Move read_tps_conf() to confio.h

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

diff --git a/src/gromacs/gmxana/gmx_chi.c b/src/gromacs/gmxana/gmx_chi.c
index 8756ac7bc17a9b90ab67c2a7e056d4aafa5909a5..0b12224e2e98d91dd060b57cd2234bd4f4b744d1 100644 (file)
--- a/src/gromacs/gmxana/gmx_chi.c
+++ b/src/gromacs/gmxana/gmx_chi.c
@@ -45,7 +45,6 @@
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxana/gstat.h"
@@ -57,6 +56,7 @@
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/topology/residuetypes.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
@@ -1251,25 +1251,27 @@ int gmx_chi(int argc, char *argv[])
         "With option [TT]-all[tt], the angles themselves as a function of time for",
         "each residue are printed to separate files [TT](dihedral)(RESIDUE)(nresnr).xvg[tt].",
         "These can be in radians or degrees.[PAR]",
-        "A log file (argument [TT]-g[tt]) is also written. This contains [BR]",
-        "(a) information about the number of residues of each type.[BR]",
-        "(b) The NMR ^3J coupling constants from the Karplus equation.[BR]",
-        "(c) a table for each residue of the number of transitions between ",
-        "rotamers per nanosecond,  and the order parameter S^2 of each dihedral.[BR]",
-        "(d) a table for each residue of the rotamer occupancy.[PAR]",
+        "A log file (argument [TT]-g[tt]) is also written. This contains",
+        "",
+        " * information about the number of residues of each type.",
+        " * The NMR ^3J coupling constants from the Karplus equation.",
+        " * a table for each residue of the number of transitions between ",
+        "   rotamers per nanosecond,  and the order parameter S^2 of each dihedral.",
+        " * a table for each residue of the rotamer occupancy.",
+        "",
         "All rotamers are taken as 3-fold, except for [GRK]omega[grk] and [GRK]chi[grk] dihedrals",
         "to planar groups (i.e. [GRK]chi[grk][SUB]2[sub] of aromatics, Asp and Asn; [GRK]chi[grk][SUB]3[sub] of Glu",
         "and Gln; and [GRK]chi[grk][SUB]4[sub] of Arg), which are 2-fold. \"rotamer 0\" means ",
         "that the dihedral was not in the core region of each rotamer. ",
         "The width of the core region can be set with [TT]-core_rotamer[tt][PAR]",
 
-        "The S^2 order parameters are also output to an [TT].xvg[tt] file",
-        "(argument [TT]-o[tt] ) and optionally as a [TT].pdb[tt] file with",
+        "The S^2 order parameters are also output to an [REF].xvg[ref] file",
+        "(argument [TT]-o[tt] ) and optionally as a [REF].pdb[ref] file with",
         "the S^2 values as B-factor (argument [TT]-p[tt]). ",
         "The total number of rotamer transitions per timestep",
         "(argument [TT]-ot[tt]), the number of transitions per rotamer",
         "(argument [TT]-rt[tt]), and the ^3J couplings (argument [TT]-jc[tt]), ",
-        "can also be written to [TT].xvg[tt] files. Note that the analysis",
+        "can also be written to [REF].xvg[ref] files. Note that the analysis",
         "of rotamer transitions assumes that the supplied trajectory frames",
         "are equally spaced in time.[PAR]",
 
@@ -1334,15 +1336,15 @@ int gmx_chi(int argc, char *argv[])
         { "-binwidth", FALSE, etINT, {&ndeg},
           "bin width for histograms (degrees)" },
         { "-core_rotamer", FALSE, etREAL, {&core_frac},
-          "only the central [TT]-core_rotamer[tt]*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0)" },
+          "only the central [TT]-core_rotamer[tt]\\*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0)" },
         { "-maxchi", FALSE, etENUM, {maxchistr},
           "calculate first ndih [GRK]chi[grk] dihedrals" },
         { "-normhisto", FALSE, etBOOL, {&bNormHisto},
           "Normalize histograms" },
         { "-ramomega", FALSE, etBOOL, {&bRamOmega},
-          "compute average omega as a function of [GRK]phi[grk]/[GRK]psi[grk] and plot it in an [TT].xpm[tt] plot" },
+          "compute average omega as a function of [GRK]phi[grk]/[GRK]psi[grk] and plot it in an [REF].xpm[ref] plot" },
         { "-bfact", FALSE, etREAL, {&bfac_init},
-          "B-factor value for [TT].pdb[tt] file for atoms with no calculated dihedral order parameter"},
+          "B-factor value for [REF].pdb[ref] file for atoms with no calculated dihedral order parameter"},
         { "-chi_prod", FALSE, etBOOL, {&bChiProduct},
           "compute a single cumulative rotamer for each residue"},
         { "-HChi", FALSE, etBOOL, {&bHChi},