Implemented the Gromacs trajectory converter

Extensions/setup.py

@@ -44,7 +44,13 @@ EXTENSIONS = [Extension('distance_histogram',
               Extension('qhull',
                         include_dirs  = QHULL_INCLUDE_DIR,
                         sources =  glob.glob(os.path.join(QHULL_DIR, 'src','*.c')) + ['qhull.pyx'],
-                        define_macros = [('qh_QHpointer','1')])
+                        define_macros = [('qh_QHpointer','1')]),
+              Extension('mdanse_xtc',
+                        include_dirs=['./xtc/include/','./xtc/'],
+                        sources=['./xtc/src/xdrfile.c',
+                                 './xtc/src/xdr_seek.c',
+                                 './xtc/src/xdrfile_xtc.c',
+                                 './xtc/xtc.pyx'])
               ]
 
 

Extensions/xtc/include/ms_stdint.h

+// ISO C9x  compliant stdint.h for Microsoft Visual Studio
+// Based on ISO/IEC 9899:TC2 Committee draft (May 6, 2005) WG14/N1124
+//
+//  Copyright (c) 2006-2013 Alexander Chemeris
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//   1. Redistributions of source code must retain the above copyright notice,
+//      this list of conditions and the following disclaimer.
+//
+//   2. 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.
+//
+//   3. Neither the name of the product 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 AUTHOR ``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 AUTHOR 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.
+//
+///////////////////////////////////////////////////////////////////////////////
+
+#ifndef _MSC_VER // [
+#error "Use this header only with Microsoft Visual C++ compilers!"
+#endif // _MSC_VER ]
+
+#ifndef _MSC_STDINT_H_ // [
+#define _MSC_STDINT_H_
+
+#if _MSC_VER > 1000
+#pragma once
+#endif
+
+#if _MSC_VER >= 1600 // [
+#include <stdint.h>
+#else // ] _MSC_VER >= 1600 [
+
+#include <limits.h>
+
+// For Visual Studio 6 in C++ mode and for many Visual Studio versions when
+// compiling for ARM we should wrap <wchar.h> include with 'extern "C++" {}'
+// or compiler give many errors like this:
+//   error C2733: second C linkage of overloaded function 'wmemchr' not allowed
+#ifdef __cplusplus
+extern "C" {
+#endif
+#  include <wchar.h>
+#ifdef __cplusplus
+}
+#endif
+
+// Define _W64 macros to mark types changing their size, like intptr_t.
+#ifndef _W64
+#  if !defined(__midl) && (defined(_X86_) || defined(_M_IX86)) && _MSC_VER >= 1300
+#     define _W64 __w64
+#  else
+#     define _W64
+#  endif
+#endif
+
+
+// 7.18.1 Integer types
+
+// 7.18.1.1 Exact-width integer types
+
+// Visual Studio 6 and Embedded Visual C++ 4 doesn't
+// realize that, e.g. char has the same size as __int8
+// so we give up on __intX for them.
+#if (_MSC_VER < 1300)
+   typedef signed char       int8_t;
+   typedef signed short      int16_t;
+   typedef signed int        int32_t;
+   typedef unsigned char     uint8_t;
+   typedef unsigned short    uint16_t;
+   typedef unsigned int      uint32_t;
+#else
+   typedef signed __int8     int8_t;
+   typedef signed __int16    int16_t;
+   typedef signed __int32    int32_t;
+   typedef unsigned __int8   uint8_t;
+   typedef unsigned __int16  uint16_t;
+   typedef unsigned __int32  uint32_t;
+#endif
+typedef signed __int64       int64_t;
+typedef unsigned __int64     uint64_t;
+
+
+// 7.18.1.2 Minimum-width integer types
+typedef int8_t    int_least8_t;
+typedef int16_t   int_least16_t;
+typedef int32_t   int_least32_t;
+typedef int64_t   int_least64_t;
+typedef uint8_t   uint_least8_t;
+typedef uint16_t  uint_least16_t;
+typedef uint32_t  uint_least32_t;
+typedef uint64_t  uint_least64_t;
+
+// 7.18.1.3 Fastest minimum-width integer types
+typedef int8_t    int_fast8_t;
+typedef int16_t   int_fast16_t;
+typedef int32_t   int_fast32_t;
+typedef int64_t   int_fast64_t;
+typedef uint8_t   uint_fast8_t;
+typedef uint16_t  uint_fast16_t;
+typedef uint32_t  uint_fast32_t;
+typedef uint64_t  uint_fast64_t;
+
+// 7.18.1.4 Integer types capable of holding object pointers
+#ifdef _WIN64 // [
+   typedef signed __int64    intptr_t;
