Merge pull request #62 from SystemsBioinformatics/dev

fixed typo
SystemsBioinformatics · Nov 2, 2023 · aac43c5 · aac43c5
2 parents 0146bad + 54beff7
commit aac43c5
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Showing 7 changed files with 36 additions and 4 deletions.
diff --git a/cbmpy/CBModel.py b/cbmpy/CBModel.py
@@ -1570,7 +1570,7 @@ def convertUserConstraintsToUserDefinedConstraints(self):
 
             ucnew = self.createUserDefinedConstraint(u, lb, ub, components)
             self.addUserDefinedConstraint(ucnew)
-        print("Markging up model V2 --> V3")
+        print("Marking up model V2 --> V3")
         self.__FBC_VERSION__ = 3
 
         self.user_constraints.clear()
@@ -1596,7 +1596,7 @@ def copyUserDefinedConstraintsToUserConstraints(self):
                 ub = numpy.Inf
                 lb = rhs = udc.getLowerBound()
             elif udc.getLowerBound() == numpy.NINF:
-                operator == "L"
+                operator = "L"
                 lb = numpy.NINF
                 ub = rhs = udc.getUpperBound()
             else:

diff --git a/develop-fbcv3/QP/dbg.lp b/develop-fbcv3/QP/dbg.lp
@@ -26,6 +26,7 @@ Subject To
  cons1: R16 + R15  = 0.8
  cons2: R15 >= 0.1
  cons3: R14 >= 0.1
+ cons4: R15 <= 1
 Bounds
  0 <= R01 <= 1
  0 <= R10 <= 1000

diff --git a/develop-fbcv3/QP/test_new_ucs.py b/develop-fbcv3/QP/test_new_ucs.py
@@ -39,6 +39,7 @@
 print(old_cons[2] - new_cons[2] == 0)
 
 
+
 for uc in ucmod.user_defined_constraints:
     uc.setAnnotation('secret', uc.getId())
     for var in uc.constraint_components:

diff --git a/develop-fbcv3/QP/test_user_def_rc.py b/develop-fbcv3/QP/test_user_def_rc.py
@@ -11,6 +11,7 @@
 test.addUserConstraint('cons1', fluxes=[(1, 'R16'), (1, 'R15')], operator='=', rhs=0.8)
 test.addUserConstraint('cons2', fluxes=[(1, 'R15')], operator='>=', rhs=0.1)
 test.addUserConstraint('cons3', fluxes=[(1, 'R14')], operator='>=', rhs=0.1)
+test.addUserConstraint('cons4', fluxes=[(1, 'R15')], operator='<=', rhs=1.0)
 
 lp = cbmpy.CBSolver.cplx_analyzeModel(
     test,

diff --git a/develop-fbcv3/QP/test_user_def_rc.xml b/develop-fbcv3/QP/test_user_def_rc.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<!-- SBML created with CBMPy (0.8.7) on Mon, 30 Oct 2023 23:09:17 -->
+<!-- SBML created with CBMPy (0.8.8) on Thu, 02 Nov 2023 15:35:00 -->
 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:html="http://www.w3.org/1999/xhtml" level="3" version="1" fbc:required="false">
   <model metaid="meta_sbml_model" id="sbml_model" substanceUnits="mmol_per_gdw" timeUnits="hour" extentUnits="mmol_per_gdw" fbc:strict="true">
     <notes>

diff --git a/develop-fbcv3/QP/test_user_def_rc.xml.user_constraints.json b/develop-fbcv3/QP/test_user_def_rc.xml.user_constraints.json
@@ -36,5 +36,16 @@
     ],
     "operator": "G",
     "rhs": 0.1
+  },
+  "cons4": {
+    "fluxes": [
+      [
+        1,
+        "R15",
+        "linear"
+      ]
+    ],
+    "operator": "L",
+    "rhs": 1.0
   }
 }
diff --git a/develop-fbcv3/QP/the_third.fbc3.xml b/develop-fbcv3/QP/the_third.fbc3.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<!-- SBML created with CBMPy (0.8.7) on Mon, 30 Oct 2023 23:01:37 -->
+<!-- SBML created with CBMPy (0.8.8) on Thu, 02 Nov 2023 15:35:10 -->
 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version3" xmlns:html="http://www.w3.org/1999/xhtml" level="3" version="1" fbc:required="false">
   <model metaid="meta_sbml_model" id="sbml_model" substanceUnits="mmol_per_gdw" timeUnits="hour" extentUnits="mmol_per_gdw" fbc:strict="true">
     <notes>
@@ -120,6 +120,8 @@
       <parameter metaid="meta_udcc_cons2_ub" id="udcc_cons2_ub" name="udcc_cons2_ub" value="INF" constant="true"/>
       <parameter metaid="meta_udcc_cons3_lb" id="udcc_cons3_lb" name="udcc_cons3_lb" value="0.1" constant="true"/>
       <parameter metaid="meta_udcc_cons3_ub" id="udcc_cons3_ub" name="udcc_cons3_ub" value="INF" constant="true"/>
+      <parameter metaid="meta_udcc_cons4_lb" id="udcc_cons4_lb" name="udcc_cons4_lb" value="-INF" constant="true"/>
+      <parameter metaid="meta_udcc_cons4_ub" id="udcc_cons4_ub" name="udcc_cons4_ub" value="1" constant="true"/>
     </listOfParameters>
     <listOfReactions>
       <reaction metaid="meta_R01" id="R01" name="R01" reversible="false" fast="false" fbc:lowerFluxBound="bnd_par0" fbc:upperFluxBound="bnd_par1">
@@ -709,6 +711,22 @@
           </fbc:userDefinedConstraintComponent>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
+      <fbc:userDefinedConstraint fbc:id="cons4" fbc:lowerBound="udcc_cons4_lb" fbc:upperBound="udcc_cons4_ub">
+        <annotation>
+          <listOfKeyValuePairs xmlns="http://sbml.org/fbc/keyvaluepair">
+            <keyValuePair key="secret" value="cons4"/>
+          </listOfKeyValuePairs>
+        </annotation>
+        <fbc:listOfUserDefinedConstraintComponents>
+          <fbc:userDefinedConstraintComponent fbc:id="udcc_cons4_R15" fbc:coefficient="1" fbc:variable="R15" fbc:variableType="linear">
+            <annotation>
+              <listOfKeyValuePairs xmlns="http://sbml.org/fbc/keyvaluepair">
+                <keyValuePair key="secret" value="udcc_cons4_R15"/>
+              </listOfKeyValuePairs>
+            </annotation>
+          </fbc:userDefinedConstraintComponent>
+        </fbc:listOfUserDefinedConstraintComponents>
+      </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>
   </model>
 </sbml>