added packmol to environment and changed the default behavior of the …

…REMD simulations to chdir into the working directory and run packmol there, rather than running from the top directory. fortran seems to have a limit on the string length it can use, so I cannot feed packmol long abspath file names

setup.py

@@ -26,27 +26,6 @@
 except:
     long_description = "\n".join(short_description[2:]),
 
-class PostDevelopCommand(develop):
-    """Post-installation for development mode."""
-    def run(self):
-        develop.run(self)
-        start_dir = os.path.abspath('')
-        os.chdir('submodules/packmol')
-        check_call('./configure'.split())
-        check_call('make'.split())
-        os.chdir(start_dir)
-        # PUT YOUR POST-INSTALL SCRIPT HERE or CALL A FUNCTION
-
-class PostInstallCommand(install):
-    """Post-installation for installation mode."""
-    def run(self):
-        install.run(self)
-        start_dir = os.path.abspath('')
-        os.chdir('submodules/packmol')
-        check_call('./configure'.split())
-        check_call('make'.split())
-        os.chdir(start_dir)
-
 setup(
     # Self-descriptive entries which should always be present
     name='terphenyl_simulations',
@@ -56,10 +35,7 @@ def run(self):
     long_description=long_description,
     long_description_content_type="text/markdown",
     version=versioneer.get_version(),
-    cmdclass={
-        'develop': PostDevelopCommand,
-        'install': PostInstallCommand,
-        },
+    cmdclass=versioneer.get_cmdclass(),
     license='MIT',
 
     # Which Python importable modules should be included when your package is installed

terphenyl_simulations/analysis_workflows/remd.py

@@ -51,15 +51,26 @@ def build_foldamer(job):
     foldamer_builder = terphenyl_simulations.build.FoldamerBuilder(job.sp['build_foldamer'])
     foldamer_builder.build_foldamer(path = job.fn(""))
 
+@FlowProject.pre.after(build_foldamer)
 @FlowProject.operation
 def parameterize_foldamer(job):
     pass
 
+@FlowProject.post((lambda job: os.path.exists(job.fn('solvated_' + job.doc['build_parameters']['structure_file'] + '.pdb'))))
 @FlowProject.operation
 def build_system(job):
-    packmol_builder = terphenyl_simulations.build.SystemBuilder(job.sp['build_foldamer'], path = job.fn(''))
+    top_dir = os.path.abspath('.')
+    os.chdir(job.fn(''))
+    packmol_builder = terphenyl_simulations.build.SystemBuilder(job.sp['build_foldamer'])
     packmol_builder.build_packmol_inp()
     packmol_builder.build_system()
+    os.chdir(top_dir)
+
+@FlowProject.pre.after(build_system)
+@FlowProject.operation
+def parameterize_system(job):
+    pass
+
 
 def main():
     if not os.path.isdir('workspace'):

terphenyl_simulations/build.py

@@ -85,6 +85,29 @@ def build_packmol_inp(self):
             self.output_file
         )
 
+        # Get solvent PDB location
+
+        # Check top signac directory
+        solvent_pdb = self.build_params['system']['solvent'] + '.pdb'
+        print(os.listdir(os.path.join(ROOT_DIR, 'data/solvents/')))
+
+        # Check stored solvent pdbs
+        if not os.path.exists(solvent_pdb) and solvent_pdb in os.listdir(os.path.join(ROOT_DIR, 'data/solvents/')):
+            print('Using ' + solvent_pdb + ' from the internal library of solvents. If this ' + \
+                  'is not the behavior you intend, please include the solvent pdb you wish ' + \
+                  'to solvate the system with in your working directory.')
+            solvent_pdb = os.path.join(ROOT_DIR, 'data/solvents/', self.build_params['system']['solvent'] + '.pdb')
+
+        # Copy to path directory
+            shutil.copy(
+                solvent_pdb,
+                os.path.join(self.path, solvent_pdb.split('/')[-1])
+            )
+        else:
+            warnings.warn('Warning! Unable to find ' + solvent_pdb + ' in the working directory \
+                          or the internal library.')
+
+
         # Make replacements to the template inp file
         replace_all_pattern('OUTPUT_FILENAME', os.path.join(self.path, 'solvated_' + self.build_params['structure_file'] + '.pdb'), self.output_file)
         replace_all_pattern('SOLUTE_PDB', os.path.join(self.path, self.build_params['structure_file'] + '.pdb'), self.output_file)
@@ -100,18 +123,6 @@ def build_packmol_inp(self):
         ]
         solute_position_str = [str(round(n, 1)) for n in solute_position]
         replace_all_pattern('SOLUTE_POSITION', ' '.join(solute_position_str), self.output_file)
-
-        # Get solvent PDB location
-        solvent_pdb = self.build_params['system']['solvent'] + '.pdb'
-        print(os.listdir(os.path.join(ROOT_DIR, 'data/solvents/')))
-        if not os.path.exists(solvent_pdb) and solvent_pdb in os.listdir(os.path.join(ROOT_DIR, 'data/solvents/')):
-            print('Using ' + solvent_pdb + ' from the internal library of solvents. If this ' + \
-                  'is not the behavior you intend, please include the solvent pdb you wish ' + \
-                  'to solvate the system with in your working directory.')
-            solvent_pdb = os.path.join(ROOT_DIR, 'data/solvents/', self.build_params['system']['solvent'] + '.pdb')
-        else:
-            warnings.warn('Warning! Unable to find ' + solvent_pdb + ' in the working directory \
-                          or the internal library.')
         replace_all_pattern('SOLVENT_PDB', solvent_pdb, self.output_file)
         replace_all_pattern('N_SOLVENT', str(self.build_params['system']['n_solvent']), self.output_file)
 
@@ -133,6 +144,7 @@ def build_system(self):
         with open('temp', 'w') as f:
             f.write(cmdline_entry)
 
+        print(cmdline_entry)
         process = Popen(['bash temp'], shell = True, stdin=PIPE)
         process.wait()
         os.remove('temp')

terphenyl_simulations/clustering.py

@@ -244,7 +244,7 @@ def torsion_clustering_grid_search(
         min_samples_values,
         [round(eps, 2) for eps in eps_values],
         "Min. Samples",
-        "$\epsilon_{DBSCAN}$",
+        "$\\epsilon_{DBSCAN}$",
         prefix  + "_" + plot_filename,
         "Avg. Silhouette Score"
     )
@@ -368,7 +368,7 @@ def clustering_grid_search(
         min_samples_values,
         [round(eps, 2) for eps in eps_values],
         "Min. Samples",
-        "$\epsilon_{DBSCAN}$",
+        "$\\epsilon_{DBSCAN}$",
         prefix  + "_" + plot_filename,
         "Avg. Silhouette Score"
     )

terphenyl_simulations/plotting.py

@@ -262,8 +262,8 @@ def plot_ramachandran_plot(traj_file, top_file, prefix = "remd", bins = 50, titl
 
     plt.figure(figsize=[5,5])
     plt.hist2d(phi_angles, psi_angles, bins = np.linspace(-180, 180, bins + 1))
-    plt.xlabel("$\Phi$ Angle (Degrees)")
-    plt.ylabel("$\Psi$ Angle (Degrees)")
+    plt.xlabel("$\\Phi$ Angle (Degrees)")
+    plt.ylabel("$\\Psi$ Angle (Degrees)")
 
     for scatter_points_file in scatter_points_files:
         frame = md.load(scatter_points_file)