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Commit 6e0506e6 authored by Remi Perenon's avatar Remi Perenon
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Merge branch 'feature-gromacs_converter' into 'develop' 

Feature gromacs converter

See merge request !23
parents 49648644 ec1b7f45
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CHANGELOG
View file @ 6e0506e6
version 1.2.0
--------------
* ADDED issue #10 Implemented Gromacs trajectory converter
* FIXED issue #21 "Save a template for new analysis" button produced an error
* CHANGED (internal) MDANSE is now built with system python (2.7.10)
......
Data/Trajectories/Gromacs/md.pdb 0 → 100644
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Extensions/setup.py
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......@@ -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=[numpy.get_include(),'./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 0 → 100644
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// 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 0 → 100644
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#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 0 → 100644
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#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.h 0 → 100644
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/* -*- 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.
*/
/*! \file xdrfile.h
* \brief Interface to read/write portabile binary files using XDR.
*
* This file provides an interface to read & write portably binary files,
* using XDR - the external data representation standard defined in RFC 1014.
*
* There are several advantages to the XDR approach:
*
* -# It is portable. And not just portable between big/small integer endian,
* but truly portable if you have system XDR routines. For example:
* - It doesn't matter if the character representation is ASCII or EBCDIC.
* - Some systems are small endian but use big endian order of the two
* dword in a double precision floating-point variable. The system XDR
* libraries will read/write this correctly.
* - Some systems (VAX...) don't use IEEE floating point. Their system
* XDR libraries will convert to/from this automatically.
* -# XDR libraries are required for NFS and lots of other network functions.
* This means there isn't a single Unix-like system that doesn't have them.
* -# There is NO extra metadata whatsoever, and we write plain XDR files.
* If you write a float, it will take exactly 4 bytes in the file.
* (All basic datatypes are 4 bytes, double fp 8 bytes).
* -# You can read/write the files by calling the system XDR routines directly
* too - you don't have to use the routines defined in this file.
* -# It is no problem if your system doesn't have XDR libraries (MS Windows).
* We have written our own versions of the necessary routines that work if
* your system uses ASCII for strings and IEEE floating-point. All types
* of byte and dword endian for integer and floating-point are supported.
* -# You can use these routines for any type of data, but since we designed
* them for Gromacs we also provide a special routine to write coordinates
* with (adjustable) lossy compression. The default precision will give you
* three decimals guaranteed accuracy, and reduces the filesize to 1/10th
* of normal binary data.
*
* We do not support getting or setting positions in XDR files, since it can
* break in horrible ways for large (64-bit) files, resulting in silent data
* corruption. Note that it works great to open/read/write 64-bit files if
* your system supports it; it is just the random access we cannot trust!
*
* We also provide wrapper routines so this module can be used from FORTRAN -
* see the file xdrfile_fortran.txt in the Gromacs distribution for
* documentation on the FORTRAN interface!
*/
#ifndef _XDRFILE_H_
#define _XDRFILE_H_
#ifdef __cplusplus
extern "C"
{
#endif
/*! \brief Abstract datatype for an portable binary file handle
*
* This datatype essentially works just like the standard FILE type in C.
* The actual contents is hidden in the implementation, so you can only
* define pointers to it, for use with the xdrfile routines.
*
* If you \a really need to see the definition it is in xdrfile.c, but you
* cannot access elements of the structure outside that file.
*
* \warning The implementation is completely different from the C standard
* library FILE, so don't even think about using an XDRFILE pointer as an
* argument to a routine that needs a standard FILE pointer.
*/
typedef struct XDRFILE XDRFILE;
enum { exdrOK, exdrHEADER, exdrSTRING, exdrDOUBLE,
exdrINT, exdrFLOAT, exdrUINT, exdr3DX, exdrCLOSE, exdrMAGIC,
exdrNOMEM, exdrENDOFFILE, exdrFILENOTFOUND, exdrNR };
extern char *exdr_message[exdrNR];
#define DIM 3
typedef float matrix[DIM][DIM];
typedef float rvec[DIM];
typedef int mybool;
/*! \brief Open a portable binary file, just like fopen()
*
* Use this routine much like calls to the standard library function
* fopen(). The only difference is that the returned pointer should only
* be used with routines defined in this header.
*
* \param path Full or relative path (including name) of the file
* \param mode "r" for reading, "w" for writing, "a" for append.
*
* \return Pointer to abstract xdr file datatype, or NULL if an error occurs.
*
*/
XDRFILE *
xdrfile_open (const char * path,
const char * mode);
/*! \brief Close a previously opened portable binary file, just like fclose()
*
* Use this routine much like calls to the standard library function
* fopen(). The only difference is that it is used for an XDRFILE handle
* instead of a FILE handle.
*
* \param xfp Pointer to an abstract XDRFILE datatype
*
* \return 0 on success, non-zero on error.
*/
int
xdrfile_close (XDRFILE * xfp);
/*! \brief Read one or more \a char type variable(s)
*
* \param ptr Pointer to memory where data should be written
* \param ndata Number of characters to read
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of characters read
*/
int
xdrfile_read_char(char * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Write one or more \a characters type variable(s)
*
* \param ptr Pointer to memory where data should be read
* \param ndata Number of characters to write.
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of characters written
*/
int
xdrfile_write_char(char * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Read one or more \a unsigned \a char type variable(s)
*
* \param ptr Pointer to memory where data should be written
* \param ndata Number of unsigned characters to read
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of unsigned characters read
*/
int
xdrfile_read_uchar(unsigned char * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Write one or more \a unsigned \a characters type variable(s)
*
* \param ptr Pointer to memory where data should be read
* \param ndata Number of unsigned characters to write.
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of unsigned characters written
*/
int
xdrfile_write_uchar(unsigned char * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Read one or more \a short type variable(s)
*
* \param ptr Pointer to memory where data should be written
* \param ndata Number of shorts to read
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of shorts read
*/
int
xdrfile_read_short(short * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Write one or more \a short type variable(s)
*
* \param ptr Pointer to memory where data should be read
* \param ndata Number of shorts to write.
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of shorts written
*/
int
xdrfile_write_short(short * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Read one or more \a unsigned \a short type variable(s)
*
* \param ptr Pointer to memory where data should be written
* \param ndata Number of unsigned shorts to read
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of unsigned shorts read
*/
int
xdrfile_read_ushort(unsigned short * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Write one or more \a unsigned \a short type variable(s)
*
* \param ptr Pointer to memory where data should be read
* \param ndata Number of unsigned shorts to write.
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of unsigned shorts written
*/
int
xdrfile_write_ushort(unsigned short * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Read one or more \a integer type variable(s)
*
* \param ptr Pointer to memory where data should be written
* \param ndata Number of integers to read
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of integers read
*
* The integer data type is assumed to be less than or equal to 32 bits.
*
* We do not provide any routines for reading/writing 64-bit integers, since
* - Not all XDR implementations support it
* - Not all machines have 64-bit integers
*
* Split your 64-bit data into two 32-bit integers for portability!
*/
int
xdrfile_read_int(int * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Write one or more \a integer type variable(s)
*
* \param ptr Pointer to memory where data should be read
* \param ndata Number of integers to write.
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of integers written