def loadSBML( self, aSBMLDocument ):
if type( aSBMLDocument ) == str:
self.theSBMLDocument = libsbml.readSBML( aSBMLDocument )
elif type( self.theSBMLDocument ) == file:
self.theSBMLDocument = libsbml.readSBMLFromString( aSBMLDocument.read() )
else:
self.theSBMLDocument = aSBMLDocument
if self.theSBMLDocument.getLevel() != 2:
self.theSBMLDocument.setLevel( 2 )
aXMLNamespaceList = self.theSBMLDocument.getNamespaces()
anURI = aXMLNamespaceList.getURI( ECELL_XML_NAMESPACE_PREFIX )
if anURI != ECELL_XML_NAMESPACE_URI:
if anURI == '':
aXMLNamespaceList.add( ECELL_XML_NAMESPACE_PREFIX, \
ECELL_XML_NAMESPACE_URI )
else:
raise SBMLConvertError, 'Wrong URI [%s] is already assinged to xmlns:%s. Remove or correct it by yourself' % ( anURI, ECELL_XML_NAMESPACE_PREFIX )
if self.theSBMLDocument.getNumFatals() > 0:
fatalerrorList = []
for i in range( self.theSBMLDocument.getNumFatals() ):
fatalerrorList.append( self.theSBMLDocument.getFatal( i ).getMessage() )
self.theSBMLDocument = None
raise SBMLConvertError, \
'This SBML document is invalid:\n %s' \
% ( ', '.join( fatalerrorList ) )
if not self.theSBMLDocument.getModel():
self.theSBMLDocument.createModel()
self.__createIdDict()
def read_sbml(
source: Union[Path, str],
promote: bool = False,
validate: bool = False,
log_errors: bool = True,
units_consistency: bool = True,
modeling_practice: bool = True,
internal_consistency: bool = True,
) -> libsbml.SBMLDocument:
"""Read SBMLDocument from given source.
:param source: SBML path or string
:param promote: promote local parameters to global parameters
:param validate: validate file
:param log_errors: validation flag
:param units_consistency: validation flag
:param modeling_practice: validation flag
:param internal_consistency: validation flag
:return: SBMLDocument
"""
if isinstance(source, str) and "<sbml" in source:
doc = libsbml.readSBMLFromString(source)
else:
if not isinstance(source, Path):
logger.error(f"All SBML paths should be of type 'Path', but "
f"'{type(source)}' found for: {source}")
source = Path(source)
doc = libsbml.readSBMLFromFile(
str(source)) # type: libsbml.SBMLDocument
# promote local parameters
if promote:
doc = promote_local_variables(doc) # type: libsbml.SBMLDocument
# check for errors
if doc.getNumErrors() > 0:
if doc.getError(0).getErrorId() == libsbml.XMLFileUnreadable:
err_message = f"Unreadable SBML file"
elif doc.getError(0).getErrorId() == libsbml.XMLFileOperationError:
err_message = "Problems reading SBML file: XMLFileOperationError"
else:
err_message = "SBMLDocumentErrors encountered while reading the SBML file."
validation.log_sbml_errors_for_doc(doc)
err_message = f"read_sbml error '{source}': {err_message}"
logger.error(err_message)
if validate:
validation.validate_doc(
doc=doc,
name=source,
log_errors=log_errors,
units_consistency=units_consistency,
modeling_practice=modeling_practice,
internal_consistency=internal_consistency,
)
return doc
def create_parts(self):
import libsbml
from tellurium.analysis import _annotations
self.set_visible(3)
uri_id = self.widgets['ontologyResults'].value
if self.widgets['ontologySelect'].value == 'ChEBI':
matched_ids = self.bm.getModelsIdByChEBIId(uri_id)
elif self.widgets['ontologySelect'].value == 'GO':
matched_ids = self.bm.getModelsIdByGO(uri_id)
else:
raise Exception('No ontology selected')
if not matched_ids:
print 'No biomodels containing %s' % uri_id
return
self.matched_sbml = [libsbml.readSBMLFromString(
self.bm.getModelSBMLById(id).encode('utf-8'))
for id in matched_ids]
self.matched_sbml_lookup = dict(zip(matched_ids, self.matched_sbml))
self.matched_reactions = [_annotations.matching_reactions(sbml, uri_id)
for sbml in self.matched_sbml]
values = {}
for r in sum(self.matched_reactions, []):
msg = '%s: %s' % (
_annotations.get_biomodel_id(r.model.getSBMLDocument()),
r.__str__())
values[msg] = r
self.widgets['reactionResults'].values = values
def update_node_dimensions(sbml_layout,
fig_dpi,
fig_width_pixels,
fig_height_pixels,
node_multiplier=1.0):
"""Increase the size of the node boxes, if necessary, to fit the text.
Args:
sbml_layout (libsbml_draw.model.SBMLlayout): current SBML model
fig_dpi (int): dots-per-inch setting for the figure
fig_width_pixels (int): width of the figure in pixels
fig_height_pixels (int): height of the figure in pixels
node_multiplier (optional, float): multiplier to achieve a width of
the node box beyond what's needed for the text itself, eg. 1.1
represents an extra 10%
Returns: None
"""
nodes = sbml_layout._SBMLlayout__network.nodes.values()
nw_width_data_coords = (max([node.center.x for node in nodes]) -
min([node.center.x
for node in nodes])) + SBNW_NODE_WIDTH
nw_height_data_coords = (max([node.center.y for node in nodes]) -
min([node.center.y
for node in nodes])) + SBNW_NODE_HEIGHT
for node in nodes:
width, height = compute_node_dimensions(
node_multiplier * (len(node.name) + 0) * node.font_size,
node_multiplier * (node.font_size + 0), fig_dpi, fig_width_pixels,
fig_height_pixels, nw_width_data_coords, nw_height_data_coords)
h_node_id = node.id.encode('utf-8')
h_node = sbnw.nw_getNodepFromId(sbml_layout._SBMLlayout__h_network,
h_node_id)
sbnw.node_setWidth(h_node, width)
node.width = width
sbnw.node_setHeight(h_node, height)
node.height = height
node.lower_left_point = [
node.center.x - node.width / 2, node.center.y - node.height / 2
]
# h_reaction = sbnw.nw_getReactionp(self.__h_network, nr)
# sbnw.reaction_recenter(h_reaction)
# sbnw.nw_recenterJunctions(sbml_layout._SBMLlayout__h_network)
# sbnw.nw_rebuildCurves(sbml_layout._SBMLlayout__h_network)
# sbml_layout._SBMLlayout__updateNetworkLayout()
sbml_layout._SBMLlayout__doc = libsbml.readSBMLFromString(
sbml_layout._SBMLlayout__getSBMLWithLayoutString())
def get_initial_assignments_dict(model):
sbml = model.getSBML()
sbml_document = libsbml.readSBMLFromString(sbml)
sbml_model = sbml_document.getModel()
assignments = {}
for ia in sbml_model.getListOfInitialAssignments():
assignments[ia.getId()] = libsbml.formulaToString(ia.getMath())
return assignments
def readrpSBMLtar(inputTar):
rpsbml_paths = {}
with tarfile.open(inputTar) as tar:
for member in tar.getmembers():
rpsbml_paths[member.name] = rpRanker.rpSBML(
member.name,
libsbml.readSBMLFromString(
tar.extractfile(member).read().decode("utf-8")))
return rpsbml_paths
def parseSBML(self):
if not hasattr(self, '_sbml_document'):
# self.sbml_file = ForeignKey
# self.sbml_file.file = FileField on Attachment
# self.sbml_file.file.file = File object on FileField
contents = self.sbml_file.file.file.read()
import libsbml
self._sbml_document = libsbml.readSBMLFromString(contents)
return self._sbml_document
def runSingleSBML(rpcofactors, member_name, rpsbml_string, path_id,
compartment_id):
#open one of the rp SBML files
rpsbml = rpSBML.rpSBML(member_name,
libsbml.readSBMLFromString(rpsbml_string))
#rpcofactors = rpRanker.rpCofactors()
if rpcofactors.addCofactors(rpsbml, compartment_id, path_id):
return libsbml.writeSBMLToString(rpsbml.document).encode('utf-8')
else:
return ''
def biomodels_info():
'''
fetch latest biomodels release from ftp
extract
parse all curated models
'''
import ftplib
import tarfile
import libsbml
import re
import os
if not os.path.exists('release.tar.bz2'):
ftp = ftplib.FTP("ftp.ebi.ac.uk")
ftp.login()
ftp.cwd("/pub/databases/biomodels/releases/latest/")
file_list = []
ftp.dir(file_list.append)
ftp_file = [x for x in file_list if x.endswith('pub-sbml_files.tar.bz2')][0].split()[-1]
try:
ftp.retrbinary('RETR %s' % ftp_file, open('release.tar.bz2', 'wb').write)
except ftplib.error_perm:
print 'ERROR: cannot read file "%s"' % ftp_file
import os
os.unlink(ftp_file)
return
#print '*** Downloaded "%s" to CWD' % ftp_file
else:
print 'used release.tar.bz2 in current folder! remove to redownload'
#Unpack and read info
tar = tarfile.open('release.tar.bz2', 'r:bz2')
curated_files = [x for x in tar.getnames() if '/curated/' in x]
items = []
notes_items = []
for fn in curated_files:
#print fn[-19:-4]
try:
cur_file = tar.extractfile(fn).read()
doc = libsbml.readSBMLFromString(cur_file)
model = doc.getModel()
notes = re.sub('body', 'div', model.getNotes().getChild(0).toXMLString())
model_id = fn[-19:-4]
name = model.getName()
items.append([model_id, '<li><q><span bla="%s">%s: %s</span> <a href="{{=URL(r=request,f="biomodels_info_notes.html#%s")}}" target="_blank">notes</a></q></li>' % (model_id, model_id, name, model_id)])
notes_items.append('<div id="%s">%s</div>' % (model_id, notes))
except:
pass
#print model.getName(), model.getId(),
items.sort()
biomodels_list = "<ul class='biomodels_select'>%s\n</ul>" % "\n".join([x for y,x in items])
notes = "<div class='biomodels_notes'>%s</div><br/><br/><br/><br/><br/><br/><br/><br/>" % ''.join(notes_items)
open('biomodels_info_list.html', 'w').write(biomodels_list)
open('biomodels_info_notes.html', 'w').write(notes)
def libSBML_read():
with open(file_path, 'r') as file:
SBML = file.read()
SBML = libsbml.readSBMLFromString(SBML)
model = SBML.getModel()
species = model.getListOfSpecies()
print(species.get(1))
def translate():
data = request.get_json()
sbml = data.get('sbml')
doc = libsbml.readSBMLFromString(sbml.encode('utf-8'))
if doc.getNumErrors() > 0:
messages = ['Invalid SBML!\n']
for i in xrange(0, doc.getNumErrors()):
error = doc.getError(i)
messages.append(error.getMessage())
return ''.join(messages)
else:
return sbml
def parseSBML(self):
if not hasattr(self, "_sbml_document"):
# self.sbml_file = ForeignKey
# self.sbml_file.file = FileField on Attachment
# self.sbml_file.file.file = File object on FileField
# self.sbml_file.file.file.name = path to file
import libsbml
with self.sbml_file.file.open() as upload:
text = upload.read().decode("utf-8")
self._sbml_document = libsbml.readSBMLFromString(text)
return self._sbml_document
def __init__(self, sbml):
'''
sbml -- an SBML string, libsbml.SBMLDocument object, or libsbml.Model object
'''
if isinstance(sbml, basestring):
self.doc = libsbml.readSBMLFromString(sbml)
self.model = self.doc.getModel()
elif isinstance(sbml, libsbml.SBMLDocument):
self.doc = sbml
self.model = self.doc.getModel()
elif isinstance(sbml, libsbml.Model):
self.model = sbml
else:
raise Exception('SBML Input is not valid')
self.G = nx.DiGraph()
self.labels = {}
self.species = []
self.reactions = []
for i, s in enumerate(self.model.species):
self.G.add_node(s.getId())
self.species.append(s.getId())
for i, r in enumerate(self.model.reactions):
self.G.add_node(r.getId())
self.reactions.append(r.getId())
for s in r.reactants:
self.G.add_edge(s.getSpecies(), r.getId(), kind='reactant')
for s in r.products:
self.G.add_edge(r.getId(), s.getSpecies(), kind='product')
for s in r.modifiers:
self.G.add_edge(s.getSpecies(), r.getId(), kind='modifier')
self.modifier_edges = [key for key, val in nx.get_edge_attributes(self.G, 'kind').items() if val == 'modifier']
self.product_edges = [key for key, val in nx.get_edge_attributes(self.G, 'kind').items() if val == 'product']
self.reactant_edges = [key for key, val in nx.get_edge_attributes(self.G, 'kind').items() if val == 'reactant']
#mass_transfer_edges = [key for key, val in nx.get_edge_attributes(G, 'kind').items() if val != 'modifier']
# Default drawing options
self.options = {}
self.options['species'] = {
'size': 500,
'color': 'r',
'alpha': 0.8,
'label_size': 16
}
self.options
def __init__(self, sbml):
'''
Initialize with from either SBML string or SBML Document object
'''
import libsbml
if isinstance(sbml, libsbml.SBMLDocument):
self.document = sbml
elif isinstance(sbml, basestring):
self.document = libsbml.readSBMLFromString(sbml)
else:
raise Exception("Model is not a string or SBML document object")
if self.document.getNumErrors() > 0:
raise Exception('SBML document contains erros')
self.model = self.document.getModel()
def get_model_from_gzip_sbml(stream: bytes) -> "Model":
"""
Generate a model instance from a gzip-compressed, UTF-8 encoded SBML document.
