Finish io

setup.py

@@ -90,8 +90,10 @@ def read(*names, **kwargs):
         "click",
         "future",
         "MDAnalysis",
+        "MDAnalysisTests",
         "numpy",
         "pandas",
+        "pytest",
         "scipy",
         "scikit-learn",
     ],

src/fluctmatch/__init__.py

@@ -1,19 +1,40 @@
-# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
-# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
+# -*- coding: utf-8 -*-
 #
-# fluctmatch --- https://github.com/tclick/python-fluctmatch
-# Copyright (c) 2013-2017 The fluctmatch Development Team and contributors
-# (see the file AUTHORS for the full list of names)
+#  python-fluctmatch -
+#  Copyright (c) 2019 Timothy H. Click, Ph.D.
 #
-# Released under the New BSD license.
+#  All rights reserved.
 #
-# Please cite your use of fluctmatch in published work:
+#  Redistribution and use in source and binary forms, with or without
+#  modification, are permitted provided that the following conditions are met:
 #
-# Timothy H. Click, Nixon Raj, and Jhih-Wei Chu.
-# Calculation of Enzyme Fluctuograms from All-Atom Molecular Dynamics
-# Simulation. Meth Enzymology. 578 (2016), 327-342,
-# doi:10.1016/bs.mie.2016.05.024.
+#  Redistributions of source code must retain the above copyright notice, this
+#  list of conditions and the following disclaimer.
 #
+#  Redistributions in binary form must reproduce the above copyright notice,
+#  this list of conditions and the following disclaimer in the documentation
+#  and/or other materials provided with the distribution.
+#
+#  Neither the name of the author nor the names of its contributors may be used
+#  to endorse or promote products derived from this software without specific
+#  prior written permission.
+#
+#  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS”
+#  AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+#  IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+#  ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR
+#  ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+#  DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+#  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+#  CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+#  OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+#  OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+#  Timothy H. Click, Nixon Raj, and Jhih-Wei Chu.
+#  Simulation. Meth Enzymology. 578 (2016), 327-342,
+#  Calculation of Enzyme Fluctuograms from All-Atom Molecular Dynamics
+#  doi:10.1016/bs.mie.2016.05.024.
+
 import logging
 
 __version__: str = "3.4.1"
@@ -27,4 +48,4 @@
 from .coordinates import COR
 from .intcor import IC
 from .parameter import PRM
-from .topology import PSFParser, RTF, STR
+from .topology import CORParser, PSFParser, RTF, STR

src/fluctmatch/coordinates/COR.py

@@ -1,46 +1,51 @@
-# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
-# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
+# -*- coding: utf-8 -*-
 #
-# fluctmatch --- https://github.com/tclick/python-fluctmatch
-# Copyright (c) 2013-2017 The fluctmatch Development Team and contributors
-# (see the file AUTHORS for the full list of names)
+#  python-fluctmatch -
+#  Copyright (c) 2019 Timothy H. Click, Ph.D.
 #
-# Released under the New BSD license.
+#  All rights reserved.
 #
-# Please cite your use of fluctmatch in published work:
+#  Redistribution and use in source and binary forms, with or without
+#  modification, are permitted provided that the following conditions are met:
 #
-# Timothy H. Click, Nixon Raj, and Jhih-Wei Chu.
-# Calculation of Enzyme Fluctuograms from All-Atom Molecular Dynamics
-# Simulation. Meth Enzymology. 578 (2016), 327-342,
-# doi:10.1016/bs.mie.2016.05.024.
+#  Redistributions of source code must retain the above copyright notice, this
+#  list of conditions and the following disclaimer.
 #
-"""COR structure files in fluctmatch --- :mod:`MDAnalysis.coordinates.CRD`
-===========================================================================
-
-Read and write coordinates in CHARMM CARD coordinate format (suffix
-"cord"). The CHARMM "extended format" is handled automatically.
-"""
-from __future__ import (
-    absolute_import,
-    division,
-    print_function,
-    unicode_literals,
-)
-from future.builtins import (
-    open,
-    range,
-    str,
-    super,
-    zip,
-)
+#  Redistributions in binary form must reproduce the above copyright notice,
+#  this list of conditions and the following disclaimer in the documentation
+#  and/or other materials provided with the distribution.
+#
+#  Neither the name of the author nor the names of its contributors may be used
+#  to endorse or promote products derived from this software without specific
+#  prior written permission.
+#
+#  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS”
+#  AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+#  IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+#  ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR
+#  ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+#  DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+#  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+#  CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+#  OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+#  OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+#  Timothy H. Click, Nixon Raj, and Jhih-Wei Chu.
+#  Simulation. Meth Enzymology. 578 (2016), 327-342,
+#  Calculation of Enzyme Fluctuograms from All-Atom Molecular Dynamics
+#  doi:10.1016/bs.mie.2016.05.024.
+"""CHARMM coordinate file reader and writer for viewing in VMD."""
 
