
# ColumnSpec('foo', 'Column 1', width=1),
# ColumnSpec('bar', 'Column 2', width=1),
# ColumnSpec('baz', 'Column 3', width=1),
# ColumnSpec('qux', 'Column 4', width=4))
#
# subrow1 = RowSpec(
# ColumnSpec('subfoo1', 'First wide column', bold=True, span=2, width=2),
# ColumnSpec('subbar1', 'Second wide column', span=2))
#
# subrow2 = RowSpec(
# ColumnSpec('subfoo2', 'A table-wide column', span=4))
#
# summaryrow = RowSpec(
# ColumnSpec('junk1', span=2, width=2),
# ColumnSpec('baz', bold=True, width=1),
# ColumnSpec('junk2'))
#
# lines = []
# lines.append([mainrs({'foo': 1, 'bar': 2, 'baz': 3, 'qux': 'Bar. ' * 30}),
# subrow1({'subfoo1': 'And', 'subbar1': 'another'}),
# subrow2({'subfoo2': 'This is a test. ' * 15}),
# subrow2({'subfoo2': 'And another test'})])
# for i in range(5):
# lines.append(mainrs({'foo': i, 'bar': 14, 'baz': 15, 'qux': 'extra'}))
# lines.append(summaryrow({'junk1': None, 'baz': 'Summary!', 'junk2': None}))
#
# for tableclass, extension in exampletypes:
# outfile = open('showcase.%s' % extension, 'wb')
# if tableclass is HTMLTable:
# outfile.write(htmlheader)
# outfile.write(tableclass('Sample Table',
# '%s test' % extension.upper(),
# headers=[mainrs, subrow1, subrow2]).render(lines))
# if tableclass is HTMLTable:
# outfile.write(htmlfooter)
#### Converting species dictionary from RMG-Java in bond connectivity
# format into the smile and
import decimal
import random
import numpy as np
import csv
import itertools
from rmgpy.molecule import Molecule
#reading text file of species
groups= []
uniquekeys = []
def isa_group_separator(line):
return line=='\n'
with open('Species_Dictionary.txt') as f:
for key,group in itertools.groupby(f,isa_group_separator):
groups.append(list(group))
uniquekeys.append(key)
#print groups , len(groups)
# Since empty lines are appered as seperate lists in the groups lis,
# this section is removing them from the final list
groupsb = list()
for sublist in groups:
if not any(map(str.strip, sublist)): # this detects blanks
continue # it was blank, so skip it
if sublist not in groupsb: # this detects duplicates
groupsb.append(sublist)
#print groupsb , len (groupsb)
# remove '\n' from each item in list
def stripp(x):
return x.strip('\n')
groupsb=[list(map(stripp,x)) for x in groupsb]
#print groupsb
rows = []
for index, adjacency_list in enumerate(groupsb, start=1):
species_name = adjacency_list[0]
mol = Molecule().fromAdjacencyList('\n'.join(adjacency_list))
smiles = mol.toSMILES()
rows.append({'Index': index,
'Species': species_name,
'SMILES': smiles,
'Molecule': mol,
})
print "Made {num} rows".format(num=len(rows))
invoicerow = RowSpec(ColumnSpec('Index', 'Index #'),
ColumnSpec('Species', 'Species Name'),
ColumnSpec('SMILES', 'SMILES'),
ColumnSpec('Molecule', 'Molecule'),
)
lines = invoicerow.makeall(rows)
def image(mol):
from base64 import b64encode
src = mol._repr_png_()
encoded = b64encode(src)
return '<img alt="{name}" src="data:image/png;base64,{data}" />'.format(name=mol.toSMILES(), data=encoded)
image.htmlsafe = True
def blank(mol):
return ''
for tableclass, extension in exampletypes:
outfile = open('Species.%s' % extension, 'wb')
if tableclass is HTMLTable:
tableclass.castfunctions[Molecule] = image
else:
tableclass.castfunctions[Molecule] = blank
if tableclass is HTMLTable:
outfile.write(htmlheader)
outfile.write(tableclass('Species dictionary',
'species list from RMG-java generated mechanism for bio-oil gasification',
headers=invoicerow).render(lines))
if tableclass is HTMLTable:
outfile.write(htmlfooter)
def example():
"""Create a set of sample tables"""