Parameters
----------
stream : bytes
A gzip-compressed, UTF-8 encoded SBML document.
Returns
-------
Model
A model instance generated from the SBML document.
"""
return _sbml_to_model(
libsbml.readSBMLFromString(gzip.decompress(stream).decode("utf-8")))
def __init__(self, sbml,
species={},
reactions={},
reactants={},
products={},
modifiers={}):
'''
sbml -- an SBML string, libsbml.SBMLDocument object, or
libsbml.Model object
'''
import pygraphviz as pgv
import libsbml
if isinstance(sbml, basestring):
self.doc = libsbml.readSBMLFromString(sbml)
self.model = self.doc.getModel()
elif isinstance(sbml, libsbml.SBMLDocument):
self.doc = sbml
self.model = self.doc.getModel()
elif isinstance(sbml, libsbml.Model):
self.model = sbml
else:
raise Exception('SBML Input is not valid')
self.G = pgv.AGraph(strict=False, directed=True)
for i, s in enumerate(self.model.species):
if s.getName():
label = s.getName() + ' ({})'.format(s.getId())
else:
label = s.getId()
self.G.add_node(s.getId(), label=label, **species)
for i, r in enumerate(self.model.reactions):
if r.getName():
label = r.getName() + ' ({})'.format(r.getId())
else:
label = r.getId()
self.G.add_node(r.getId(), label=label, **reactions)
for s in r.reactants:
self.G.add_edge(s.getSpecies(), r.getId(), **reactants)
for s in r.products:
self.G.add_edge(r.getId(), s.getSpecies(), **products)
for s in r.modifiers:
self.G.add_edge(s.getSpecies(), r.getId(), **modifiers)
def loadSBML(self, aSBMLDocument):
if type(aSBMLDocument) == str:
self.theSBMLDocument = libsbml.readSBML(aSBMLDocument)
elif type(aSBMLDocument) == file:
self.theSBMLDocument = libsbml.readSBMLFromString(aSBMLDocument.read())
else:
self.theSBMLDocument = aSBMLDocument
if self.theSBMLDocument.getLevel() != 2:
self.theSBMLDocument.setLevel(2)
if self.theSBMLDocument.getNumFatals() > 0:
fatalerrorList = []
for i in range(self.theSBMLDocument.getNumFatals()):
fatalerrorList.append(self.theSBMLDocument.getFatal(i))
self.theSBMLDocument = None
raise SBMLConvertError, "This SBML document is invalid: %s" % (", ".join(fatalerrorList))
def species_df(r: roadrunner.RoadRunner) -> pd.DataFrame:
"""
Create FloatingSpecies DataFrame.
:return: pandas DataFrame
"""
r_model = r.model # type: roadrunner.ExecutableModel
sbml_str = r.getCurrentSBML()
doc = libsbml.readSBMLFromString(sbml_str) # type: libsbml.SBMLDocument
model = doc.getModel() # type: libsbml.Model
sids = r_model.getFloatingSpeciesIds() + r_model.getBoundarySpeciesIds()
species = [model.getSpecies(sid)
for sid in sids] # type: List[libsbml.Species]
data = {
'sid':
sids,
'concentration':
np.concatenate([
r_model.getFloatingSpeciesConcentrations(),
r_model.getBoundarySpeciesConcentrations()
],
axis=0),
'amount':
np.concatenate([
r.model.getFloatingSpeciesAmounts(),
r.model.getBoundarySpeciesAmounts()
],
axis=0),
'unit': [s.getUnits() for s in species],
'constant': [s.getConstant() for s in species],
'boundaryCondition': [s.getBoundaryCondition() for s in species],
'name': [s.getName() for s in species],
}
return pd.DataFrame(data,
columns=[
'sid', 'concentration', 'amount', 'unit',
'constant', 'boundaryCondition', 'species', 'name'
])
def clamp_species(r: roadrunner.RoadRunner,
sids,
boundary_condition=True) -> roadrunner.RoadRunner:
""" Clamp/Free specie(s) via setting boundaryCondition=True/False.
This requires changing the SBML and ODE system.
:param r: roadrunner.RoadRunner
:param sids: sid or iterable of sids
:param boundary_condition: boolean flag to clamp (True) or free (False) species
:return: modified roadrunner.RoadRunner
"""
# get model for current SBML state
sbml_str = r.getCurrentSBML()
doc = libsbml.readSBMLFromString(sbml_str) # type: libsbml.SBMLDocument
model = doc.getModel() # type: libsbml.Model
if isinstance(sids, str):
sids = [sids]
for sid in sids:
# set boundary conditions
sbase = model.getElementBySId(sid) # type: libsbml.SBase
if not sbase:
logging.error("No element for SId in model: {}".format(sid))
return None
else:
if sbase.getTypeCode() == libsbml.SBML_SPECIES:
species = sbase # type: libsbml.Species
species.setBoundaryCondition(boundary_condition)
else:
logging.error(
"SId in clamp does not match species: {}".format(sbase))
return None
# create modified roadrunner instance
sbmlmod_str = libsbml.writeSBMLToString(doc)
rmod = load_model(sbmlmod_str) # type: roadrunner.RoadRunner
set_timecourse_selections(rmod, r.timeCourseSelections)
return rmod
def loadSBML( self, aSBMLDocument ):
if type( aSBMLDocument ) == str:
self.theSBMLDocument = libsbml.readSBML( aSBMLDocument )
elif type( aSBMLDocument ) == file:
self.theSBMLDocument = libsbml.readSBMLFromString( aSBMLDocument.read() )
else:
self.theSBMLDocument = aSBMLDocument
if self.theSBMLDocument.getLevel() != 2:
self.theSBMLDocument.setLevel( 2 )
if self.theSBMLDocument.getNumFatals() > 0:
fatalerrorList = []
for i in range( self.theSBMLDocument.getNumFatals() ):
fatalerrorList.append( self.theSBMLDocument.getFatal( i ) )
self.theSBMLDocument = None
raise SBMLConvertError, \
'This SBML document is invalid: %s' \
% ( ', '.join( fatalerrorList ) )
def create(id, DIR_REPOS, VERSION):
'''
Generates repo contents for a specific model
'''
import bioservices
import _template as t
s = bioservices.BioModels()
sbml = s.getModelSBMLById(id)
mkdirp(os.path.join(DIR_REPOS, id, id))
setup_params = {
'name': id,
'version': VERSION,
'description': '%s from BioModels' % id,
'url': 'http://www.ebi.ac.uk/biomodels-main/%s' % id
}
model_params = {
'path': '%s.xml' % id
}
init_params = {}
import libsbml
doc = libsbml.readSBMLFromString(sbml.encode('utf-8'))
model = doc.getModel()
notes = h.handle(model.getNotesString().decode('utf-8'))
with open(os.path.join(DIR_REPOS, id, 'setup.py'), 'w') as f:
f.write(t.setuppy_template(setup_params))
with open(os.path.join(DIR_REPOS, id, id, 'model.py'), 'w') as f:
f.write(t.modelpy_template(model_params))
with open(os.path.join(DIR_REPOS, id, id, id + '.xml'), 'w') as f:
f.write(sbml.encode('utf-8'))
with open(os.path.join(DIR_REPOS, id, id, '__init__.py'), 'w') as f:
f.write(t.initpy_template(init_params))
with open(os.path.join(DIR_REPOS, id, 'README.md'), 'w') as f:
f.write(notes.encode('utf-8'))
def parameter_df(r: roadrunner.RoadRunner) -> pd.DataFrame:
"""
Create GlobalParameter DataFrame.
:return: pandas DataFrame
"""
r_model = r.model # type: roadrunner.ExecutableModel
doc = libsbml.readSBMLFromString(
r.getCurrentSBML()) # type: libsbml.SBMLDocument
model = doc.getModel() # type: libsbml.Model
sids = r_model.getGlobalParameterIds()
parameters = [model.getParameter(sid)
for sid in sids] # type: List[libsbml.Parameter]
data = {
'sid': sids,
'value': r_model.getGlobalParameterValues(),
'unit': [p.units for p in parameters],
'constant': [p.constant for p in parameters],
'name': [p.name for p in parameters],
}
df = pd.DataFrame(data,
columns=['sid', 'value', 'unit', 'constant', 'name'])
return df
def __init__(self,
sbml,
species={},
reactions={},
reactants={},
products={},
modifiers={}):
"""
:param sbml: SBML string, libsbml.SBMLDocument object, or libsbml.Model object
:param species:
:type species:
:param reactions:
:type reactions:
:param reactants:
:type reactants:
:param products:
:type products:
:param modifiers:
:type modifiers:
"""
# load model
if isinstance(sbml, basestring):
self.doc = libsbml.readSBMLFromString(sbml)
self.model = self.doc.getModel()
elif isinstance(sbml, libsbml.SBMLDocument):
self.doc = sbml
self.model = self.doc.getModel()
elif isinstance(sbml, libsbml.Model):
self.model = sbml
else:
raise Exception('SBML Input is not valid')
# create graph
self.g = SBMLDiagram._createGraph(self.model,
species=species,
reactions=reactions,
reactants=reactants,
products=products,
modifiers=modifiers)
def __init__(self, sbmlFileContents=None, exceptionOnError=True):
self.model_name = None
self.model_notes = {}
self.metList = None
self.reactionList = None
self.initialSetFluxesCount = None
self.initialBoundedFluxesCount = None
self.initialCloselyBoundedFluxesCount = None
self.errorCount = 0
self.logStrings = []
if not isinstance(sbmlFileContents, basestring):
self.errorCount = 1
self.logStrings = [
'No SBML string provided (object is not a string).'
