Fix concentration setting (#453)

* Fix setting of concentrations * Bump to 1.1.6 * minor GUI improvements * Fix freezing with empty search string * variable rename * GUI improvements * cleanup * Add thermodynamic FBA * Clean-up * Fix clean-up Co-authored-by: axelvonkamp <[email protected]>
cnapy-org · Jan 27, 2023 · d563b14 · d563b14
1 parent 2f5fd16
commit d563b14
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Showing 18 changed files with 156 additions and 51 deletions.
diff --git a/README.md b/README.md
@@ -61,13 +61,13 @@ Everyone is welcome to contribute to CNApy's development. [See our contribution
 3. Create a conda environment with all dependencies
 
     ```sh
-    conda create -n cnapy-1.1.5 -c conda-forge -c cnapy cnapy=1.1.5
+    conda create -n cnapy-1.1.6 -c conda-forge -c cnapy cnapy=1.1.6
     ```
 
 4. Activate the cnapy conda environment
 
     ```sh
-    conda activate cnapy-1.1.5
+    conda activate cnapy-1.1.6
     ```
 
 5. Run CNApy within you activated conda environment

diff --git a/cnapy/appdata.py b/cnapy/appdata.py
@@ -24,7 +24,7 @@ class AppData:
     ''' The application data '''
 
     def __init__(self):
-        self.version = "cnapy-1.1.5"
+        self.version = "cnapy-1.1.6"
         self.format_version = 2
         self.unsaved = False
         self.project = ProjectData()

diff --git a/cnapy/core.py b/cnapy/core.py
@@ -229,7 +229,7 @@ def make_scenario_feasible(cobra_model: cobra.Model, scen_values: Dict[str, Tupl
                     if v != 0:
                         print(s.name, format_string.format(v, v/abs(coeff)))
                         bm_mod[m] = v
-                if gam_mets_param is not None:
+                if len(gam_mets) > 0:
                     gam_adjust = gam_max_change * model.solver.variables["gam_slack"].primal
             else:
                 for m,_,coeff,(s_p,s_n) in bm_coeff_var:
@@ -241,7 +241,7 @@ def make_scenario_feasible(cobra_model: cobra.Model, scen_values: Dict[str, Tupl
                     if v != 0:
                         print(s_n.name, format_string.format(v, v/abs(coeff)))
                         bm_mod[m] = -v
-                if gam_mets_param is not None:
+                if len(gam_mets) > 0:
                     gam_adjust = gam_max_change * \
                         (model.solver.variables["gam_slack_pos"].primal - model.solver.variables["gam_slack_neg"].primal)
             if len(gam_mets) > 0:

diff --git a/cnapy/gui_elements/central_widget.py b/cnapy/gui_elements/central_widget.py
@@ -309,6 +309,9 @@ def delete_map(self, idx: int):
     def update_selected(self):
         string = self.searchbar.text()
 
+        if string == "":
+            return
+
         idx = self.tabs.currentIndex()
         with_annotations = self.search_annotations.isChecked() and self.search_annotations.isEnabled()
         if idx == ModelTabIndex.Reactions:

diff --git a/cnapy/gui_elements/flux_feasibility_dialog.py b/cnapy/gui_elements/flux_feasibility_dialog.py
@@ -1,8 +1,10 @@
 from math import copysign
 from qtpy.QtCore import Qt, Slot, QSignalBlocker
 from qtpy.QtWidgets import (QDialog, QGroupBox, QHBoxLayout, QTableWidget, QCheckBox, QMainWindow,
-                            QLabel, QLineEdit, QMessageBox, QPushButton, QAbstractItemView,
-                            QRadioButton, QVBoxLayout, QTableWidgetItem, QButtonGroup, QStyledItemDelegate)
+                            QLabel, QLineEdit, QMessageBox, QPushButton, QAbstractItemView, QAction,
+                            QRadioButton, QVBoxLayout, QTableWidgetItem, QButtonGroup, 
+                            QStyledItemDelegate, QTableWidgetSelectionRange)
+from qtpy.QtGui import QGuiApplication
 
