merging

Author: sbillinge

.gitignore

@@ -43,3 +43,6 @@ nosetests.xml
 setup.cfg
 /DistancePrinter/version.cfg
 /DistancePrinter/gitarchive.cfg
+
+# test output
+actual.res

DistancePrinter/distanceprinter.py

@@ -12,9 +12,7 @@
 #
 ##############################################################################
 
-import os
 import sys
-import itertools
 import numpy as np
 
 from diffpy.pdffit2 import PdfFit
@@ -38,14 +36,14 @@ def calDistance(strufile, atomi, atomj, lb, ub, complete):
     distlist = np.zeros(len(dij), dtype=dtypec)
 
     if not complete:
-        for i, dist, dd, ij in itertools.izip(range(len(dij)), dij, ddij, ij0):
+        for i, dist, dd, ij in zip(range(len(dij)), dij, ddij, ij0):
             if ij[0] > ij[1]:
                 distlist[i] = (dist, dd, ele[ij[1]], ele[ij[0]])
             else:
                 distlist[i] = (dist, dd, ele[ij[0]], ele[ij[1]])
         distlist = np.unique(distlist)
     else:
-        for i, dist, dd, ij in itertools.izip(range(len(dij)), dij, ddij, ij0):
+        for i, dist, dd, ij in zip(range(len(dij)), dij, ddij, ij0):
             distlist[i] = (dist, dd, '%s.%i' % (ele[ij[0]], ij[0]), '%s.%i' % (ele[ij[1]], ij[1]))
 
     distlist.sort(order='distance')
@@ -78,18 +76,30 @@ def formatResults(stru, distlist, complete, all0ddij, **kw):
 
     if complete:
         for dist in distlist:
-            lines.append('%s-%s:\t%2.6f' % (dist[2], dist[3], dist[0]))
+            try:
+                lines.append('%s-%s:\t%2.6f' % (dist[2].decode('utf-8'), dist[3].decode('utf-8'), dist[0]))
+            except AttributeError:
+                lines.append('%s-%s:\t%2.6f' % (dist[2], dist[3], dist[0]))
     else:
         for dist in distlist:
-            lines.append('%s-%s:\t%2.6f (%1.1e)' % (dist[2], dist[3], dist[0], dist[1]))
+            try:
+                lines.append('%s-%s:\t%2.6f (%1.1e)' % (dist[2].decode('utf-8'), dist[3].decode('utf-8'), dist[0], dist[1]))
+            except AttributeError:
+                lines.append('%s-%s:\t%2.6f (%1.1e)' % (dist[2], dist[3], dist[0], dist[1]))
     rv = '\n'.join(lines)
     return rv
 
 def writeToFile(filename, rv):
-    f = file(filename, 'w')
-    f.write(rv)
-    f.close()
-    return
+    f = open(filename, 'w', encoding="utf-8")
+    try:
+        rv = rv.decode('utf-8')
+        f.write(rv)
+        f.close()
+    except AttributeError:
+        # No need to decode in python 3
+        f.write(rv)
+        f.close()
+        pass
 
 def main():
     sysargv = sys.argv[1:]

tests/data/Ni-9008476.cif

@@ -0,0 +1,250 @@
+#------------------------------------------------------------------------------
+#$Date: 2017-10-15 03:23:08 +0300 (Sun, 15 Oct 2017) $
+#$Revision: 202022 $
+#$URL: file:///home/coder/svn-repositories/cod/cif/9/00/84/9008476.cif $
+#------------------------------------------------------------------------------
+#
+# This file is available in the Crystallography Open Database (COD),
+# http://www.crystallography.net/. The original data for this entry
+# were provided the American Mineralogist Crystal Structure Database,
+# http://rruff.geo.arizona.edu/AMS/amcsd.php
+#
+# The file may be used within the scientific community so long as
+# proper attribution is given to the journal article from which the
+# data were obtained.
+#
+data_9008476
+loop_
+_publ_author_name
+'Wyckoff, R. W. G.'
+_publ_section_title
+;
+ Second edition. Interscience Publishers, New York, New York
+ Cubic closest packed, ccp, structure
+;
+_journal_name_full               'Crystal Structures'
+_journal_page_first              7
+_journal_page_last               83
+_journal_volume                  1
+_journal_year                    1963
+_chemical_formula_sum            Ni
+_chemical_name_mineral           Nickel
+_space_group_IT_number           225
+_symmetry_space_group_name_Hall  '-F 4 2 3'
+_symmetry_space_group_name_H-M   'F m -3 m'
+_cell_angle_alpha                90
+_cell_angle_beta                 90
+_cell_angle_gamma                90
+_cell_length_a                   3.52387
+_cell_length_b                   3.52387
+_cell_length_c                   3.52387
+_cell_volume                     43.758
+_exptl_crystal_density_diffrn    8.909
+_cod_original_sg_symbol_H-M      'F m 3 m'
+_cod_database_code               9008476
+loop_
+_symmetry_equiv_pos_as_xyz
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+loop_
+_atom_site_label
+_atom_site_fract_x
+_atom_site_fract_y
+_atom_site_fract_z
+Ni 0.00000 0.00000 0.00000
+loop_
+_cod_related_entry_id
+_cod_related_entry_database
+_cod_related_entry_code
+1 ChemSpider 910
+2 MPOD 1000037