Minor changes.

nmrstarlib/__init__.py

@@ -1,3 +1,6 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
 """Routines for working with BMRB NMR-STAR format files.
 
 This package includes the following modules:
@@ -20,13 +23,21 @@
     JSONized file format.
 
 ``csviewer``
-    This module provides the :func:`~nmrstarlib.csviewer.csviewer` function that visualizes
+    This module provides the :class:`~nmrstarlib.csviewer.CSViewer` class that visualizes
     chemical shift values using the Graphviz (http://www.graphviz.org/) DOT Languge description.
 """
 
 import os
 from . import nmrstarlib
 
 this_directory = os.path.dirname(__file__)
-config_file = os.path.join(this_directory, '../conf/constants.json')
-nmrstarlib.update_constants(config_file)
+
+if nmrstarlib.NMRSTAR_VERSION == "3":
+    config_filepath = os.path.join(this_directory, '../conf/constants_nmrstar3.json')
+elif nmrstarlib.NMRSTAR_VERSION == "2":
+    config_filepath = os.path.join(this_directory, '../conf/constants_nmrstar2.json')
+else:
+    config_filepath = os.path.join(this_directory, '../conf/constants_nmrstar3.json')
+
+with open(config_filepath, "r") as infile:
+    nmrstarlib.update_constants(infile)

nmrstarlib/bmrblex.py

@@ -114,16 +114,6 @@ def get_token(self):
         raw = self._read_token()
         return raw
 
-    def _get_nextchar(self):
-        nextchar = self.instream.read(1)
-        self.streamposition += 1
-        return nextchar
-
-    def _get_nextnextchar(self):
-        nextnextchar = self.instream.read(1)
-        self.instream.seek(self.streamposition + 1)
-        return nextnextchar
-
     def _read_token(self):
         """Read token based on the parsing rules.
 
@@ -137,17 +127,15 @@ def _read_token(self):
         while self.streamposition+1 < self.streamlength-1:
             nextchar = self.instream.read(1)
             self.streamposition += 1
-            # nextchar = self._get_nextchar()
 
             nextnextchar = self.instream.read(1)       # look up 1 char ahead
             self.instream.seek(self.streamposition+1)  # return to current stream position
-            # nextnextchar = self._get_nextnextchar()
 
             if self.state is None:
-                self.token = ''        # past end of file
+                self.token = ""        # past end of file
                 break
 
-            elif self.state == ' ':
+            elif self.state == " ":
                 if not nextchar:
                     self.state = None  # end of file
                     break
@@ -233,13 +221,13 @@ def _read_token(self):
                 else:
                     self.token = self.token + nextchar
 
-            #
-            elif self.state == 'a':
+            # process regular token (unquoted text)
+            elif self.state == "a":
                 if not nextchar:
                     self.state = None   # end of file
                     break
                 elif nextchar in self.whitespace:
-                    self.state = ' '
+                    self.state = " "
                     if self.token or quoted:
                         break   # emit current token
                     else:

nmrstarlib/csviewer.py

@@ -15,7 +15,7 @@
 class CSViewer(object):
     """Chemical Shifts Viewer: uses:meth:`nmrstarlib.nmrstarlib.StarFile.chem_shifts_by_residue`
     method chemical shifts organized by residue and visualizes chemical shifts values using the
-    Graphviz(http: // www.graphviz.org /) DOT Languge description.
+    Graphviz (http://www.graphviz.org/) DOT Languge description.
     """
 
     dot_template = '''digraph {{