Main

README.md

@@ -50,7 +50,7 @@ conda install -c conda-forge rplibs
 softwareupdate --install-rosetta --agree-to-license
 ```
 
-### 2. Install rpLibs
+### 2. Install
 
 ```bash
 CONDA_SUBDIR=osx-64 conda install -c conda-forge rplibs
@@ -68,11 +68,16 @@ CONDA_SUBDIR=osx-64 mamba install -c conda-forge rplibs
 conda config --env --set subdir osx-64
 ```
 
-### 5. Verify installation
+### 4. Verify installation
 
 ```bash
 python -c "import rplibs; print('rplibs installed successfully')"
-python -c "import cobra; print(cobra.__version__)"
+```
+
+### 5. (Optional) Dev installation
+
+```bash
+CONDA_SUBDIR=osx-64 conda env create -f environment.yaml
 ```
 
 ---

environment.yaml

@@ -8,6 +8,7 @@ dependencies:
   - networkx>=2.5
   - filetype
   - brs_utils>=1.26.0
-  - chemlite
+  - chemlite>=2.8.0
   - rr_cache
   - cobra
+  - libsbml

rplibs/rpPathway.py

@@ -74,7 +74,6 @@ def __init__(
         )
         rpObject.__init__(self, logger)
         self.__species_groups = {}
-        self.set_target_id(None)
         self.__unit_def = {}
         self.__compartments = {}
         self.add_compartment(
@@ -206,9 +205,9 @@ def get_rxn_target(self) -> rpReaction:
         the target compound of the pathway."""
         return self.get_reaction(self.get_target_rxn_id())
 
-    def get_target_id(self) -> str:
-        """Get the ID of the pathway target compound."""
-        return self.__target_id
+    # def get_target_id(self) -> str:
+    #     """Get the ID of the pathway target compound."""
+    #     return self.__target_id
 
     def get_target(self) -> rpCompound:
         """Get the object of the pathway target compound."""
@@ -462,18 +461,18 @@ def set_sink_species(self, species: List[str]) -> None:
         self.__build_intermediate_species()
         # self.__sink = deepcopy(sink)
 
-    def set_target_id(self, id: str) -> None:
-        """Set the ID of the pathway target.
-        After that, 'intermediate' species group is rebuilt.
+    # def set_target_id(self, id: str) -> None:
+    #     """Set the ID of the pathway target.
+    #     After that, 'intermediate' species group is rebuilt.
 
-        Parameters
-        ----------
-        id: str
-            ID of the species to set as the pathway target.
-        """
-        self.__target_id = id
-        # (re-)build intermediate species group
-        self.__build_intermediate_species()
+    #     Parameters
+    #     ----------
+    #     id: str
+    #         ID of the species to set as the pathway target.
+    #     """
+    #     self.__target_id = id
+    #     # (re-)build intermediate species group
+    #     self.__build_intermediate_species()
 
     def add_unit_def(
         self, id: str, kind: int, exp: int, scale: int, mult: float
@@ -632,9 +631,9 @@ def __import_rpSBML(
             rxn_infos["fbc_units"] = self.get_parameter_units(
                 rxn_infos["fbc_lower_value"]
             )
-            reaction, target_id = rpReaction.build(rxn_id, rxn_infos, logger)
+            reaction = rpReaction.build(rxn_id, rxn_infos, logger)
             # Add the reaction to the pathway
-            self.add_reaction(rxn=reaction, target_id=target_id)
+            self.add_reaction(rxn=reaction)
 
         ## GROUPS
         for group in rpsbml.getPlugin("groups").getListOfGroups():
@@ -801,7 +800,11 @@ def to_rpSBML(self, cache: rrCache = None, local_cache: dict = {}) -> rpSBML:
         rpsbml.create_enriched_group(
             group_id="rp_pathway",
             members=self.get_reactions_ids(),
-            infos={**rpObject._to_dict(self), "global_score": self.get_global_score()},
+            infos={
+                **rpObject._to_dict(self),
+                "global_score": self.get_global_score(),
+                "target_id": self.get_target_id(),
+            },
         )
         for group_id, group_members in self.get_species_groups().items():
             _members = [local_cache.get(spe_id, spe_id) for spe_id in group_members]
@@ -828,27 +831,27 @@ def from_rpSBML(rpsbml: rpSBML) -> "rpPathway":
         pathway.__import_rpSBML(rpsbml)
         return pathway
 
-    def add_reaction(
-        self, rxn: rpReaction, rxn_id: str = None, target_id: str = None
-    ) -> None:
-        """
-        Add a reaction to the pathway.
