def makeArcsFromProcess(process, iarc, dids):
arcs = []
for reactant in process.getReactants():
arc = libsbgn.arc()
start = libsbgn.startType(0, 0)
end = libsbgn.endType(0, 0)
arc.set_source(dids[reactant.getId()])
# arc.set_target("{0}.1".format(process.getId()))
arc.set_target(dids[process.getId()])
arc.set_id("arc{0}".format(iarc))
iarc += 1
arc.set_start(start)
arc.set_end(end)
arc.set_class(libsbgn.ArcClass.CONSUMPTION)
arcs.append(arc)
for product in process.getProducts():
arc = libsbgn.arc()
start = libsbgn.startType(0, 0)
end = libsbgn.endType(0, 0)
# arc.set_source("{0}.2".format(process.getId()))
arc.set_source(dids[process.getId()])
arc.set_target(dids[product.getId()])
arc.set_id("arc{0}".format(iarc))
iarc += 1
arc.set_start(start)
arc.set_end(end)
arc.set_class(libsbgn.ArcClass.PRODUCTION)
arcs.append(arc)
return iarc, arcs
def makeArcsFromProcess(process, iarc, dids):
arcs = []
for reactant in process.getReactants():
arc = libsbgn.arc()
start = libsbgn.startType(0, 0)
end = libsbgn.endType(0, 0)
arc.set_source(dids[reactant.getId()])
# arc.set_target("{0}.1".format(process.getId()))
arc.set_target(dids[process.getId()])
arc.set_id("arc{0}".format(iarc))
iarc += 1
arc.set_start(start)
arc.set_end(end)
arc.set_class(libsbgn.ArcClass.CONSUMPTION)
arcs.append(arc)
for product in process.getProducts():
arc = libsbgn.arc()
start = libsbgn.startType(0, 0)
end = libsbgn.endType(0, 0)
# arc.set_source("{0}.2".format(process.getId()))
arc.set_source(dids[process.getId()])
arc.set_target(dids[product.getId()])
arc.set_id("arc{0}".format(iarc))
iarc += 1
arc.set_start(start)
arc.set_end(end)
arc.set_class(libsbgn.ArcClass.PRODUCTION)
arcs.append(arc)
return iarc, arcs
def _make_arcs_from_process(process, dids):
arcs = []
if hasattr(process, "reactants"):
for reactant in process.reactants:
arc = libsbgn.arc()
start = libsbgn.startType(0, 0)
end = libsbgn.endType(0, 0)
arc.set_source(dids[str(reactant)])
# arc.set_target("{0}.1".format(process.getId()))
arc.set_target(dids[str(process)])
arc.set_id("cons_{0}_{1}".format(dids[str(reactant)],
dids[str(process)]))
arc.set_start(start)
arc.set_end(end)
arc.set_class(libsbgn.ArcClass.CONSUMPTION)
arcs.append(arc)
if hasattr(process, "products"):
for product in process.products:
arc = libsbgn.arc()
start = libsbgn.startType(0, 0)
end = libsbgn.endType(0, 0)
# arc.set_source("{0}.2".format(process.getId()))
arc.set_source(dids[str(process)])
arc.set_target(dids[str(product)])
arc.set_id("prod_{0}_{1}".format(dids[str(process)],
dids[str(product)]))
arc.set_start(start)
arc.set_end(end)
arc.set_class(libsbgn.ArcClass.PRODUCTION)
arcs.append(arc)
return arcs
def add_arc_glyph(self, glyph, side="left", stoichiometry=None):
"""Method for adding specific arc with all needed parameters and right direction.
It can be CONSUMPTION, PRODUCTION or MODULATION arc.
:param glyph: Glyph from arc should start or end.
:param side: determine direction and type of arc
:return:
"""
if side == "left":
x_start, y_start = glyph.bbox.get_x() + glyph.bbox.get_w(
), glyph.bbox.get_y() + (glyph.bbox.get_h() / 2)
x_end, y_end = self.port_in["x"], self.port_in["y"]
arc = libsbgn.arc(class_=ArcClass.CONSUMPTION,
source=glyph.get_id()[0],
target=self.port_in["id"],
id=glyph.get_id()[0] + "_in")
arc.set_start(libsbgn.startType(x=x_start, y=y_start))
arc.set_end(libsbgn.endType(x=x_end, y=y_end))
elif side == "right":
x_start, y_start = self.port_out["x"], self.port_out["y"]
x_end, y_end = glyph.bbox.get_x(), glyph.bbox.get_y() + (
glyph.bbox.get_h() / 2)
arc = libsbgn.arc(class_=ArcClass.PRODUCTION,
source=self.port_out["id"],
target=glyph.get_id()[0],
id=glyph.get_id()[0] + "_out")
arc.set_start(libsbgn.startType(x=x_start, y=y_start))
arc.set_end(libsbgn.endType(x=x_end, y=y_end))
