From 9bad8e731e7dfb647552683fff8b0c08a000ca94 Mon Sep 17 00:00:00 2001
From: Max Linke <max_linke@gmx.de>
Date: Sun, 28 Aug 2016 19:08:42 +0200
Subject: [PATCH] read DCD Header

and fixes other issue I set by accident
---
 package/MDAnalysis/lib/formats/libdcd.pyx | 51 +++++++----------------
 1 file changed, 14 insertions(+), 37 deletions(-)

diff --git a/package/MDAnalysis/lib/formats/libdcd.pyx b/package/MDAnalysis/lib/formats/libdcd.pyx
index d9da15afccb..fec875a9ac6 100644
--- a/package/MDAnalysis/lib/formats/libdcd.pyx
+++ b/package/MDAnalysis/lib/formats/libdcd.pyx
@@ -14,23 +14,16 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 
-# This is not tested but should serve as an example how to enable windows
-# support in the future
-IF UNAME_SYSNAME == "Windows":
-    cdef extern from 'windows.h':
-        ctypedef HANDLE fio_fd
-ELSE:
-    from libc.stdio cimport SEEK_SET, SEEK_CUR, SEEK_END, FILE
-    ctypedef FILE * fio_fd;
-    _whence_vals = {"FIO_SEEK_SET": SEEK_SET,
-                    "FIO_SEEK_CUR": SEEK_CUR,
-                    "FIO_SEEK_END": SEEK_END}
+from libc.stdio cimport SEEK_SET, SEEK_CUR, SEEK_END
+ctypedef int fio_fd;
+_whence_vals = {"FIO_SEEK_SET": SEEK_SET,
+                "FIO_SEEK_CUR": SEEK_CUR,
+                "FIO_SEEK_END": SEEK_END}
 
 cdef enum:
     FIO_READ = 0x01
     FIO_WRITE = 0x02
 
-cdef enum:
 DCD_ERRORS = {
     0: 'No Problem',
     -1: 'Normal EOF',
@@ -55,40 +48,23 @@ cdef extern from 'include/readdcd.h':
                        int *nsavc, double *delta, int *nfixed, int **freeind,
                        float **fixedcoords, int *reverse, int *charmm,
                        char **remarks, int *len_remarks)
-    int read_dcdstep(fio_fd fd, int natoms, float *x, float *y, float *z,
-                     float *unitcell, int nfixed, int first, int *freeind,
-                     float *fixedcoords, int reverse, int charmm)
-    int read_dcdsubset(fio_fd fd, int natoms, int lowerb, int upperb, float *x,
-                       float *y, float *z, float *unitcell, int nfixed,
-                       int first, int *freeind, float *fixedcoords, int reverse,
-                       int charmm)
-    int skip_dcdstep(fio_fd fd, int natoms, int nfixed, int charmm, int numstep)
-    void close_dcd_read(int *freeind, float *fixedcoords)
-    int write_dcdheader(fio_fd fd, const char *remarks, int natoms,
-                        int istart, int nsavc, double delta, int with_unitcell,
-                        int charmm)
-    int write_dcdstep(fio_fd fd, int curstep, int curframe,
-                      int natoms, const float *x, const float *y, const float *z,
-                      const double *unitcell, int charmm)
-    int skip_dcdstep(fio_fd fd, int natoms, int nfixed, int charmm, int numsteps)
 
 
 cdef class DCDFile:
     cdef fio_fd fp
     cdef readonly fname
     cdef int is_open
-
     cdef int natoms
     cdef int nsets
     cdef int istart
     cdef int nsavc
     cdef double delta
     cdef int nfixed
-    cdef int **freeind
-    cdef float **fixedcords
+    cdef int *freeind
+    cdef float *fixedcoords
     cdef int reverse
     cdef int charmm
-    cdef char **remarks
+    cdef char *remarks
     cdef int len_remarks
 
     def __cinit__(self, fname, mode='r'):
@@ -134,10 +110,11 @@ cdef class DCDFile:
         if not self.is_open:
             raise RuntimeError("No file open")
 
-        ok = read_dcdheader(self.fd, <int*>&self.natoms, <int*>&self.nsets,
-                            <int*>&self.istart, <int*>&self.nsavc, self.delta,
-                            <int*>self.nfixed, self.freeind, self.fixedcoords,
-                            <int*>self.reverse, <int>*self.reverse,
-                            self.remarks, <int*>&self.len_remarks)
+        ok = read_dcdheader(self.fp, &self.natoms, &self.nsets, &self.istart,
+                            &self.nsavc, &self.delta, &self.nfixed, &self.freeind,
+                            &self.fixedcoords, &self.reverse,
+                            &self.charmm, &self.remarks, &self.len_remarks)
         if ok != 0:
             raise IOError("Reading DCD header failed: {}".format(DCD_ERRORS[ok]))
+
+        print(self.natoms)