Merge d2e2e2e into e511aac

CHANGELOG.rst

@@ -6,6 +6,32 @@ Changelog
 ------------
 Added
 ~~~~~
+- ``numba`` added as dependency
+Changed
+~~~~~~~
+- ``SequenceFile.calculate_freq`` backend changed from ``numpy`` to ``numba`` for faster computation
+- ``SequenceFile.calculate_weights`` backend changed from ``numpy`` to ``numba`` for faster computation
+- ``SequenceFile.filter`` backend changed from ``numpy`` to ``numba`` for faster computation
+- ``SequenceFile.filter_gapped`` backend changed from ``numpy`` to ``numba`` for faster computation
+- ``SequenceFile.calculate_weights`` renamed to ``SequenceFile.get_weights``
+- ``SequenceFile.compute_freq`` renamed to ``SequenceFile.get_frequency``
+- ``ContactMap.singletons`` backend changed from ``numpy`` to ``numba`` for faster computation
+- ``Bandwidth`` backend changed from ``numpy`` to ``numba`` for faster computation
+- ``ContactMap.short_range_contacts`` renamed to ``ContactMap.short_range``
+- ``ContactMap.medium_range_contacts`` renamed to ``ContactMap.medium_range``
+- ``ContactMap.long_range_contacts`` renamed to ``ContactMap.long_range``
+- ``ContactMap.calculate_scalar_score`` renamed to ``ContactMap.set_scalar_score``
+- ``ContactMap.calculate_contact_density`` renamed to ``ContactMap.get_contact_density``
+- ``ContactMap.calculate_jaccard_index`` renamed to ``ContactMap.get_jaccard_index``
+Fixed
+~~~~~
+- Bug fix in ``SequenceFile.filter`` to remove ``Sequence`` entries reliably
+- Bug fix in ``ContactMapMatrixFigure`` when ``gap`` variable was less than 1
+
+[0.9]
+-----
+Added
+~~~~~
 - ``conkit.plot`` subpackage refactored to allow ``matplotlib`` access of ``Figure`` instances. This provides
   functionality similar to ``seaborn``, so ``matplotlib.Axes`` can be provided into which a plot is drawn.
 - ``ContactMap.as_list`` function to represent the contact map as a 2D-list of residue indexes

CONTRIB.rst

@@ -9,3 +9,4 @@ This is a list of people who have made contributions to ConKit.
 - `Felix Simkovic <https://github.com/fsimkovic>`_
 - `Jens Thomas <https://github.com/linucks>`_
 - `Stefan Seemayer <https://github.com/sseemayer>`_
+- `Chunan Liu <https://github.com/biochunan>`_

conkit/command_line/conkit_plot.py

@@ -268,7 +268,7 @@ def main():
         con = conkit.io.read(args.confile, args.conformat)[0]
 
         con.sequence = seq
-        con.assign_sequence_register()
+        con.set_sequence_register()
         con.remove_neighbors(min_distance=args.dtn, inplace=True)
         ncontacts = int(seq.seq_len * args.dfactor)
         con.sort('raw_score', reverse=True, inplace=True)
@@ -277,7 +277,7 @@ def main():
         if args.otherfile:
             other = conkit.io.read(args.otherfile, args.otherformat)[0]
             other.sequence = seq
-            other.assign_sequence_register()
+            other.set_sequence_register()
             other.remove_neighbors(min_distance=args.dtn, inplace=True)
             other.sort('raw_score', reverse=True, inplace=True)
             other_sliced = other[:ncontacts]
@@ -341,7 +341,7 @@ def altloc_remove(cmap):
         con = conkit.io.read(args.confile, args.conformat)[0]
 
         con.sequence = seq
-        con.assign_sequence_register()
+        con.set_sequence_register()
         con.remove_neighbors(min_distance=args.dtn, inplace=True)
         con.sort('raw_score', reverse=True, inplace=True)
         ncontacts = int(seq.seq_len * args.dfactor)
@@ -356,12 +356,12 @@ def altloc_remove(cmap):
         con = conkit.io.read(args.confile, args.conformat)[0]
 
         con.sequence = seq
-        con.assign_sequence_register()
+        con.set_sequence_register()
 
         if args.otherfile:
             other = conkit.io.read(args.otherfile, args.otherformat)[0]
             other.sequence = seq
-            other.assign_sequence_register()
+            other.set_sequence_register()
         else:
             other = con
 
@@ -377,7 +377,7 @@ def altloc_remove(cmap):
         con = conkit.io.read(args.confile, args.conformat)[0]
 
         con.sequence = seq
-        con.assign_sequence_register()
+        con.set_sequence_register()
         con.remove_neighbors(min_distance=args.dtn, inplace=True)
         con.sort('raw_score', reverse=True, inplace=True)
         ncontacts = int(seq.seq_len * args.dfactor)
@@ -399,7 +399,7 @@ def altloc_remove(cmap):
         con = conkit.io.read(args.confile, args.conformat)[0]
 
         con.sequence = seq
-        con.assign_sequence_register()
+        con.set_sequence_register()
         con.remove_neighbors(min_distance=args.dtn, inplace=True)
         con.sort('raw_score', reverse=True, inplace=True)
 

conkit/command_line/conkit_precision.py

@@ -77,7 +77,7 @@ def main():
     con = conkit.io.read(args.confile, args.conformat)[0]
 
     con.sequence = seq
-    con.assign_sequence_register()
+    con.set_sequence_register()
 
     logger.info('Min sequence separation for contacting residues: %d', args.dtn)
     logger.info('Contact list cutoff factor: %f * L', args.dfactor)