 from cnapy.utils import QComplReceivLineEdit
 from cnapy.core import make_scenario_feasible, QPnotSupportedException
@@ -93,11 +95,16 @@ def __init__(self, main_window: QMainWindow):
         self.bm_constituents.setSortingEnabled(True)
         self.bm_constituents.verticalHeader().setVisible(False)
         self.bm_constituents.setEditTriggers(QAbstractItemView.NoEditTriggers)
+        self.bm_constituents.setSelectionMode(QAbstractItemView.ContiguousSelection)
         self.bm_constituents.resizeColumnsToContents()
         coefficient_delegate = CoefficientDelegate()
         self.bm_constituents.setItemDelegateForColumn(3, coefficient_delegate)
         self.bm_constituents.setItemDelegateForColumn(4, coefficient_delegate)
         self.bm_constituents.setItemDelegateForColumn(5, coefficient_delegate)
+        copy_action = QAction("Copy", self.bm_constituents)
+        copy_action.setShortcut("Ctrl+C")
+        copy_action.triggered.connect(self.copy_table_selection)
+        self.bm_constituents.addAction(copy_action)
         vbox_bm_coeff.addWidget(self.bm_constituents)
         hbox = QHBoxLayout()
         hbox.addWidget(QLabel("Maximal relative coefficient change [%]:"))
@@ -182,6 +189,12 @@ def compute(self):
         abs_flux_weights: bool = False
         weights_key: str = None
 
+        # clear previous results
+        self.gam_adjustment.setText("")
+        for i in range(self.bm_constituents.rowCount()):
+            self.bm_constituents.setItem(i, 4, None)
+            self.bm_constituents.setItem(i, 5, None)
+
         if self.flux_group.isChecked():
             if self.abs_flux_weights_button.isChecked():
                 abs_flux_weights = True
@@ -212,8 +225,6 @@ def compute(self):
                     checkbox = self.bm_constituents.cellWidget(i, 0)
                     if checkbox is not None and checkbox.isChecked():
                         variable_constituents.append(self.bm_constituents.item(i, 1).data(Qt.UserRole))
-                    self.bm_constituents.setItem(i, 4, None)
-                    self.bm_constituents.setItem(i, 5, None)
                 try:
                     max_coeff_change = float(self.max_coeff_change.text())
                 except ValueError:
@@ -333,7 +344,7 @@ def compute(self):
                         self.appdata.project.scen_values.reactions[self.bm_mod_reac_id] = \
                             [{met.id: coeff for met, coeff in bm_reac_mod.metabolites.items()}, fixed_growth_rate, fixed_growth_rate]
                         self.main_window.centralWidget().tabs.widget(ModelTabIndex.Scenario).recreate_scenario_items_needed = True
-                if self.adjust_gam.isChecked():
+                if self.bm_group.isChecked() and self.adjust_gam.isChecked():
                     self.gam_adjustment.setText("Calculated GAM adjustment: "+coefficient_format.format(gam_adjust))
                 self.main_window.centralWidget().update()
             else:
@@ -409,3 +420,26 @@ def enable_biomass_equation_modifications(self, enable: bool):
         self.bm_group.setChecked(enable)
         self.adjust_bm_coeff.setEnabled(enable)
         self.adjust_gam.setEnabled(enable)
+
+    @Slot()
+    def copy_table_selection(self):
+        selection_range: QTableWidgetSelectionRange = self.bm_constituents.selectedRanges()[0]
+        table = []
+        r = selection_range.topRow()
+        while r <= selection_range.bottomRow():
+            row = []
+            c = selection_range.leftColumn()
+            while c <= selection_range.rightColumn():
+                if c == 0:
+                    row.append(str(self.bm_constituents.cellWidget(r, c).isChecked()))
+                else:
+                    item: QTableWidgetItem = self.bm_constituents.item(r, c)
+                    if item is None:
+                        row.append("")
+                    else:
+                        row.append(str(item.data(Qt.DisplayRole)))
+                c += 1
+            table.append('\t'.join(row))
+            r += 1
+        clipboard = QGuiApplication.clipboard()
+        clipboard.setText('\r'.join(table))
diff --git a/cnapy/gui_elements/main_window.py b/cnapy/gui_elements/main_window.py
@@ -45,7 +45,7 @@
 from cnapy.gui_elements.flux_optimization_dialog import FluxOptimizationDialog
 from cnapy.gui_elements.configuration_cplex import CplexConfigurationDialog
 from cnapy.gui_elements.configuration_gurobi import GurobiConfigurationDialog
-from cnapy.gui_elements.thermodynamics_dialog import ThermodynamicDialog
+from cnapy.gui_elements.thermodynamics_dialog import ThermodynamicAnalysisTypes, ThermodynamicDialog
 import cnapy.utils as utils
 
 
@@ -398,6 +398,9 @@ def __init__(self, appdata: AppData):
         optmdf_action.triggered.connect(self.perform_optmdfpathway)
         self.analysis_menu.addAction(optmdf_action)
 
