def ExportJSONFiles():
options, _ = MakeOpts().parse_args(sys.argv)
print "Using the database file: " + options.public_db
print "Using the NIST table: " + options.nist_table
print "Saving the data to the CSV file: " + options.output_csv
db = SqliteDatabase(options.public_db)
csv_writer = csv.writer(open(options.output_csv, 'w'))
csv_writer.writerow([
'url', 'reference_id', 'method', 'evaluation', 'ec', 'enzyme',
'kegg_reaction', 'reaction', 'K', 'K_tag', 'T (K)', 'I (M)', 'pH',
'pMg'
])
for row in db.DictReader(options.nist_table):
csvrow = [
row[t] for t in [
'url', 'reference_id', 'method', 'evaluation', 'ec', 'enzyme',
'kegg_reaction', 'reaction'
]
]
csvrow += [
reformat_number_string(row['K'], '%.3e'),
reformat_number_string(row['K_tag'], '%.3e'),
reformat_number_string(row['T'], '%.2f'),
reformat_number_string(row['I'], '%.2f'),
reformat_number_string(row['pH'], '%.2f'),
reformat_number_string(row['pMg'], '%.2f')
]
csv_writer.writerow(csvrow)
def setUp(self):
fake_csv_file = StringIO(CSV_DATA)
csv_reader = csv.DictReader(fake_csv_file)
self.fake_thermo_csv = PsuedoisomerTableThermodynamics()
self.fake_thermo_csv = PsuedoisomerTableThermodynamics._FromDictReader(
csv_reader, self.fake_thermo_csv, warn_for_conflicting_refs=False)
db = SqliteDatabase(PUBLIC_DB_FNAME)
db_reader = db.DictReader('fake_pseudoisomers')
self.fake_thermo_db = PsuedoisomerTableThermodynamics()
self.fake_thermo_db = PsuedoisomerTableThermodynamics._FromDictReader(
db_reader, self.fake_thermo_db, warn_for_conflicting_refs=False)
def compare_charges():
#db_public = SqliteDatabase('../data/public_data.sqlite')
db_gibbs = SqliteDatabase('../res/gibbs.sqlite')
print "Writing Compare Charges report to ../res/groups_report.html"
html_writer = HtmlWriter("../res/groups_report.html")
kegg = Kegg.getInstance()
#pH, I, pMg, T = default_pH, default_I, default_pMg, default_T
pH, I, pMg, T = default_pH, 0, 14, default_T
cid2error = {}
for row_dict in db_gibbs.DictReader("gc_errors"):
cid = int(row_dict['cid'])
cid2error[cid] = row_dict['error']
estimators = {}
estimators['hatzi'] = Hatzi(use_pKa=False)
estimators['milo'] = PsuedoisomerTableThermodynamics.FromDatabase(
db_gibbs, 'gc_pseudoisomers', name='Milo Group Contribution')
all_cids = set(lsum([e.get_all_cids() for e in estimators.values()]))
dict_list = []
for cid in all_cids:
try:
name = kegg.cid2name(cid)
link = kegg.cid2compound(cid).get_link()
except KeyError:
name = "unknown"
link = ""
row_dict = {
'cid': '<a href="%s">C%05d</a>' % (link, cid),
'name': name,
'error': cid2error.get(cid, None)
}
for key, est in estimators.iteritems():
try:
pmap = est.cid2PseudoisomerMap(cid)
dG0, dG0_tag, nH, z, nMg = pmap.GetMostAbundantPseudoisomer(
pH, I, pMg, T)
except MissingCompoundFormationEnergy:
dG0, dG0_tag, nH, z, nMg = "", "", "", "", ""
row_dict['nH_' + key] = nH
row_dict['charge_' + key] = z
row_dict['nMg_' + key] = nMg
row_dict['dG0_' + key] = dG0
row_dict['dG0_tag_' + key] = dG0_tag
dict_list.append(row_dict)
html_writer.write_table(
dict_list,
headers=['cid', 'name', 'charge_hatzi', 'charge_milo', 'error'])
html_writer.close()
def ExportJSONFiles():
estimators = LoadAllEstimators()
options, _ = MakeOpts(estimators).parse_args(sys.argv)
thermo_list = []
thermo_list.append(estimators[options.thermodynamics_source])
thermo_list.append(
PsuedoisomerTableThermodynamics.FromCsvFile(
options.thermodynamics_csv))
# Make sure we have all the data.
kegg = Kegg.getInstance()
for i, thermo in enumerate(thermo_list):
print "Priority %d - formation energies of: %s" % (i + 1, thermo.name)
kegg.AddThermodynamicData(thermo, priority=(i + 1))
db = SqliteDatabase('../res/gibbs.sqlite')
print 'Exporting Group Contribution Nullspace matrix as JSON.'