-
-        Parameters
-        ----------
-        rxn: rpReaction
-            Reaction object to add
-        rxn_id: str, optional
-            ID of the reaction within the pathway
-        target_id: str, optional
-            ID of the compound if it is the pathway target
-        """
-
-        super().add_reaction(rxn, rxn_id)
-
-        # TARGET
-        if target_id is not None:
-            self.set_target_id(target_id)
+    # def add_reaction(
+    #     self, rxn: rpReaction, rxn_id: str = None, target_id: str = None
+    # ) -> None:
+    #     """
+    #     Add a reaction to the pathway.
+
+    #     Parameters
+    #     ----------
+    #     rxn: rpReaction
+    #         Reaction object to add
+    #     rxn_id: str, optional
+    #         ID of the reaction within the pathway
+    #     target_id: str, optional
+    #         ID of the compound if it is the pathway target
+    #     """
+
+    #     super().add_reaction(rxn, rxn_id)
+
+    #     # TARGET
+    #     if target_id is not None:
+    #         self.set_target_id(target_id)
 
     ## MISC
     def rename_compound(self, id: str, new_id: str) -> None:

rplibs/rpReaction.py

@@ -79,22 +79,23 @@ def build(
         )
         # Add additional infos
         write_to(infos["brsynth"], reaction)
-        # Detects if the current reaction produces the target
-        target_id = [
-            spe_id for spe_id in reaction.get_products_ids() if "TARGET" in spe_id
-        ]
-        if target_id != []:
-            target_id = target_id[0]
-        else:
-            # If not, detects if the current reaction consumes the target
-            target_id = [
-                spe_id for spe_id in reaction.get_reactants_ids() if "TARGET" in spe_id
-            ]
-            if target_id != []:
-                target_id = target_id[0]
-            else:
-                target_id = None
-        return reaction, target_id
+        # # Detects if the current reaction produces the target
+        # target_id = [
+        #     spe_id for spe_id in reaction.get_products_ids() if "TARGET" in spe_id
+        # ]
+        # if target_id != []:
+        #     target_id = target_id[0]
+        # else:
+        #     # If not, detects if the current reaction consumes the target
+        #     target_id = [
+        #         spe_id for spe_id in reaction.get_reactants_ids() if "TARGET" in spe_id
+        #     ]
+        #     if target_id != []:
+        #         target_id = target_id[0]
+        #     else:
+        #         target_id = None
+        # return reaction, target_id
+        return reaction
 
     def __init__(
         self,

tests/data/lycopene.sbml

@@ -546,6 +546,7 @@
                   <brsynth:units value="kilojoule / mole"/>
                 </brsynth:thermo_dG>
                 <brsynth:global_score value="0.9892438888549804"/>
+                <brsynth:target_id value="TARGET_0000000001"/>
               </brsynth:brsynth>
             </rdf:BRSynth>
           </rdf:RDF>

tests/test_rpPathway.py

@@ -20,7 +20,10 @@ class Test_rpPathway(Main_rplibs):
     def setUp(self):
         self.target = rpCompound(
             id="TARGET_0000000001",
-            smiles="[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]",
+            smiles="[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H]",
+            inchi="InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3",
+            inchikey="OAIJSZIZWZSQBC-UHFFFAOYSA-N",
+            formula="",
         )
         # species = {
         #     # "TARGET_0000000001": rpCompound(
@@ -196,17 +199,16 @@ def setUp(self):
                 {"kind": 13, "exponent": -1, "scale": 1, "multiplier": 1.0},
             ],
         }
-        self.pathway = rpPathway(
-            id=self.id,
-        )
+        self.pathway = rpPathway(id=self.id)