# In practice, you'd most likely be embedding your HTML tables in
# a web page template. For demonstration purposes, we'll create a
# simple page with a few default styles.
htmlheader = """\
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01//EN">
<html>
<head>
<title>Sample table</title>
<style type="text/css">
body { font-family: Helvetica,Arial,FreeSans; }
table.reporttable { border-style: solid; border-width: 1px; }
table.reporttable tr.tr_odd { background-color: #eee; }
table.reporttable tr.tr_even { background-color: #bbb; }
table.reporttable th { background-color: blue; color: white; }
table.reporttable td.cell_bold { font-weight: bold; }
table.reporttable td.cell_money { text-align: right; font-family: monospace; }
</style>
</head>
<body>
"""
htmlfooter = """\
</body>
</html>"""
exampletypes = ((PDFTable, 'pdf'), (HTMLTable, 'html'), (SpreadsheetTable,
'xls'))
#### Example with several row types
# mainrs = RowSpec(
# ColumnSpec('foo', 'Column 1', width=1),
# ColumnSpec('bar', 'Column 2', width=1),
# ColumnSpec('baz', 'Column 3', width=1),
# ColumnSpec('qux', 'Column 4', width=4))
#
# subrow1 = RowSpec(
# ColumnSpec('subfoo1', 'First wide column', bold=True, span=2, width=2),
# ColumnSpec('subbar1', 'Second wide column', span=2))
#
# subrow2 = RowSpec(
# ColumnSpec('subfoo2', 'A table-wide column', span=4))
#
# summaryrow = RowSpec(
# ColumnSpec('junk1', span=2, width=2),
# ColumnSpec('baz', bold=True, width=1),
# ColumnSpec('junk2'))
#
# lines = []
# lines.append([mainrs({'foo': 1, 'bar': 2, 'baz': 3, 'qux': 'Bar. ' * 30}),
# subrow1({'subfoo1': 'And', 'subbar1': 'another'}),
# subrow2({'subfoo2': 'This is a test. ' * 15}),
# subrow2({'subfoo2': 'And another test'})])
# for i in range(5):
# lines.append(mainrs({'foo': i, 'bar': 14, 'baz': 15, 'qux': 'extra'}))
# lines.append(summaryrow({'junk1': None, 'baz': 'Summary!', 'junk2': None}))
#
# for tableclass, extension in exampletypes:
# outfile = open('showcase.%s' % extension, 'wb')
# if tableclass is HTMLTable:
# outfile.write(htmlheader)
# outfile.write(tableclass('Sample Table',
# '%s test' % extension.upper(),
# headers=[mainrs, subrow1, subrow2]).render(lines))
# if tableclass is HTMLTable:
# outfile.write(htmlfooter)
#### Converting species dictionary from RMG-Java in bond connectivity
# format into the smile and
import decimal
import random
import numpy as np
import csv
import itertools
from rmgpy.molecule import Molecule
#reading text file of species
groups = []
uniquekeys = []
def isa_group_separator(line):
return line == '\n'
with open('Species_Dictionary.txt') as f:
for key, group in itertools.groupby(f, isa_group_separator):
groups.append(list(group))
uniquekeys.append(key)
#print groups , len(groups)
# Since empty lines are appered as seperate lists in the groups lis,
# this section is removing them from the final list
groupsb = list()
for sublist in groups:
if not any(map(str.strip, sublist)): # this detects blanks
continue # it was blank, so skip it
if sublist not in groupsb: # this detects duplicates
groupsb.append(sublist)
#print groupsb , len (groupsb)
# remove '\n' from each item in list
def stripp(x):
return x.strip('\n')
groupsb = [list(map(stripp, x)) for x in groupsb]
#print groupsb
rows = []
for index, adjacency_list in enumerate(groupsb, start=1):
species_name = adjacency_list[0]
