Remove remaining uses of programs.txt

Other uses have been replaced with direct generation from the wrapper
binary.  Since the manual no longer has the program man pages, there is
no particular need to list the programs either, in particular since this
is potentially more maintenance.  A reference to the online help and/or
'gmx help' should be sufficient.

Related to #685.

Change-Id: Ie865e955416cdc28f654cf2f988994bac7550ac6

diff --git a/admin/mktex b/admin/mktex
deleted file mode 100755 (executable)
index b55ed87..0000000
--- a/admin/mktex
+++ /dev/null
@@ -1,51 +0,0 @@
-#!/bin/csh -f
-
-if ( $#argv < 2 ) then
-  echo "Error: provide the binary directory as first argument,"
-  echo "and the location of programs.txt as the second."
-  echo "Proglist.tex will be written in the current directory."
-  exit
-endif
-
-set GMXBINDIR   = $1
-set PROGFILE   = $2
-
-set dir = $cwd
-
-set VER                = 4.5
-set TEXIDX     = proglist.tex
-
-set GENERAL    = "getting_started:Getting_Started flow:Flow_Chart files:File_Formats mdp_opt:mdp_options"
-
-cd $GMXBINDIR
-set PROGRAMS = [a-z]*
-cd $dir
-
-echo ""
-echo "generating latex page $TEXIDX"
-echo "--------------------------------"
-
-if ( -f $TEXIDX ) \rm $TEXIDX
-touch $TEXIDX
-
-echo "\\begin{description}" >> $TEXIDX
-awk -F '|' -v longest="mk\\_angndx" '{\
-  gsub("_","\\_",$0);\
-  gsub("%","\\%",$0);\
-  if (NF) {\
-    if ( $1 == "LONGEST" ) {\
-      longest = $2;\
-    } else if ( $1 == "HEAD" ) {\
-      printf("\\item {\\large\\bf %s}\n",$2);\
-      printf("\\vspace{-2ex}\\begin{tabbing}\n");\
-      printf("{\\bf %s} \\= \\kill\n",longest);\
-    } else if ( $1 == "END" ) {\
-      printf("\\end{tabbing}\\vspace{-2ex}\n\n");\
-    } else {\
-      printf("{\\bf %s} \\> %s \\\\\n",$1,$2);\
-    }\
-  }\
-}' $PROGFILE | sed -e 's/e\.g\./{\\eg}/g' >> $TEXIDX
-echo "\\end{description}" >> $TEXIDX
-
-#last line