 import itertools
 import logging
+import warnings
+from pathlib import Path
+from typing import ClassVar, Dict, Mapping, Optional, Any, List, Generator, Union
 
 import numpy as np
+import MDAnalysis as mda
 from MDAnalysis.coordinates import CRD
 from MDAnalysis.exceptions import NoDataError
-from MDAnalysis.lib import util
 
 logger = logging.getLogger(__name__)
 
@@ -52,8 +57,27 @@ class CORReader(CRD.CRDReader):
        Now returns a ValueError instead of FormatError.
        Frames now 0-based instead of 1-based.
     """
-    format = "COR"
-    units = {"time": None, "length": "Angstrom"}
+    format: ClassVar[str] = "COR"
+    units: ClassVar[Dict[str, Optional[str]]] = dict(time=None,
+                                                        length="Angstrom")
+
+    def __init__(self, filename: Union[str, Path], convert_units: bool=None,
+                 n_atoms: int=None, **kwargs: Mapping):
+        super().__init__(filename, convert_units, n_atoms, **kwargs)
+
+    @staticmethod
+    def parse_n_atoms(filename: Union[str, Path], **kwargs: Mapping) -> int:
+        n_atoms: int
+        with open(filename) as crdfile:
+            for linenum, line in enumerate(crdfile):
+                if line.strip().startswith('*') or line.strip() == "":
+                    continue  # ignore TITLE and empty lines
+                fields: List[str] = line.split()
+                if len(fields) <= 2:
+                    # should be the natoms line
+                    n_atoms: int = int(fields[0])
+                    break
+        return n_atoms
 
 
 class CORWriter(CRD.CRDWriter):
@@ -73,130 +97,128 @@ class CORWriter(CRD.CRDWriter):
     .. versionchanged:: 0.11.0
        Frames now 0-based instead of 1-based
     """
-    format = "COR"
-    units = {"time": None, "length": "Angstrom"}
+    format: ClassVar[str] = "COR"
+    units: ClassVar[Dict[str, Optional[str]]] = {"time": None, "length": "Angstrom"}
 
-    fmt = dict(
+    fmt: Dict[str, str] = dict(
         # crdtype = "extended"
         # fortran_format = "(2I10,2X,A8,2X,A8,3F20.10,2X,A8,2X,A8,F20.10)"
         ATOM_EXT=("{serial:10d}{totRes:10d}  {resname:<8.8s}  {name:<8.8s}"
                   "{pos[0]:20.10f}{pos[1]:20.10f}{pos[2]:20.10f}  "
-                  "{chainID:<8.8s}  {resSeq:<8d}{tempfactor:20.10f}\n"),
-        NUMATOMS_EXT="{0:10d} EXT\n",
+                  "{chainID:<8.8s}  {resSeq:<8d}{tempfactor:20.10f}"),
+        NUMATOMS_EXT="{0:10d}  EXT",
         # crdtype = "standard"
         # fortran_format = "(2I5,1X,A4,1X,A4,3F10.5,1X,A4,1X,A4,F10.5)"
         ATOM=("{serial:5d}{totRes:5d} {resname:<4.4s} {name:<4.4s}"
               "{pos[0]:10.5f}{pos[1]:10.5f}{pos[2]:10.5f} "
-              "{chainID:<4.4s} {resSeq:<4d}{tempfactor:10.5f}\n"),
+              "{chainID:<4.4s} {resSeq:<4d}{tempfactor:10.5f}"),
         TITLE="* FRAME {frame} FROM {where}",
-        NUMATOMS="{0:5d}\n",
+        NUMATOMS="{0:5d}",
     )
 
-    def __init__(self, filename, **kwargs):
+    def __init__(self, filename: Union[str, Path], **kwargs: Mapping):
         """
         Parameters
         ----------
         filename : str or :class:`~MDAnalysis.lib.util.NamedStream`
              name of the output file or a stream
         """
         super().__init__(filename, **kwargs)
-        self.filename = util.filename(filename, ext="cor")
-        self.crd = None
 
-    def write(self, selection, frame=None):
+        self.filename: Path = Path(filename).with_suffix(".cor")
+        self.crd: Optional[str] = None
+
+    def write(self, selection: Union[mda.Universe, mda.AtomGroup],
+              frame: Optional[int]=None):
         """Write selection at current trajectory frame to file.
 
         write(selection,frame=FRAME)
 
         selection         MDAnalysis AtomGroup
         frame             optionally move to frame FRAME
         """
-        u = selection.universe
+        u: mda.Universe = selection.universe
         if frame is not None:
             u.trajectory[frame]  # advance to frame
         else:
             try:
-                frame = u.trajectory.ts.frame
+                frame: int = u.trajectory.ts.frame
             except AttributeError:
-                frame = 0  # should catch cases when we are analyzing a single PDB (?)
+                frame: int = 0
 
-        atoms = selection.atoms  # make sure to use atoms (Issue 46)
-        coor = atoms.positions  # can write from selection == Universe (Issue 49)
+        atoms: mda.AtomGroup = selection.atoms
+        coor: np.ndarray = atoms.positions
 
