Adding Appending Functionality method to WriterBase

package/MDAnalysis/coordinates/CRD.py

@@ -110,7 +110,7 @@ def Writer(self, filename, **kwargs):
         return CRDWriter(filename, **kwargs)
 
 
-class CRDWriter(base.WriterBase):
+class CRDWriter(base.SingleFrameWriterBase):
     """CRD writer that implements the CHARMM CRD coordinate format.
 
     It automatically writes the CHARMM EXT extended format if there
@@ -148,13 +148,16 @@ class CRDWriter(base.WriterBase):
         "NUMATOMS": "{0:5d}\n",
     }
 
-    def __init__(self, filename, **kwargs):
+    def __init__(self, filename, n_atoms=None, append=False, **kwargs):
         """
         Parameters
         ----------
         filename : str or :class:`~MDAnalysis.lib.util.NamedStream`
              name of the output file or a stream
-
+        n_atoms : int (optional)
+                number of atoms in the coordinate file;
+        append : bool (optional)
+                append to an existing CRD file; default is to overwrite
         extended : bool (optional)
              By default, noextended CRD format is used [``False``].
              However, extended CRD format can be forced by
@@ -165,13 +168,14 @@ def __init__(self, filename, **kwargs):
              .. versionadded:: 2.2.0
         """
 
-        self.filename = util.filename(filename, ext='crd')
+        filename = util.filename(filename, ext='crd')
+        super().__init__(filename, n_atoms, append)
         self.crd = None
 
         # account for explicit crd format, if requested
         self.extended = kwargs.pop("extended", False)
 
-    def write(self, selection, frame=None):
+    def _write_next_frame(self, selection, frame=None):
         """Write selection at current trajectory frame to file.
 
         Parameters

package/MDAnalysis/coordinates/DCD.py

@@ -338,6 +338,7 @@ class DCDWriter(base.WriterBase):
     def __init__(self,
                  filename,
                  n_atoms,
+                 append=False,
                  convert_units=True,
                  step=1,
                  dt=1,
@@ -351,6 +352,9 @@ def __init__(self,
             filename of trajectory
         n_atoms : int
             number of atoms to be written
+        append : bool (optional)
+            append to an existing trajectory if True, default is to
+            overwrite an existing file: ``False``
         convert_units : bool (optional)
             convert from MDAnalysis units to format specific units
         step : int (optional)
@@ -376,11 +380,10 @@ def __init__(self,
             General writer arguments
 
         """
-        self.filename = filename
         self._convert_units = convert_units
         if n_atoms is None:
             raise ValueError("n_atoms argument is required")
-        self.n_atoms = n_atoms
+        super().__init__(filename, n_atoms, append)
         self._file = DCDFile(self.filename, 'w')
         self.step = step
         self.dt = dt

package/MDAnalysis/coordinates/FHIAIMS.py

@@ -205,7 +205,7 @@ def Writer(self, filename, n_atoms=None, **kwargs):
         return FHIAIMSWriter(filename, n_atoms=n_atoms, **kwargs)
 
 
-class FHIAIMSWriter(base.WriterBase):
+class FHIAIMSWriter(base.SingleFrameWriterBase):
     """FHI-AIMS Writer.
 
        Single frame writer for the `FHI-AIMS`_ format.  Writes geometry (3D and
@@ -228,7 +228,8 @@ class FHIAIMSWriter(base.WriterBase):
         'box_triclinic': "lattice_vector {box[0]:12.8f} {box[1]:12.8f} {box[2]:12.8f}\nlattice_vector {box[3]:12.8f} {box[4]:12.8f} {box[5]:12.8f}\nlattice_vector {box[6]:12.8f} {box[7]:12.8f} {box[8]:12.8f}\n"
     }
 
-    def __init__(self, filename, convert_units=True, n_atoms=None, **kwargs):
+    def __init__(self, filename, convert_units=True, n_atoms=None,
+                 append=False, **kwargs):
         """Set up the FHI-AIMS Writer
 
         Parameters
@@ -239,8 +240,8 @@ def __init__(self, filename, convert_units=True, n_atoms=None, **kwargs):
             number of atoms
 