diff --git a/admin/programs.txt b/admin/programs.txt
deleted file mode 100644 (file)
index 1aaa7a5..0000000
--- a/admin/programs.txt
+++ /dev/null
@@ -1,168 +0,0 @@
-HEAD|Generating topologies and coordinates
-editconf|edits the box and writes subgroups 
-g_protonate|protonates structures
-g_x2top|generates a primitive topology from coordinates 
-genbox|solvates a system
-genconf|multiplies a conformation in 'random' orientations
-genion|generates mono atomic ions on energetically favorable positions
-genrestr|generates position restraints or distance restraints for index groups
-pdb2gmx|converts coordinate files to topology and FF-compliant coordinate files
-END
-
-HEAD|Running a simulation
-grompp|makes a run input file
-mdrun|performs a simulation, do a normal mode analysis or an energy minimization
-tpbconv|makes a run input file for restarting a crashed run
-END
-
-HEAD|Viewing trajectories
-g_nmtraj|generate a virtual trajectory from an eigenvector
-ngmx|displays a trajectory
-END
-
-HEAD|Processing energies
-g_enemat|extracts an energy matrix from an energy file
-g_energy|writes energies to xvg files and displays averages
-mdrun|with -rerun (re)calculates energies for trajectory frames
-END
-
-HEAD|Converting files
-editconf|converts and manipulates structure files
-eneconv|converts energy files
-g_sigeps|convert c6/12 or c6/cn combinations to and from sigma/epsilon
-trjcat|concatenates trajectory files
-trjconv|converts and manipulates trajectory files
-xpm2ps|converts XPM matrices to encapsulated postscript (or XPM)
-END
-
-HEAD|Tools
-g_analyze|analyzes data sets
-g_dyndom|interpolate and extrapolate structure rotations
-g_filter|frequency filters trajectories, useful for making smooth movies
-g_lie|free energy estimate from linear combinations
-g_morph|linear interpolation of conformations 
-g_pme_error|estimates the error of using PME with a given input file
-g_select|selects groups of atoms based on flexible textual selections
-g_sham|read/write xmgr and xvgr data sets
-g_spatial|calculates the spatial distribution function
-g_traj|plots x, v and f of selected atoms/groups (and more) from a trajectory
-g_tune_pme|time mdrun as a function of PME nodes to optimize settings
-g_wham|weighted histogram analysis after umbrella sampling
-gmxcheck|checks and compares files
-gmxdump|makes binary files human readable
-make_ndx|makes index files
-mk_angndx|generates index files for g_angle
-trjorder|orders molecules according to their distance to a group
-xpm2ps|convert XPM (XPixelMap) file to postscript
-END
-
-HEAD|Distances between structures
-g_cluster|clusters structures
-g_confrms|fits two structures and calculates the rmsd 
-g_rms|calculates rmsd's with a reference structure and rmsd matrices
-g_rmsf|calculates atomic fluctuations
-END
-
-HEAD|Distances in structures over time
-g_bond|calculates distances between atoms
-g_dist|calculates the distances between the centers of mass of two groups
-g_mindist|calculates the minimum distance between two groups
-g_mdmat|calculates residue contact maps
-g_polystat|calculates static properties of polymers
-g_rmsdist|calculates atom pair distances averaged with power -2, -3 or -6
-END
-
-HEAD|Mass distribution properties over time
-g_gyrate|calculates the radius of gyration
-g_msd|calculates mean square displacements
-g_polystat|calculates static properties of polymers
-g_rdf|calculates radial distribution functions
-g_rotacf|calculates the rotational correlation function for molecules
-g_rotmat|plots the rotation matrix for fitting to a reference structure
-g_sans|computes the small angle neutron scattering spectra
-g_saxs|computes the small angle X-Ray scattering spectra
-g_traj|plots x, v, f, box, temperature and rotational energy
-g_vanhove|calculates Van Hove displacement functions
-END
-
-HEAD|Analyzing bonded interactions
-g_angle|calculates distributions and correlations for angles and dihedrals
-g_bond|calculates bond length distributions
-mk_angndx|generates index files for g_angle
-END
-
-HEAD|Structural properties
-g_anadock|cluster structures from Autodock runs
-g_bundle|analyzes bundles of axes, e.g. helices
-g_clustsize|calculate size distributions of atomic clusters
-g_disre|analyzes distance restraints
-g_hbond|computes and analyzes hydrogen bonds
-g_order|computes the order parameter per atom for carbon tails
-g_principal|calculates axes of inertia for a group of atoms
-g_rdf|calculates radial distribution functions
-g_saltbr|computes salt bridges
-g_sas|computes solvent accessible surface area
-g_sgangle|computes the angle and distance between two groups
-g_sorient|analyzes solvent orientation around solutes
-g_spol|analyzes solvent dipole orientation and polarization around solutes
-END
-
-HEAD|Kinetic properties
-g_bar|calculates free energy difference estimates through Bennett's acceptance ratio
-g_current|calculate current autocorrelation function of system
-g_dos|analyzes density of states and properties based on that
-g_dyecoupl|extracts dye dynamics from trajectories
-g_kinetics|analyzes kinetic constants from properties based on the Eyring model
-g_principal|calculate principal axes of inertion for a group of atoms
-g_tcaf|calculates viscosities of liquids
-g_traj|plots x, v, f, box, temperature and rotational energy
-g_vanhove|compute Van Hove correlation function
-g_velacc|calculates velocity autocorrelation functions
-END
-
-HEAD|Electrostatic properties
-g_current|calculates dielectric constants for charged systems
-g_dielectric|calculates frequency dependent dielectric constants
-g_dipoles|computes the total dipole plus fluctuations
-g_potential|calculates the electrostatic potential across the box
-g_spol|analyze dipoles around a solute
-genion|generates mono atomic ions on energetically favorable positions
-END
-
-HEAD|Protein-specific analysis
-do_dssp|assigns secondary structure and calculates solvent accessible surface area
-g_chi|calculates everything you want to know about chi and other dihedrals
-g_helix|calculates basic properties of alpha helices
-g_helixorient|calculates local pitch/bending/rotation/orientation inside helices
-g_rama|computes Ramachandran plots
-g_wheel|plots helical wheels
-g_xrama|shows animated Ramachandran plots
-END
-
-HEAD|Interfaces
-g_bundle|analyzes bundles of axes, e.g. transmembrane helices
-g_density|calculates the density of the system
-g_densmap|calculates 2D planar or axial-radial density maps
-g_densorder|calculate surface fluctuations
-g_h2order|computes the orientation of water molecules
-g_hydorder|computes tetrahedrality parameters around a given atom
-g_order|computes the order parameter per atom for carbon tails
-g_membed|embeds a protein into a lipid bilayer
-g_potential|calculates the electrostatic potential across the box
-END
-
-
-HEAD|Covariance analysis
-g_anaeig|analyzes the eigenvectors
-g_covar|calculates and diagonalizes the covariance matrix
-make_edi|generate input files for essential dynamics sampling
-END
-
-HEAD|Normal modes
-g_anaeig|analyzes the normal modes
-g_nmeig|diagonalizes the Hessian 
-g_nmtraj|generate oscillating trajectory of an eigenmode
-g_nmens|generates an ensemble of structures from the normal modes
-grompp|makes a run input file
-mdrun|finds a potential energy minimum and calculates the Hessian
-END

diff --git a/manual/CMakeLists.txt b/manual/CMakeLists.txt
index a83f2cc454771b9b97c2c5bb50097d4435a85f59..8d52c41190a308b8bea954bacfb0a22b13fe93aa 100644 (file)
--- a/manual/CMakeLists.txt
+++ b/manual/CMakeLists.txt
@@ -81,11 +81,6 @@ if(MANUAL_BUILD_IS_POSSIBLE)
         DEPENDS mkmdp ${CMAKE_SOURCE_DIR}/share/html/online/mdp_opt.html
         )
 