else:
if glyph.bbox.get_y() > self.port_in["y"]:
x_start, y_start = glyph.bbox.get_x(
) + glyph.bbox.get_w() / 2, glyph.bbox.get_y()
x_end, y_end = self.port_in["x"] + self.pg_size, self.port_in[
"y"] + (self.pg_size / 2)
else:
x_start, y_start = glyph.bbox.get_x() + glyph.bbox.get_w(
) / 2, glyph.bbox.get_y() + glyph.bbox.get_h()
x_end, y_end = self.port_in["x"] + self.pg_size, self.port_in[
"y"] - (self.pg_size / 2)
arc = libsbgn.arc(class_=ArcClass.MODULATION,
source=glyph.get_id()[0],
target=self.port_in["id"],
id=glyph.get_id()[0] + "_modifier")
arc.set_start(libsbgn.startType(x=x_start, y=y_start))
arc.set_end(libsbgn.endType(x=x_end, y=y_end))
if stoichiometry and stoichiometry != 0:
stoichiometry_glyph = libsbgn.glyph(
class_=GlyphClass.STOICHIOMETRY, id=str(hash(glyph)))
stoichiometry_glyph.set_label(libsbgn.label(text=stoichiometry))
x, y = self._get_middle_of_edge(x_start, y_start, x_end, y_end)
stoichiometry_glyph.set_bbox(
libsbgn.bbox(x=x,
y=y,
w=STOICHIOMETRY_GLYPH_SIZE,
h=STOICHIOMETRY_GLYPH_SIZE))
self.map.add_glyph(stoichiometry_glyph)
arc.add_glyph(stoichiometry_glyph)
self.map.add_arc(arc)
def _make_arc_from_modulation(modulation, dids):
arc = libsbgn.arc()
start = libsbgn.startType(0, 0)
end = libsbgn.endType(0, 0)
arc.set_source(dids[str(modulation.source)])
arc.set_target(dids[str(modulation.target)])
arc.set_id(modulation.id)
arc.set_start(start)
arc.set_end(end)
arc.set_class(libsbgn.ArcClass[ModulationEnum(modulation.__class__).name])
return arc
def makeArcFromModulation(modulation, iarc, dids):
arc = libsbgn.arc()
start = libsbgn.startType(0, 0)
end = libsbgn.endType(0, 0)
arc.set_source(dids[modulation.getSource().getId()])
arc.set_target(dids[modulation.getTarget().getId()])
arc.set_id("arc{0}".format(iarc))
iarc += 1
arc.set_start(start)
arc.set_end(end)
arc.set_class(libsbgn.ArcClass[modulation.getClazz().name])
return iarc, arc
def makeArcFromModulation(modulation, iarc, dids):
arc = libsbgn.arc()
start = libsbgn.startType(0, 0)
end = libsbgn.endType(0, 0)
arc.set_source(dids[modulation.getSource().getId()])
arc.set_target(dids[modulation.getTarget().getId()])
arc.set_id("arc{0}".format(iarc))
iarc += 1
arc.set_start(start)
arc.set_end(end)
arc.set_class(libsbgn.ArcClass[modulation.getClazz().name])
return iarc, arc
def _make_arcs_from_lo(op, dids):
arcs = []
for child in op.children:
arc = libsbgn.arc()
start = libsbgn.startType(0, 0)
end = libsbgn.endType(0, 0)
arc.set_source(dids[str(child)])
arc.set_target(dids[str(op)])
arc.set_id("log_{0}_{1}".format(dids[str(child)], dids[str(op)]))
arc.set_start(start)
arc.set_end(end)
arc.set_class(libsbgn.ArcClass["LOGIC_ARC"])
arcs.append(arc)
return arcs
def sbgn():
""" Fixture provides sbgn test data via sbgn argument. """
# create empty sbgn
sbgn = libsbgn.sbgn()
# create map, set language and set in sbgn
sbgn_map = libsbgn.map()
sbgn_map.set_language(Language.PD)
sbgn.set_map(sbgn_map)
# create a bounding box for map
box = libsbgn.bbox(x=0, y=0, w=363, h=253)
sbgn_map.set_bbox(box)
# create some glyphs
# class attribute is named 'class_' ! in glyphs and arcs
# glyphs with labels
g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id="glyph1")
g.set_label(libsbgn.label(text="Ethanol"))
g.set_bbox(libsbgn.bbox(x=40, y=120, w=60, h=60))
sbgn_map.add_glyph(g)
# glyph with ports (process)
g = libsbgn.glyph(class_=GlyphClass.PROCESS,
id="pn1",
orientation=Orientation.HORIZONTAL)
g.set_bbox(libsbgn.bbox(x=148, y=168, w=24, h=24))
g.add_port(libsbgn.port(x=136, y=180, id="pn1.1"))
g.add_port(libsbgn.port(x=184, y=180, id="pn1.2"))
sbgn_map.add_glyph(g)
# arcs
# create arcs and set the start and end points
a = libsbgn.arc(class_=ArcClass.CONSUMPTION,
source="glyph1",
target="pn1.1",
