Resolve merge conflicts.

dfhahn · Jan 24, 2022 · fe2ae9a · fe2ae9a
2 parents bdd3286 + 1ea7b75
commit fe2ae9a
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Showing 4 changed files with 15 additions and 24 deletions.
diff --git a/pmx/workflow/workflow2_make_perturbations.py b/pmx/workflow/workflow2_make_perturbations.py
@@ -69,10 +69,9 @@ def atomsToMorph(pwf):
         process = subprocess.Popen(command,
                                    stdout=subprocess.PIPE,
                                    stderr=subprocess.PIPE)
-        process.wait()
+        out = process.communicate()
 
         if pwf.verbose:
-            out = process.communicate()
             print('STDERR{} '.format(out[1].decode("utf-8")))
             print('STDOUT{} '.format(out[0].decode("utf-8")))
 
@@ -133,10 +132,9 @@ def makeHybrid(pwf):
         process = subprocess.Popen(command, 
                                    stdout=subprocess.PIPE,
                                    stderr=subprocess.PIPE)
-        process.wait()
+        out = process.communicate()
 
         if pwf.verbose:
-            out = process.communicate()
             print('STDERR{} '.format(out[1].decode("utf-8")))
             print('STDOUT{} '.format(out[0].decode("utf-8")))
 
@@ -167,10 +165,9 @@ def oneffFile(pwf):
         process = subprocess.Popen(command,
                                    stdout=subprocess.PIPE,
                                    stderr=subprocess.PIPE)
-        process.wait()
+        out = process.communicate()
 
         if pwf.verbose:
-            out = process.communicate()
             print('STDERR{} '.format(out[1].decode("utf-8")))
             print('STDOUT{} '.format(out[0].decode("utf-8")))
 

diff --git a/pmx/workflow/workflow3_solvate.py b/pmx/workflow/workflow3_solvate.py
@@ -49,10 +49,9 @@ def solvateLigand(pwf):
                                     '-d', str(1.5)],
                                    stdout=subprocess.PIPE,
                                    stderr=subprocess.PIPE)
-        process.wait()
+        out = process.communicate()
 
         if pwf.verbose:
-            out = process.communicate()
             print('STDERR{} '.format(out[1].decode("utf-8")))
             print('STDOUT{} '.format(out[0].decode("utf-8")))
 
@@ -67,10 +66,9 @@ def solvateLigand(pwf):
                                     '-p', topology],
                                    stdout=subprocess.PIPE,
                                    stderr=subprocess.PIPE)
-        process.wait()
+        out = process.communicate()
 
         if pwf.verbose:
-            out = process.communicate()
             print('STDERR{} '.format(out[1].decode("utf-8")))
             print('STDOUT{} '.format(out[0].decode("utf-8")))
 
@@ -82,16 +80,16 @@ def solvateLigand(pwf):
         process = subprocess.Popen(['gmx', 'grompp',
                                     '-p', topology,
                                     '-c', water,
+                                    '-r', water,
                                     '-o', tprfile,
                                     '-f', mdpemA,
                                     '-po', mdout,
                                     '-maxwarn', str(2)],
                                    stdout=subprocess.PIPE,
                                    stderr=subprocess.PIPE)
-        process.wait()
+        out = process.communicate()
 
         if pwf.verbose:
-            out = process.communicate()
             print('STDERR{} '.format(out[1].decode("utf-8")))
             print('STDOUT{} '.format(out[0].decode("utf-8")))
 
@@ -125,9 +123,9 @@ def addIonsLigand(pwf):
                                         stdout=subprocess.PIPE,
                                         stderr=subprocess.PIPE)
             process.stdin.write('SOL'.encode())
+            out = process.communicate()
 
             if pwf.verbose:
-                out = process.communicate()
                 print('STDERR{} '.format(out[1].decode("utf-8")))
                 print('STDOUT{} '.format(out[0].decode("utf-8")))
 
@@ -213,8 +211,7 @@ def combineProteinLigand(pwf):
             includes = ['ffMOL.itp', 'merged.itp']
 
         # protein
-        includes += list(filter(lambda x: x.endswith('.itp') and not  x.startswith('ff'), os.listdir(f'{pwf.protPath}/top/amber99sb-star-ildn-mut.ff/')))
-
+        includes += list(filter(lambda x: x.endswith('.itp') and not  x.startswith('ff') and not x.startswidth('posre'), os.listdir(f'{pwf.protPath}/top/amber99sb-star-ildn-mut.ff/')))
 
         # molecules to be included
         molecules = []
@@ -272,10 +269,9 @@ def solvateComplex(pwf):
                                     '-d', str(1.5)],
                                    stdout=subprocess.PIPE,
                                    stderr=subprocess.PIPE)
-        process.wait()
+        out = process.communicate()
 
         if pwf.verbose:
-            out = process.communicate()
             print('STDOUT{} '.format(out[0].decode("utf-8")))
             print('STDERR{} '.format(out[1].decode("utf-8")))
 
@@ -289,10 +285,9 @@ def solvateComplex(pwf):
                                     '-p', topology],
                                    stdout=subprocess.PIPE,
                                    stderr=subprocess.PIPE)
-        process.wait()
+        out = process.communicate()
 
         if pwf.verbose:
-            out = process.communicate()
             print('STDOUT{} '.format(out[0].decode("utf-8")))
             print('STDERR{} '.format(out[1].decode("utf-8")))
 
@@ -303,16 +298,16 @@ def solvateComplex(pwf):
         process = subprocess.Popen(['gmx', 'grompp',
                                     '-p', topology,
                                     '-c', water,
+                                    '-r', water,
                                     '-o', tprfile,
                                     '-f', mdpemA,
                                     '-po', mdout,
                                     '-maxwarn', str(3)],
                                    stdout=subprocess.PIPE,
                                    stderr=subprocess.PIPE)
-        process.wait()
+        out = process.communicate()
 
         if pwf.verbose:
-            out = process.communicate()
             print('STDOUT{} '.format(out[0].decode("utf-8")))
             print('STDERR{} '.format(out[1].decode("utf-8")))
 
@@ -356,8 +351,9 @@ def addIonsComplex(pwf):
                                        stderr=subprocess.PIPE)
             process.stdin.write('SOL'.encode())
 
+            out = process.communicate()
+
             if pwf.verbose:
-                out = process.communicate()
                 print('STDOUT{} '.format(out[0].decode("utf-8")))
                 print('STDERR{} '.format(out[1].decode("utf-8")))
 

diff --git a/pmx/workflow/workflow4_write_scripts.py b/pmx/workflow/workflow4_write_scripts.py
@@ -243,7 +243,6 @@ def prepareSimulations(pwf, runtype, queueType):
                         metavar='FORCEFIELD',
                         type=str,
                         default='smirnoff99Frosst-1.1.0.offxml',
-                        choices=['smirnoff99Frosst-1.1.0.offxml', 'openff-1.0.0.offxml', 'gaff2'],
                         help='The force field used.')
     parser.add_argument('-p',
                         '--path',

diff --git a/pmx/workflow/workflow7_analyse.py b/pmx/workflow/workflow7_analyse.py
@@ -121,7 +121,6 @@ def analyzeSimulations(pwf):
     with Pool(16) as p:
         p.map(run_commands, commands)
 
-
 def unite_results(pwf):
     bootnum = 1000
     ######## read into a data frame #########