+        tfba_action = QAction("Thermodynamic FBA...", self)
+        tfba_action.triggered.connect(self.perform_thermodynamic_fba)
+        self.analysis_menu.addAction(tfba_action)
 
         bottleneck_action = QAction("Thermodynamic bottleneck analysis...", self)
         bottleneck_action.triggered.connect(self.perform_bottleneck_analysis)
@@ -1878,14 +1881,32 @@ def set_status_unknown(self):
 
     @Slot()
     def perform_optmdfpathway(self):
+        # Has to be in self to keep computation thread
         self.optmdfpathway_dialog = ThermodynamicDialog(
-            self.appdata, self.centralWidget(), bottleneck_analysis=False)
+            self.appdata,
+            self.centralWidget(),
+            analysis_type=ThermodynamicAnalysisTypes.OPTMDFPATHWAY
+        )
         self.optmdfpathway_dialog.exec_()
 
+    @Slot()
+    def perform_thermodynamic_fba(self):
+        # Has to be in self to keep computation thread
+        self.thermodynamic_fba_dialog = ThermodynamicDialog(
+            self.appdata,
+            self.centralWidget(),
+            analysis_type=ThermodynamicAnalysisTypes.THERMODYNAMIC_FBA
+        )
+        self.thermodynamic_fba_dialog.exec_()
+
     @Slot()
     def perform_bottleneck_analysis(self):
+        # Has to be in self to keep computation thread
         self.bottleneck_dialog = ThermodynamicDialog(
-            self.appdata, self.centralWidget(), bottleneck_analysis=True)
+            self.appdata,
+            self.centralWidget(),
+            analysis_type=ThermodynamicAnalysisTypes.BOTTLENECK_ANALYSIS
+        )
         self.bottleneck_dialog.exec_()
 
     def _load_json(self) -> Dict[Any, Any]:
@@ -1933,6 +1954,9 @@ def _set_concentrations(self, concentrations):
             else:
                 lb = concentrations[metabolite.id]["min"]
                 ub = concentrations[metabolite.id]["max"]
+
+            metabolite.annotation["Cmin"] = lb
+            metabolite.annotation["Cmax"] = ub
         self.centralWidget().update()
         self.unsaved_changes()
 

diff --git a/cnapy/gui_elements/scenario_tab.py b/cnapy/gui_elements/scenario_tab.py
@@ -42,7 +42,7 @@ def __init__(self, central_widget):
         self.use_scenario_objective.setEnabled(True)
         self.use_scenario_objective.stateChanged.connect(self.use_scenario_objective_changed)
         self.objective_group_layout.addWidget(self.use_scenario_objective)
-        self.scenario_objective = QComplReceivLineEdit(self, [])
+        self.scenario_objective = QComplReceivLineEdit(self, [], reject_empty_string=False)
         self.scenario_objective.set_wordlist(self.reaction_ids, replace_completer_model=False)
         self.scenario_objective.set_completer_model(self.reaction_ids_model)
         self.objective_group_layout.addWidget(self.scenario_objective)
@@ -55,6 +55,7 @@ def __init__(self, central_widget):
         layout.addWidget(group)
 
         label = QLabel("Scenario reactions")
+        label.setToolTip("The IDs of the scenario reactions must be distinct from those in the network.\nYou may introduce new metabolites in scenario reactions.")
         hbox = QHBoxLayout()
         hbox.addWidget(label)
         self.add_reaction = QPushButton("+")
@@ -76,6 +77,7 @@ def __init__(self, central_widget):
         layout.addWidget(self.equation)
 
         label = QLabel("Scenario constraints")
+        label.setToolTip('Formulated as linear inequality constraints over the reactions,\ne.g. "R1 + R2 >= 10"\nmeans that the sum of fluxes through R1 and R2 must be at least 10.')
         hbox = QHBoxLayout()
         hbox.addWidget(label)
         self.add_constraint_button = QPushButton("+")
@@ -407,13 +409,13 @@ def change_scenario_objective_coefficients(self, text_correct: bool):
                     self.objectiveSetupChanged.emit()
             self.use_scenario_objective.setEnabled(True)
         else:
-            self.appdata.project.scen_values.objective_coefficients.clear()
             self.use_scenario_objective.setEnabled(False)
 
     @Slot()
     def validate_objective(self):
         if not self.scenario_objective.is_valid and self.appdata.project.scen_values.use_scenario_objective:
-            self.use_scenario_objective.setChecked(False)
+            self.appdata.project.scen_values.objective_coefficients.clear()
+            self.use_scenario_objective.setChecked(False) # triggers use_scenario_objective_changed
 
     @Slot(int)
     def use_scenario_objective_changed(self, state: int):