id="a01")
a.set_start(libsbgn.startType(x=98, y=160))
a.set_end(libsbgn.endType(x=136, y=180))
sbgn_map.add_arc(a)
return sbgn
def sbgn():
""" Fixture provides sbgn test data via sbgn argument. """
# create empty sbgn
sbgn = libsbgn.sbgn()
# create map, set language and set in sbgn
sbgn_map = libsbgn.map()
sbgn_map.set_language(Language.PD)
sbgn.set_map(sbgn_map)
# create a bounding box for map
box = libsbgn.bbox(x=0, y=0, w=363, h=253)
sbgn_map.set_bbox(box)
# create some glyphs
# class attribute is named 'class_' ! in glyphs and arcs
# glyphs with labels
g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id='glyph1')
g.set_label(libsbgn.label(text='Ethanol'))
g.set_bbox(libsbgn.bbox(x=40, y=120, w=60, h=60))
sbgn_map.add_glyph(g)
# glyph with ports (process)
g = libsbgn.glyph(class_=GlyphClass.PROCESS, id='pn1',
orientation=Orientation.HORIZONTAL)
g.set_bbox(libsbgn.bbox(x=148, y=168, w=24, h=24))
g.add_port(libsbgn.port(x=136, y=180, id="pn1.1"))
g.add_port(libsbgn.port(x=184, y=180, id="pn1.2"))
sbgn_map.add_glyph(g)
# arcs
# create arcs and set the start and end points
a = libsbgn.arc(class_=ArcClass.CONSUMPTION, source="glyph1", target="pn1.1", id="a01")
a.set_start(libsbgn.startType(x=98, y=160))
a.set_end(libsbgn.endType(x=136, y=180))
sbgn_map.add_arc(a)
return sbgn
g.set_label(libsbgn.label(text='NADH')) g.set_bbox(libsbgn.bbox(x=300, y=150, w=60, h=60)) map.add_glyph(g) # glyph with ports (process) g = libsbgn.glyph(class_=GlyphClass.PROCESS, id='pn1', orientation=Orientation.HORIZONTAL) g.set_bbox(libsbgn.bbox(x=148, y=168, w=24, h=24)) g.add_port(libsbgn.port(x=136, y=180, id="pn1.1")) g.add_port(libsbgn.port(x=184, y=180, id="pn1.2")) map.add_glyph(g) # arcs # create arcs and set the start and end points a = libsbgn.arc(class_=ArcClass.CONSUMPTION, source="glyph1", target="pn1.1", id="a01") a.set_start(libsbgn.startType(x=98, y=160)) a.set_end(libsbgn.endType(x=136, y=180)) map.add_arc(a) a = libsbgn.arc(class_=ArcClass.PRODUCTION, source="pn1.2", target="glyph_nadh", id="a02") a.set_start(libsbgn.startType(x=184, y=180)) a.set_end(libsbgn.endType(x=300, y=180)) map.add_arc(a) a = libsbgn.arc(class_=ArcClass.CATALYSIS, source="glyph_adh1", target="pn1", id="a03") a.set_start(libsbgn.startType(x=160, y=80)) a.set_end(libsbgn.endType(x=160, y=168)) map.add_arc(a) a = libsbgn.arc(class_=ArcClass.PRODUCTION, source="pn1.2", target="glyph_h", id="a04") a.set_start(libsbgn.startType(x=184, y=180))
apd_arc_name = list(set(apd_synonyms).intersection(set(arc_names)))
if apd_arc_name:
apd_sbgn_arc = arc_dic[apd_arc_name[0]]
print(pn)
print(apd_arc_name[0])
else:
apd_sbgn_arc = ArcClass.UNKNOWN_INFLUENCE
for sub in subj:
a = libsbgn.arc(class_=sub_subgn_arc,
source=ent_dic[str(sub)],
target='pn' + str(pn) + '.1',
id="a" + str(an))
a.set_start(libsbgn.startType(x=98, y=160))
a.set_end(libsbgn.endType(x=136, y=180))
map.add_arc(a)
an = an + 1
for ob in obj:
a = libsbgn.arc(class_=sbgn_arc,
source='pn' + str(pn) + '.2',
target=ent_dic[str(ob)],
id="a" + str(an))
a.set_start(libsbgn.startType(x=98, y=160))
a.set_end(libsbgn.endType(x=136, y=180))
map.add_arc(a)
an = an + 1
for ap in apd:
def save_as_sbgn(n2lo, e2lo, model, out_sbgn):
"""
Converts a model with the given node and edge layout to SBGN PD (see http://www.sbgn.org/).
:param n2lo: node layout as a dictionary {node_id: ((x, y), (w, h)) if node is not ubiquitous
else node_id : {r_ids: ((x, y), (w, h)) for r_ids of
reactions using each duplicated metabolite}}
:param e2lo: edge layout as a dictionary {edge_id: [(x_start, y_start), (x_bend_0, y_bend_0),..,(x_end, y_end)]},
where edge_id = "-".join(sorted((metabolite_id, reaction_id))).
:param model: SBML model
:param out_sbgn: path where to save the resulting SBGN file.