]
elif sbmlFileContents.strip() == '':
self.errorCount = 1
self.logStrings = ['No SBML string provided (string is empty).']
else:
# Not saving a local pointer to sbmlDoc, in order to circumvent this error when attempting to deepcopy:
# TypeError: object.__new__(SwigPyObject) is not safe, use SwigPyObject.__new__()
sbmlDoc = libsbml.readSBMLFromString(sbmlFileContents)
self.errorCount = sbmlDoc.getNumErrors()
if self.errorCount:
errs = sbmlDoc.getErrorLog()
for x in range(self.errorCount):
err = errs.getError(x)
self.logStrings.append(err.getMessage())
self.parseSBMLDoc(sbmlDoc)
if self.errorCount > 0 and exceptionOnError:
raise Exception('Errors parsing SBML:\n%s' %
('\n'.join(self.logStrings)))
def __init__(self, sbml,
species={},
reactions={},
reactants={},
products={},
modifiers={}):
"""
:param sbml: SBML string, libsbml.SBMLDocument object, or libsbml.Model object
:param species:
:type species:
:param reactions:
:type reactions:
:param reactants:
:type reactants:
:param products:
:type products:
:param modifiers:
:type modifiers:
"""
# load model
if isinstance(sbml, basestring):
self.doc = libsbml.readSBMLFromString(sbml)
self.model = self.doc.getModel()
elif isinstance(sbml, libsbml.SBMLDocument):
self.doc = sbml
self.model = self.doc.getModel()
elif isinstance(sbml, libsbml.Model):
self.model = sbml
else:
raise Exception('SBML Input is not valid')
# create graph
self.g = SBMLDiagram._createGraph(self.model,
species=species,
reactions=reactions,
reactants=reactants,
products=products,
modifiers=modifiers)
def runSingleSBML(member_name, rpsbml_string, inSBML, isMerge, path_id):
#open one of the rp SBML files
input_rpsbml = rpSBML.rpSBML('inputMergeModel',
libsbml.readSBMLFromFile(inSBML))
rpsbml = rpSBML.rpSBML(member_name,
libsbml.readSBMLFromString(rpsbml_string))
#read the input GEM sbml model
#input_rpsbml = rpSBML.rpSBML('inputMergeModel', libsbml.readSBMLFromString(inSBML_string))
#print(input_rpsbml)
#print(input_rpsbml.model)
rpsbml.mergeModels(input_rpsbml.model)
rpfba = rpFBA.rpFBA(input_rpsbml)
rpfba.allObj(path_id)
if isMerge:
##### pass FBA results to the original model ####
groups = rpfba.rpsbml.model.getPlugin('groups')
rp_pathway = groups.getGroup(path_id)
for member in rp_pathway.getListOfMembers():
reacFBA = rpfba.rpsbml.model.getReaction(member.getIdRef())
reacIN = rpsbml.model.getReaction(member.getIdRef())
reacIN.setAnnotation(reacFBA.getAnnotation())
return libsbml.writeSBMLToString(rpsbml.document).encode('utf-8')
else:
return libsbml.writeSBMLToString(input_rpsbml.document).encode('utf-8')
def _parameters_for_sensitivity(r, exclude_filter=None,
exclude_zero: bool = True,
zero_eps: float = 1E-8):
""" Get parameter ids for sensitivity analysis.
Values around current model state are used.
:param r:
:param exclude_filter: filter function to exclude parameters
:param exclude_zero: exclude parameters which are zero
:return:
"""
doc = libsbml.readSBMLFromString(
r.getSBML()) # type: libsbml.SBMLDocument
model = doc.getModel() # type: libsbml.Model
# constant parameters
pids_const = []
for p in model.getListOfParameters():
if p.getConstant() is True:
pids_const.append(p.getId())
# filter parameters
parameters = OrderedDict()
for pid in sorted(pids_const):
if exclude_filter and exclude_filter(pid):
continue
value = r[pid]
if exclude_zero:
if np.abs(value) < zero_eps:
continue
parameters[pid] = value
return parameters
def test_sbml(self):
fwd = Direction.forward()
rev = Direction.reversible()
a = M("A_c")
b = M("B_c")
c = M("C_e")
e = M("E_e", boundary=True)
model = Model()
model.reactions = [
R("R1", 1*a, 3*b, direction=fwd, bounds=Bounds(-100, 100)),
R("R2", 1*c, 3*b, direction=fwd, bounds=Bounds(-100, 100)),
R("R3", 1*b + 1*c, 1*e, direction=rev, bounds=Bounds(-100, 100))]
import libsbml
import converter
sbml = converter.Bioopt2SbmlConverter().convert(model)
sbml_export = libsbml.writeSBMLToString(sbml)
doc = libsbml.readSBMLFromString(sbml_export)
self.assertEquals(0, doc.getNumErrors())
exp_export = """<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3">
<model>
<listOfUnitDefinitions>
<unitDefinition id="mmol_per_gDW_per_hr">
<listOfUnits>
<unit kind="mole" scale="-3"/>
<unit kind="second" exponent="-1" multiplier="0.00027778"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment id="C_0001" name="c"/>
<compartment id="C_0002" name="e"/>
</listOfCompartments>
<listOfSpecies>
<species id="M_0001_c" name="A_c" compartment="C_0001" initialAmount="0" boundaryCondition="false"/>
<species id="M_0002_b" name="E_e" compartment="C_0002" initialAmount="0" boundaryCondition="true"/>
<species id="M_0003_e" name="C_e" compartment="C_0002" initialAmount="0" boundaryCondition="false"/>
<species id="M_0004_c" name="B_c" compartment="C_0001" initialAmount="0" boundaryCondition="false"/>
</listOfSpecies>
<listOfReactions>
<reaction id="R_0001" name="R1" reversible="false">
<listOfReactants>
<speciesReference species="M_0001_c" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="M_0004_c" stoichiometry="3"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> FLUX_VALUE </ci>
</math>
<listOfParameters>
<parameter id="LOWER_BOUND" value="-100" units="mmol_per_gDW_per_hr"/>
<parameter id="UPPER_BOUND" value="100" units="mmol_per_gDW_per_hr"/>
<parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
<parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction id="R_0002" name="R2" reversible="false">
<listOfReactants>
<speciesReference species="M_0003_e" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="M_0004_c" stoichiometry="3"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> FLUX_VALUE </ci>
</math>
<listOfParameters>
<parameter id="LOWER_BOUND" value="-100" units="mmol_per_gDW_per_hr"/>
<parameter id="UPPER_BOUND" value="100" units="mmol_per_gDW_per_hr"/>
<parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
<parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction id="R_0003" name="R3" reversible="true">
<listOfReactants>
<speciesReference species="M_0004_c" stoichiometry="1"/>
<speciesReference species="M_0003_e" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="M_0002_b" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> FLUX_VALUE </ci>
</math>
<listOfParameters>
<parameter id="LOWER_BOUND" value="-100" units="mmol_per_gDW_per_hr"/>
<parameter id="UPPER_BOUND" value="100" units="mmol_per_gDW_per_hr"/>
<parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
<parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
</listOfParameters>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
"""
exp_export = sbml_export # TODO: we have a stochioustic processes in metabolite id generation so strings can't be used to assert
self.assertEquals(exp_export, sbml_export)
def flattenExternalModelDefinitions(doc):
""" Converts all ExternalModelDefinitions to ModelDefinitions.
I.e. the definition of models in external files are read
and directly included in the top model. The resulting
comp model consists than only of a single file.
The model refs in the submodel do not change in the process,
so no need to update the submodels.
:param doc: SBMLDocument
:return: SBMLDocument with ExternalModelDefinitions replaced
"""
# FIXME: handle /multiple levels of hierarchies recursively (ExternalModelDefinitions of submodels)
model = doc.getModel()
if model is None:
return doc
comp_doc = doc.getPlugin("comp")
emd_list = comp_doc.getListOfExternalModelDefinitions()
# no ExternalModelDefinitions
if (emd_list is None) or (len(emd_list) == 0):
return doc
# ExternalModelDefinitions set as ModelDefinitions
emd_ids = []
mds = []
for emd in emd_list:
emd_ids.append(emd.getId())
# get the model definition from the model
ref_model = emd.getReferencedModel()
# store model definition
md = libsbml.ModelDefinition(ref_model)
mds.append(md)
packages = []
for emd in emd_list:
# get the model definition from the model
ref_model = emd.getReferencedModel()
ref_doc = ref_model.getSBMLDocument()
# print('\n', ref_model)
for k in range(ref_doc.getNumPlugins()):
plugin = ref_doc.getPlugin(k)
uri = plugin.getURI()
prefix = plugin.getPrefix()
name = plugin.getPackageName()
required = None
if ref_doc.isSetPackageRequired(name):
required = ref_doc.getPackageRequired(name)
packages.append({
'model': ref_model,
'uri': uri,
'prefix': prefix,
'name': name,
'required': required
})
# remove emds from model (do not remove while iterating over the list)
for emd_id in emd_ids:
comp_doc.removeExternalModelDefinition(emd_id)
# activate all the packages
from pprint import pprint
pprint(packages)
for pdict in packages:
doc.enablePackage(pdict['uri'], pdict['prefix'], True)
doc.setPackageRequired(pdict['name'], pdict['required'])
# now add the model definitions
for md in mds:
comp_doc.addModelDefinition(md)
sbml_str = libsbml.writeSBMLToString(doc)
doc = libsbml.readSBMLFromString(sbml_str)
# replacement finished, now go through all ModelDefinitions
# and add things the packages require
print("-" * 80)
for k in range(doc.getNumPlugins()):
plugin = doc.getPlugin(k)
name = plugin.getPackageName()
print(name, '\n')
md_list = comp_doc.getListOfModelDefinitions()
for md_model in md_list:
# if a package needs something on
# a model we have to write it on all ModelDefinitions
# this will break on a package per package basis ! We know about fbc it needs
# a strict tag so writing this here
if name == "fbc":