         """
-        self.filename = util.filename(filename, ext='.in', keep=True)
-        self.n_atoms = n_atoms
+        filename = util.filename(filename, ext='.in', keep=True)
+        super().__init__(filename, n_atoms, append)
 
     def _write_next_frame(self, obj):
         """Write selection at current trajectory frame to file.

package/MDAnalysis/coordinates/GRO.py

@@ -261,7 +261,7 @@ def Writer(self, filename, n_atoms=None, **kwargs):
         return GROWriter(filename, n_atoms=n_atoms, **kwargs)
 
 
-class GROWriter(base.WriterBase):
+class GROWriter(base.SingleFrameWriterBase):
     """GRO Writer that conforms to the Trajectory API.
 
     Will attempt to write the following information from the topology:
@@ -311,7 +311,8 @@ class GROWriter(base.WriterBase):
     }
     fmt['xyz_v'] = fmt['xyz'][:-1] + "{vel[0]:8.4f}{vel[1]:8.4f}{vel[2]:8.4f}\n"
 
-    def __init__(self, filename, convert_units=True, n_atoms=None, **kwargs):
+    def __init__(self, filename, convert_units=True, n_atoms=None,
+                 append=False, **kwargs):
         """Set up a GROWriter with a precision of 3 decimal places.
 
         Parameters
@@ -326,7 +327,9 @@ def __init__(self, filename, convert_units=True, n_atoms=None, **kwargs):
             By default, all the atoms were reindexed to have a atom id starting
             from 1. [``True``] However, this behaviour can be turned off by
             specifying `reindex` ``=False``.
-
+        append : bool (optional)
+            If ``True``, open file in append mode. [``False``]
+
         Note
         ----
         To use the reindex keyword, user can follow the two examples given
@@ -344,13 +347,13 @@ def __init__(self, filename, convert_units=True, n_atoms=None, **kwargs):
                w.write(u.atoms)
 
         """
-        self.filename = util.filename(filename, ext='gro', keep=True)
-        self.n_atoms = n_atoms
+        filename = util.filename(filename, ext='gro', keep=True)
+        super().__init__(filename, n_atoms, append)
         self.reindex = kwargs.pop('reindex', True)
 
         self.convert_units = convert_units  # convert length and time to base units
 
-    def write(self, obj):
+    def _write_next_frame(self, obj):
         """Write selection at current trajectory frame to file.
 
         Parameters

package/MDAnalysis/coordinates/H5MD.py

@@ -1050,7 +1050,8 @@ class H5MDWriter(base.WriterBase):
     @due.dcite(Doi("10.1016/j.cpc.2014.01.018"),
                description="Specifications of the H5MD standard",
                path=__name__, version='1.1')
-    def __init__(self, filename, n_atoms, n_frames=None, driver=None,
+    def __init__(self, filename, n_atoms, 
+                 append=False, n_frames=None, driver=None,
                  convert_units=True, chunks=None, compression=None,
                  compression_opts=None, positions=True, velocities=True,
                  forces=True, timeunit=None, lengthunit=None,
@@ -1060,14 +1061,13 @@ def __init__(self, filename, n_atoms, n_frames=None, driver=None,
 
         if not HAS_H5PY:
             raise RuntimeError("H5MDWriter: Please install h5py")
-        self.filename = filename
         if n_atoms == 0:
             raise ValueError("H5MDWriter: no atoms in output trajectory")
+        super().__init__(filename, n_atoms, append)
         self._driver = driver
         if self._driver == 'mpio':
             raise ValueError("H5MDWriter: parallel writing with MPI I/O "
                              "is not currently supported.")
-        self.n_atoms = n_atoms
         self.n_frames = n_frames
         self.chunks = (1, n_atoms, 3) if chunks is None else chunks
         if self.chunks is False and self.n_frames is None:

package/MDAnalysis/coordinates/MOL2.py

@@ -287,17 +287,21 @@ class MOL2Writer(base.WriterBase):
     multiframe = True
     units = {'time': None, 'length': 'Angstrom'}
 
-    def __init__(self, filename, n_atoms=None, convert_units=True):
+    def __init__(self, filename, n_atoms=None, append=False, 
+                 convert_units=True):
         """Create a new MOL2Writer
 