"""
# let's scale the map so that a minimal node has a width == 16 (so that the labels fit)
h_min, (x_shift, y_shift), (w, h) = get_layout_characteristics(n2lo)
scale_factor = MARGIN * 1.0 / h_min if h_min else 1
(w, h) = scale((w, h), scale_factor)
(x_shift, y_shift) = shift(scale((x_shift, y_shift), scale_factor), MARGIN, MARGIN)
# create empty sbgn
sbgn = libsbgn.sbgn()
# create map, set language and set in sbgn
sbgn_map = libsbgn.map()
sbgn_map.set_language(Language.PD)
sbgn.set_map(sbgn_map)
# create a bounding box for the map
box = libsbgn.bbox(0, 0, w + 2 * MARGIN, h + 2 * MARGIN)
sbgn_map.set_bbox(box)
# glyphs with labels
for comp in model.getListOfCompartments():
c_id = comp.getId()
c_name = comp.getName()
if not c_name:
c_name = c_id
if c_id in n2lo:
(x, y), (w, h) = transform(n2lo[c_id], x_shift, y_shift, scale_factor)
g = libsbgn.glyph(class_=GlyphClass.COMPARTMENT, id=c_id)
g.set_label(libsbgn.label(text=c_name, bbox=libsbgn.bbox(x, y, w, h)))
g.set_bbox(libsbgn.bbox(x, y, w, h))
sbgn_map.add_glyph(g)
for species in model.getListOfSpecies():
s_id = species.getId()
s_name = species.getName()
glyph_type = GlyphClass.UNSPECIFIED_ENTITY
sbo_term = species.getSBOTermID()
if sbo_term:
sbo_term = sbo_term.upper().strip()
if sbo_term in SBO_2_GLYPH_TYPE:
glyph_type = SBO_2_GLYPH_TYPE[sbo_term]
if not s_name:
s_name = s_id
if s_id in n2lo:
if isinstance(n2lo[s_id], dict):
elements = n2lo[s_id].items()
else:
elements = [('', n2lo[s_id])]
for r_ids, coords in elements:
if not r_ids or next((it for it in (model.getReaction(r_id) for r_id in r_ids) if it), False):
(x, y), (w, h) = transform(coords, x_shift, y_shift, scale_factor)
g = libsbgn.glyph(class_=glyph_type, id="%s_%s" % (s_id, '_'.join(r_ids)) if r_ids else s_id,
compartmentRef=species.getCompartment())
g.set_label(libsbgn.label(text=s_name,
bbox=libsbgn.bbox(x + w * 0.1, y + h * 0.1, w * 0.8, h * 0.8)))
g.set_bbox(libsbgn.bbox(x, y, w, h))
sbgn_map.add_glyph(g)
# glyph with ports (process)
for reaction in model.getListOfReactions():
r_id = reaction.getId()
if r_id in n2lo:
(x, y), (w, h) = transform(n2lo[r_id], x_shift, y_shift, scale_factor)
g = libsbgn.glyph(class_=GlyphClass.PROCESS, id=r_id)
g.set_bbox(libsbgn.bbox(x, y, w, h))
rev = reaction.getReversible()
in_port = None
for s_id in (species_ref.getSpecies() for species_ref in reaction.getListOfReactants()):
edge_id = "-".join(sorted((s_id, r_id)))
if edge_id in e2lo:
xy_list = e2lo[edge_id]
if not in_port:
port_x, port_y = shift(scale(xy_list[-2] if len(xy_list) > 2 else xy_list[-1], scale_factor),
x_shift, y_shift)
in_port = libsbgn.port(x=port_x, y=port_y, id="%s__in" % r_id)
g.add_port(in_port)
sref_id = s_id
if isinstance(n2lo[s_id], dict):
for r_ids in n2lo[s_id].keys():
if r_id in r_ids:
sref_id = "%s_%s" % (s_id, '_'.join(r_ids))
a = libsbgn.arc(class_=ArcClass.PRODUCTION if rev else ArcClass.CONSUMPTION,
target=sref_id if rev else in_port.get_id(),
source=in_port.get_id() if rev else sref_id, id="a_%s_%s" % (s_id, r_id))
s_x, s_y = shift(scale(xy_list[0], scale_factor), x_shift, y_shift)
a.set_start(libsbgn.startType(x=in_port.get_x() if rev else s_x, y=in_port.get_y() if rev else s_y))
a.set_end(libsbgn.endType(x=s_x if rev else in_port.get_x(), y=s_y if rev else in_port.get_y()))
sbgn_map.add_arc(a)
out_port = None
for s_id in (species_ref.getSpecies() for species_ref in reaction.getListOfProducts()):
edge_id = "-".join(sorted((s_id, r_id)))
if edge_id in e2lo:
xy_list = e2lo[edge_id]
if not out_port:
port_x, port_y = shift(scale(xy_list[1] if len(xy_list) > 2 else xy_list[0], scale_factor),
x_shift, y_shift)
out_port = libsbgn.port(x=port_x, y=port_y, id="%s__out" % r_id)
g.add_port(out_port)
sref_id = s_id
if isinstance(n2lo[s_id], dict):
for r_ids in n2lo[s_id].keys():
if r_id in r_ids:
sref_id = "%s_%s" % (s_id, '_'.join(r_ids))
a = libsbgn.arc(class_=ArcClass.PRODUCTION, target=sref_id, source=out_port.get_id(),
id="a_%s_%s" % (r_id, s_id))
s_x, s_y = shift(scale(xy_list[-1], scale_factor), x_shift, y_shift)
a.set_end(libsbgn.startType(x=s_x, y=s_y))
a.set_start(libsbgn.endType(x=out_port.get_x(), y=out_port.get_y()))
sbgn_map.add_arc(a)
sbgn_map.add_glyph(g)
