Added an initial version for the coordinate reader which just calls ASE.

python/nomadcore/coordinate_reader.py

+import ase.io
+import logging
+logger = logging.getLogger(__name__)
+
+
+#===============================================================================
+class CoordinateReader(object):
+    """Used to parse various different atomic coordinate files.
+
+    See the dictionary 'formats' for all the supported formats and a brief
+    explanation. Reading is primarily done by ASE, but in some cases own
+    implementation must be used. Returns all coordinates as numpy arrays.
+    """
+    def __init__(self):
+        self.formats = {
+            "xyz":    CoordinateFormat(".xyz", "The XYZ file format.", self.ase_iread),
+            "cif":    CoordinateFormat(".cif", "Crystallographic Information File", self.ase_iread),
+            "pdb":    CoordinateFormat(".pdb", "Protein Data Bank", self.ase_iread),
+        }
+
+    def iread(self, file_handle, format):
+        """Returns an iterator that goes through the given trajectory file one
+        configuration at a time.
+
+        Args:
+            file_handle: A file object pointing to the coordinate file.
+            format: String containing one of the supported formats.
+        """
+        if not self.check_format_support(format):
+            return
+
+        iread_function = self.formats[format].function
+        return iread_function(file_handle, format)
+
+    def n_atoms(self, file_handle, format):
+        """Read the first configuration of the coordinate file to extract the
+        number of atoms in it.
+        """
+        iterator = self.iread(file_handle, format)
+        pos = iterator.next()
+        return pos.shape[0]
+
+    def check_format_support(self, format):
+        """Check if the given format is supported.
+        """
+
+        if format not in self.formats:
+            logger.error("The format '{}' is not supported by CoordinateReader.".format(format))
+            return False
+        else:
+            return True
+
+    def ase_iread(self, file_handle, format):
+        """Wrapper for ASE's iread function. Returns numpy arrays instead of
+        Atoms objects.
+        """
+        # The newest ASE version found in Github has an iread function.
+        # After reading the ASE source code, it seems that the ASE iread does
+        # actually read the entire file into memory and the yields the
+        # configurations from it. Should be checked at some point.
+        def ase_generator(iterator):
+            """Used to wrap an iterator returned by ase.io.iread so that it returns
+            the positions instead of the ase.Atoms object.
+            """
+            for value in iterator:
+                yield value.get_positions()
+
+        iterator = ase.io.read(file_handle, index=":", format=format)
+        return ase_generator(iterator)
+
+    def custom_iread(self, file_handle, format):
+        """
+        """
+        pass
+
+
+#===============================================================================
+class CoordinateFormat(object):
+    """Represents a coordinate format.
+    """
+    def __init__(self, extension, info, function):
+        self.extension = extension
+        self.info = info
+        self.function = function