From 38ecae7adc571686b09a354be2443343f18a3cdc Mon Sep 17 00:00:00 2001
From: tlfobe <lenny@DESKTOP-HTCAJ46>
Date: Fri, 1 Mar 2024 18:01:40 -0700
Subject: [PATCH] adding workflow functions to parameterize entire box

---
 terphenyl_simulations/analysis_workflows/remd.py |  8 +++++---
 terphenyl_simulations/gromacs_wrapper.py         | 10 +++++++++-
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/terphenyl_simulations/analysis_workflows/remd.py b/terphenyl_simulations/analysis_workflows/remd.py
index 6d617fb..2cc4581 100644
--- a/terphenyl_simulations/analysis_workflows/remd.py
+++ b/terphenyl_simulations/analysis_workflows/remd.py
@@ -88,6 +88,10 @@ def build_system(job):
     packmol_builder.solvate_system()
     os.chdir(top_dir)
 
+@FlowProject.operation
+def parameterize_solvated_system(job):
+    pass
+
 
 @FlowProject.pre.after(build_foldamer)
 @FlowProject.post(
@@ -113,14 +117,12 @@ def minimize_foldamer(job):
     os.chdir(job.fn(""))
     gmx_wrapper = terphenyl_simulations.gromacs_wrapper.GromacsWrapper(job.sp['gromacs_exe'])
     out_name = job.doc['foldamer_gro'].split('.gro')[0] + '_centered.gro'
-    gmx_wrapper.center(job.doc['foldamer_gro'], out_name)
+    gmx_wrapper.center_configuration(job.doc['foldamer_gro'], out_name)
     job.doc['foldamer_gro'] = out_name
     gmx_wrapper.minimize(job.doc['foldamer_gro'], job.doc['foldamer_topology'])
-    
     os.chdir(top_dir)
 
 
-
 @FlowProject.pre.after(build_system)
 @FlowProject.operation
 def parameterize_system(job):
diff --git a/terphenyl_simulations/gromacs_wrapper.py b/terphenyl_simulations/gromacs_wrapper.py
index 60d2c0c..3bf4d13 100644
--- a/terphenyl_simulations/gromacs_wrapper.py
+++ b/terphenyl_simulations/gromacs_wrapper.py
@@ -30,13 +30,21 @@ def __init__(self, gromacs_exe = None, path = '.'):
             self.mpi = True
             self.gmx = 'mpirun -np 1 ' + self.gmx
 
-    def center(self, gro_file, out_file):
+    def center_configuration(self, gro_file, out_file):
         editconf_call = self.gmx + ' editconf -f ' + gro_file + \
                                             ' -c yes' + \
                                             ' -o ' + out_file
         process = subprocess.Popen(editconf_call.split(' '))
         process.wait()
 
+    def add_box(self, gro_file, box_size, out_file):
+        editconf_call = self.gmx + ' editconf -f ' + gro_file + \
+                                            ' -box ' + str(box_size) +  \
+                                            ' -o ' + out_file
+        process = subprocess.Popen(editconf_call.split(' '))
+        process.wait()
+
+
     def minimize(self, gro_file, top_file, prefix = 'em', mdp = 'em.mdp'):
         # Check for mdp file
         if not mdp in os.listdir(self.path):