def __init__(self, sparse, arrow='<=>', rid=None):
for cid, coeff in sparse.iteritems():
if not (isinstance(coeff, float) or isinstance(coeff, int)):
raise ValueError(
'All values in KeggReaction must be integers or floats')
self.sparse = dict(filter(lambda (k, v): v, sparse.items()))
self.arrow = arrow
self.rid = rid
self.ccache = CompoundCacher()
def main(fname, pH, I, T):
ccache = CompoundCacher()
for row in csv.reader(open(fname, 'r'), delimiter='\t'):
compound_id = re.findall('(C[0-9]+)_10', row[0])[0]
dG0 = float(row[1])
comp = ccache.get_compound(compound_id)
dG0_prime = dG0 + comp.transform_neutral(pH, I, T)
print '%s\t%f\t%f' % (compound_id, dG0, dG0_prime)
ccache.dump()
def get_ddG0(rxn_dict, pH, I, novel_mets):
ccache = CompoundCacher()
# ddG0 = get_transform_ddG0(rxn_dict, ccache, pH, I, T)
T = 298.15
ddG0_forward = 0
for compound_id, coeff in rxn_dict.items():
if novel_mets != None and compound_id in novel_mets:
comp = novel_mets[compound_id]
else:
comp = ccache.get_compound(compound_id)
ddG0_forward += coeff * comp.transform_pH7(pH, I, T)
return ddG0_forward
def __init__(self, S, cids, rids=None):
self.S = S
self.cids = cids
self.rids = rids
assert len(self.cids) == self.S.shape[0]
if self.rids is not None:
assert len(self.rids) == self.S.shape[1]
self.ccache = CompoundCacher()
# remove H+ from the stoichiometric matrix if it exists
if 'C00080' in self.cids:
i = self.cids.index('C00080')
self.S = np.vstack((self.S[:i, :], self.S[i + 1:, :]))
self.cids.pop(i)
# -*- coding: utf-8 -*-
"""
Created on Thu Aug 7 21:00:31 2014
@author: eladn
"""
import sys
from compound_cacher import CompoundCacher
compound_id = sys.argv[1]
CompoundCacher.RebuildCompoundJSON()
ccache = CompoundCacher()
sys.stderr.write('removing %s from cache ...\n' % compound_id)
ccache.remove(compound_id)
sys.stderr.write('recalculating SMILES and pKa values ...\n')
comp = ccache.get_compound(compound_id)
sys.stderr.write('writing new data to cache ...\n')
ccache.dump()
d = comp.to_json_dict()
sys.stderr.write(''.join(['%20s : %s\n' % (k, v) for (k, v) in d.iteritems()]))
import sys
sys.path.append('../python')
import inchi2gv
from compound_cacher import CompoundCacher
from molecule import Molecule
#logger = logging.getLogger('')
#logger.setLevel(logging.DEBUG)
ccache = CompoundCacher('../cache/compounds.json')
groups_data = inchi2gv.init_groups_data()
group_list = groups_data.GetGroupNames()
group_names = groups_data.GetGroupNames()
decomposer = inchi2gv.InChIDecomposer(groups_data)
# test the decomposition of ATP into groups
ATP_inchi = ccache.get_compound('C00002').inchi
group_def = decomposer.inchi_to_groupvec(ATP_inchi)
for j, group_name in enumerate(group_names):
if group_def[j] != 0:
print group_name, ' x %d' % group_def[j]
patterns = ['c~[O;+0]', 'c~[O;+1]', 'c~[n;+1]~c', 'c~[n;+0]~c', 'c~[n;-1]~c']
for cid in ['C00255', 'C01007']:
comp = ccache.get_compound(cid)
print "-" * 50, '\n%s' % cid
inchi = comp.inchi
mol = Molecule.FromInChI(inchi)
print mol.ToSmiles()
'phase': 'aqueous',
'dG0_f': np.round(dG0_f, 2),
'nH': nH,
'z': z,
'nMg': 0
}
yield d
if __name__ == '__main__':
import sys, json
logger = logging.getLogger('')
logger.setLevel(logging.DEBUG)
from compound_cacher import CompoundCacher, CompoundEncoder
from molecule import Molecule, OpenBabelError
ccache = CompoundCacher(cache_fname=None)
for compound_id in ['C00087', 'C00282', 'C00237']:
comp = Compound.from_kegg(compound_id)
try:
mol = Molecule.FromInChI(str(comp.inchi))
sys.stderr.write(
'%s : formula = %s, nE = %s' %
(str(comp.inchi), mol.GetFormula(), mol.GetNumElectrons()))
except OpenBabelError:
pass
ccache.add(comp)
sys.stderr.write(
'\ncompound id = %s, nH = %s, z = %s, pKa = %s, bag = %s\n\n\n' %
(compound_id, str(comp.nHs), str(comp.zs), str(
comp.pKas), str(comp.atom_bag)))
def load_compound_cache():
ccache = CompoundCacher()
return ccache