nullspace_vectors = []
for row in db.DictReader('ugc_conservations'):
d = {'msg': row['msg']}
sparse = json.loads(row['json'])
d['reaction'] = []
for cid, coeff in sparse.iteritems():
d['reaction'].append([coeff, "C%05d" % int(cid)])
nullspace_vectors.append(d)
WriteJSONFile(nullspace_vectors, options.nullspace_out_filename)
print 'Exporting KEGG compounds as JSON.'
WriteJSONFile(kegg.AllCompounds(), options.compounds_out_filename)
print 'Exporting KEGG reactions as JSON.'
WriteJSONFile(kegg.AllReactions(), options.reactions_out_filename)
print 'Exporting KEGG enzymes as JSON.'
WriteJSONFile(kegg.AllEnzymes(), options.enzymes_out_filename)
class Nist(object):
def __init__(self, T_range=(298, 314)):
self.db = SqliteDatabase('../data/public_data.sqlite')
self.kegg = Kegg.getInstance()
self.T_range = T_range
self.pH_range = None
self.override_I = None
self.override_pMg = None
self.override_T = None
self.FromDatabase()
self.BalanceReactions()
def FromDatabase(self):
self.data = []
self.cid2count = {}
logging.info('Reading NIST reaction data from database ...')
for i, row_dict in enumerate(self.db.DictReader('nist_equilibrium')):
nist_row_data = NistRowData()
try:
nist_row_data.ReadFromDatabase('nist%05d' % i, row_dict)
self.data.append(nist_row_data)
for cid in nist_row_data.GetAllCids():
self.cid2count[cid] = self.cid2count.setdefault(cid, 0) + 1
except NistMissingCrucialDataException as e:
logging.debug(str(e))
logging.info('Total of %d rows read from the NIST database' %
len(self.data))
def BalanceReactions(self, balance_water=True):
for row in self.data:
try:
row.reaction.Balance(balance_water)
except KeggReactionNotBalancedException as e:
raise Exception(
str(e) + '\n' + str(row.reaction) + '\n' + row.url)
def GetAllCids(self):
return sorted(self.cid2count.keys())
def AnalyzeStats(self, html_writer):
"""
Produces a set of plots that show some statistics about the NIST database
"""
logging.info('Calculating statistics for NIST database (%d rows)' %
len(self.data))
if not self.data:
raise Exception("The database has no rows in it")
T_list = []
I_list = []
pH_list = []
pMg_list = []
year_list = []
for nist_row_data in self.data:
pH_list.append(nist_row_data.pH)
T_list.append(nist_row_data.T - 273.15)
if nist_row_data.I:
I_list.append(nist_row_data.I)
if nist_row_data.pMg:
pMg_list.append(nist_row_data.pMg)
year = nist_row_data.GetYear()
if year:
year_list.append(year)
html_writer.write("<p><h2>NIST database statistics</h2>\n")
fig = plt.figure()
plt.title("Temperature histogram")
plt.hist(T_list, np.arange(int(min(T_list)), int(max(T_list) + 1),
2.5))
plt.xlabel("Temperature (C)")
plt.ylabel("No. of measurements")
html_writer.embed_matplotlib_figure(fig,
width=320,
height=240,
name='hist_T')
fig = plt.figure()
plt.hist(pMg_list, np.arange(0, 10.1, 0.1))
plt.title("pMg histogram")
plt.xlabel("pMg")
plt.ylabel("No. of measurements")
html_writer.embed_matplotlib_figure(fig,
width=320,
height=240,
name='hist_pMg')
fig = plt.figure()
plt.hist(pH_list, np.arange(4, 11, 0.1))
plt.title("pH histogram")
plt.xlabel("pH")
plt.ylabel("No. of measurements")
html_writer.embed_matplotlib_figure(fig,
width=320,
height=240,
name='hist_pH')
fig = plt.figure()
plt.hist(I_list, np.arange(0, 1, 0.025))
plt.title("Ionic Strength histogram")
plt.xlabel("Ionic Strength [M]")
