Move read_tps_conf() to confio.h

[alexxy/gromacs.git] / src / gromacs / gmxana / gmx_rmsf.c

diff --git a/src/gromacs/gmxana/gmx_rmsf.c b/src/gromacs/gmxana/gmx_rmsf.c
index f96663cb77f6665ed674c7bec00c0ba8c8a003b5..223a1d7d5995684f3ace3de3cb19a4dfedb0b48d 100644 (file)
--- a/src/gromacs/gmxana/gmx_rmsf.c
+++ b/src/gromacs/gmxana/gmx_rmsf.c
@@ -41,7 +41,6 @@
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
@@ -54,6 +53,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
@@ -191,22 +191,22 @@ int gmx_rmsf(int argc, char *argv[])
         "deviation) of atomic positions in the trajectory (supplied with [TT]-f[tt])",
         "after (optionally) fitting to a reference frame (supplied with [TT]-s[tt]).[PAR]",
         "With option [TT]-oq[tt] the RMSF values are converted to B-factor",
-        "values, which are written to a [TT].pdb[tt] file with the coordinates, of the",
-        "structure file, or of a [TT].pdb[tt] file when [TT]-q[tt] is specified.",
+        "values, which are written to a [REF].pdb[ref] file with the coordinates, of the",
+        "structure file, or of a [REF].pdb[ref] file when [TT]-q[tt] is specified.",
         "Option [TT]-ox[tt] writes the B-factors to a file with the average",
         "coordinates.[PAR]",
         "With the option [TT]-od[tt] the root mean square deviation with",
         "respect to the reference structure is calculated.[PAR]",
         "With the option [TT]-aniso[tt], [THISMODULE] will compute anisotropic",
         "temperature factors and then it will also output average coordinates",
-        "and a [TT].pdb[tt] file with ANISOU records (corresonding to the [TT]-oq[tt]",
+        "and a [REF].pdb[ref] file with ANISOU records (corresonding to the [TT]-oq[tt]",
         "or [TT]-ox[tt] option). Please note that the U values",
         "are orientation-dependent, so before comparison with experimental data",
         "you should verify that you fit to the experimental coordinates.[PAR]",
-        "When a [TT].pdb[tt] input file is passed to the program and the [TT]-aniso[tt]",
+        "When a [REF].pdb[ref] input file is passed to the program and the [TT]-aniso[tt]",
         "flag is set",
         "a correlation plot of the Uij will be created, if any anisotropic",
-        "temperature factors are present in the [TT].pdb[tt] file.[PAR]",
+        "temperature factors are present in the [REF].pdb[ref] file.[PAR]",
         "With option [TT]-dir[tt] the average MSF (3x3) matrix is diagonalized.",
         "This shows the directions in which the atoms fluctuate the most and",
         "the least."
@@ -224,7 +224,6 @@ int gmx_rmsf(int argc, char *argv[])
     int              step, nre, natoms, i, g, m, teller = 0;
     real             t, lambda, *w_rls, *w_rms;
 
-    t_tpxheader      header;
     t_inputrec       ir;
     t_topology       top;
     int              ePBC;