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/*
Theseus - maximum likelihood superpositioning of macromolecular structures
Copyright (C) 2004-2014 Douglas L. Theobald
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the:
Free Software Foundation, Inc.,
59 Temple Place, Suite 330,
Boston, MA 02111-1307 USA
-/_|:|_|_\-
*/
#ifndef THESEUS_SEEN
#define THESEUS_SEEN
#if __STDC__ != 1
#error NOT a Standard C environment
#endif
/* Temporary workaround for broken OSX system headers, shipped in
XCode 1.5. They're declaring stuff 'static inline', and this is
incompatible with the '-ansi' flag I pass to gcc.
See Apple bug #3805571. */
#if defined(__APPLE__) && !defined(inline)
#define inline __inline__
#endif
#include <pthread.h>
#include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include <unistd.h>
#include <getopt.h>
#include <ctype.h>
#include <math.h>
#include <time.h>
#include <signal.h>
#include <dirent.h>
#include <sys/time.h>
#include <sys/stat.h>
#ifndef __MINGW32__
#include <sys/resource.h>
#endif
#include <sys/types.h>
#include <gsl/gsl_sf_gamma.h>
#include "Error.h"
#include "CovMat.h"
#include "DLTmath.h"
#include "distfit.h"
#include "Embed.h"
#include "FragDist.h"
#include "pdbUtils.h"
#include "pdbMalloc.h"
#include "pdbStats.h"
#include "pdbIO.h"
#include "PCAstats.h"
#include "RandCds.h"
#include "MultiPose.h"
#include "MultiPose2MSA.h"
#include "MultiPoseMix.h"
#include "QuarticHornFrag.h"
#include "GibbsMet.h"
#include "ProcGSLSVDNu.h"
#include "termcol.h"
static void
ParseCmdLine(int argc, char *argv[], CdsArray *baseA);
static void
PrintSuperposStats(CdsArray *cdsA);
#endif
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