# for some ModelDefinitions we don't get the fbc Plugin ???
fbc_model = md_model.getPlugin(name)
print('\tModel:', md_model)
print('\tFBCModelPlugin:', fbc_model, type(fbc_model))
# setting because it is required (if unlucky additional info required)
# but we can't set it because we can't access the FBCModelPlugins of the ModelDefinitions
if fbc_model is not None:
if not fbc_model.isSetStrict():
fbc_model.setStrict(False)
else:
print(
"WARNING: This should never happen. All ModelDefinitions should have a FBCModelPlugin"
)
doc.checkInternalConsistency()
doc.printErrors()
return doc
def convertSBML2EML( aSBMLString ):
aSBMLDocument = libsbml.readSBMLFromString( aSBMLString )
aSBMLModel = aSBMLDocument.getModel()
theModel = SBML_Model( aSBMLDocument, aSBMLModel )
theCompartment = SBML_Compartment( theModel )
theParameter = SBML_Parameter( theModel )
theSpecies = SBML_Species( theModel )
theRule = SBML_Rule( theModel )
theReaction = SBML_Reaction( theModel )
# theEvent = SBML_Event( theModel )
anEml = Eml()
# ------------------------------
# Set Stepper
# ------------------------------
anEml.createStepper( 'ODEStepper', 'DE' )
## anEml.createStepper( 'ODE45Stepper', 'DE' )
# ------------------------------
# Set Compartment ( System )
# ------------------------------
# setFullID
aSystemFullID='System::/'
anEml.createEntity( 'System', aSystemFullID )
anEml.setEntityProperty( aSystemFullID, 'StepperID', ['DE'] )
anEml.setEntityProperty( aSystemFullID, 'Name', ['Default'] )
for aCompartment in ( theModel.CompartmentList ):
# initialize
theCompartment.initialize( aCompartment )
# getPath
if ( theModel.Level == 1 ):
aPath = theModel.getPath( aCompartment[1] )
elif ( theModel.Level == 2 ):
aPath = theModel.getPath( aCompartment[0] )
# setFullID
if( aPath == '/' ):
aSystemFullID = 'System::/'
else:
aSystemFullID = theCompartment.getCompartmentID( aCompartment )
anEml.createEntity( 'System', aSystemFullID )
# setStepper
anEml.setEntityProperty( aSystemFullID, 'StepperID', ['DE'] )
# setName( default = [] )
if ( theModel.Level == 2 ):
if ( aCompartment[1] != '' ):
anEml.setEntityProperty( aSystemFullID,
'Name',
aCompartment[1:2] )
# setDimensions( default = 3 )
aDimensionsFullID = 'Variable:' + aPath + ':Dimensions'
anEml.createEntity( 'Variable', aDimensionsFullID )
aTmpList = [ str( aCompartment[2] ) ]
anEml.setEntityProperty( aDimensionsFullID, 'Value', aTmpList[0:1] )
# setSIZE
aSizeFullID = 'Variable:' + aPath + ':SIZE'
anEml.createEntity( 'Variable', aSizeFullID )
aSizeValue = theCompartment.getCompartmentSize( aCompartment )
aSizeUnit = theCompartment.getCompartmentUnit( aCompartment )
# convert to ECELL Unit
if ( aSizeUnit != '' ):
aSizeValue = theModel.convertUnit( aSizeUnit, aSizeValue )
aTmpList = [ str( aSizeValue ) ]
anEml.setEntityProperty( aSizeFullID, 'Value', aTmpList[0:1] )
# setConstant( default = 1 )
if ( aCompartment[7] == 1 ):
anEml.setEntityProperty( aSizeFullID, 'Fixed', ['1',] )
# ------------------------------
# Set GlobalParameter ( Variable )
# ------------------------------
if ( theModel.ParameterList != [] ):
# setGlobalParameterSystem
aSystemFullID='System:/:SBMLParameter'
anEml.createEntity( 'System', aSystemFullID )
anEml.setEntityProperty( aSystemFullID, 'StepperID', ['DE'] )
anEml.setEntityProperty( aSystemFullID, 'Name', ['Global Parameter'] )
for aParameter in theModel.ParameterList:
# setFullID
aSystemFullID = theParameter.getParameterID( aParameter )
anEml.createEntity( 'Variable', aSystemFullID )
# setName
if ( aParameter[1] != '' ):
anEml.setEntityProperty( aSystemFullID, 'Name', aParameter[1:2] )
# setValue
aTmpList = [ str( theParameter.getParameterValue( aParameter ) ) ]
anEml.setEntityProperty( aSystemFullID, 'Value', aTmpList[0:1] )
# setFixed ( default = 1 )
if ( aParameter[4] == 1 ):
# aTmpList = [ str( aParameter[4] ) ]
aTmpList = [ '1' ]
anEml.setEntityProperty( aSystemFullID, 'Fixed', aTmpList[0:1] )
# ------------------------------
# Set Species ( Variable )
# ------------------------------
for aSpecies in theModel.SpeciesList:
### setFullID ###
aSystemFullID = theSpecies.getSpeciesID( aSpecies )
anEml.createEntity( 'Variable', aSystemFullID )
### setName ###
if( theModel.Level == 2 ):
if ( aSpecies[1] != '' ):
anEml.setEntityProperty( aSystemFullID, 'Name', aSpecies[1:2] )
### setValue ###
aTmpList = [ str( theSpecies.getSpeciesValue( aSpecies ) ) ]
anEml.setEntityProperty( aSystemFullID, 'Value', aTmpList[0:1] )
### setFixed ###
aConstant = theSpecies.getConstant( aSpecies )
anEml.setEntityProperty( aSystemFullID,
'Fixed',
[ str( aConstant ) ] )
# ------------------------------
# Set Rule ( Process )
# ------------------------------
if ( theModel.RuleList != [] ):
### make Rule System ###
aSystemFullID='System:/:SBMLRule'
anEml.createEntity( 'System', aSystemFullID )
anEml.setEntityProperty( aSystemFullID,
'Name',
['System for SBML Rule'] )
anEml.setEntityProperty( aSystemFullID, 'StepperID', ['DE'] )
for aRule in theModel.RuleList:
theRule.initialize()
### setFullID ###
aSystemFullID = theRule.getRuleID()
### Algebraic Rule ###
if ( aRule[0] == libsbml.SBML_ALGEBRAIC_RULE ):
anEml.createEntity( 'ExpressionAlgebraicProcess', aSystemFullID )
### Assignment Rule ###
elif ( aRule[0] == libsbml.SBML_ASSIGNMENT_RULE or
aRule[0] == libsbml.SBML_SPECIES_CONCENTRATION_RULE or
aRule[0] == libsbml.SBML_COMPARTMENT_VOLUME_RULE or
aRule[0] == libsbml.SBML_PARAMETER_RULE ):
anEml.createEntity( 'ExpressionAssignmentProcess', aSystemFullID )
aVariableType = theRule.getVariableType( aRule[2] )
if ( aVariableType == libsbml.SBML_SPECIES ):
theRule.setSpeciesToVariableReference( aRule[2], '1' )
elif ( aVariableType == libsbml.SBML_PARAMETER ):
theRule.setParameterToVariableReference( aRule[2], '1' )
elif ( aVariableType == libsbml.SBML_COMPARTMENT ):
theRule.setCompartmentToVariableReference( aRule[2], '1' )
else:
raise TypeError,\
"Variable type must be Species, Parameter, or Compartment"
### Rate Rule ###
elif ( aRule[0] == libsbml.SBML_RATE_RULE ):
anEml.createEntity( 'ExpressionFluxProcess', aSystemFullID )
aVariableType = theRule.getVariableType( aRule[2] )
if ( aVariableType == libsbml.SBML_SPECIES ):
theRule.setSpeciesToVariableReference( aRule[2], '1' )
elif ( aVariableType == libsbml.SBML_PARAMETER ):
theRule.setParameterToVariableReference( aRule[2], '1' )
elif ( aVariableType == libsbml.SBML_COMPARTMENT ):
theRule.setCompartmentToVariableReference( aRule[2], '1' )
else:
raise TypeError,\
"Variable type must be Species, Parameter, or Compartment"
else:
raise TypeError,\
" The type of Rule must be Algebraic, Assignment or Rate Rule"
# convert SBML formula to E-Cell formula
convertedFormula = [ str( theRule.convertRuleFormula( aRule[1] ) ) ]
# set Expression Property
anEml.setEntityProperty( aSystemFullID,
'Expression',
convertedFormula )
# setVariableReferenceList
anEml.setEntityProperty( aSystemFullID,
'VariableReferenceList',
theRule.VariableReferenceList )
# ------------------------------
# Set Reaction ( Process )
# ------------------------------
for aReaction in theModel.ReactionList:
theReaction.initialize()
# setFullID
aSystemFullID = theReaction.getReactionID( aReaction )
anEml.createEntity( 'ExpressionFluxProcess', aSystemFullID )
# setName
if ( theModel.Level == 2 ):
if( aReaction[1] != '' ):
anEml.setEntityProperty( aSystemFullID, 'Name', aReaction[1:2] )
# setSubstrate
for aSubstrate in aReaction[5]:
aSubstrateList = []
aSubstrateList.append( 'S' + str( theReaction.SubstrateNumber ) )
theReaction.SubstrateNumber = theReaction.SubstrateNumber + 1
aSubstrateID = theModel.getSpeciesReferenceID( aSubstrate[0] )
if ( aSubstrateID == None ):
raise NameError,"Species "+aSubstrate[0]+" not found"
aSubstrateList.append( 'Variable:' + aSubstrateID )
if ( aSubstrate[2] != 1 ):
raise Exception,"Stoichiometry Error : E-Cell System can't set a floating Stoichiometry"
aSubstrateList.append( str( -1 * theReaction.getStoichiometry(
aSubstrate[0], aSubstrate[1] ) ) )
theReaction.VariableReferenceList.append( aSubstrateList )
# setProduct
for aProduct in aReaction[6]:
aProductList = []
aProductList.append( 'P' + str(theReaction.ProductNumber) )
theReaction.ProductNumber = theReaction.ProductNumber + 1
aProductID = theModel.getSpeciesReferenceID( aProduct[0] )
if ( aProductID == None ):
raise NameError,"Species "+aProduct[0]+" not found"
aProductList.append( 'Variable:' + aProductID )
if ( aProduct[2] != 1 ):
raise Exception,"Stoichiometry Error : E-Cell System can't set a floating Stoichiometry"
aProductList.append( str( 1 * theReaction.getStoichiometry(
aProduct[0], aProduct[1] ) ) )
theReaction.VariableReferenceList.append( aProductList )
# setCatalyst
for aModifier in aReaction[7]:
aModifierList = []
aModifierList.append( 'C' + str( theReaction.ModifierNumber ) )
theReaction.ModifierNumber = theReaction.ModifierNumber + 1
aModifierID = theModel.getSpeciesReferenceID( aModifier )
if ( aModifierID == None ):
raise NameError,"Species "+aModifier[0]+" not found"
aModifierList.append( 'Variable:' + aModifierID )
aModifierList.append( '0' )
theReaction.VariableReferenceList.append( aModifierList )
# setProperty
if( aReaction[2] != [] ):
if( aReaction[2][4] != [] ):
for aParameter in aReaction[2][4]:
if ( aParameter[2] != '' ):
aTmpList = [ str( aParameter[2] ) ]
if ( theModel.Level == 1 ):
anEml.setEntityProperty\
( aSystemFullID, aParameter[1], aTmpList[0:1] )
elif ( theModel.Level == 2 ):