plt.ylabel("No. of measurements")
html_writer.embed_matplotlib_figure(fig,
width=320,
height=240,
name='hist_I')
# histogram of publication years
fig = plt.figure()
plt.hist(year_list, np.arange(1930, 2010, 5))
plt.title("Year of publication histogram")
plt.xlabel("Year of publication")
plt.ylabel("No. of measurements")
html_writer.embed_matplotlib_figure(fig,
width=320,
height=240,
name='hist_year')
db_public = SqliteDatabase('../data/public_data.sqlite')
alberty = PsuedoisomerTableThermodynamics.FromDatabase(
db_public, 'alberty_pseudoisomers')
alberty_cids = set(alberty.get_all_cids())
nist_cids = set(self.GetAllCids())
count_list = [
"Alberty #compounds = %d" % len(alberty_cids),
"NIST #compounds = %d" % len(nist_cids),
"intersection #compounds = %d" %
len(alberty_cids.intersection(nist_cids))
]
html_writer.write_ul(count_list)
N = 60 # cutoff for the number of counts in the histogram
hist_a = np.zeros(N)
hist_b = np.zeros(N)
for cid, cnt in self.cid2count.iteritems():
if cnt >= N:
cnt = N - 1
if cid in alberty_cids:
hist_a[cnt] += 1
else:
hist_b[cnt] += 1
hist_a[0] = len(alberty_cids.difference(self.cid2count.keys()))
fig = plt.figure()
plt.rc('font', size=10)
plt.hold(True)
p1 = plt.bar(range(N), hist_a, color='b')
p2 = plt.bar(range(N), hist_b, color='r', bottom=hist_a[0:N])
plt.text(N - 1,
hist_a[N - 1] + hist_b[N - 1],
'> %d' % (N - 1),
fontsize=10,
horizontalalignment='right',
verticalalignment='baseline')
plt.title("Overlap with Alberty's database")
plt.xlabel("N reactions")
plt.ylabel("no. of compounds measured in N reactions")
plt.legend((p1[0], p2[0]),
("Exist in Alberty's database", "New compounds"))
html_writer.embed_matplotlib_figure(fig,
width=320,
height=240,
name='connectivity')
def AnalyzeConnectivity(self, html_writer):
def cid2name(cid, KEGG):
return "\"" + KEGG.cid2name(cid) + "\""
def load_cid_set(train_csv_fname):
"""
Read the training data from a CSV file
"""
cid_set = set()
for row in csv.DictReader(open(train_csv_fname)):
#(smiles, cid, compoud_name, dG0, dH0, z, nH, Mg, use_for, ref, remark) = row
if (row['use for'] in ['skip']):
continue
cid = int(row['cid'])
if cid > 0:
cid_set.add(cid)
return cid_set
known_cids = load_cid_set('../data/thermodynamics/dG0_seed.csv')
one_step_cids = set()
coupled_cids = set()
Gdot = pydot.Dot()
for nist_row_data in nist.data:
unknown_cids = list(
nist_row_data.GetAllCids().difference(known_cids))
if len(unknown_cids) == 1:
one_step_cids.add(unknown_cids[0])
elif len(unknown_cids) == 2:
coupled_cids.add((min(unknown_cids), max(unknown_cids)))
for cid in one_step_cids:
#Gdot.add_node(pydot.Node(cid2name(cid, KEGG), None))
Gdot.add_node(pydot.Node("C%05d" % cid, None))
for (cid1, cid2) in coupled_cids:
Gdot.add_edge(pydot.Edge("C%05d" % cid1, "C%05d" % cid2, None))
html_writer.write("<p><h2>Connectivity</h2>\n")
html_writer.embed_dot_inline(Gdot, width=640, height=480)
html_writer.write("</p>\n")
#win = xdot.DotWindow()
#win.connect('destroy', gtk.main_quit)
#win.set_filter('dot')
#util._mkdir('../res/nist')
#dot_fname = '../res/nist/connectivity.dot'
#Gdot.write(dot_fname, format='dot')
#win.open_file(dot_fname)
#gtk.main()
def verify_formation(self, html_writer, thermodynamics, name=None):
cid2errors = defaultdict(list)
cid2refs = defaultdict(set)