         self.pathway.set_parameters(self.parameters)
         self.pathway.set_unit_defs(self.unit_def)
         self.rxn.set_rp2_transfo_id(self.rp2_transfo_id)
         self.rxn.set_rule_ids(self.rule_ids)
         self.rxn.set_tmpl_rxn_ids(self.tmpl_rxn_ids)
         self.rxn.set_idx_in_path(self.idx_in_path)
         self.rxn.set_rule_score(self.rule_score)
-        self.pathway.add_reaction(rxn=self.rxn, target_id=self.target.get_id())
+        self.pathway.add_reaction(rxn=self.rxn)
+        self.pathway.set_target_id(self.target.get_id())
         for rxn in self.reactions[1:]:
             self.pathway.add_reaction(rxn)
         self.sink = ["MNXM23", "MNXM6", "MNXM13"]
@@ -215,6 +217,8 @@ def setUp(self):
             self.pathway.add_thermo_info(key, value)
         self.pathway.set_fba_fraction(self.fba)
 
+        self.rpsbml_lycopene = rpPathway(infile=self.rpsbml_lycopene_path)
+
     ## READ METHODS
     def test__to_dict(self):
         self.assertDictEqual(
@@ -302,7 +306,20 @@ def test_get_rxn_target(self):
         self.assertEqual(self.pathway.get_rxn_target(), self.rxn)
 
     def test_get_target(self):
-        self.assertEqual(self.pathway.get_target(), self.target)
+        # Compare ID, name, smiles, inchi, inchikey, formula, but not annotations, to avoid issues with the cache
+        self.__compare_compound(self.pathway.get_target(), self.target)
+
+    def __compare_compound(self, cmpd1: rpCompound, reference: rpCompound):
+        self.assertEqual(cmpd1.get_id(), reference.get_id())
+        self.assertEqual(cmpd1.get_name(), reference.get_name())
+        self.assertEqual(cmpd1.get_smiles(), reference.get_smiles())
+        self.assertEqual(cmpd1.get_inchi(), reference.get_inchi())
+        self.assertEqual(cmpd1.get_inchikey(), reference.get_inchikey())
+        self.assertEqual(cmpd1.get_formula(), reference.get_formula())
+
+    def test_read_target(self):
+        target = rpPathway(infile=self.rpsbml_lycopene_path).get_target()
+        self.__compare_compound(target, self.target)
 
     def test_get_parameters(self):
         self.assertDictEqual(self.pathway.get_parameters(), self.parameters)
@@ -317,21 +334,21 @@ def test_get_fba(self):
     def test_get_thermo(self):
         self.assertDictEqual(self.pathway.get_thermo(), self.thermo)
 
-    def test_rpSBML_rpsbml(self):
+    def test_rpPathway2rpSBML2rpPathway(self):
         self.assertEqual(
             self.pathway, rpPathway.from_rpSBML(rpsbml=self.pathway.to_rpSBML())
         )
 
-    def test_rpSBML_file(self):
-        with NamedTemporaryFile(delete=False) as tempf:
-            tempf.close()
-            self.assertEqual(
-                self.pathway, rpPathway.from_rpSBML(self.pathway.to_rpSBML())
-            )
-            tempf.close()
-            remove(tempf.name)
+    # def test_rpSBML_file(self):
+    #     with NamedTemporaryFile(delete=False) as tempf:
+    #         tempf.close()
+    #         self.assertEqual(
+    #             self.pathway, rpPathway.from_rpSBML(self.pathway.to_rpSBML())
+    #         )
+    #         tempf.close()
+    #         remove(tempf.name)
 
-    def test_rpSBML_file_rpsbml(self):
+    def test_rpPathway2SBML2rpPathway(self):
         with NamedTemporaryFile(delete=False) as tempf:
             self.pathway.to_rpSBML().write_to_file(tempf.name)
             self.assertEqual(self.pathway, rpPathway(infile=tempf.name))
@@ -380,7 +397,8 @@ def test_add_parameter(self):
 
     def test_eq(self):
         pathway = rpPathway(id="test_pathway")
-        pathway.add_reaction(rxn=self.rxn, target_id="TARGET_0000000001")
+        pathway.add_reaction(rxn=self.rxn)
+        pathway.set_target_id("TARGET_0000000001")
         for rxn in self.reactions[1:]:
             pathway.add_reaction(rxn)
         self.assertEqual(self.pathway, pathway)