+   typedef unsigned __int64  uintptr_t;
+#else // _WIN64 ][
+   typedef _W64 signed int   intptr_t;
+   typedef _W64 unsigned int uintptr_t;
+#endif // _WIN64 ]
+
+// 7.18.1.5 Greatest-width integer types
+typedef int64_t   intmax_t;
+typedef uint64_t  uintmax_t;
+
+
+// 7.18.2 Limits of specified-width integer types
+
+#if !defined(__cplusplus) || defined(__STDC_LIMIT_MACROS) // [   See footnote 220 at page 257 and footnote 221 at page 259
+
+// 7.18.2.1 Limits of exact-width integer types
+#define INT8_MIN     ((int8_t)_I8_MIN)
+#define INT8_MAX     _I8_MAX
+#define INT16_MIN    ((int16_t)_I16_MIN)
+#define INT16_MAX    _I16_MAX
+#define INT32_MIN    ((int32_t)_I32_MIN)
+#define INT32_MAX    _I32_MAX
+#define INT64_MIN    ((int64_t)_I64_MIN)
+#define INT64_MAX    _I64_MAX
+#define UINT8_MAX    _UI8_MAX
+#define UINT16_MAX   _UI16_MAX
+#define UINT32_MAX   _UI32_MAX
+#define UINT64_MAX   _UI64_MAX
+
+// 7.18.2.2 Limits of minimum-width integer types
+#define INT_LEAST8_MIN    INT8_MIN
+#define INT_LEAST8_MAX    INT8_MAX
+#define INT_LEAST16_MIN   INT16_MIN
+#define INT_LEAST16_MAX   INT16_MAX
+#define INT_LEAST32_MIN   INT32_MIN
+#define INT_LEAST32_MAX   INT32_MAX
+#define INT_LEAST64_MIN   INT64_MIN
+#define INT_LEAST64_MAX   INT64_MAX
+#define UINT_LEAST8_MAX   UINT8_MAX
+#define UINT_LEAST16_MAX  UINT16_MAX
+#define UINT_LEAST32_MAX  UINT32_MAX
+#define UINT_LEAST64_MAX  UINT64_MAX
+
+// 7.18.2.3 Limits of fastest minimum-width integer types
+#define INT_FAST8_MIN    INT8_MIN
+#define INT_FAST8_MAX    INT8_MAX
+#define INT_FAST16_MIN   INT16_MIN
+#define INT_FAST16_MAX   INT16_MAX
+#define INT_FAST32_MIN   INT32_MIN
+#define INT_FAST32_MAX   INT32_MAX
+#define INT_FAST64_MIN   INT64_MIN
+#define INT_FAST64_MAX   INT64_MAX
+#define UINT_FAST8_MAX   UINT8_MAX
+#define UINT_FAST16_MAX  UINT16_MAX
+#define UINT_FAST32_MAX  UINT32_MAX
+#define UINT_FAST64_MAX  UINT64_MAX
+
+// 7.18.2.4 Limits of integer types capable of holding object pointers
+#ifdef _WIN64 // [
+#  define INTPTR_MIN   INT64_MIN
+#  define INTPTR_MAX   INT64_MAX
+#  define UINTPTR_MAX  UINT64_MAX
+#else // _WIN64 ][
+#  define INTPTR_MIN   INT32_MIN
+#  define INTPTR_MAX   INT32_MAX
+#  define UINTPTR_MAX  UINT32_MAX
+#endif // _WIN64 ]
+
+// 7.18.2.5 Limits of greatest-width integer types
+#define INTMAX_MIN   INT64_MIN
+#define INTMAX_MAX   INT64_MAX
+#define UINTMAX_MAX  UINT64_MAX
+
+// 7.18.3 Limits of other integer types
+
+#ifdef _WIN64 // [
+#  define PTRDIFF_MIN  _I64_MIN
+#  define PTRDIFF_MAX  _I64_MAX
+#else  // _WIN64 ][
+#  define PTRDIFF_MIN  _I32_MIN
+#  define PTRDIFF_MAX  _I32_MAX
+#endif  // _WIN64 ]
+
+#define SIG_ATOMIC_MIN  INT_MIN
+#define SIG_ATOMIC_MAX  INT_MAX
+
+#ifndef SIZE_MAX // [
+#  ifdef _WIN64 // [
+#     define SIZE_MAX  _UI64_MAX
+#  else // _WIN64 ][
+#     define SIZE_MAX  _UI32_MAX
+#  endif // _WIN64 ]
+#endif // SIZE_MAX ]
+
+// WCHAR_MIN and WCHAR_MAX are also defined in <wchar.h>
+#ifndef WCHAR_MIN // [
+#  define WCHAR_MIN  0
+#endif  // WCHAR_MIN ]
+#ifndef WCHAR_MAX // [
+#  define WCHAR_MAX  _UI16_MAX
+#endif  // WCHAR_MAX ]
+
+#define WINT_MIN  0
+#define WINT_MAX  _UI16_MAX
+
+#endif // __STDC_LIMIT_MACROS ]
+
+
+// 7.18.4 Limits of other integer types
+
+#if !defined(__cplusplus) || defined(__STDC_CONSTANT_MACROS) // [   See footnote 224 at page 260
+
+// 7.18.4.1 Macros for minimum-width integer constants
+
+#define INT8_C(val)  val##i8
+#define INT16_C(val) val##i16
+#define INT32_C(val) val##i32
+#define INT64_C(val) val##i64
+
+#define UINT8_C(val)  val##ui8
+#define UINT16_C(val) val##ui16
+#define UINT32_C(val) val##ui32
+#define UINT64_C(val) val##ui64
+
+// 7.18.4.2 Macros for greatest-width integer constants
+// These #ifndef's are needed to prevent collisions with <boost/cstdint.hpp>.
+// Check out Issue 9 for the details.
+#ifndef INTMAX_C //   [
+#  define INTMAX_C   INT64_C
+#endif // INTMAX_C    ]
+#ifndef UINTMAX_C //  [
+#  define UINTMAX_C  UINT64_C
+#endif // UINTMAX_C   ]
+
+#endif // __STDC_CONSTANT_MACROS ]
+
+#endif // _MSC_VER >= 1600 ]
+
+#endif // _MSC_STDINT_H_ ]

