Update setup_options.py

Added additional sessions

openmmdl/openmmdl_setup/setup_options.py

@@ -1,11 +1,16 @@
-
+from flask import session, request
 
 class SetupOptionsConfigurator:
     def __init__(self, session):
         self.session = session
 
     def configure_default_options(self):
-        """Select default options based on the file format and force field."""
+        """
+        Sets default simulation options based on session data.
+        
+        Updates parameters for ensemble type, platform, cutoff, tolerances,
+        simulation length, and output files.
+        """
         implicitWater = False
         self.session["restart_checkpoint"] = False
         self.session["mdtraj_output"] = "mdtraj_pdb_dcd"
@@ -33,7 +38,7 @@ def configure_default_options(self):
         self.session["hmr"] = True
         self.session["hmrMass"] = "1.5"
         self.session["dt"] = "0.002"
-        self.session["sim_length"] = "30"
+        self.session["sim_length"] = "50"
         self.session["equilibration"] = "equilibration"
         self.session["temperature"] = "300"
         self.session["friction"] = "1.0"
@@ -68,7 +73,11 @@ def configure_default_options(self):
         self.session["md_postprocessing"] = "True"
 
     def configureDefaultAmberOptions(self):
-        """Select default options based on the file format and force field."""
+        """
+        Sets default options for ligand, receptor, and solvation in Amber.
+    
+        Configures force fields, ion types, water model, and lipid properties.
+        """
         # Ligand
         self.session["nmLig"] = ""
         self.session["spLig"] = ""
@@ -98,13 +107,30 @@ def configureDefaultAmberOptions(self):
         self.session["pos_ion"] = "Na+"
         self.session["neg_ion"] = "Cl-"
         self.session["ionConc"] = "0.15"
-
-
+        
+        
 class RequestSessionManager:
     def __init__(self, form):
         self.form = form
 
-    def setAmberOptions_update_session(self):
+    def setAmberOptions_rcp_session(self):
+        """
+        Sets receptor-related Amber options from form data.
+        """
+        session["rcpType"] = self.form.get("rcpType", "")
+        session["prot_ff"] = self.form.get("prot_ff", "")
+        session["other_prot_ff_input"] = self.form.get("other_prot_ff_input", "")
+        session["dna_ff"] = self.form.get("dna_ff", "")
+        session["other_dna_ff_input"] = self.form.get("other_dna_ff_input", "")
+        session["rna_ff"] = self.form.get("rna_ff", "")
+        session["other_rna_ff_input"] = self.form.get("other_rna_ff_input", "")
+        session["carbo_ff"] = self.form.get("carbo_ff", "")
+        session["other_carbo_ff_input"] = self.form.get("other_carbo_ff_input", "")
+
+    def setAmberOptions_water_membrane_session(self):
+        """
+        Sets water and membrane-related Amber options from form data.
+        """
         session["addType"] = self.form.get("addType", "")
         session["boxType"] = self.form.get("boxType", "")
         session["dist"] = self.form.get("dist", "")
@@ -118,3 +144,54 @@ def setAmberOptions_update_session(self):
         session["pos_ion"] = self.form.get("pos_ion", "")
         session["neg_ion"] = self.form.get("neg_ion", "")
         session["ionConc"] = self.form.get("ionConc", "")
+
+    def addhydrogens_add_water_or_membrane_session(self):
+        """
+        Configures water or membrane settings based on form data.
+        """
+        if "addWater" in self.form:
+            session["solvent"] = True
+            session["add_membrane"] = False
+            padding, boxSize, boxShape = None, None, None
+
+            if self.form["boxType"] == "geometry":
+                session["water_padding"] = True
+                session["water_padding_distance"] = float(self.form["geomPadding"])
+                session["water_boxShape"] = self.form["geometryDropdown"]
+            else:
+                session["water_padding"] = False
+                session["box_x"] = float(self.form["boxx"])
+                session["box_y"] = float(self.form["boxy"])
+                session["box_z"] = float(self.form["boxz"])
+                boxSize = (
+                    float(self.form["boxx"]),
+                    float(self.form["boxy"]),
+                    float(self.form["boxz"]),
+                )
+            session["water_ionicstrength"] = float(self.form["ionicstrength"])
+            session["water_positive"] = self.form["positiveion"] + "+"
+            session["water_negative"] = self.form["negativeion"] + "-"
+
+        elif "addMembrane" in self.form:
+            session["solvent"] = True
+            session["add_membrane"] = True
+            session["lipidType"] = self.form["lipidType"]
+            session["membrane_padding"] = float(self.form["membranePadding"])
+            session["membrane_ionicstrength"] = float(self.form["ionicstrength"])
+            session["membrane_positive"] = self.form["positiveion"] + "+"
+            session["membrane_negative"] = self.form["negativeion"] + "-"
+
+    def simulationoptions_add_general_settings(self):
+        """
+        Adds general simulation settings from form data to the session.
+        """
+        for key in self.form:
+            session[key] = self.form[key]
+        session["ligand"] = "ligand" in self.form
+        session["writeDCD"] = "writeDCD" in self.form
+        session["writeData"] = "writeData" in self.form
+        session["writeCheckpoint"] = "writeCheckpoint" in self.form
+        session["dataFields"] = self.form.getlist("dataFields")
+        session["hmr"] = "hmr" in self.form
+        session["writeSimulationXml"] = "writeSimulationXml" in self.form
+        session["writeFinalState"] = "writeFinalState" in self.form