-        n_atoms = len(atoms)
+        n_atoms: int = atoms.n_atoms
         # Detect which format string we"re using to output (EXT or not)
         # *len refers to how to truncate various things,
         # depending on output format!
-        at_fmt = self.fmt["ATOM_EXT"]
-        serial_len = 10
-        resid_len = 8
-        totres_len = 10
+        at_fmt: str = self.fmt["ATOM_EXT"]
+        serial_len: int = 10
+        resid_len: int = 8
+        totres_len: int = 10
 
         # Check for attributes, use defaults for missing ones
-        attrs = {}
-        missing_topology = []
+        attrs: Dict[str, Any] = {}
+        missing_topology: List[Any] = []
         for attr, default in (
-            ("resnames", itertools.cycle(("UNK", ))),
+            ("resnames", itertools.cycle(("UNK",))),
                 # Resids *must* be an array because we index it later
             ("resids", np.ones(n_atoms, dtype=np.int)),
             ("names", itertools.cycle(("X", ))),
-            ("tempfactors", itertools.cycle((0.0, ))),
+            ("tempfactors", itertools.cycle((0.0,))),
         ):
             try:
-                attrs[attr] = getattr(atoms, attr)
+                attrs[attr]: Any = getattr(atoms, attr)
             except (NoDataError, AttributeError):
-                attrs[attr] = default
+                attrs[attr]: Any = default
                 missing_topology.append(attr)
         # ChainIDs - Try ChainIDs first, fall back to Segids
         try:
-            attrs["chainIDs"] = atoms.segids
+            attrs["chainIDs"]: str = atoms.segids
         except (NoDataError, AttributeError):
             # try looking for segids instead
             try:
-                attrs["chainIDs"] = atoms.chainIDs
+                attrs["chainIDs"]: np.ndarray = atoms.chainIDs
             except (NoDataError, AttributeError):
-                attrs["chainIDs"] = itertools.cycle(("", ))
+                attrs["chainIDs"]: Generator = itertools.cycle(("", ))
                 missing_topology.append(attr)
         if missing_topology:
-            logger.warn(
-                "Supplied AtomGroup was missing the following attributes: "
-                "{miss}. These will be written with default values. "
-                "".format(miss=", ".join(missing_topology)))
-
-        with open(self.filename, "wb") as crd:
+            miss: str = ", ".join(missing_topology)
+            warnings.warn(f"Supplied AtomGroup was missing the following "
+                          f"attributes: {miss}. These will be written with "
+                          f"default values.")
+            logger.warning(f"Supplied AtomGroup was missing the following "
+                           f"attributes: {miss}. These will be written with "
+                           f"default values.")
+
+        with open(self.filename, "w") as crd:
             # Write Title
-            logger.info("Writing {}".format(self.filename))
-            crd.write(self.fmt["TITLE"].format(
-                frame=frame, where=u.trajectory.filename).encode())
-            crd.write("\n".encode())
-            crd.write("*\n".encode())
+            logger.info(f"Writing {self.filename}")
+            print(self.fmt["TITLE"].format(frame=frame,
+                                           where=u.trajectory.filename),
+                  file=crd)
+            print("*", file=crd)
 
             # Write NUMATOMS
-            crd.write(self.fmt["NUMATOMS_EXT"].format(n_atoms).encode())
+            print(self.fmt["NUMATOMS_EXT"].format(n_atoms), file=crd)
 
             # Write all atoms
-
-            current_resid = 1
-            resids = attrs["resids"]
+            current_resid: int = 1
+            resids: List[int] = attrs["resids"]
             for i, pos, resname, name, chainID, resid, tempfactor in zip(
                     range(n_atoms), coor, attrs["resnames"], attrs["names"],
                     attrs["chainIDs"], attrs["resids"], attrs["tempfactors"]):
                 if not i == 0 and resids[i] != resids[i - 1]:
                     current_resid += 1
 
                 # Truncate numbers
-                serial = int(str(i + 1)[-serial_len:])
-                resid = int(str(resid)[-resid_len:])
-                current_resid = int(str(current_resid)[-totres_len:])
-
-                crd.write(
-                    at_fmt.format(
-                        serial=serial,
-                        totRes=current_resid,
-                        resname=resname,
-                        name=name,
-                        pos=pos,
-                        chainID=chainID,
-                        resSeq=resid,
-                        tempfactor=tempfactor).encode())
+                serial: int = int(str(i + 1)[-serial_len:])
+                resid: int = int(str(resid)[-resid_len:])
+                current_resid: int = int(str(current_resid)[-totres_len:])
+
+                print(at_fmt.format(serial=serial, totRes=current_resid,
+                                    resname=resname, name=name, pos=pos,
+                                    chainID=chainID, resSeq=resid,
+                                    tempfactor=tempfactor), file=crd)
             logger.info("Coordinate file successfully written.")