         Parameters
         ----------
         filename: str
             name of output file
+        append: bool (optional)
+            If ``True``, append to an existing file. If ``False``, overwrite
+            the file. Default is ``False``.
         convert_units: bool (optional)
             units are converted to the MDAnalysis base format; [``True``]
         """
-        self.filename = filename
+        super().__init__(filename, n_atoms, append)
         self.convert_units = convert_units  # convert length and time to base units
 
         self.frames_written = 0

package/MDAnalysis/coordinates/NAMDBIN.py

@@ -91,7 +91,7 @@ def Writer(self, filename, **kwargs):
         return NAMDBINWriter(filename, **kwargs)
 
 
-class NAMDBINWriter(base.WriterBase):
+class NAMDBINWriter(base.SingleFrameWriterBase):
     """Writer for NAMD binary coordinate files.
 
 
@@ -100,7 +100,7 @@ class NAMDBINWriter(base.WriterBase):
     format = ['COOR', 'NAMDBIN']
     units = {'time': None, 'length': 'Angstrom'}
 
-    def __init__(self, filename, n_atoms=None, **kwargs):
+    def __init__(self, filename, n_atoms=None, append=False, **kwargs):
         """
         Parameters
         ----------
@@ -109,7 +109,8 @@ def __init__(self, filename, n_atoms=None, **kwargs):
         n_atoms  : int
             number of atoms for the output coordinate
         """
-        self.filename = util.filename(filename)
+        filename = util.filename(filename)
+        super().__init__(filename, n_atoms, append)
 
     def _write_next_frame(self, obj):
         """Write information associated with ``obj`` at current frame into

package/MDAnalysis/coordinates/PDB.py

@@ -461,7 +461,7 @@ def close(self):
         self._pdbfile.close()
 
 
-class PDBWriter(base.WriterBase):
+class PDBWriter(base.SingleFrameWriterBase):
     """PDB writer that implements a subset of the `PDB 3.3 standard`_ .
 
     PDB format as used by NAMD/CHARMM: 4-letter resnames and segID are allowed,
@@ -612,7 +612,8 @@ class PDBWriter(base.WriterBase):
 
     def __init__(self, filename, bonds="conect", n_atoms=None, start=0, step=1,
                  remarks="Created by PDBWriter",
-                 convert_units=True, multiframe=None, reindex=True):
+                 convert_units=True, multiframe=None, reindex=True,
+                 append=False):
         """Create a new PDBWriter
 
         Parameters
@@ -643,15 +644,17 @@ def __init__(self, filename, bonds="conect", n_atoms=None, start=0, step=1,
         reindex: bool (optional)
             If ``True`` (default), the atom serial is set to be consecutive
             numbers starting at 1. Else, use the atom id.
-
+        append: bool (optional)
+            If ``True``, append to an existing file. If ``False``, overwrite
+            the file. [``False``]
         """
         # n_atoms = None : dummy keyword argument
         # (not used, but Writer() always provides n_atoms as the second argument)
 
         # TODO: - remarks should be a list of lines and written to REMARK
         #       - additional title keyword could contain line for TITLE
 
-        self.filename = filename
+        super().__init__(filename, n_atoms, append)
         # convert length and time to base units
         self.convert_units = convert_units
         self._multiframe = self.multiframe if multiframe is None else multiframe
@@ -895,32 +898,7 @@ def _update_frame(self, obj):
         # hack...
         self.obj = obj
         self.ts = obj.universe.trajectory.ts
-
-    def write(self, obj):
-        """Write object *obj* at current trajectory frame to file.
-
-        *obj* can be a selection (i.e. a
-        :class:`~MDAnalysis.core.groups.AtomGroup`) or a whole
-        :class:`~MDAnalysis.core.universe.Universe`.
-
-        The last letter of the :attr:`~MDAnalysis.core.groups.Atom.segid` is
-        used as the PDB chainID (but see :meth:`~PDBWriter.ATOM` for
-        details).
-
-        Parameters
-        ----------
-        obj
-            The :class:`~MDAnalysis.core.groups.AtomGroup` or
-            :class:`~MDAnalysis.core.universe.Universe` to write.
-        """
-
-        self._update_frame(obj)
-        self._write_pdb_header()
-        # Issue 105: with write() ONLY write a single frame; use
-        # write_all_timesteps() to dump everything in one go, or do the
-        # traditional loop over frames
-        self._write_next_frame(self.ts, multiframe=self._multiframe)
-        # END and CONECT records are written when file is being close()d
+
 
