Add verbose option

FRETpredict/__init__.py

@@ -4,6 +4,6 @@
 from .lennardjones import lj_parameters
 from .libraries import *
 
-__version__ = '0.2.1'
+__version__ = '0.2.2'
 
 

FRETpredict/utils.py

@@ -307,7 +307,7 @@ def rotamer_placement(self, universe, prot_atoms, lib):
         # Save aligned rotamers
         if self.verbose:
             rotamers = universe.select_atoms("all")
-            with MDAnalysis.Writer(lib.name.replace(' ','_')+'.pdb', rotamers.n_atoms) as W:
+            with MDAnalysis.Writer(self.output_prefix+'_'+lib.name.replace(' ','_')+'.pdb', rotamers.n_atoms) as W:
                 for ts in universe.trajectory:
                     W.write(rotamers)
 

tests/test_Hsp90.py

@@ -21,7 +21,8 @@ def test_Hsp90_R0_calculation():
                    electrostatic=True,
                    libname_1='AlexaFluor 594 C1R cutoff30',
                    libname_2='AlexaFluor 568 C1R cutoff30',
-                   output_prefix='tests/test_systems/Hsp90/output/E30')
+                   output_prefix='tests/test_systems/Hsp90/output/E30',
+                   verbose=True)
 
     # Run FRETpredict calculations
     FRET.run()
@@ -43,7 +44,8 @@ def test_Hsp90_fixed_R0():
                            fixed_R0=True, r0=5.5, electrostatic=True,
                            libname_1='AlexaFluor 594 C1R cutoff30',
                            libname_2='AlexaFluor 568 C1R cutoff30',
-                           output_prefix='tests/test_systems/Hsp90/output/E30_fixedR0')
+                           output_prefix='tests/test_systems/Hsp90/output/E30_fixedR0',
+                           verbose=True)
 
     # Run FRETpredict calculations
     FRET_fixedR0.run()
@@ -53,7 +55,3 @@ def test_Hsp90_fixed_R0():
     assert np.abs(pd.read_pickle('tests/test_systems/Hsp90/output/E30_fixedR0-data-452-637.pkl')['Estatic'] - 0.538) < 1e-3,  \
     "Could not read FRET data from file (fixed R0)"
 
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-
-
-