reaction2errors = defaultdict(list)
reaction2refs = defaultdict(set)
for row_data in self.SelectRowsFromNist():
dG0_est = row_data.PredictReactionEnergy(thermodynamics)
if np.isnan(dG0_est):
continue
err = row_data.dG0_r - dG0_est
for cid in row_data.GetAllCids():
cid2errors[cid].append(err)
cid2refs[cid].add((row_data.ref_id, row_data.url))
reaction2errors[row_data.reaction].append(err)
reaction2refs[row_data.reaction].add(
(row_data.ref_id, row_data.url))
rowdicts = []
for cid, err_list in cid2errors.iteritems():
refs = cid2refs[cid]
urls = ', '.join([
'<a href="%s">%s</a>' % (url, ref_id) for ref_id, url in refs
])
rowdict = {
'cid': 'C%05d' % cid,
'name': self.kegg.cid2name(cid),
'RMSE': rms_flat(err_list),
'E[err]': np.mean(err_list),
'#err': len(err_list),
'std[err]': np.std(err_list),
'URLs': urls
}
rowdicts.append(rowdict)
rowdicts.sort(key=lambda x: x['RMSE'], reverse=True)
html_writer.write_table(
rowdicts,
['#', 'cid', 'name', 'RMSE', '#err', 'E[err]', 'std[err]', 'URLs'],
decimal=1)
rowdicts = []
for reaction, err_list in reaction2errors.iteritems():
refs = reaction2refs[reaction]
urls = ', '.join([
'<a href="%s">%s</a>' % (url, ref_id) for ref_id, url in refs
])
rowdict = {
'reaction': reaction.to_hypertext(show_cids=False),
'RMSE': rms_flat(err_list),
'E[err]': np.mean(err_list),
'#err': len(err_list),
'std[err]': np.std(err_list),
'URLs': urls
}
rowdicts.append(rowdict)
rowdicts.sort(key=lambda x: x['RMSE'], reverse=True)
html_writer.write_table(
rowdicts,
['#', 'reaction', 'RMSE', '#err', 'E[err]', 'std[err]', 'URLs'],
decimal=1)
def verify_results(self, html_writer, thermodynamics, name=None):
"""Calculate all the dG0_r for the reaction from NIST and compare to
the measured data.
Write results to HTML.
Args:
thermodynamics: a Thermodynamics object that provides dG estimates.
ignore_I: whether or not to ignore the ionic strength in NIST.
"""
dG0_obs_vec = []
dG0_est_vec = []
# A mapping from each evaluation method (NIST calls separates them to
# A, B, C and D) to the results of the relevant measurements
evaluation_map = {}
rowdicts = []
finite_rowdicts = []
eval_to_label = {
'A': 'high quality',
'B': 'low quality',
'C': 'low quality',
'D': 'low quality',
'E': 'low quality'
}
for row_data in self.SelectRowsFromNist():
rowdict = {}
label = eval_to_label[row_data.evaluation]
if label not in evaluation_map:
evaluation_map[label] = ([], [])
rowdict[symbol_dr_G0_prime + ' (obs)'] = np.round(
row_data.dG0_r, 1)
rowdict['_reaction'] = row_data.reaction
rowdict['reaction'] = row_data.reaction.to_hypertext(
show_cids=False)
if row_data.reaction.rid is not None:
rowdict['rid'] = '<a href="%s">R%05d</a>' % (
row_data.reaction.get_link(), row_data.reaction.rid)
else:
rowdict['rid'] = ''
rowdict['pH'] = row_data.pH
rowdict['pMg'] = row_data.pMg
rowdict['I'] = row_data.I
rowdict['T'] = row_data.T
rowdict['eval.'] = row_data.evaluation
rowdict['url'] = '<a href="%s">%s</a>' % (row_data.url,
row_data.ref_id)
dG0_est = row_data.PredictReactionEnergy(thermodynamics)
if np.isfinite(dG0_est):
dG0_obs_vec.append(row_data.dG0_r)
dG0_est_vec.append(dG0_est)
evaluation_map[label][0].append(row_data.dG0_r)
evaluation_map[label][1].append(dG0_est)
rowdict[symbol_dr_G0_prime + ' (est)'] = np.round(dG0_est, 1)
rowdict['residual'] = np.round(row_data.dG0_r - dG0_est, 3)