anEml.setEntityProperty\
( aSystemFullID, aParameter[0], aTmpList[0:1] )
# --------------------------
# set "Expression" Property
# --------------------------
# convert SBML format formula to E-Cell format formula
if( aReaction[2][0] != '' ):
anExpression =\
[ str( theReaction.convertKineticLawFormula( aReaction[2][0] ) ) ]
# set Expression Property for ExpressionFluxProcess
anEml.setEntityProperty( aSystemFullID,
'Expression',
anExpression )
# setVariableReferenceList
anEml.setEntityProperty( aSystemFullID,
'VariableReferenceList',
theReaction.VariableReferenceList )
return anEml
def __init__(self, sbml_to_compare):
'''
sbml_to_compare -- list of two SBML strings, libsbml.SBMLDocument objects, or
libsbml.Model objects, to compare
'''
import pygraphviz as pgv
import libsbml
from tellurium.analysis import getMatchingSpecies, getMatchingReactions
# List of the two sbml documents to create diff
self.doc = []
# Dict of species id (from model 1) to description of match in model 2
self.matches = [dict(), dict()]
# The pygraphviz graph object
self.G = pgv.AGraph(strict=False, directed=True)
for sbml in sbml_to_compare:
if isinstance(sbml, basestring):
self.doc.append(libsbml.readSBMLFromString(sbml))
elif isinstance(sbml, libsbml.SBMLDocument):
self.doc.append(sbml)
elif isinstance(sbml, libsbml.Model):
self.doc.append(sbml.getSBMLDocument())
else:
raise Exception('SBML Input is not valid')
matching_species = getMatchingSpecies(self.doc[0].model, self.doc[1].model)
# Create set of overlapping species IDs
for entry in matching_species:
self.matches[0][entry['id']] = entry
for sub_entry in entry['children'] + entry['parents'] + entry['exact']:
self.matches[1][sub_entry['id']] = entry
first_color = 'blue'
second_color = 'red'
match_color = 'green'
# Creating graph for first model
for s in self.doc[0].model.species:
if s.getName():
label = s.getName()
else:
label = s.getId()
if s.getId() in self.matches[0]:
label += " ({})".format(self._create_matched_description(s.getId()))
if s.getId() in self.matches[0]:
color = match_color
else:
color = first_color
self.G.add_node(s.getId(), label=label, color=color)
for r in self.doc[0].model.reactions:
if r.getName():
label = r.getName()
else:
label = r.getId()
self.G.add_node(r.getId(), label=label, shape='box', color=first_color)
for s in r.reactants:
self.G.add_edge(s.getSpecies(), r.getId(), arrowhead='none', color=first_color)
for s in r.products:
self.G.add_edge(r.getId(), s.getSpecies(), color=first_color)
for s in r.modifiers:
self.G.add_edge(s.getSpecies(), r.getId(), arrowhead='odot', color=first_color)
# Creating graph for second model
for s in self.doc[1].model.species:
# Skip creating species node for matches
if s.getId() in self.matches[1]:
continue
if s.getName():
label = s.getName() + ' ({})'.format(s.getId())
else:
label = s.getId()
self.G.add_node(s.getId(), label=label, color=second_color)
for r in self.doc[1].model.reactions:
if r.getName():
label = r.getName() + ' ({})'.format(r.getId())
else:
label = r.getId()
self.G.add_node(r.getId(), label=label, shape='box', color=second_color)
for s in r.reactants:
if s.getSpecies() in self.matches[1]:
matched_id = self.matches[1][s.getSpecies()]['id']
self.G.add_edge(matched_id, r.getId(), arrowhead='none', color=second_color)
else:
self.G.add_edge(s.getSpecies(), r.getId(), arrowhead='none', color=second_color)
for s in r.products:
if s.getSpecies() in self.matches[1]:
matched_id = self.matches[1][s.getSpecies()]['id']
self.G.add_edge(r.getId(), matched_id, color=second_color)
else:
self.G.add_edge(r.getId(), s.getSpecies(), color=second_color)
for s in r.modifiers:
if s.getSpecies() in self.matches[1]:
matched_id = self.matches[1][s.getSpecies()]['id']
self.G.add_edge(matched_id, r.getId(), arrowhead='odot', color=second_color)
else:
self.G.add_edge(s.getSpecies(), r.getId(), arrowhead='odot', color=second_color)
def get_ia_and_rules(model):
sbml = model.getSBML()
sbml_document = libsbml.readSBMLFromString(sbml)
sbml_model = sbml_document.getModel()
return _get_sbml_ini_dict(sbml_model), _get_sbml_rule_dict(sbml_model)
from __future__ import print_function, division
import libsbml
import tellurium as te
import lxml.etree as ET
from io import StringIO
import tempfile
r = te.loada('''
J0: S1 -> S2; k1*S1;
S1=10.0; S2=0.0; k1=1.0;
''')
# create SBML file
f = tempfile.NamedTemporaryFile('w', suffix=".xml")
r.exportToSBML(f.name)
# create C14N canonical XML
et = ET.parse(f.name)
output = StringIO.StringIO()
et.write_c14n(output)
c14n_xml = output.getvalue()
# TODO: in addition sort all elements of the listOfs
# read with libsbml
doc = libsbml.readSBMLFromString(c14n_xml)
# read with roadrunner
te.loadSBMLModel(c14n_xml)
def convertSBML2EML(aSBMLString):
aSBMLDocument = libsbml.readSBMLFromString(aSBMLString)
aSBMLModel = aSBMLDocument.getModel()
theModel = SBML_Model(aSBMLDocument, aSBMLModel)
theCompartment = SBML_Compartment(theModel)
theParameter = SBML_Parameter(theModel)
theSpecies = SBML_Species(theModel)
theRule = SBML_Rule(theModel)
theReaction = SBML_Reaction(theModel)
# theEvent = SBML_Event( theModel )
anEml = Eml()
# ------------------------------
# Set Stepper
# ------------------------------
anEml.createStepper('ODEStepper', 'DE')
## anEml.createStepper( 'ODE45Stepper', 'DE' )
# ------------------------------
# Set Compartment ( System )
# ------------------------------
# setFullID
aSystemFullID = 'System::/'
anEml.createEntity('System', aSystemFullID)
anEml.setEntityProperty(aSystemFullID, 'StepperID', ['DE'])
anEml.setEntityProperty(aSystemFullID, 'Name', ['Default'])
for aCompartment in (theModel.CompartmentList):
# initialize
theCompartment.initialize(aCompartment)
# getPath
if (theModel.Level == 1):
aPath = theModel.getPath(aCompartment[1])
elif (theModel.Level == 2):
aPath = theModel.getPath(aCompartment[0])
# setFullID
if (aPath == '/'):
aSystemFullID = 'System::/'
else:
aSystemFullID = theCompartment.getCompartmentID(aCompartment)
anEml.createEntity('System', aSystemFullID)
# setStepper
anEml.setEntityProperty(aSystemFullID, 'StepperID', ['DE'])
# setName( default = [] )
if (theModel.Level == 2):
if (aCompartment[1] != ''):
anEml.setEntityProperty(aSystemFullID, 'Name',
aCompartment[1:2])
# setDimensions( default = 3 )
aDimensionsFullID = 'Variable:' + aPath + ':Dimensions'
anEml.createEntity('Variable', aDimensionsFullID)
aTmpList = [str(aCompartment[2])]
anEml.setEntityProperty(aDimensionsFullID, 'Value', aTmpList[0:1])
# setSIZE
aSizeFullID = 'Variable:' + aPath + ':SIZE'
anEml.createEntity('Variable', aSizeFullID)
aSizeValue = theCompartment.getCompartmentSize(aCompartment)
aSizeUnit = theCompartment.getCompartmentUnit(aCompartment)
# convert to ECELL Unit
if (aSizeUnit != ''):
aSizeValue = theModel.convertUnit(aSizeUnit, aSizeValue)
aTmpList = [str(aSizeValue)]
anEml.setEntityProperty(aSizeFullID, 'Value', aTmpList[0:1])
# setConstant( default = 1 )
if (aCompartment[7] == 1):
anEml.setEntityProperty(aSizeFullID, 'Fixed', [
'1',
])
# ------------------------------
# Set GlobalParameter ( Variable )
# ------------------------------
if (theModel.ParameterList != []):
# setGlobalParameterSystem
aSystemFullID = 'System:/:SBMLParameter'
anEml.createEntity('System', aSystemFullID)
anEml.setEntityProperty(aSystemFullID, 'StepperID', ['DE'])
anEml.setEntityProperty(aSystemFullID, 'Name', ['Global Parameter'])
for aParameter in theModel.ParameterList:
# setFullID
aSystemFullID = theParameter.getParameterID(aParameter)
anEml.createEntity('Variable', aSystemFullID)
# setName
if (aParameter[1] != ''):
anEml.setEntityProperty(aSystemFullID, 'Name', aParameter[1:2])
# setValue
aTmpList = [str(theParameter.getParameterValue(aParameter))]
anEml.setEntityProperty(aSystemFullID, 'Value', aTmpList[0:1])
# setFixed ( default = 1 )
if (aParameter[4] == 1):
# aTmpList = [ str( aParameter[4] ) ]
aTmpList = ['1']
anEml.setEntityProperty(aSystemFullID, 'Fixed', aTmpList[0:1])
# ------------------------------
# Set Species ( Variable )
# ------------------------------
for aSpecies in theModel.SpeciesList:
### setFullID ###
aSystemFullID = theSpecies.getSpeciesID(aSpecies)
anEml.createEntity('Variable', aSystemFullID)
### setName ###
if (theModel.Level == 2):
if (aSpecies[1] != ''):
anEml.setEntityProperty(aSystemFullID, 'Name', aSpecies[1:2])
### setValue ###
aTmpList = [str(theSpecies.getSpeciesValue(aSpecies))]
anEml.setEntityProperty(aSystemFullID, 'Value', aTmpList[0:1])
### setFixed ###
aConstant = theSpecies.getConstant(aSpecies)
anEml.setEntityProperty(aSystemFullID, 'Fixed', [str(aConstant)])
# ------------------------------
# Set Rule ( Process )
# ------------------------------
if (theModel.RuleList != []):
### make Rule System ###
aSystemFullID = 'System:/:SBMLRule'
anEml.createEntity('System', aSystemFullID)
anEml.setEntityProperty(aSystemFullID, 'Name',
['System for SBML Rule'])
anEml.setEntityProperty(aSystemFullID, 'StepperID', ['DE'])
for aRule in theModel.RuleList:
theRule.initialize()
### setFullID ###
aSystemFullID = theRule.getRuleID()
### Algebraic Rule ###
if (aRule[0] == libsbml.SBML_ALGEBRAIC_RULE):
anEml.createEntity('ExpressionAlgebraicProcess', aSystemFullID)
### Assignment Rule ###
elif (aRule[0] == libsbml.SBML_ASSIGNMENT_RULE
or aRule[0] == libsbml.SBML_SPECIES_CONCENTRATION_RULE
or aRule[0] == libsbml.SBML_COMPARTMENT_VOLUME_RULE
or aRule[0] == libsbml.SBML_PARAMETER_RULE):
anEml.createEntity('ExpressionAssignmentProcess', aSystemFullID)
