From 93953cec30011ab08526a8976a608b035c644b1a Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Fri, 9 Aug 2024 13:48:06 +0200
Subject: [PATCH] Create setup_options.py

Added File and Class to move default configuration settings from openmmdl setup
---
 openmmdl/openmmdl_setup/setup_options.py | 68 ++++++++++++++++++++++++
 1 file changed, 68 insertions(+)
 create mode 100644 openmmdl/openmmdl_setup/setup_options.py

diff --git a/openmmdl/openmmdl_setup/setup_options.py b/openmmdl/openmmdl_setup/setup_options.py
new file mode 100644
index 00000000..a2fd10d5
--- /dev/null
+++ b/openmmdl/openmmdl_setup/setup_options.py
@@ -0,0 +1,68 @@
+
+
+class SimulationOptionsConfigurator:
+    def __init__(self, session):
+        self.session = session
+
+    def configure_default_options(self):
+        """Select default options based on the file format and force field."""
+        implicitWater = False
+        self.session["restart_checkpoint"] = False
+        self.session["mdtraj_output"] = "mdtraj_pdb_dcd"
+        self.session["mdtraj_removal"] = "False"
+        self.session["mda_output"] = "mda_pdb_dcd"
+        self.session["mda_selection"] = "mda_prot_lig_all"
+        self.session["openmmdl_analysis"] = "No"
+        self.session["analysis_selection"] = "analysis_all"
+        self.session["binding_mode"] = "40"
+        self.session["min_transition"] = "1"
+        self.session["rmsd_diff"] = "No"
+        self.session["pml_generation"] = "True"
+        self.session["stable_water"] = "Yes"
+        self.session["wc_distance"] = "1.0"
+        
+        if self.session["fileType"] == "pdb" and self.session["waterModel"] == "implicit":
+            implicitWater = True
+        
+        self.session["ensemble"] = "nvt" if implicitWater else "npt"
+        self.session["platform"] = "CUDA"
+        self.session["precision"] = "mixed"
+        self.session["cutoff"] = "2.0" if implicitWater else "1.0"
+        self.session["ewaldTol"] = "0.0005"
+        self.session["constraintTol"] = "0.000001"
+        self.session["hmr"] = True
+        self.session["hmrMass"] = "1.5"
+        self.session["dt"] = "0.002"
+        self.session["sim_length"] = "30"
+        self.session["equilibration"] = "equilibration"
+        self.session["temperature"] = "300"
+        self.session["friction"] = "1.0"
+        self.session["pressure"] = "1.0"
+        self.session["barostatInterval"] = "25"
+        self.session["nonbondedMethod"] = "CutoffNonPeriodic" if implicitWater else "PME"
+        self.session["writeDCD"] = True
+        self.session["dcdFilename"] = "trajectory.dcd"
+        self.session["dcdFrames"] = "1000"
+        self.session["pdbInterval_ns"] = "10"
+        self.session["writeData"] = True
+        self.session["dataFilename"] = "log.txt"
+        self.session["dataInterval"] = "1000"
+        self.session["dataFields"] = [
+            "step",
+            "speed",
+            "progress",
+            "potentialEnergy",
+            "temperature",
+        ]
+        self.session["writeCheckpoint"] = True
+        self.session["checkpointFilename"] = "checkpoint.chk"
+        self.session["checkpointInterval_ns"] = "0.02"
+        self.session["writeSimulationXml"] = False
+        self.session["systemXmlFilename"] = "system.xml"
+        self.session["integratorXmlFilename"] = "integrator.xml"
+        self.session["writeFinalState"] = False
+        self.session["finalStateFileType"] = "stateXML"
+        self.session["finalStateFilename"] = "final_state.xml"
+        self.session["constraints"] = "hbonds"
+        self.session["rmsd"] = "True"
+        self.session["md_postprocessing"] = "True"