Work around more DX parsing issues by other apps

AUTHORS

@@ -15,4 +15,5 @@ Contributors:
 * Max Linke <kain88-de>
 * Jan Domanski <jandom>
 * Dominik Mierzejewski <rathann>
-* Tyler Luchko <tluchko>
+* Tyler Luchko <tluchko>
+* Giacomo Fiorin <giacomofiorin>

CHANGELOG

@@ -12,6 +12,15 @@ The rules for this file:
   * accompany each entry with github issue/PR number (Issue #xyz)
 
 ------------------------------------------------------------------------------
+??/??/2019 giacomofiorin
+
+  * 0.5.0
+
+  Fixes
+
+  * Allow parsing DX files by NAMD's GridForces module (typequote keyword, #58)
+  * Allow parsing DX files by Pymol's buggy floating-point parser (#58)
+
 04/06/2019 rathann, tluchko, orbeckst
 
   * 0.4.1

gridData/OpenDX.py

@@ -301,7 +301,8 @@ class array(DXclass):
         # "string" not automatically supported
     }
 
-    def __init__(self, classid, array=None, type=None, **kwargs):
+    def __init__(self, classid, array=None, type=None, typequote='"',
+                 **kwargs):
         """
         Parameters
         ----------
@@ -347,6 +348,7 @@ def __init__(self, classid, array=None, type=None, **kwargs):
                                   "types are: {1}".format(type,
                                                           list(self.dx_types.values()))))
             self.type = type
+        self.typequote = typequote
 
     def write(self, file):
         """Write the *class array* section.
@@ -367,18 +369,23 @@ def write(self, file):
                               "Supported valus are: {}\n"
                               "Use the type=<type> keyword argument.").format(
                                   self.type, list(self.dx_types.keys())))
+        typelabel = (self.typequote+self.type+self.typequote)
         DXclass.write(self,file,
-                      'type "{0}" rank 0 items {1} data follows'.format(
-                          self.type, self.array.size))
+                      'type {0} rank 0 items {1} data follows'.format(
+                          typelabel, self.array.size))
         # grid data, serialized as a C array (z fastest varying)
         # (flat iterator is equivalent to: for x: for y: for z: grid[x,y,z])
         # VMD's DX reader requires exactly 3 values per line
+        fmt_string = "{:d}"
+        if (self.array.dtype.kind == 'f' or self.array.dtype.kind == 'c'):
+            precision = numpy.finfo(self.array.dtype).precision
+            fmt_string = "{:."+"{:d}".format(precision)+"f}"
         values_per_line = 3
         values = self.array.flat
         while 1:
             try:
                 for i in range(values_per_line):
-                    file.write(str(next(values)) + "\t")
+                    file.write(fmt_string.format(next(values)) + "\t")
                 file.write('\n')
             except StopIteration:
                 file.write('\n')

gridData/core.py

@@ -407,7 +407,7 @@ def _load_plt(self, filename):
         grid, edges = g.histogramdd()
         self.__init__(grid=grid, edges=edges, metadata=self.metadata)
 
-    def export(self, filename, file_format=None, type=None):
+    def export(self, filename, file_format=None, type=None, typequote='"'):
         """export density to file using the given format.
 
         The format can also be deduced from the suffix of the filename
@@ -426,25 +426,34 @@ def export(self, filename, file_format=None, type=None):
 
         Parameters
         ----------
+
         filename : str
             name of the output file
+
         file_format : {'dx', 'pickle', None} (optional)
             output file format, the default is "dx"
+
         type : str (optional)
-            for DX, set the output DX array type, e.g., "double" or
-            "float"; note that PyMOL only understands "double" (see
-            issue `#35`_). By default (``None``), the DX type is
-            determined from the numpy dtype of the array of the grid
-            (and this will typically result in "double").
+            for DX, set the output DX array type, e.g., "double" or "float".
+            By default (``None``), the DX type is determined from the numpy
+            dtype of the array of the grid (and this will typically result in
+            "double").
 
             .. versionadded:: 0.4.0
 
-
         .. _`#35`: https://github.com/MDAnalysis/GridDataFormats/issues/35
 
+        typequote : str (optional)
+            For DX, set the character used to quote the type string;
+            by default this is a double-quote character, '"'.
+            Custom parsers like the one from NAMD-GridForces (backend for MDFF)
+            expect no quotes, and typequote='' may be used to appease them.
+
+            .. versionadded:: 0.5.0
+
         """
         exporter = self._get_exporter(filename, file_format=file_format)
-        exporter(filename, type=type)
+        exporter(filename, type=type, typequote=typequote)
 
     # note: the _export_FORMAT() methods all take the filename as a mandatory
     # argument. They can process kwargs but they are not required to do
@@ -460,7 +469,7 @@ def _export_python(self, filename, **kwargs):
         with open(filename, 'wb') as f:
             cPickle.dump(data, f, cPickle.HIGHEST_PROTOCOL)
 
-    def _export_dx(self, filename, type=None, **kwargs):
+    def _export_dx(self, filename, type=None, typequote='"', **kwargs):
         """Export the density grid to an OpenDX file.
 
         The file format is the simplest regular grid array and it is
@@ -494,7 +503,7 @@ def _export_dx(self, filename, type=None, **kwargs):
             positions=OpenDX.gridpositions(1, self.grid.shape, self.origin,
                                            self.delta),
             connections=OpenDX.gridconnections(2, self.grid.shape),
-            data=OpenDX.array(3, self.grid, type=type),
+            data=OpenDX.array(3, self.grid, type=type, typequote=typequote),
         )
         dx = OpenDX.field('density', components=components, comments=comments)
         dx.write(filename)