rowdict['|error|'] = abs(rowdict['residual'])
rowdict['sort_key'] = -rowdict['|error|']
finite_rowdicts.append(rowdict)
else:
rowdict['sort_key'] = 1
rowdicts.append(rowdict)
rowdicts.sort(key=lambda x: x['sort_key'])
if not dG0_obs_vec:
return 0, 0
unique_reaction_dict = defaultdict(list)
for rowdict in finite_rowdicts:
unique_reaction_dict[rowdict['_reaction']].append(
rowdict['|error|'])
unique_rmse_list = [
rms_flat(error_list)
for error_list in unique_reaction_dict.values()
]
unique_rmse = rms_flat(unique_rmse_list)
resid = np.array(dG0_obs_vec) - np.array(dG0_est_vec)
rmse = rms_flat(resid.flat)
# plot the profile graph
plt.rcParams['text.usetex'] = False
plt.rcParams['legend.fontsize'] = 10
plt.rcParams['font.family'] = 'sans-serif'
plt.rcParams['font.size'] = 12
plt.rcParams['lines.linewidth'] = 1
plt.rcParams['lines.markersize'] = 3
fig1 = plt.figure(figsize=(6, 6), dpi=90)
plt.hold(True)
colors = ['purple', 'orange']
for i, label in enumerate(sorted(evaluation_map.keys())):
measured, predicted = evaluation_map[label]
plt.plot(measured,
predicted,
marker='.',
linestyle='None',
markerfacecolor=colors[i],
markeredgecolor=colors[i],
markersize=5,
label=label,
figure=fig1)
plt.legend(loc='lower right')
plt.text(-50,
40,
r'RMSE = %.1f [kJ/mol]' % (unique_rmse),
fontsize=14,
figure=fig1)
plt.xlabel(r'observed $\Delta_r G^{\'\circ}$ [kJ/mol]',
fontsize=14,
figure=fig1)
plt.ylabel(r'estimated $\Delta_r G^{\'\circ}$ [kJ/mol]',
fontsize=14,
figure=fig1)
#min_x = min(dG0_obs_vec)
#max_x = max(dG0_obs_vec)
plt.plot([-60, 60], [-60, 60], 'k--', figure=fig1)
plt.axis([-60, 60, -60, 60])
if name:
html_writer.embed_matplotlib_figure(fig1, name=name + "_eval")
else:
html_writer.embed_matplotlib_figure(fig1)
fig2 = plt.figure(figsize=(6, 6), dpi=90)
binned_plot(x=[rowdict['pH'] for rowdict in finite_rowdicts],
y=[rowdict['|error|'] for rowdict in finite_rowdicts],
bins=[5, 6, 7, 8, 9],
y_type='rmse',
figure=fig2)
plt.xlim((4, 11))
plt.ylim((0, 12))
plt.title(r'effect of pH', fontsize=14, figure=fig2)
plt.xlabel('pH', fontsize=14, figure=fig2)
plt.ylabel(r'RMSE ($\Delta_r G^{\'\circ}$) [kJ/mol]',
fontsize=14,
figure=fig2)
if name:
html_writer.embed_matplotlib_figure(fig2, name=name + "_pH")
else:
html_writer.embed_matplotlib_figure(fig2)
fig3 = plt.figure(figsize=(6, 6), dpi=90)
plt.hist([rowdict['residual'] for rowdict in finite_rowdicts],
bins=np.arange(-50, 50, 0.5))
plt.title(r'RMSE = %.1f [kJ/mol]' % rmse, fontsize=14, figure=fig3)
plt.xlabel(r'residual $\Delta_r G^{\'\circ}$ [kJ/mol]',
fontsize=14,
figure=fig3)
plt.ylabel(r'no. of measurements', fontsize=14, figure=fig3)
if name:
html_writer.embed_matplotlib_figure(fig3, name=name + "_hist")
else:
html_writer.embed_matplotlib_figure(fig3)
table_headers = [
"#", "|error|", symbol_dr_G0_prime + " (obs)",
symbol_dr_G0_prime + " (est)", "reaction", "rid", "pH", "pMg", "I",
"T", "eval.", "url"
]
html_writer.write_table(rowdicts, table_headers, decimal=1)
return len(dG0_obs_vec), unique_rmse
def two_way_comparison(self, html_writer, thermo1, thermo2, name=None):
"""
Compare the estimation errors of two different evaluation methods.
Write results to HTML.
Args:
thermo1: a Thermodynamics object that provides dG estimates.
thermo2: a Thermodynamics object that provides dG estimates.