Extensions/xtc/include/trr_header.h

+#ifndef _trr_header_h_
+#define _trr_header_h_
+
+typedef struct		/* This struct describes the order and the	*/
+/* sizes of the structs in a trjfile, sizes are given in bytes.	*/
+{
+    int  bDouble;        /* Double precision?                            */
+    int	ir_size;	/* Backward compatibility		        */
+    int	e_size;		/* Backward compatibility		        */
+    int	box_size;	/* Non zero if a box is present			*/
+    int   vir_size;       /* Backward compatibility		        */
+    int   pres_size;      /* Backward compatibility		        */
+    int	top_size;	/* Backward compatibility		        */
+    int	sym_size;	/* Backward compatibility		        */
+    int	x_size;		/* Non zero if coordinates are present		*/
+    int	v_size;		/* Non zero if velocities are present		*/
+    int	f_size;		/* Non zero if forces are present		*/
+
+    int	natoms;		/* The total number of atoms			*/
+    int	step;		/* Current step number				*/
+    int	nre;		/* Backward compatibility		        */
+    float	tf;		/* Current time					*/
+    float	lambdaf;		/* Current value of lambda			*/
+    double	td;		/* Current time					*/
+    double	lambdad;		/* Current value of lambda			*/
+} t_trnheader;
+
+int do_trnheader(XDRFILE *xd, char bRead, t_trnheader *sh);
+
+#endif

Extensions/xtc/include/xdr_seek.h

+#ifndef _xdr_seek_h
+#define _xdr_seek_h
+
+// for int64_t on older M$ Visual Studio
+#if _MSC_VER && _MSVC_VER < 1600 && !__INTEL_COMPILER
+	#include "ms_stdint.h"
+#else
+	#include <stdint.h>
+#endif
+
+#include "xdrfile.h"
+
+int64_t xdr_tell(XDRFILE *xd);
+int xdr_seek(XDRFILE *xd, int64_t pos, int whence);
+
+#endif

Extensions/xtc/include/xdrfile_trr.h

+ /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
+ *
+ * $Id$
+ *
+ * Copyright (c) 2009-2014, Erik Lindahl & David van der Spoel
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice, this
+ * list of conditions and the following disclaimer.
+ *
+ * 2. 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.
+ *
+ * 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 COPYRIGHT HOLDER 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.
+ */
+
+#ifndef _xdrfile_trr_h
+#define _xdrfile_trr_h
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#include "xdrfile.h"
+  
+  /* All functions return exdrOK if successful.
+   * (error codes defined in xdrfile.h).
+   */  
+   
+  /* This function returns the number of atoms in the xtc file in *natoms */
+  extern int read_trr_natoms(char *fn,int *natoms);
+  extern int read_trr_nframes(char* fn, unsigned long *nframes);
+  
+  /* Read one frame of an open xtc file. If either of x,v,f,box are
+     NULL the arrays will be read from the file but not used.  */
+  extern int read_trr(XDRFILE *xd,int natoms,int *step,float *t,float *lambda,
+		      matrix box,rvec *x,rvec *v,rvec *f);
+
+  /* Write a frame to xtc file */
+  extern int write_trr(XDRFILE *xd,int natoms,int step,float t,float lambda,
+		       matrix box,rvec *x,rvec *v,rvec *f);
+
+  
+#ifdef __cplusplus
+}
+#endif
+
+#endif

Extensions/xtc/include/xdrfile_xtc.h

+ /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
+ *
+ * $Id$
+ *
+ * Copyright (c) 2009-2014, Erik Lindahl & David van der Spoel
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice, this
+ * list of conditions and the following disclaimer.
+ *
+ * 2. 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.
+ *
+ * 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 COPYRIGHT HOLDER 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.
+ */