partial support for DCD files

src/euston/io.py

@@ -9,6 +9,11 @@
 
 # third-party modules
 import numpy as np
+try:
+    import MDAnalysis as mda
+    HAS_MDA = True
+except:
+    HAS_MDA = False
 
 # custom modules
 import geometry as geo
@@ -47,6 +52,13 @@ class HoldsCoordinates(object):
     def get_coordinates(self):
         pass
 
+class HoldsUnitcell(object):
+    __metaclass__ = abc.ABCMeta
+
+    @abc.abstractmethod
+    def get_h_matrix(self):
+        pass
+
 def anyopen(filename):
     rawname = filename
     gzip = '.gz .gzip'.split()
@@ -57,6 +69,9 @@ def anyopen(filename):
     if rawname.endswith('.xyz'):
         return XYZ(filename=filename)
 
+    if rawname.endswith('.dcd'):
+        return DCD(filename=filename)
+
 class FileIO(object):
     """Abstract base class for all file objects with support for gzipped input files.."""
 
@@ -97,6 +112,30 @@ def _parse(self):
         """Finalises file content parsing."""
         self._parsed = True
 
+class DCD(HoldsCoordinates, HoldsUnitcell, FileIO):
+    @require_loaded
+    def _parse(self):
+        if not HAS_MDA:
+            raise TypeError('MDAnalysis required in order to load a DCD file.')
+        reader = mda.coordinates.DCD.DCDReader(self._fh.name)
+        self._hmat = geo.abc_to_hmatrix(*reader.ts.dimensions, degrees=True)
+        self._coordinates = np.zeros((reader.ts.numatoms, 3))
+        self._coordinates[:, 0] = reader.ts._x
+        self._coordinates[:, 1] = reader.ts._y
+        self._coordinates[:, 2] = reader.ts._z
+
+        super(DCD, self)._parse()
+
+    @require_loaded
+    @require_parsed
+    def get_coordinates(self):
+        return self._coordinates
+
+    @require_loaded
+    @require_parsed
+    def get_h_matrix(self):
+        return self._hmat
+
 class XYZ(HoldsCoordinates, FileIO):
     @require_loaded
     def count_atoms(self):
@@ -394,7 +433,7 @@ def get_cell_vectors(self):
         return (a, b, c)
 
 
-class CubeFile(FileIO):
+class CubeFile(HoldsUnitcell, FileIO):
     def count_atoms(self):
         return self._natoms
 

src/tools/es_cellmultiply.py

@@ -8,11 +8,15 @@
 Supported File Formats
 ----------------------
 
-====== ====== ====== =========
-Format Input  Output Extension
-====== ====== ====== =========
-XYZ    Native Native .xyz
-====== ====== ====== =========
+Most of the file formats require external python packages like MDAnalysis or mdtraj. Only native formats can be
+used without any further packages.
+
+====== ===================== ===================== =========
+Format Input                 Output                Extension
+====== ===================== ===================== =========
+XYZ    Native                Native                .xyz
+DCD    MDAnalysis            --                    .dcd
+====== ===================== ===================== =========
 
 Command Line Interface
 ----------------------
@@ -86,10 +90,15 @@ def main(args):
     :param args: Arguments as from argparse.ArgumentParser.parse_args
     """
 
-    xyz = io.XYZ(args.input)
+    inputfile = io.anyopen(args.input)
+    if not isinstance(inputfile, io.HoldsCoordinates):
+        print 'Input file has to contain atom positions.'
 
     hmat = None
-    if not (args.sc_in and args.sc_out):
+    if isinstance(inputfile, io.HoldsUnitcell):
+        hmat = inputfile.get_h_matrix()
+
+    if not (args.sc_in and args.sc_out) and (hmat is None):
         if (args.hmat is None and args.abc is None) or (args.hmat is not None and args.abc is not None):
             print 'Please specify either the H matrix or lattice constants unless input and output are scaled.'
             exit(1)
@@ -118,11 +127,15 @@ def main(args):
             print 'Invalid multiplier setting - has to be at least one.'
             exit(4)
 
-    multiplied = geo.cell_multiply(xyz.get_coordinates(), args.X, args.Y, args.Z, h_matrix=hmat, scaling_in=args.sc_in, scaling_out=args.sc_out)
+    multiplied = geo.cell_multiply(inputfile.get_coordinates(), args.X, args.Y, args.Z, h_matrix=hmat, scaling_in=args.sc_in, scaling_out=args.sc_out)
     factor = args.X*args.Y*args.Z
 
     output = io.XYZ()
-    output.set_data(xyz.get_labels()*factor, multiplied)
+    try:
+        labels = inputfile.get_labels()
+    except:
+        labels = ['X'] * inputfile.get_coordinates().shape[0]
+    output.set_data(labels*factor, multiplied)
     io.write_lines(args.output, output.to_string())
 
 if __name__ == '__main__':