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Commit 762f63c2 authored by eric pellegrini's avatar eric pellegrini Committed by Remi Perenon
Browse files

Implemented the Gromacs trajectory converter

parent 49648644
This diff is collapsed.
......@@ -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'])
]
......
// 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_ ]
#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
#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
This diff is collapsed.
/* -*- 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
/* -*- 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_xtc_h
#define _xdrfile_xtc_h
#ifdef __cplusplus
extern "C" {
#endif
#include "xdrfile.h"
/* All functions return exdrOK if succesfull.
* (error codes defined in xdrfile.h).
*/
/* This function returns the number of atoms in the xtc file in *natoms */
extern int read_xtc_natoms(char *fn,int *natoms);
int read_xtc_nframes(char* fn, unsigned long *nframes);
/* Read one frame of an open xtc file */
extern int read_xtc(XDRFILE *xd,int natoms,int *step,float *time,
matrix box,rvec *x,float *prec);
/* Write a frame to xtc file */
extern int write_xtc(XDRFILE *xd,
int natoms,int step,float time,
matrix box,rvec *x,float prec);
#ifdef __cplusplus
}
#endif
#endif
/* 64 bit fileseek operations */
#define _FILE_OFFSETS_BITS 64
#include "xdr_seek.h"
#include <stdio.h>
/// copied from xtcfile.c (version 1.1.4)
struct XDRFILE
{
FILE * fp; /**< pointer to standard C library file handle */
void * /*this used to be (XDR*) */ xdr; /**< pointer to corresponding XDR handle */
char mode; /**< r=read, w=write, a=append */
int * buf1; /**< Buffer for internal use */
int buf1size; /**< Current allocated length of buf1 */
int * buf2; /**< Buffer for internal use */
int buf2size; /**< Current allocated length of buf2 */
};
//// end of copied
int64_t xdr_tell(XDRFILE *xd)
{
FILE* fptr = xd->fp;
#ifndef _WIN32
// use posix 64 bit ftell version
return ftello(fptr);
#elif defined(_MSVC_VER) && !__INTEL_COMPILER
return _ftelli64(fptr);
#else
return ftell(fptr);
#endif
}
int xdr_seek(XDRFILE *xd, int64_t pos, int whence)
{
int result = 1;
FILE* fptr = xd->fp;
#ifndef _WIN32
// use posix 64 bit ftell version
result = fseeko(fptr, pos, whence) < 0 ? exdrNR : exdrOK;
#elif _MSVC_VER && !__INTEL_COMPILER
result = _fseeki64(fptr, pos, whence) < 0 ? exdrNR : exdrOK;
#else
result = fseek(fptr, pos, whence) < 0 ? exdrNR : exdrOK;
#endif
if (result != exdrOK)
return result;
return exdrOK;
}
This diff is collapsed.
/* -*- 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.
*/
#include <stdlib.h>
#include <string.h>
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "xdrfile.h"
#include "xdrfile_trr.h"
#define BUFSIZE 128
#define GROMACS_MAGIC 1993
typedef struct /* This struct describes the order and the */
/* sizes of the structs in a trjfile, sizes are given in bytes. */
{
mybool 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;
static int nFloatSize(t_trnheader *sh,int *nflsz)
{
int nflsize=0;
if (sh->box_size)
nflsize = sh->box_size/(DIM*DIM);
else if (sh->x_size)
nflsize = sh->x_size/(sh->natoms*DIM);
else if (sh->v_size)
nflsize = sh->v_size/(sh->natoms*DIM);
else if (sh->f_size)
nflsize = sh->f_size/(sh->natoms*DIM);
else
return exdrHEADER;
if (((nflsize != sizeof(float)) && (nflsize != sizeof(double))))
return exdrHEADER;
*nflsz = nflsize;
return exdrOK;
}
extern int do_trnheader(XDRFILE *xd,mybool bRead,t_trnheader *sh)
{
int magic=GROMACS_MAGIC;
int nflsz,slen,result;
char *version = "GMX_trn_file";
char buf[BUFSIZE];
if (xdrfile_read_int(&magic,1,xd) != 1) {
/* modification by RTM to return the right EOF code
this is what's happening in the XTC code */
if (bRead)
return exdrENDOFFILE;
else
return exdrINT;
}
if (magic != GROMACS_MAGIC)
return exdrMAGIC;
if (bRead)
{
if (xdrfile_read_int(&slen,1,xd) != 1)
return exdrINT;
if (slen != strlen(version)+1)
return exdrSTRING;
if (xdrfile_read_string(buf,BUFSIZE,xd) <= 0)
return exdrSTRING;
}