mol = Molecule().fromAdjacencyList('\n'.join(adjacency_list))
smiles = mol.toSMILES()
rows.append({
'Index': index,
'Species': species_name,
'SMILES': smiles,
'Molecule': mol,
})
print "Made {num} rows".format(num=len(rows))
invoicerow = RowSpec(
ColumnSpec('Index', 'Index #'),
ColumnSpec('Species', 'Species Name'),
ColumnSpec('SMILES', 'SMILES'),
ColumnSpec('Molecule', 'Molecule'),
)
lines = invoicerow.makeall(rows)
def image(mol):
from base64 import b64encode
src = mol._repr_png_()
encoded = b64encode(src)
return '<img alt="{name}" src="data:image/png;base64,{data}" />'.format(
name=mol.toSMILES(), data=encoded)
image.htmlsafe = True
def blank(mol):
return ''
for tableclass, extension in exampletypes:
outfile = open('Species.%s' % extension, 'wb')
if tableclass is HTMLTable:
tableclass.castfunctions[Molecule] = image
else:
tableclass.castfunctions[Molecule] = blank
if tableclass is HTMLTable:
outfile.write(htmlheader)
outfile.write(
tableclass(
'Species dictionary',
'species list from RMG-java generated mechanism for bio-oil gasification',
headers=invoicerow).render(lines))
if tableclass is HTMLTable:
outfile.write(htmlfooter)
with open(f) as thermofile:
line = thermofile.readline()
match = re.match('InChI = "(.*?)(\/mult\d)*"',line)
if not match: continue
inchi = match.group(1)
mult = match.group(2)
if mult: continue
mol = Molecule()
mol.fromInChI(inchi)
mmol = rmgpy.qm.mopac.MopacMolPM3(mol, settings)
print mmol.uniqueID, f
thermo = mmol.loadThermoData()
if not thermo: continue
assert inchi.startswith('InChI=1S/')
inchimain = inchi[9:]
keystart = keydict[inchimain]
jthermo = thermodict[keystart]
print mol.toSMILES()
print inchi
print keystart
print thermo
print jthermo
print 'H', thermo.H298.value/jthermo.H298.value, thermo.H298.value-jthermo.H298.value
print 'S', thermo.S298.value/jthermo.S298.value, thermo.S298.value-jthermo.S298.value
print 'Cp', thermo.Cpdata.values/jthermo.Cpdata.values
print
MaxCarbonNumberPerSpecies: 20
MaxOxygenNumberPerSpecies: 20
MaxRadicalNumberPerSpecies: 20
MaxSulfurNumberPerSpecies: 20
MaxSiliconNumberPerSpecies: 20
MaxHeavyAtomNumberPerSpecies: 100
MaxCycleNumberPerSpecies: 20
END
PrimaryThermoLibrary:
Name: RMG-minimal
Location: primaryThermoLibrary
END
""")
for f in os.listdir(folder):
f = os.path.join(folder, f)
stem, ext = os.path.splitext(f)
if ext != '.thermo':
continue
data = rmgpy.qm.molecule.loadThermoDataFile(f)
mol = Molecule().fromAdjacencyList(data['adjacencyList'])
output.write('// {0!s}\n'.format(data['InChI']))
output.write('// {0!r}\n'.format(data['thermoData']).replace(
'),', '),\n// '))
output.write(mol.toSMILES())
output.write(data['adjacencyList'] + '\n')
MaxCarbonNumberPerSpecies: 20
MaxOxygenNumberPerSpecies: 20
MaxRadicalNumberPerSpecies: 20
MaxSulfurNumberPerSpecies: 20
MaxSiliconNumberPerSpecies: 20
MaxHeavyAtomNumberPerSpecies: 100
MaxCycleNumberPerSpecies: 20
END
PrimaryThermoLibrary:
Name: RMG-minimal
Location: primaryThermoLibrary
END
""")
for f in os.listdir(folder):
f = os.path.join(folder,f)
stem, ext = os.path.splitext(f)
if ext != '.thermo':
continue
data = rmgpy.qm.molecule.loadThermoDataFile(f)
mol = Molecule().fromAdjacencyList(data['adjacencyList'])
output.write('// {0!s}\n'.format(data['InChI']))
output.write('// {0!r}\n'.format(data['thermoData']).replace('),','),\n// '))
output.write(mol.toSMILES())
output.write(data['adjacencyList']+'\n')