# write everything to a file
sbgn.write_file(out_sbgn)
def test_basestring_issue():
"""
This tests issue: https://github.com/matthiaskoenig/libsbgn-python/issues/4
"""
# create empty sbgn
sbgn = libsbgn.sbgn()
# create map, set language and set in sbgn
sbgn_map = libsbgn.map()
sbgn_map.set_language(Language.PD)
sbgn.set_map(sbgn_map)
# create a bounding box for the map
box = libsbgn.bbox(0, 0, 100, 100)
sbgn_map.set_bbox(box)
# glyphs with labels
for comp in ('Cytoplasm', ):
c_id = comp
c_name = comp
(x, y), (w, h) = (10, 10), (90, 90)
g = libsbgn.glyph(class_=GlyphClass.COMPARTMENT, id=c_id)
g.set_label(libsbgn.label(text=c_name, bbox=libsbgn.bbox(x, y, w, h)))
g.set_bbox(libsbgn.bbox(x, y, w, h))
sbgn_map.add_glyph(g)
s2xy = {'H2': (20, 20), 'O2': (20, 80), 'H2O': (80, 60)}
for species, (x, y) in s2xy.items():
s_id = species
s_name = species
glyph_type = GlyphClass.UNSPECIFIED_ENTITY
glyph_type = GlyphClass.SIMPLE_CHEMICAL
(w, h) = (5, 5)
g = libsbgn.glyph(class_=glyph_type, id=s_id, compartmentRef='Cytoplasm')
g.set_label(libsbgn.label(text=s_name,
bbox=libsbgn.bbox(x + w * 0.1, y + h * 0.1, w * 0.8, h * 0.8)))
g.set_bbox(libsbgn.bbox(x, y, w, h))
sbgn_map.add_glyph(g)
# glyph with ports (process)
r_id = 'Water'
(x, y), (w, h) = (60, 60), (4, 4)
g = libsbgn.glyph(class_=GlyphClass.PROCESS, id=r_id)
g.set_bbox(libsbgn.bbox(x, y, w, h))
in_port = None
for s_id in ('O2', 'H2'):
edge_id = "-".join(sorted((s_id, r_id)))
if not in_port:
port_x, port_y = (61, 62)
in_port = libsbgn.port(x=port_x, y=port_y, id="%s__in" % r_id)
g.add_port(in_port)
sref_id = s_id
a = libsbgn.arc(class_=ArcClass.CONSUMPTION,
target=in_port.get_id(),
source=sref_id, id="a_%s_%s" % (s_id, r_id))
s_x, s_y = s2xy[s_id]
a.set_start(libsbgn.startType(x=s_x, y=s_y))
a.set_end(libsbgn.endType(x=in_port.get_x(), y=in_port.get_y()))
sbgn_map.add_arc(a)
out_port = None
for s_id in ('H2O', ):
edge_id = "-".join(sorted((s_id, r_id)))
if not out_port:
port_x, port_y = (63, 62)
out_port = libsbgn.port(x=port_x, y=port_y, id="%s__out" % r_id)
g.add_port(out_port)
sref_id = s_id
a = libsbgn.arc(class_=ArcClass.PRODUCTION, target=sref_id, source=out_port.get_id(),
id="a_%s_%s" % (r_id, s_id))
s_x, s_y = s2xy[s_id]
a.set_end(libsbgn.startType(x=s_x, y=s_y))
a.set_start(libsbgn.endType(x=out_port.get_x(), y=out_port.get_y()))
sbgn_map.add_arc(a)
sbgn_map.add_glyph(g)
# write everything to a file
f_tmp = tempfile.NamedTemporaryFile(suffix=".sbgn")
sbgn.write_file(f_tmp.name)
def write_sbgn_02(f):
""" Create SBGN document and write to file.
:param f:
:return:
"""
# create empty sbgn
sbgn = libsbgn.sbgn()
# create map, set language and set in sbgn
map = libsbgn.map()
map.set_language(Language.PD)
sbgn.set_map(map)
# create a bounding box for map
# <bbox x="0" y="0" w="363" h="253"/>
# [1] de novo and set all attributes
# box = libsbgn.bbox()
# box.set_x(0)
# box.set_y(0)
# box.set_w(363)
# box.set_h(253)
# [2] de novo with attributes at creation
box = libsbgn.bbox(x=0, y=0, w=363, h=253)
map.set_bbox(box)
# create some glyphs
# class attribute is named 'class_' ! in glyphs and arcs
'''
<glyph class="simple chemical" id="glyph1">
<label text="Ethanol"/> <!-- fontsize="" etc -->
<!-- Line breaks are allowed in the text attribute -->
<bbox x="40" y="120" w="60" h="60"/>
</glyph>
'''
# glyphs with labels
g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id='glyph1')
g.set_label(libsbgn.label(text='Ethanol'))
g.set_bbox(libsbgn.bbox(x=40, y=120, w=60, h=60))
map.add_glyph(g)
g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id='glyph_ethanal')
g.set_label(libsbgn.label(text='Ethanal'))
g.set_bbox(libsbgn.bbox(x=220, y=110, w=60, h=60))
map.add_glyph(g)
g = libsbgn.glyph(class_=GlyphClass.MACROMOLECULE, id='glyph_adh1')
g.set_label(libsbgn.label(text='ADH1'))
g.set_bbox(libsbgn.bbox(x=106, y=20, w=108, h=60))
map.add_glyph(g)
g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id='glyph_h')
g.set_label(libsbgn.label(text='H+'))
g.set_bbox(libsbgn.bbox(x=220, y=190, w=60, h=60))
map.add_glyph(g)
g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id='glyph_nad')
g.set_label(libsbgn.label(text='NAD+'))
g.set_bbox(libsbgn.bbox(x=40, y=190, w=60, h=60))
map.add_glyph(g)
