DCDwriter now has a option to set istart

Programs who use DCD have different conventions for istart, the starting frame
of the trajectory. Because of this we now allow it to be set by the user.

Author: kain88-de

package/MDAnalysis/coordinates/DCD.py

@@ -358,6 +358,7 @@ def __init__(self,
                  dt=1,
                  remarks='',
                  nsavc=1,
+                 istart=0,
                  **kwargs):
         """Parameters
         ----------
@@ -380,6 +381,8 @@ def __init__(self,
             how many MD steps is a frame saved to the DCD). By default, this
             number is just set to one and this should be sufficient for almost
             all cases but if required, nsavc can be changed.
+        istart : int (optional)
+            starting frame number. CHARMM defaults to 1.
         **kwargs : dict
             General writer arguments
 
@@ -400,7 +403,7 @@ def __init__(self,
             nsavc=nsavc,
             delta=delta,
             is_periodic=1,
-            istart=0)
+            istart=istart)
 
     def write_next_timestep(self, ts):
         """Write timestep object into trajectory.

testsuite/MDAnalysisTests/coordinates/test_dcd.py

@@ -284,6 +284,16 @@ def test_writer_trajectory_no_natoms(tmpdir, universe_dcd):
         universe_dcd.trajectory.Writer("foo.dcd")
 
 
+@pytest.mark.parametrize('istart', (0, 1, 2, 3))
+def test_write_istart(universe_dcd, tmpdir, istart):
+    u = universe_dcd
+    outfile = str(tmpdir.join('test.dcd'))
+    with mda.Writer(outfile, u.atoms.n_atoms, istart=istart) as w:
+        w.write(u.atoms)
+    u = mda.Universe(PSF, outfile)
+    assert u.trajectory._file.header['istart'] == istart
+
+
 class RefCHARMMtriclinicDCD(object):
     topology = PSF_TRICLINIC
     trajectory = DCD_TRICLINIC