Updated tests.

Fixed bugs within the various I/O files.
Added CHARMM input files.
Added fluctuation matching code.

Signed-off-by: Timothy Click <tcthepoet@yahoo.com>

src/fluctmatch/coordinates/CRD.py

@@ -34,21 +34,19 @@
     unicode_literals,
 )
 
-=from future.builtins import (
-    range,
-    str,
-    super,
-    zip,
-)
-
 import itertools
 import warnings
 
 import numpy as np
-
 from MDAnalysis.coordinates import CRD
 from MDAnalysis.exceptions import NoDataError
 from MDAnalysis.lib import util
+from future.builtins import (
+    range,
+    str,
+    super,
+    zip,
+)
 
 
 class CRDWriter(CRD.CRDWriter):
@@ -88,7 +86,7 @@ class CRDWriter(CRD.CRDWriter):
 
     def __init__(self, filename, **kwargs):
         self.filename = util.filename(filename, ext="crd")
-        super().__init__(self.filename, **kwargs)
+        super().__init__(filename, **kwargs)
         self.crd = None
 
     def write(self, selection, frame=None):

src/fluctmatch/fluctmatch/base.py

@@ -0,0 +1,129 @@
+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
+#
+
+from __future__ import (
+    absolute_import,
+    division,
+    print_function,
+    unicode_literals,
+)
+
+import abc
+import os
+
+from future.builtins import (
+    dict,
+)
+from future.utils import (
+    with_metaclass,
+)
+
+
+class FluctMatch(with_metaclass(abc.ABCMeta, object)):
+    """Base class for fluctuation matching."""
+    parameters = dict()
+    target = dict()
+
+    def __init__(self, *args, **kwargs):
+        """Initialization of fluctuation matching.
+
+        Parameters
+        ----------
+        topology : filename or Topology object
+            A CHARMM/XPLOR PSF topology file, PDB file or Gromacs GRO file; used to
+            define the list of atoms. If the file includes bond information,
+            partial charges, atom masses, ... then these data will be available to
+            MDAnalysis. A "structure" file (PSF, PDB or GRO, in the sense of a
+            topology) is always required. Alternatively, an existing
+            :class:`MDAnalysis.core.topology.Topology` instance may also be given.
+        extended
+            Renames the residues and atoms according to the extended CHARMM PSF format.
+            Standard CHARMM PSF limits the residue and atom names to four characters,
+            but the extended CHARMM PSF permits eight characters. The residues and
+            atoms are renamed according to the number of segments (1: A, 2: B, etc.)
+            and then the residue number or atom index number.
+         xplor
+            Assigns the atom type as either a numerical or an alphanumerical
+            designation. CHARMM normally assigns a numerical designation, but the
+            XPLOR version permits an alphanumerical designation with a maximum
+            size of 4. The numerical form corresponds to the atom index number plus a
+            factor of 100, and the alphanumerical form will be similar the standard
+            CHARMM atom name.
+        topology_format
+            Provide the file format of the topology file; ``None`` guesses it from
+            the file extension [``None``] Can also pass a subclass of
+            :class:`MDAnalysis.topology.base.TopologyReaderBase` to define a custom
+            reader to be used on the topology file.
+        format
+            Provide the file format of the coordinate or trajectory file; ``None``
+            guesses it from the file extension. Note that this keyword has no
+            effect if a list of file names is supplied because the "chained" reader
+            has to guess the file format for each individual list member.
+            [``None``] Can also pass a subclass of
+            :class:`MDAnalysis.coordinates.base.ProtoReader` to define a custom
+            reader to be used on the trajectory file.
+        guess_bonds : bool, optional
+            Once Universe has been loaded, attempt to guess the connectivity
+            between atoms.  This will populate the .bonds .angles and .dihedrals
+            attributes of the Universe.
+        vdwradii : dict, optional
+            For use with *guess_bonds*. Supply a dict giving a vdwradii for each
+            atom type which are used in guessing bonds.
+        is_anchor : bool, optional
+            When unpickling instances of
+            :class:`MDAnalysis.core.groups.AtomGroup` existing Universes are
+            searched for one where to anchor those atoms. Set to ``False`` to
+            prevent this Universe from being considered. [``True``]
+        anchor_name : str, optional
+            Setting to other than ``None`` will cause
+            :class:`MDAnalysis.core.groups.AtomGroup` instances pickled from the
+            Universe to only unpickle if a compatible Universe with matching
+            *anchor_name* is found. Even if *anchor_name* is set *is_anchor* will
+            still be honored when unpickling.
+        in_memory
+            After reading in the trajectory, transfer it to an in-memory
+            representations, which allow for manipulation of coordinates.
+        in_memory_step
+            Only read every nth frame into in-memory representation.
+        outdir
+            Output directory
+        temperature
+            Temperature (in K)
+        rmin
+            Minimum distance to consider for bond lengths.
+        rmax
+            Maximum distance to consider for bond lengths.
+        """
+        self.outdir = kwargs.get("outdir", os.curdir)
+        self.temperature = kwargs.get("temperature", 300.0)
+        self.args = args
+        self.kwargs = kwargs
+
+    @abc.abstractmethod
+    def initialize(self, restart=False):
+        """Create an elastic network model from a basic coarse-grain model.
+
+        :param restart: reinitialize tye object
+        """
+        pass
+
+    @abc.abstractmethod
+    def run(self, nma_exec=None, tol=1.e-4, n_cycles=250):
+        """Perform a self-consistent fluctuation matching
+
+        :param nma_exec: executable file for normal mode analysis
+        :param tol: error tolerance
+        :param n_cycles: number of fluctuation matching cycles
+        """
+        pass
+
+    @abc.abstractmethod
+    def restart(self, nma_exec=None, tol=1.e-4, n_cycles=250):
+        """Restart a simulation.
+
+        :param nma_exec: executable file for normal mode analysis
+        :param tol: error tolerance
+        :param n_cycles: number of fluctuation matching cycles
+        """
+        pass