g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id='glyph_nadh')
g.set_label(libsbgn.label(text='NADH'))
g.set_bbox(libsbgn.bbox(x=300, y=150, w=60, h=60))
map.add_glyph(g)
# glyph with ports (process)
g = libsbgn.glyph(class_=GlyphClass.PROCESS, id='pn1', orientation=Orientation.HORIZONTAL)
g.set_bbox(libsbgn.bbox(x=148, y=168, w=24, h=24))
g.add_port(libsbgn.port(x=136, y=180, id="pn1.1"))
g.add_port(libsbgn.port(x=184, y=180, id="pn1.2"))
map.add_glyph(g)
# arcs
# create arcs and set the start and end points
a = libsbgn.arc(class_=ArcClass.CONSUMPTION, source="glyph1", target="pn1.1", id="a01")
a.set_start(libsbgn.startType(x=98, y=160))
a.set_end(libsbgn.endType(x=136, y=180))
map.add_arc(a)
a = libsbgn.arc(class_=ArcClass.PRODUCTION, source="pn1.2", target="glyph_nadh", id="a02")
a.set_start(libsbgn.startType(x=184, y=180))
a.set_end(libsbgn.endType(x=300, y=180))
map.add_arc(a)
a = libsbgn.arc(class_=ArcClass.CATALYSIS, source="glyph_adh1", target="pn1", id="a03")
a.set_start(libsbgn.startType(x=160, y=80))
a.set_end(libsbgn.endType(x=160, y=168))
map.add_arc(a)
a = libsbgn.arc(class_=ArcClass.PRODUCTION, source="pn1.2", target="glyph_h", id="a04")
a.set_start(libsbgn.startType(x=184, y=180))
a.set_end(libsbgn.endType(x=224, y=202))
map.add_arc(a)
a = libsbgn.arc(class_=ArcClass.PRODUCTION, source="pn1.2", target="glyph_ethanal", id="a05")
a.set_start(libsbgn.startType(x=184, y=180))
a.set_end(libsbgn.endType(x=224, y=154))
map.add_arc(a)
a = libsbgn.arc(class_=ArcClass.CONSUMPTION, source="glyph_nad", target="pn1.1", id="a06")
a.set_start(libsbgn.startType(x=95, y=202))
a.set_end(libsbgn.endType(x=136, y=180))
map.add_arc(a)
# write to file
sbgn.write_file(f)
def test_basestring_issue():
"""
This tests issue: https://github.com/matthiaskoenig/libsbgn-python/issues/4
"""
# create empty sbgn
sbgn = libsbgn.sbgn()
# create map, set language and set in sbgn
sbgn_map = libsbgn.map()
sbgn_map.set_language(Language.PD)
sbgn.set_map(sbgn_map)
# create a bounding box for the map
box = libsbgn.bbox(0, 0, 100, 100)
sbgn_map.set_bbox(box)
# glyphs with labels
for comp in ("Cytoplasm",):
c_id = comp
c_name = comp
(x, y), (w, h) = (10, 10), (90, 90)
g = libsbgn.glyph(class_=GlyphClass.COMPARTMENT, id=c_id)
g.set_label(libsbgn.label(text=c_name, bbox=libsbgn.bbox(x, y, w, h)))
g.set_bbox(libsbgn.bbox(x, y, w, h))
sbgn_map.add_glyph(g)
s2xy = {"H2": (20, 20), "O2": (20, 80), "H2O": (80, 60)}
for species, (x, y) in s2xy.items():
s_id = species
s_name = species
glyph_type = GlyphClass.UNSPECIFIED_ENTITY
glyph_type = GlyphClass.SIMPLE_CHEMICAL
(w, h) = (5, 5)
g = libsbgn.glyph(class_=glyph_type, id=s_id, compartmentRef="Cytoplasm")
g.set_label(
libsbgn.label(
text=s_name,
bbox=libsbgn.bbox(x + w * 0.1, y + h * 0.1, w * 0.8, h * 0.8),
)
)
g.set_bbox(libsbgn.bbox(x, y, w, h))
sbgn_map.add_glyph(g)
# glyph with ports (process)
r_id = "Water"
(x, y), (w, h) = (60, 60), (4, 4)
g = libsbgn.glyph(class_=GlyphClass.PROCESS, id=r_id)
g.set_bbox(libsbgn.bbox(x, y, w, h))
in_port = None
for s_id in ("O2", "H2"):
edge_id = "-".join(sorted((s_id, r_id)))
if not in_port:
port_x, port_y = (61, 62)
in_port = libsbgn.port(x=port_x, y=port_y, id="%s__in" % r_id)
g.add_port(in_port)
sref_id = s_id
a = libsbgn.arc(
class_=ArcClass.CONSUMPTION,
target=in_port.get_id(),
source=sref_id,
id="a_%s_%s" % (s_id, r_id),
)
s_x, s_y = s2xy[s_id]
a.set_start(libsbgn.startType(x=s_x, y=s_y))
a.set_end(libsbgn.endType(x=in_port.get_x(), y=in_port.get_y()))
sbgn_map.add_arc(a)
out_port = None
for s_id in ("H2O",):
edge_id = "-".join(sorted((s_id, r_id)))
if not out_port:
port_x, port_y = (63, 62)
out_port = libsbgn.port(x=port_x, y=port_y, id="%s__out" % r_id)
g.add_port(out_port)
sref_id = s_id
a = libsbgn.arc(
class_=ArcClass.PRODUCTION,
target=sref_id,
source=out_port.get_id(),
id="a_%s_%s" % (r_id, s_id),
)
s_x, s_y = s2xy[s_id]
a.set_end(libsbgn.startType(x=s_x, y=s_y))
a.set_start(libsbgn.endType(x=out_port.get_x(), y=out_port.get_y()))
sbgn_map.add_arc(a)
sbgn_map.add_glyph(g)
# write everything to a file
f_tmp = tempfile.NamedTemporaryFile(suffix=".sbgn")
sbgn.write_file(f_tmp.name)
def write_sbgn_02(f):
"""Create SBGN document and write to file.