aVariableType = theRule.getVariableType(aRule[2])
if (aVariableType == libsbml.SBML_SPECIES):
theRule.setSpeciesToVariableReference(aRule[2], '1')
elif (aVariableType == libsbml.SBML_PARAMETER):
theRule.setParameterToVariableReference(aRule[2], '1')
elif (aVariableType == libsbml.SBML_COMPARTMENT):
theRule.setCompartmentToVariableReference(aRule[2], '1')
else:
raise TypeError,\
"Variable type must be Species, Parameter, or Compartment"
### Rate Rule ###
elif (aRule[0] == libsbml.SBML_RATE_RULE):
anEml.createEntity('ExpressionFluxProcess', aSystemFullID)
aVariableType = theRule.getVariableType(aRule[2])
if (aVariableType == libsbml.SBML_SPECIES):
theRule.setSpeciesToVariableReference(aRule[2], '1')
elif (aVariableType == libsbml.SBML_PARAMETER):
theRule.setParameterToVariableReference(aRule[2], '1')
elif (aVariableType == libsbml.SBML_COMPARTMENT):
theRule.setCompartmentToVariableReference(aRule[2], '1')
else:
raise TypeError,\
"Variable type must be Species, Parameter, or Compartment"
else:
raise TypeError,\
" The type of Rule must be Algebraic, Assignment or Rate Rule"
# convert SBML formula to E-Cell formula
convertedFormula = [str(theRule.convertRuleFormula(aRule[1]))]
# set Expression Property
anEml.setEntityProperty(aSystemFullID, 'Expression', convertedFormula)
# setVariableReferenceList
anEml.setEntityProperty(aSystemFullID, 'VariableReferenceList',
theRule.VariableReferenceList)
# ------------------------------
# Set Reaction ( Process )
# ------------------------------
for aReaction in theModel.ReactionList:
theReaction.initialize()
# setFullID
aSystemFullID = theReaction.getReactionID(aReaction)
anEml.createEntity('ExpressionFluxProcess', aSystemFullID)
# setName
if (theModel.Level == 2):
if (aReaction[1] != ''):
anEml.setEntityProperty(aSystemFullID, 'Name', aReaction[1:2])
# setSubstrate
for aSubstrate in aReaction[5]:
aSubstrateList = []
aSubstrateList.append('S' + str(theReaction.SubstrateNumber))
theReaction.SubstrateNumber = theReaction.SubstrateNumber + 1
aSubstrateID = theModel.getSpeciesReferenceID(aSubstrate[0])
if (aSubstrateID == None):
raise NameError, "Species " + aSubstrate[0] + " not found"
aSubstrateList.append('Variable:' + aSubstrateID)
if (aSubstrate[2] != 1):
raise Exception, "Stoichiometry Error : E-Cell System can't set a floating Stoichiometry"
aSubstrateList.append(
str(-1 * theReaction.getStoichiometry(aSubstrate[0],
aSubstrate[1])))
theReaction.VariableReferenceList.append(aSubstrateList)
# setProduct
for aProduct in aReaction[6]:
aProductList = []
aProductList.append('P' + str(theReaction.ProductNumber))
theReaction.ProductNumber = theReaction.ProductNumber + 1
aProductID = theModel.getSpeciesReferenceID(aProduct[0])
if (aProductID == None):
raise NameError, "Species " + aProduct[0] + " not found"
aProductList.append('Variable:' + aProductID)
if (aProduct[2] != 1):
raise Exception, "Stoichiometry Error : E-Cell System can't set a floating Stoichiometry"
aProductList.append(
str(1 *
theReaction.getStoichiometry(aProduct[0], aProduct[1])))
theReaction.VariableReferenceList.append(aProductList)
# setCatalyst
for aModifier in aReaction[7]:
aModifierList = []
aModifierList.append('C' + str(theReaction.ModifierNumber))
theReaction.ModifierNumber = theReaction.ModifierNumber + 1
aModifierID = theModel.getSpeciesReferenceID(aModifier)
if (aModifierID == None):
raise NameError, "Species " + aModifier[0] + " not found"
aModifierList.append('Variable:' + aModifierID)
aModifierList.append('0')
theReaction.VariableReferenceList.append(aModifierList)
# setProperty
if (aReaction[2] != []):
if (aReaction[2][4] != []):
for aParameter in aReaction[2][4]:
if (aParameter[2] != ''):
aTmpList = [str(aParameter[2])]
if (theModel.Level == 1):
anEml.setEntityProperty\
( aSystemFullID, aParameter[1], aTmpList[0:1] )
elif (theModel.Level == 2):
anEml.setEntityProperty\
( aSystemFullID, aParameter[0], aTmpList[0:1] )
# --------------------------
# set "Expression" Property
# --------------------------
# convert SBML format formula to E-Cell format formula
if (aReaction[2][0] != ''):
anExpression =\
[ str( theReaction.convertKineticLawFormula( aReaction[2][0] ) ) ]
# set Expression Property for ExpressionFluxProcess
anEml.setEntityProperty(aSystemFullID, 'Expression',
anExpression)
# setVariableReferenceList
anEml.setEntityProperty(aSystemFullID, 'VariableReferenceList',
theReaction.VariableReferenceList)
return anEml
def runSingleSBML(rpthermo, member_name, rpsbml_string, path_id):
#open one of the rp SBML files
rpsbml = rpSBML.rpSBML(member_name,
libsbml.readSBMLFromString(rpsbml_string))
rpthermo.pathway_drG_prime_m(rpsbml, path_id)
return libsbml.writeSBMLToString(rpsbml.document).encode('utf-8')
def readrpSBMLzip(inputZip):
input_zip = zipfile.ZipFile(inputZip)
rpsbml_paths = {}
for name in input_zip.namelist():
rpsbml_paths[name] = rpFBA.rpSBML(name, libsbml.readSBMLFromString(input_zip.read(name).decode("utf-8")))
return rpsbml_paths
def flattenExternalModelDefinitions(doc):
""" Converts all ExternalModelDefinitions to ModelDefinitions.
I.e. the definition of models in external files are read
and directly included in the top model. The resulting
comp model consists than only of a single file.
The model refs in the submodel do not change in the process,
so no need to update the submodels.
:param doc: SBMLDocument
:return: SBMLDocument with ExternalModelDefinitions replaced
"""
# FIXME: handle /multiple levels of hierarchies recursively (ExternalModelDefinitions of submodels)
model = doc.getModel()
if model is None:
return doc
comp_doc = doc.getPlugin("comp")
emd_list = comp_doc.getListOfExternalModelDefinitions()
# no ExternalModelDefinitions
if (emd_list is None) or (len(emd_list) == 0):
return doc
# ExternalModelDefinitions set as ModelDefinitions
emd_ids = []
mds = []
for emd in emd_list:
emd_ids.append(emd.getId())
# get the model definition from the model
ref_model = emd.getReferencedModel()
# store model definition
md = libsbml.ModelDefinition(ref_model)
mds.append(md)
packages = []
for emd in emd_list:
# get the model definition from the model
ref_model = emd.getReferencedModel()
ref_doc = ref_model.getSBMLDocument()
# print('\n', ref_model)
for k in range(ref_doc.getNumPlugins()):
plugin = ref_doc.getPlugin(k)
uri = plugin.getURI()
prefix = plugin.getPrefix()
name = plugin.getPackageName()
required = None
if ref_doc.isSetPackageRequired(name):
required = ref_doc.getPackageRequired(name)
packages.append({
'model': ref_model,
'uri': uri,
'prefix': prefix,
'name': name,
'required': required
})
# remove emds from model (do not remove while iterating over the list)
for emd_id in emd_ids:
comp_doc.removeExternalModelDefinition(emd_id)
# activate all the packages
from pprint import pprint
pprint(packages)
for pdict in packages:
doc.enablePackage(pdict['uri'], pdict['prefix'], True)
doc.setPackageRequired(pdict['name'], pdict['required'])
# now add the model definitions
for md in mds:
comp_doc.addModelDefinition(md)
sbml_str = libsbml.writeSBMLToString(doc)
doc = libsbml.readSBMLFromString(sbml_str)
# replacement finished, now go through all ModelDefinitions
# and add things the packages require
print("-"*80)
for k in range(doc.getNumPlugins()):
plugin = doc.getPlugin(k)
name = plugin.getPackageName()
print(name, '\n')
md_list = comp_doc.getListOfModelDefinitions()
for md_model in md_list:
# if a package needs something on
# a model we have to write it on all ModelDefinitions
# this will break on a package per package basis ! We know about fbc it needs
# a strict tag so writing this here
if name == "fbc":
# for some ModelDefinitions we don't get the fbc Plugin ???
fbc_model = md_model.getPlugin(name)
print('\tModel:', md_model)
print('\tFBCModelPlugin:', fbc_model, type(fbc_model))
# setting because it is required (if unlucky additional info required)
# but we can't set it because we can't access the FBCModelPlugins of the ModelDefinitions
if fbc_model is not None:
if not fbc_model.isSetStrict():
fbc_model.setStrict(False)
else:
print("WARNING: This should never happen. All ModelDefinitions should have a FBCModelPlugin")
doc.checkInternalConsistency()
doc.printErrors()
return doc
def convertSBML2EML(
aSBMLString,
anODEStepper="ODEStepper",
aFixedODEStepper='FixedODE1Stepper',
aDiscreteStepper='DiscreteTimeStepper'): ## 'PassiveStepper'
theDefaultStepperID = 'Default'
theDefaultODEStepperID = 'ODE'
theDefaultDiscreteStepperID = 'Discrete'
Steppers = dict(ODE=anODEStepper,
FixedODE=aFixedODEStepper,
Discrete=aDiscreteStepper)
StepperIDs = dict(default=theDefaultStepperID,
ODE=theDefaultODEStepperID,
Discrete=theDefaultDiscreteStepperID)
aSBMLDocument = libsbml.readSBMLFromString(aSBMLString)
# ------------------------------
# Function Definition Converter
# ------------------------------
theFunctionDefinitionConverter = libsbml.SBMLFunctionDefinitionConverter()
theFunctionDefinitionConverter.setDocument(aSBMLDocument)
print " FunctionDefinitionConverter: %s" % \
libsbml.OperationReturnValue_toString( theFunctionDefinitionConverter.convert() )
# ------------------------------
# Initial Assignment Converter
# ------------------------------
theInitialAssignmentConverter = libsbml.SBMLInitialAssignmentConverter()
theInitialAssignmentConverter.setDocument(aSBMLDocument)
print " InitialAssignmentConverter: %s" % \
libsbml.OperationReturnValue_toString( theInitialAssignmentConverter.convert() )
