Merge pull request #23 from drorlab/develop

v0.2.4

TODO.md

@@ -71,6 +71,7 @@
   - [ ] lipids
   - [ ] nucleic acids
 - [ ] Simplify adding hand-crafted features 
+- [ ] Account for [Bonferroni correction](https://en.wikipedia.org/wiki/Bonferroni_correction) in comparison.
 - [ ] Implement conformational entropy calculations
   - [ ] Read papers, e.g, [1](https://www.pnas.org/content/111/43/15396), [2](https://www.mdpi.com/2079-3197/6/1/21/htm), [3](https://pubs.acs.org/doi/10.1021/acs.jcim.0c01375)
   - [ ] Test implementations, e.g., [Xentropy](https://github.com/liedllab/X-Entropy) to find the best way to do it.

pensa/features/mda_distances.py

@@ -6,7 +6,7 @@
 import gpcrmining.gpcrdb as db
 
 
-def get_atom_self_distances(pdb, xtc, selection='all', first_frame=0, last_frame=-1, step=1):
+def get_atom_self_distances(pdb, xtc, selection='all', first_frame=0, last_frame=None, step=1):
     """
     Load distances between all selected atoms.
 
@@ -20,7 +20,7 @@ def get_atom_self_distances(pdb, xtc, selection='all', first_frame=0, last_frame
         Selection string to choose which atoms to include. Default: all.
     first_frame : int, default=0
         First frame to return of the features. Zero-based.
-    last_frame : int, default=-1
+    last_frame : int, default=None
         Last frame to return of the features. Zero-based.
     step : int, default=1
         Subsampling step width when reading the frames.
@@ -64,7 +64,7 @@ def get_atom_self_distances(pdb, xtc, selection='all', first_frame=0, last_frame
     return d_labels, data_arr
 
 
-def get_calpha_distances(pdb, xtc, first_frame=0, last_frame=-1, step=1):
+def get_calpha_distances(pdb, xtc, first_frame=0, last_frame=None, step=1):
     """
     Load distances between all C-alpha atoms.
 
@@ -76,7 +76,7 @@ def get_calpha_distances(pdb, xtc, first_frame=0, last_frame=-1, step=1):
         File name for the trajectory (xtc format).
     first_frame : int, default=0
         First frame to return of the features. Zero-based.
-    last_frame : int, default=-1
+    last_frame : int, default=None
         Last frame to return of the features. Zero-based.
     step : int, default=1
         Subsampling step width when reading the frames.
@@ -124,7 +124,7 @@ def select_gpcr_residues(gpcr_name, res_dbnum):
 
 
 def get_gpcr_calpha_distances(pdb, xtc, gpcr_name, res_dbnum,
-                              first_frame=0, last_frame=-1, step=1):
+                              first_frame=0, last_frame=None, step=1):
     """
     Load distances between all selected atoms.
 
@@ -140,7 +140,7 @@ def get_gpcr_calpha_distances(pdb, xtc, gpcr_name, res_dbnum,
         Relative GPCR residue numbers.
     first_frame : int, default=0
         First frame to return of the features. Zero-based.
-    last_frame : int, default=-1
+    last_frame : int, default=None
         Last frame to return of the features. Zero-based.
     step : int, default=1
         Subsampling step width when reading the frames.

pensa/statesinfo/discrete_states.py

@@ -439,6 +439,7 @@ def get_intersects(gaussians, distribution, Gauss_xvals, write_plots=None,write_
         plt.title(write_name)        
         plt.ioff()
         plt.savefig('ssi_plots/'+write_name+".png")
+        plt.close()
 
     return all_intersects
 

setup.py

@@ -1,7 +1,7 @@
 from setuptools import setup, find_packages
 
 setup(name='pensa',
-      version='0.2.3',
+      version='0.2.4',
       description='PENSA - protein ensemble analysis',
       url='http://github.com/drorlab/pensa',
       author='Martin Voegele, Neil Thomson, Sang Truong, Jasper McAvity',