:param f:
:return:
"""
# create empty sbgn
sbgn = libsbgn.sbgn()
# create map, set language and set in sbgn
map = libsbgn.map()
map.set_language(Language.PD)
sbgn.set_map(map)
# create a bounding box for map
# <bbox x="0" y="0" w="363" h="253"/>
# [1] de novo and set all attributes
# box = libsbgn.bbox()
# box.set_x(0)
# box.set_y(0)
# box.set_w(363)
# box.set_h(253)
# [2] de novo with attributes at creation
box = libsbgn.bbox(x=0, y=0, w=363, h=253)
map.set_bbox(box)
# create some glyphs
# class attribute is named 'class_' ! in glyphs and arcs
"""
<glyph class="simple chemical" id="glyph1">
<label text="Ethanol"/> <!-- fontsize="" etc -->
<!-- Line breaks are allowed in the text attribute -->
<bbox x="40" y="120" w="60" h="60"/>
</glyph>
"""
# glyphs with labels
g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id="glyph1")
g.set_label(libsbgn.label(text="Ethanol"))
g.set_bbox(libsbgn.bbox(x=40, y=120, w=60, h=60))
map.add_glyph(g)
g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id="glyph_ethanal")
g.set_label(libsbgn.label(text="Ethanal"))
g.set_bbox(libsbgn.bbox(x=220, y=110, w=60, h=60))
map.add_glyph(g)
g = libsbgn.glyph(class_=GlyphClass.MACROMOLECULE, id="glyph_adh1")
g.set_label(libsbgn.label(text="ADH1"))
g.set_bbox(libsbgn.bbox(x=106, y=20, w=108, h=60))
map.add_glyph(g)
g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id="glyph_h")
g.set_label(libsbgn.label(text="H+"))
g.set_bbox(libsbgn.bbox(x=220, y=190, w=60, h=60))
map.add_glyph(g)
g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id="glyph_nad")
g.set_label(libsbgn.label(text="NAD+"))
g.set_bbox(libsbgn.bbox(x=40, y=190, w=60, h=60))
map.add_glyph(g)
g = libsbgn.glyph(class_=GlyphClass.SIMPLE_CHEMICAL, id="glyph_nadh")
g.set_label(libsbgn.label(text="NADH"))
g.set_bbox(libsbgn.bbox(x=300, y=150, w=60, h=60))
map.add_glyph(g)
# glyph with ports (process)
g = libsbgn.glyph(class_=GlyphClass.PROCESS,
id="pn1",
orientation=Orientation.HORIZONTAL)
g.set_bbox(libsbgn.bbox(x=148, y=168, w=24, h=24))
g.add_port(libsbgn.port(x=136, y=180, id="pn1.1"))
g.add_port(libsbgn.port(x=184, y=180, id="pn1.2"))
map.add_glyph(g)
# arcs
# create arcs and set the start and end points
a = libsbgn.arc(class_=ArcClass.CONSUMPTION,
source="glyph1",
target="pn1.1",
id="a01")
a.set_start(libsbgn.startType(x=98, y=160))
a.set_end(libsbgn.endType(x=136, y=180))
map.add_arc(a)
a = libsbgn.arc(class_=ArcClass.PRODUCTION,
source="pn1.2",
target="glyph_nadh",
id="a02")
a.set_start(libsbgn.startType(x=184, y=180))
a.set_end(libsbgn.endType(x=300, y=180))
map.add_arc(a)
a = libsbgn.arc(class_=ArcClass.CATALYSIS,
source="glyph_adh1",
target="pn1",
id="a03")
a.set_start(libsbgn.startType(x=160, y=80))
a.set_end(libsbgn.endType(x=160, y=168))
map.add_arc(a)
a = libsbgn.arc(class_=ArcClass.PRODUCTION,
source="pn1.2",
target="glyph_h",
id="a04")
a.set_start(libsbgn.startType(x=184, y=180))
a.set_end(libsbgn.endType(x=224, y=202))
map.add_arc(a)
a = libsbgn.arc(class_=ArcClass.PRODUCTION,
source="pn1.2",
target="glyph_ethanal",
id="a05")
a.set_start(libsbgn.startType(x=184, y=180))
a.set_end(libsbgn.endType(x=224, y=154))
map.add_arc(a)
a = libsbgn.arc(class_=ArcClass.CONSUMPTION,
source="glyph_nad",
target="pn1.1",
id="a06")
a.set_start(libsbgn.startType(x=95, y=202))
a.set_end(libsbgn.endType(x=136, y=180))
map.add_arc(a)
# write to file
sbgn.write_file(f)
def save_as_sbgn(n2lo, e2lo, model, out_sbgn):
"""
Converts a model with the given node and edge layout to SBGN PD (see http://www.sbgn.org/).
:param n2lo: node layout as a dictionary {node_id: ((x, y), (w, h)) if node is not ubiquitous
else node_id : {r_ids: ((x, y), (w, h)) for r_ids of
reactions using each duplicated metabolite}}
:param e2lo: edge layout as a dictionary {edge_id: [(x_start, y_start), (x_bend_0, y_bend_0),..,(x_end, y_end)]},
where edge_id = "-".join(sorted((metabolite_id, reaction_id))).
:param model: SBML model
:param out_sbgn: path where to save the resulting SBGN file.