## FIXME: theInitialAssignmentConverter.convert() always returns None.
aSBMLModel = aSBMLDocument.getModel()
## theUndetermined =
theModel = SBML_Model(aSBMLDocument, aSBMLModel)
theCompartment = SBML_Compartment(theModel)
theParameter = SBML_Parameter(theModel)
theSpecies = SBML_Species(theModel)
theRule = SBML_Rule(theModel)
theReaction = SBML_Reaction(theModel)
theEvent = SBML_Event(theModel)
## # dump FunctionDefinition
## print "\n"
## for aFunctionDefinition in theModel.FunctionDefinitionList:
## print "FunctionDefinition: %s\n" % str( aFunctionDefinition )
anEml = Eml()
set_Steppers(theModel, anEml, Steppers, StepperIDs)
set_Compartments(theCompartment, anEml, StepperIDs)
set_GlobalParameters(theParameter, anEml, StepperIDs)
set_Species(theSpecies, anEml)
set_Rules(theRule, anEml, StepperIDs)
set_Reactions(theReaction, anEml, StepperIDs)
set_Events(theEvent, anEml, StepperIDs)
return anEml
#9) The overlap of the same changes --> might not be applicable in our case
#10) Reduced model
#11) ECM
#This is to test the good functioing of the main function and make sure that
#there are no errors
#TODO: change this to the stepTest
if __name__ == "__main__":
#read the TAR.XZ with all the SBML pathways
rpsbml_paths = {}
tar = tarfile.open('tests/testFBAin.tar.xz') #TODO: create this
rpsbml_paths = {}
for member in tar.getmembers():
rpsbml_paths[member.name] = rpFBA.rpSBML(member.name,libsbml.readSBMLFromString(tar.extractfile(member).read().decode("utf-8")))
#pass the different models to the SBML solvers and write the results to file
#rpsbml_paths = readrpSBMLzip(params.inSBMLzip)
for rpsbml_name in rpsbml_paths:
rpfba = rpFBA.rpFBA(rpsbml_paths[rpsbml_name])
rpfba.allObj()
#writerpSBMLzip(rpsbml_paths, params.outSBMLzip)
#designed to write using TAR.XZ with all the SBML pathways
with tarfile.open('testFBAout.tar.xz', 'w:xz') as tf:
for rpsbml_name in rpsbml_paths:
data = libsbml.writeSBMLToString(rpsbml_paths[rpsbml_name].document).encode('utf-8')
fiOut = BytesIO(data)
info = tarfile.TarInfo(rpsbml_name)
info.size = len(data)
tf.addfile(tarinfo=info, fileobj=fiOut)
from __future__ import print_function, division
import libsbml
import tellurium as te
import lxml.etree as ET
from io import StringIO
import tempfile
r = te.loada('''
J0: S1 -> S2; k1*S1;
S1=10.0; S2=0.0; k1=1.0;
''')
# create SBML file
f = tempfile.NamedTemporaryFile('w', suffix=".xml")
r.exportToSBML(f.name)
# create C14N canonical XML
et = ET.parse(f.name)
output = StringIO.StringIO()
et.write_c14n(output)
c14n_xml = output.getvalue()
# TODO: in addition sort all elements of the listOfs
# read with libsbml
doc = libsbml.readSBMLFromString(c14n_xml)
# read with roadrunner
te.loadSBMLModel(c14n_xml)
import os
path = os.path.dirname(os.path.realpath(__file__))
sbmlFilePath = os.path.join(path, 'MODEL0911989198.xml')
with open(sbmlFilePath,'r') as f:
sbmlString = f.read()
def module_exists(module_name):
try:
__import__(module_name)
except ImportError:
return False
else:
return True
if module_exists('libsbml'):
import libsbml
sbml = libsbml.readSBMLFromString(sbmlString)
def reversibilityIndex():
"""Quantitative measure for the reversibility of a reaction by taking into consideration the concentration of the substrate and products
"""
return False
if __name__ == "__main__":
#READ THE TAR.XZ FILE
rpsbml_paths = {}
tar = tarfile.open('tests/testTHERMOin.tar.xz') #TODO: create this
rpsbml_paths = {}
for member in tar.getmembers():
rpsbml_paths[member.name] = rpFBA.rpSBML(
member.name,
libsbml.readSBMLFromString(
tar.extractfile(member).read().decode("utf-8")))
###
rpthermo = rpThermo()
for rpsbml_name in rpsbml_paths:
rpthermo.pathway_drG_prime_m(rpsbml_paths[rpsbml_name])
#WRITE THE TAR.XZ FILE
with tarfile.open('testFBAout.tar.xz', 'w:xz') as tf:
for rpsbml_name in rpsbml_paths:
data = libsbml.writeSBMLToString(
rpsbml_paths[rpsbml_name].document).encode('utf-8')
fiOut = BytesIO(data)
info = tarfile.TarInfo(rpsbml_name)
info.size = len(data)
tf.addfile(tarinfo=info, fileobj=fiOut)
def biomodels_info():
'''
fetch latest biomodels release from ftp
extract
parse all curated models
'''
import ftplib
import tarfile
import libsbml
import re
import os
if not os.path.exists('release.tar.bz2'):
ftp = ftplib.FTP("ftp.ebi.ac.uk")
ftp.login()
ftp.cwd("/pub/databases/biomodels/releases/latest/")
file_list = []
ftp.dir(file_list.append)
ftp_file = [
x for x in file_list if x.endswith('pub-sbml_files.tar.bz2')
][0].split()[-1]
try:
ftp.retrbinary('RETR %s' % ftp_file,
open('release.tar.bz2', 'wb').write)
except ftplib.error_perm:
print 'ERROR: cannot read file "%s"' % ftp_file
import os
os.unlink(ftp_file)
return
#print '*** Downloaded "%s" to CWD' % ftp_file
else:
print 'used release.tar.bz2 in current folder! remove to redownload'
#Unpack and read info
tar = tarfile.open('release.tar.bz2', 'r:bz2')
curated_files = [x for x in tar.getnames() if '/curated/' in x]
items = []
notes_items = []
for fn in curated_files:
#print fn[-19:-4]
try:
cur_file = tar.extractfile(fn).read()
doc = libsbml.readSBMLFromString(cur_file)
model = doc.getModel()
notes = re.sub('body', 'div',
model.getNotes().getChild(0).toXMLString())
model_id = fn[-19:-4]
name = model.getName()
items.append([
model_id,
'<li><q><span bla="%s">%s: %s</span> <a href="{{=URL(r=request,f="biomodels_info_notes.html#%s")}}" target="_blank">notes</a></q></li>'
% (model_id, model_id, name, model_id)
])
notes_items.append('<div id="%s">%s</div>' % (model_id, notes))
except:
pass
#print model.getName(), model.getId(),
items.sort()
biomodels_list = "<ul class='biomodels_select'>%s\n</ul>" % "\n".join(
[x for y, x in items])
notes = "<div class='biomodels_notes'>%s</div><br/><br/><br/><br/><br/><br/><br/><br/>" % ''.join(
notes_items)
open('biomodels_info_list.html', 'w').write(biomodels_list)
open('biomodels_info_notes.html', 'w').write(notes)
import libsbml
import roadrunner
sbml_path = "body19_livertoy_flat.xml"
r = roadrunner.RoadRunner("body19_livertoy_flat.xml") # type: roadrunner.RoadRunner
sbml_str = r.getCurrentSBML()
doc1 = libsbml.readSBMLFromFile(sbml_path) # type: libsbml.SBMLDocument
doc2 = libsbml.readSBMLFromString(sbml_str) # type: libsbml.SBMLDocument
docs = {"sbml": doc1, "roadrunner": doc2}
for key, doc in docs.items():
print(key)
model = doc.getModel() # type: libsbml.Model
s = model.getSpecies("Ave_glc") # type: libsbml.Species
print(s)
print("initial concentration: ", s.getInitialConcentration())
print("initial amount: ", s.getInitialAmount())
print("-" * 80)
def convertSBML2EML( aSBMLString,
anODEStepper = "ODEStepper",
aFixedODEStepper = 'FixedODE1Stepper',
aDiscreteStepper = 'DiscreteTimeStepper' ): ## 'PassiveStepper'
theDefaultStepperID = 'Default'
theDefaultODEStepperID = 'ODE'
theDefaultDiscreteStepperID = 'Discrete'
Steppers = dict(
ODE = anODEStepper,
FixedODE = aFixedODEStepper,
Discrete = aDiscreteStepper )
StepperIDs = dict(
default = theDefaultStepperID,
ODE = theDefaultODEStepperID,
Discrete = theDefaultDiscreteStepperID )
aSBMLDocument = libsbml.readSBMLFromString( aSBMLString )
# ------------------------------
# Function Definition Converter
# ------------------------------
theFunctionDefinitionConverter = libsbml.SBMLFunctionDefinitionConverter()
theFunctionDefinitionConverter.setDocument( aSBMLDocument )
print " FunctionDefinitionConverter: %s" % \
libsbml.OperationReturnValue_toString( theFunctionDefinitionConverter.convert() )
# ------------------------------
# Initial Assignment Converter
# ------------------------------
theInitialAssignmentConverter = libsbml.SBMLInitialAssignmentConverter()
theInitialAssignmentConverter.setDocument( aSBMLDocument )
print " InitialAssignmentConverter: %s" % \
libsbml.OperationReturnValue_toString( theInitialAssignmentConverter.convert() )
## FIXME: theInitialAssignmentConverter.convert() always returns None.
aSBMLModel = aSBMLDocument.getModel()
## theUndetermined =
theModel = SBML_Model( aSBMLDocument, aSBMLModel )
theCompartment = SBML_Compartment( theModel )
theParameter = SBML_Parameter( theModel )
theSpecies = SBML_Species( theModel )
theRule = SBML_Rule( theModel )
theReaction = SBML_Reaction( theModel )
theEvent = SBML_Event( theModel )
## # dump FunctionDefinition
## print "\n"
## for aFunctionDefinition in theModel.FunctionDefinitionList:
## print "FunctionDefinition: %s\n" % str( aFunctionDefinition )
anEml = Eml()
set_Steppers( theModel, anEml, Steppers, StepperIDs )
set_Compartments( theCompartment, anEml, StepperIDs )
set_GlobalParameters( theParameter, anEml, StepperIDs )
set_Species( theSpecies, anEml )
set_Rules( theRule, anEml, StepperIDs )
set_Reactions( theReaction, anEml, StepperIDs )
set_Events( theEvent, anEml, StepperIDs )
return anEml
def sbml2jsbgn(sbml_str, rxncon=False):
try:
import libsbml
except ImportError:
raise HTTP(500, 'Your need to install libsbml-python to use this function. For Debian/Ubuntu see http://sbos.eu/doku.php?id=installation_instructions')
doc = libsbml.readSBMLFromString(sbml_str)
model = doc.getModel()
graph = dict(nodes = [], edges = [])
compartment2species = {}
seen_species = set()
#------------------------------------------
if 'rxncon.org' in sbml_str:
import re
pattern_nd = re.compile('(.+)\(([^\)]*)\)')
def modification2statevariable(mod):
if '~' in mod:
mod_split = mod.split('~')
if mod_split[1] == 'U':
return mod_split[0]
if mod_split[0] == 'bd':
return mod_split[1]
else:
return '%s@%s'%(mod_split[1],mod_split[0])
return ''
#------------------------------------------
name_or_id = lambda x : x.getName() or x.getId()
#------------------------------------------
def add_node(species_id, source_id, target_id, edge_sbo):
species = model.getSpecies(species_id)
if species_id not in seen_species:
seen_species.add(species_id)
#-------------------------------------
if 'rxncon.org' in sbml_str:
#print species.getName()
if 'sink' in species_id:
node_item = dict( id = species_id, sbo = 291, is_abstract = 0, data = dict ( x = 0.0, y = 0.0, width = 60, height = 60))
graph['nodes'].append(node_item)
elif species.getName().startswith('xXx') and species.getName().endswith('xXx()'):
node_item = dict(id = species_id, sbo = 347, is_abstract = 0, data = dict( x = 0.0, y = 0.0, width = 90, height = 60, label=species.getName()[3:-5]))
graph['nodes'].append(node_item)
elif '__' in species.getName():
complex_item = dict(id = species_id, sbo = 253, is_abstract = 0, data = dict(x = 0.0, y = 0.0, width = 60, height = 60, subnodes=[]))
for subnode_id in species.getName().split('__'):
match = re.search(pattern_nd, subnode_id)
print 'subnode_id', subnode_id
subnode_id, mods = match.group(1), match.group(2)
if ('rna' in subnode_id.lower()) or ('dna' in subnode_id.lower()):
sbo = 250
else:
sbo = 252
node_item = dict( id = species_id+subnode_id, sbo = sbo, is_abstract = 0, data = dict ( x = 0.0, y = 0.0, width = 60, height = 60, label=subnode_id))