"""
total_list = []
for row_data in self.SelectRowsFromNist():
try:
dG0_pred1 = row_data.PredictReactionEnergy(thermo1)
dG0_pred2 = row_data.PredictReactionEnergy(thermo2)
except MissingReactionEnergy as e:
logging.debug("the reaction in (%s) cannot be estimated: %s" %
(row_data.ref_id, str(e)))
continue
total_list.append([
row_data.dG0_r, dG0_pred1, dG0_pred2, row_data.reaction,
row_data.pH, row_data.pMg, row_data.I, row_data.T,
row_data.evaluation, row_data.url
])
if not total_list:
return 0, 0
# plot the profile graph
plt.rcParams['text.usetex'] = False
plt.rcParams['font.family'] = 'sans-serif'
plt.rcParams['font.size'] = 8
plt.rcParams['lines.linewidth'] = 2
plt.rcParams['lines.markersize'] = 2
plt.rcParams['figure.dpi'] = 100
data_mat = np.array(total_list)
fig1 = plt.figure(figsize=(4, 4))
plt.hold(True)
error1 = data_mat[:, 0] - data_mat[:, 1]
error2 = data_mat[:, 0] - data_mat[:, 2]
max_err = max(error1.max(), error2.max())
min_err = min(error1.min(), error2.min())
plt.plot([min_err, max_err], [min_err, max_err], 'k--', figure=fig1)
plt.plot(error1, error2, '.', figure=fig1)
plt.title("Error Comparison per Reaction (in kJ/mol)")
plt.xlabel(thermo1.name, figure=fig1)
plt.ylabel(thermo2.name, figure=fig1)
html_writer.embed_matplotlib_figure(fig1, name=name + "_corr")
fig2 = plt.figure(figsize=(7, 3))
for i, thermo in enumerate([thermo1, thermo2]):
fig2.add_subplot(1, 2, i + 1)
plt.plot(data_mat[:, 0], data_mat[:, i + 1], 'b.')
rmse = rms_flat((data_mat[:, 0] - data_mat[:, i + 1]).flat)
plt.text(-50, 40, r'RMSE = %.1f [kJ/mol]' % (rmse))
plt.xlabel(r'observed $\Delta G_r^\circ$ from NIST [kJ/mol]')
plt.ylabel(r'estimated $\Delta G_r^\circ$ using %s [kJ/mol]' %
thermo.name)
plt.plot([-60, 60], [-60, 60], 'k--')
plt.axis([-60, 60, -60, 60])
html_writer.embed_matplotlib_figure(fig2, name=name + "_eval")
table_headers = [
"dG'0 (obs)",
"dG'0 (%s)" % thermo1.name,
"dG'0 (%s)" % thermo2.name, "reaction", "rid", "pH", "pMg", "I",
"T", "eval.", "url"
]
dict_list = []
for row in sorted(total_list,
key=lambda (x): abs(x[1] - x[2]),
reverse=True):
d = {}
d["dG'0 (obs)"] = '%.1f' % row[0]
d["dG'0 (%s)" % thermo1.name] = '%.1f' % row[1]
d["dG'0 (%s)" % thermo2.name] = '%.1f' % row[2]
d['reaction'] = row[3].to_hypertext(show_cids=False)
if row[3].rid is not None:
d['rid'] = '<a href="%s">R%05d</a>' % (row[3].get_link(),
row[3].rid)
else:
d['rid'] = ''
d['pH'] = '%.1f' % row[4]
d['pMg'] = '%.1f' % row[5]
d['I'] = '%.2f' % row[6]
d['T'] = '%.1f' % row[7]
d['eval.'] = row[8]
if row[9]:
d['url'] = '<a href="%s">link</a>' % row[9]
else:
d['url'] = ''
dict_list.append(d)
html_writer.write_table(dict_list, table_headers)
def SelectRowsFromNist(self,
reaction=None,
check_reverse=True,
T_range=None,
pH_range=None):
T_range = T_range or self.T_range
pH_range = pH_range or self.pH_range
rows = []
checklist = []
if reaction:
checklist.append(reaction)
if check_reverse:
checklist.append(reaction.reverse())
for nist_row_data in self.data:
if T_range and not (T_range[0] < nist_row_data.T < T_range[1]):
continue
if pH_range and not (pH_range[0] < nist_row_data.pH < pH_range[1]):
continue
if checklist and nist_row_data.reaction not in checklist:
continue
if self.override_pMg or self.override_I or self.override_T:
nist_row_copy = nist_row_data.Clone()
if self.override_pMg:
nist_row_copy.pMg = self.override_pMg
if self.override_I:
nist_row_copy.I = self.override_I
if self.override_T:
nist_row_copy.T = self.override_T
rows.append(nist_row_copy)
else:
rows.append(nist_row_data)
return rows
def GetUniqueReactionSet(self):
return set([row.reaction for row in self.data])