     def write_all_timesteps(self, obj):
         """Write all timesteps associated with *obj* to the PDB file.
@@ -965,15 +943,15 @@ def write_all_timesteps(self, obj):
 
         for framenumber in range(start, len(traj), step):
             traj[framenumber]
-            self._write_next_frame(self.ts, multiframe=True)
+            self._write_next_frame(obj, multiframe=True)
 
         # CONECT record is written when the file is being close()d
         self.close()
 
         # Set the trajectory to the starting position
         traj[start]
 
-    def _write_next_frame(self, ts=None, **kwargs):
+    def _write_next_frame(self, obj, **kwargs):
         '''write a new timestep to the PDB file
 
         :Keywords:
@@ -994,13 +972,17 @@ def _write_next_frame(self, ts=None, **kwargs):
         .. versionchanged:: 1.0.0
            Renamed from `write_next_timestep` to `_write_next_frame`.
         '''
-        if ts is None:
-            try:
-                ts = self.ts
-            except AttributeError:
-                errmsg = ("PBDWriter: no coordinate data to write to "
-                          "trajectory file")
-                raise NoDataError(errmsg) from None
+
+        self._update_frame(obj)
+        self._write_pdb_header()
+
+        try:
+            ts = self.ts
+        except AttributeError:
+            errmsg = ("PBDWriter: no coordinate data to write to "
+                        "trajectory file")
+            raise NoDataError(errmsg) from None
+
         self._check_pdb_coordinates()
         self._write_timestep(ts, **kwargs)
 
@@ -1360,3 +1342,21 @@ class MultiPDBWriter(PDBWriter):
     format = ['PDB', 'ENT']
     multiframe = True  # For Writer registration
     singleframe = False
+
+    def write(self, obj, **kwargs):
+        """Write current timestep, using the supplied `obj`.
+
+        Parameters
+        ----------
+        obj : :class:`~MDAnalysis.core.groups.AtomGroup` or :class:`~MDAnalysis.core.universe.Universe`
+            write coordinate information associate with `obj`
+
+        Note
+        ----
+        The size of the `obj` must be the same as the number of atoms provided
+        when setting up the trajectory.
+        """
+
+        # overwrite the default behavior of PDBWriter
+        self._n_frames_written += 1
+        return self._write_next_frame(obj, multiframe=True, **kwargs)

package/MDAnalysis/coordinates/PDBQT.py

@@ -190,7 +190,7 @@ def Writer(self, filename, **kwargs):
         return PDBQTWriter(filename, **kwargs)
 
 
-class PDBQTWriter(base.WriterBase):
+class PDBQTWriter(base.SingleFrameWriterBase):
     """PDBQT writer that implements a subset of the PDB_ 3.2 standard and the PDBQT_ spec.
 
     .. _PDB: http://www.wwpdb.org/documentation/file-format-content/format32/v3.2.html
@@ -212,14 +212,15 @@ class PDBQTWriter(base.WriterBase):
     units = {'time': None, 'length': 'Angstrom'}
     pdb_coor_limits = {"min": -999.9995, "max": 9999.9995}
 
-    def __init__(self, filename, **kwargs):
-        self.filename = util.filename(filename, ext='pdbqt')
+    def __init__(self, filename, n_atoms=None, append=False, **kwargs):
+        filename = util.filename(filename, ext='pdbqt')
+        super().__init__(filename, n_atoms, append)
         self.pdb = util.anyopen(self.filename, 'w')
 
     def close(self):
         self.pdb.close()
 
-    def write(self, selection, frame=None):
+    def _write_next_frame(self, selection, frame=None):
         """Write selection at current trajectory frame to file.
 
         Parameters