if mods:
show_mods = [modification2statevariable(mod) for mod in mods.split(',') if '!' not in mod]
node_item['data']['statevariable'] = [x for x in show_mods if x]
complex_item['data']['subnodes'].append(species_id+subnode_id)
graph['nodes'].append(node_item)
graph['nodes'].append(complex_item)
else:
match = re.search(pattern_nd, species.getName())
spec_id, mods = match.group(1),match.group(2)
if ('rna' in spec_id.lower()) or ('dna' in spec_id.lower()):
sbo = 250
else:
sbo = 252
node_item = dict( id = species_id, sbo = sbo, is_abstract = 0, data = dict ( x = 0.0, y = 0.0, width = 60, height = 60, label=spec_id))
if mods:
show_mods = [modification2statevariable(mod) for mod in mods.split(',') if '!' not in mod]
node_item['data']['statevariable'] = [x for x in show_mods if x]
graph['nodes'].append(node_item)
#-------------------------------------
else:
if 'sink' in species_id or name_or_id(species).lower() == 'emptyset':
sbo = 291
label = ''
else:
sbo = 285
#-------------------------------------
#guess sbo
for n in range(species.getNumCVTerms()):
cvt = species.getCVTerm(n)
res = cvt.getResources()
for m in range(res.getLength()):
resource = res.getValue(m)
if 'urn:miriam:obo.chebi' in resource:
sbo = 247
break
if 'urn:miriam:pubchem' in resource:
sbo = 247
break
if 'urn:miriam:uniprot' in resource:
sbo = 245
break
if ('rna' in name_or_id(species).lower()) or ('dna' in name_or_id(species).lower()):
sbo = 250
#if 'complex' in name_or_id(species).lower():
# sbo = 253
label = name_or_id(species)
#-------------------------------------
#create node
node_item = dict(
id = species_id,
sbo = sbo,
is_abstract = 0,
data = dict (
x = 0.0,
y = 0.0,
width = 60,
height = 60,
)
)
if label:
node_item['data']['label'] = label
#-------------------------------------
graph['nodes'].append(node_item)
#-------------------------------------
#create edge
edge_item = dict(
id = 'x',
source = source_id,
target = target_id,
sbo = edge_sbo,
)
graph['edges'].append(edge_item)
#-------------------------------------
#add compartment (compartments are linked from the compartment as subnodes)
if species:
#node_item['data']['compartment'] = species.getCompartment()
try:
compartment2species[species.getCompartment()].append(species.getId())
except KeyError:
compartment2species[species.getCompartment()] = [species.getId()]
return species.getCompartment()
#------------------------------------------
for reaction in model.getListOfReactions():
node_item = dict(
id = reaction.getId(),
sbo = 375,
is_abstract = 0,
data = dict (
x = 0.0,
y = 0.0,
label = name_or_id(reaction),
width = 20,
height = 20,
)
)
graph['nodes'].append(node_item)
#---------------
#reactands
comp = None
has_sink = False
if len(reaction.getListOfReactants())==0:
add_node(reaction.getId()+'sink', reaction.getId()+'sink', reaction.getId(), 394)
has_sink = reaction.getId()+'sink'
else:
for substrate in reaction.getListOfReactants():
comp = add_node(substrate.getSpecies(), substrate.getSpecies(), reaction.getId(), 394)
if comp:
compartment2species[comp].append(reaction.getId())
#---------------
#products
if len(reaction.getListOfProducts())==0:
add_node(reaction.getId()+'sink', reaction.getId(), reaction.getId()+'sink', 393)
has_sink = reaction.getId()+'sink'
else:
for product in reaction.getListOfProducts():
comp = add_node(product.getSpecies(), reaction.getId(), product.getSpecies(), 393)
if comp:
compartment2species[comp].append(reaction.getId())
if has_sink:
compartment2species[comp].append(has_sink)
#---------------
#modifiers
for modifier in reaction.getListOfModifiers():
#FIXME check sbo for edge_sbo
add_node(modifier.getSpecies(), modifier.getSpecies(), reaction.getId(), 168)
#------------------------------------------
for compartment in model.getListOfCompartments():
node_item = dict(
id = compartment.getId(),
sbo = 290,
is_abstract = 0,
data = dict (
x = 10.0,
y = 10.0,
label = name_or_id(compartment),
height = 200,
width = 200,
)
)
if compartment.getId() in compartment2species:
node_item['data']['subnodes'] = list(set(compartment2species[compartment.getId()]))
graph['nodes'].append(node_item)
for i in range(len(graph['edges'])):
graph['edges'][i]['id'] = 'edge%s'%i
#print graph
return graph
import os
path = os.path.dirname(os.path.realpath(__file__))
sbmlFilePath = os.path.join(path, 'MODEL1204280021.xml')
with open(sbmlFilePath,'r') as f:
sbmlString = f.read()
def module_exists(module_name):
try:
__import__(module_name)
except ImportError:
return False
else:
return True
if module_exists('libsbml'):
import libsbml
sbml = libsbml.readSBMLFromString(sbmlString)
def sbml2jsbgn(sbml_str, rxncon=False):
try:
import libsbml
except ImportError:
raise HTTP(
500,
'Your need to install libsbml-python to use this function. For Debian/Ubuntu see http://sbos.eu/doku.php?id=installation_instructions'
)
doc = libsbml.readSBMLFromString(sbml_str)
model = doc.getModel()
graph = dict(nodes=[], edges=[])
compartment2species = {}
seen_species = set()
#------------------------------------------
if 'rxncon.org' in sbml_str:
import re
pattern_nd = re.compile('(.+)\(([^\)]*)\)')
def modification2statevariable(mod):
if '~' in mod:
mod_split = mod.split('~')
if mod_split[1] == 'U':
return mod_split[0]
if mod_split[0] == 'bd':
return mod_split[1]
else:
return '%s@%s' % (mod_split[1], mod_split[0])
return ''
#------------------------------------------
name_or_id = lambda x: x.getName() or x.getId()
#------------------------------------------
def add_node(species_id, source_id, target_id, edge_sbo):
species = model.getSpecies(species_id)
if species_id not in seen_species:
seen_species.add(species_id)
#-------------------------------------
if 'rxncon.org' in sbml_str:
#print species.getName()
if 'sink' in species_id:
node_item = dict(id=species_id,
sbo=291,
is_abstract=0,
data=dict(x=0.0,
y=0.0,
width=60,
height=60))
graph['nodes'].append(node_item)
elif species.getName().startswith(
'xXx') and species.getName().endswith('xXx()'):
node_item = dict(id=species_id,
sbo=347,
is_abstract=0,
data=dict(x=0.0,
y=0.0,
width=90,
height=60,
label=species.getName()[3:-5]))
graph['nodes'].append(node_item)
elif '__' in species.getName():
complex_item = dict(id=species_id,
sbo=253,
is_abstract=0,
data=dict(x=0.0,
y=0.0,
width=60,
height=60,
subnodes=[]))
for subnode_id in species.getName().split('__'):
match = re.search(pattern_nd, subnode_id)
print 'subnode_id', subnode_id
subnode_id, mods = match.group(1), match.group(2)
if ('rna' in subnode_id.lower()) or (
'dna' in subnode_id.lower()):
sbo = 250
else:
sbo = 252
node_item = dict(id=species_id + subnode_id,
sbo=sbo,
is_abstract=0,
data=dict(x=0.0,
y=0.0,
width=60,
height=60,
label=subnode_id))
if mods:
show_mods = [
modification2statevariable(mod)
for mod in mods.split(',') if '!' not in mod
]
node_item['data']['statevariable'] = [
x for x in show_mods if x
]
complex_item['data']['subnodes'].append(species_id +
subnode_id)
graph['nodes'].append(node_item)
graph['nodes'].append(complex_item)
else:
match = re.search(pattern_nd, species.getName())
spec_id, mods = match.group(1), match.group(2)
if ('rna' in spec_id.lower()) or ('dna'
in spec_id.lower()):
sbo = 250
else:
sbo = 252
node_item = dict(id=species_id,
sbo=sbo,
is_abstract=0,
data=dict(x=0.0,
y=0.0,
width=60,
height=60,
label=spec_id))
if mods:
show_mods = [
modification2statevariable(mod)
for mod in mods.split(',') if '!' not in mod
]
node_item['data']['statevariable'] = [
x for x in show_mods if x
]
graph['nodes'].append(node_item)
#-------------------------------------
else:
if 'sink' in species_id or name_or_id(
species).lower() == 'emptyset':
sbo = 291
label = ''
else:
sbo = 285
#-------------------------------------
#guess sbo
for n in range(species.getNumCVTerms()):
cvt = species.getCVTerm(n)
res = cvt.getResources()
for m in range(res.getLength()):
resource = res.getValue(m)
if 'urn:miriam:obo.chebi' in resource:
sbo = 247
break
if 'urn:miriam:pubchem' in resource:
sbo = 247
break
if 'urn:miriam:uniprot' in resource:
sbo = 245
break
if ('rna' in name_or_id(species).lower()) or (
'dna' in name_or_id(species).lower()):
sbo = 250
#if 'complex' in name_or_id(species).lower():
# sbo = 253
label = name_or_id(species)
#-------------------------------------
#create node
node_item = dict(id=species_id,
sbo=sbo,
is_abstract=0,
data=dict(
x=0.0,
y=0.0,
width=60,
height=60,
))
if label:
node_item['data']['label'] = label
#-------------------------------------
graph['nodes'].append(node_item)
#-------------------------------------
#create edge
edge_item = dict(
id='x',
source=source_id,
target=target_id,
sbo=edge_sbo,
)
graph['edges'].append(edge_item)
#-------------------------------------
#add compartment (compartments are linked from the compartment as subnodes)
if species:
#node_item['data']['compartment'] = species.getCompartment()
try:
compartment2species[species.getCompartment()].append(
species.getId())
except KeyError:
compartment2species[species.getCompartment()] = [
species.getId()
]
return species.getCompartment()
#------------------------------------------
for reaction in model.getListOfReactions():
node_item = dict(id=reaction.getId(),
sbo=375,
is_abstract=0,
data=dict(
x=0.0,
y=0.0,
label=name_or_id(reaction),
width=20,
height=20,
))
graph['nodes'].append(node_item)
#---------------
#reactands
comp = None
has_sink = False
if len(reaction.getListOfReactants()) == 0:
add_node(reaction.getId() + 'sink',
reaction.getId() + 'sink', reaction.getId(), 394)
has_sink = reaction.getId() + 'sink'
else:
for substrate in reaction.getListOfReactants():
comp = add_node(substrate.getSpecies(), substrate.getSpecies(),
reaction.getId(), 394)
if comp:
compartment2species[comp].append(reaction.getId())
#---------------
#products
if len(reaction.getListOfProducts()) == 0:
add_node(reaction.getId() + 'sink', reaction.getId(),
reaction.getId() + 'sink', 393)
has_sink = reaction.getId() + 'sink'
else:
for product in reaction.getListOfProducts():
comp = add_node(product.getSpecies(), reaction.getId(),
product.getSpecies(), 393)
if comp:
compartment2species[comp].append(reaction.getId())
if has_sink:
compartment2species[comp].append(has_sink)
#---------------
#modifiers
for modifier in reaction.getListOfModifiers():
#FIXME check sbo for edge_sbo
add_node(modifier.getSpecies(), modifier.getSpecies(),
reaction.getId(), 168)
#------------------------------------------
for compartment in model.getListOfCompartments():
node_item = dict(id=compartment.getId(),
sbo=290,
is_abstract=0,
data=dict(
x=10.0,
y=10.0,
label=name_or_id(compartment),
height=200,
width=200,
))
if compartment.getId() in compartment2species:
node_item['data']['subnodes'] = list(
set(compartment2species[compartment.getId()]))
graph['nodes'].append(node_item)
for i in range(len(graph['edges'])):
graph['edges'][i]['id'] = 'edge%s' % i
#print graph
return graph