"""
# let's scale the map so that a minimal node has a width == 16 (so that the labels fit)
h_min, (x_shift, y_shift), (w, h) = get_layout_characteristics(n2lo)
scale_factor = MARGIN * 1.0 / h_min if h_min else 1
(w, h) = scale((w, h), scale_factor)
(x_shift, y_shift) = shift(scale((x_shift, y_shift), scale_factor), MARGIN,
MARGIN)
# create empty sbgn
sbgn = libsbgn.sbgn()
# create map, set language and set in sbgn
sbgn_map = libsbgn.map()
sbgn_map.set_language(Language.PD)
sbgn.set_map(sbgn_map)
# create a bounding box for the map
box = libsbgn.bbox(0, 0, w + 2 * MARGIN, h + 2 * MARGIN)
sbgn_map.set_bbox(box)
# glyphs with labels
for comp in model.getListOfCompartments():
c_id = comp.getId()
c_name = comp.getName()
if not c_name:
c_name = c_id
if c_id in n2lo:
(x, y), (w, h) = transform(n2lo[c_id], x_shift, y_shift,
scale_factor)
g = libsbgn.glyph(class_=GlyphClass.COMPARTMENT, id=c_id)
g.set_label(
libsbgn.label(text=c_name, bbox=libsbgn.bbox(x, y, w, h)))
g.set_bbox(libsbgn.bbox(x, y, w, h))
sbgn_map.add_glyph(g)
for species in model.getListOfSpecies():
s_id = species.getId()
s_name = species.getName()
glyph_type = GlyphClass.UNSPECIFIED_ENTITY
sbo_term = species.getSBOTermID()
if sbo_term:
sbo_term = sbo_term.upper().strip()
if sbo_term in SBO_2_GLYPH_TYPE:
glyph_type = SBO_2_GLYPH_TYPE[sbo_term]
if not s_name:
s_name = s_id
if s_id in n2lo:
if isinstance(n2lo[s_id], dict):
elements = n2lo[s_id].items()
else:
elements = [('', n2lo[s_id])]
for r_ids, coords in elements:
if not r_ids or next(
(it for it in (model.getReaction(r_id)
for r_id in r_ids) if it), False):
(x, y), (w, h) = transform(coords, x_shift, y_shift,
scale_factor)
g = libsbgn.glyph(
class_=glyph_type,
id="%s_%s" %
(s_id, '_'.join(r_ids)) if r_ids else s_id,
compartmentRef=species.getCompartment())
g.set_label(
libsbgn.label(text=s_name,
bbox=libsbgn.bbox(
x + w * 0.1, y + h * 0.1, w * 0.8,
h * 0.8)))
g.set_bbox(libsbgn.bbox(x, y, w, h))
sbgn_map.add_glyph(g)
# glyph with ports (process)
for reaction in model.getListOfReactions():
r_id = reaction.getId()
if r_id in n2lo:
(x, y), (w, h) = transform(n2lo[r_id], x_shift, y_shift,
scale_factor)
g = libsbgn.glyph(class_=GlyphClass.PROCESS, id=r_id)
g.set_bbox(libsbgn.bbox(x, y, w, h))
rev = reaction.getReversible()
in_port = None
for s_id in (species_ref.getSpecies()
for species_ref in reaction.getListOfReactants()):
edge_id = "-".join(sorted((s_id, r_id)))
if edge_id in e2lo:
xy_list = e2lo[edge_id]
if not in_port:
port_x, port_y = shift(
scale(
xy_list[-2] if len(xy_list) > 2 else
xy_list[-1], scale_factor), x_shift, y_shift)
in_port = libsbgn.port(x=port_x,
y=port_y,
id="%s__in" % r_id)
g.add_port(in_port)
sref_id = s_id
if isinstance(n2lo[s_id], dict):
for r_ids in n2lo[s_id].keys():
if r_id in r_ids:
sref_id = "%s_%s" % (s_id, '_'.join(r_ids))
a = libsbgn.arc(
class_=ArcClass.PRODUCTION
if rev else ArcClass.CONSUMPTION,
target=sref_id if rev else in_port.get_id(),
source=in_port.get_id() if rev else sref_id,
id="a_%s_%s" % (s_id, r_id))
s_x, s_y = shift(scale(xy_list[0], scale_factor), x_shift,
y_shift)
a.set_start(
libsbgn.startType(x=in_port.get_x() if rev else s_x,
y=in_port.get_y() if rev else s_y))
a.set_end(
libsbgn.endType(x=s_x if rev else in_port.get_x(),
y=s_y if rev else in_port.get_y()))
sbgn_map.add_arc(a)
out_port = None
for s_id in (species_ref.getSpecies()
for species_ref in reaction.getListOfProducts()):
edge_id = "-".join(sorted((s_id, r_id)))
if edge_id in e2lo:
xy_list = e2lo[edge_id]
if not out_port:
port_x, port_y = shift(
scale(
xy_list[1] if len(xy_list) > 2 else xy_list[0],
scale_factor), x_shift, y_shift)
out_port = libsbgn.port(x=port_x,
y=port_y,
id="%s__out" % r_id)
g.add_port(out_port)
sref_id = s_id
if isinstance(n2lo[s_id], dict):
for r_ids in n2lo[s_id].keys():
if r_id in r_ids:
sref_id = "%s_%s" % (s_id, '_'.join(r_ids))
a = libsbgn.arc(class_=ArcClass.PRODUCTION,
target=sref_id,
source=out_port.get_id(),
id="a_%s_%s" % (r_id, s_id))
s_x, s_y = shift(scale(xy_list[-1], scale_factor), x_shift,
y_shift)
a.set_end(libsbgn.startType(x=s_x, y=s_y))
a.set_start(
libsbgn.endType(x=out_port.get_x(),
y=out_port.get_y()))
sbgn_map.add_arc(a)
sbgn_map.add_glyph(g)
# write everything to a file
sbgn.write_file(out_sbgn)