-    ADD_CUSTOM_COMMAND(OUTPUT ${output_dir}/proglist.tex
-        COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/mkproglist ARGS ${CMAKE_SOURCE_DIR}/admin/programs.txt
-        DEPENDS mkproglist ${CMAKE_SOURCE_DIR}/admin/programs.txt
-        )
-
     # Finally, the command to build the manual.
 
     ADD_LATEX_DOCUMENT(gromacs.tex
@@ -101,7 +96,7 @@ if(MANUAL_BUILD_IS_POSSIBLE)
         # add_custom_targets() above. They should not be in the git
         # repository, or its directory, or the dependencies will not work
         # properly.
-        DEPENDS proglist.tex mdp_opt.tex
+        DEPENDS mdp_opt.tex
 
         BIBFILES monster.bib unpubl.bib
         IMAGE_DIRS plots

diff --git a/manual/mkproglist b/manual/mkproglist
deleted file mode 100755 (executable)
index e50a3e5..0000000
--- a/manual/mkproglist
+++ /dev/null
@@ -1,50 +0,0 @@
-#!/bin/bash
-
-TEXIDX=proglist.tex
-PROGFILE=$1
-
-if [ ! -f $PROGFILE ]; then
-    echo "Error: Can't find programs.txt"
-    exit 1
-fi
-
-echo "generating latex page ${TEXIDX} from ${PROGFILE}"
-
-rm -f ${TEXIDX}
-
-touch ${TEXIDX}
-
-longest=g_helixorient
-
-cat >> ${TEXIDX} << HEADER
-\newlength{\proglistwidth}
-\newsavebox{\proglistsavebox}
-\savebox{\proglistsavebox}{\ttfamily\small $longest}
-\settowidth{\proglistwidth}{\usebox{\proglistsavebox}}
-
-\begin{description}[font=\bfseries\large]
-HEADER
-
-awk -F '|' -v longest="$longest" '{\
-  gsub("_","_",$0);\
-  gsub("%","\\%",$0);\
-  if (NF) {\
-    if ( $1 == "LONGEST" ) {\
-      longest = $2;\
-    } else if ( $1 == "HEAD" ) {\
-      printf("\\item[%s] \\ \n",$2);\
-      printf("\\begin{description}[font=\\ttfamily\\small, style=nextline, leftmargin=\\proglistwidth, noitemsep, labelsep=0pt]\n");\
-    } else if ( $1 == "END" ) {\
-      printf("\\end{description}\n\n");\
-    } else {\
-      printf("\\item[%s] %s \n",$1,$2);\
-    }\
-  }\
-}' $PROGFILE | sed -e 's/e\.g\./{\\eg}/g' >> $TEXIDX
-cat >> $TEXIDX << FOOTER
-\end{description}
-
-FOOTER
-
-echo ""
-#last line

diff --git a/manual/programs.tex b/manual/programs.tex
index 58fbdb8aed3235b1eb4c892ab3eaad50b57673b4..e4b7e7780df4b43184c15b701e9cf7221a571e3b 100644 (file)
--- a/manual/programs.tex
+++ b/manual/programs.tex
@@ -42,9 +42,9 @@
 All the information in this chapter can also be found in HTML
 format in your {\gromacs} data directory. The path depends on
 where your files are installed, but the default location is
-{\tt /usr/local/gromacs/share/html/online.html}.
-If you installed from Linux packages it can be found as
-{\tt /usr/local/share/gromacs/html/online.html}.
+{\tt /usr/local/gromacs/share/gromacs/html/online.html}.
+If you installed from Linux packages it can typically be found as
+{\tt /usr/share/gromacs/html/online.html}.
 You can also use the online manual from the {\gromacs} web site,
 \url{http://manual.gromacs.org/current}.
 
@@ -53,7 +53,8 @@ you have sourced the {\tt GMXRC} script in the {\gromacs} binary directory for
 your host they should already be present in your {\tt MANPATH} environment variable, and you
 should be able to type {\eg} {\tt man gmx-grompp}. You can also use
 the {\tt -h} flag on the command line (e.g. {\tt gmx grompp -h}) to
-see the same information.
+see the same information, as well as {\tt gmx help grompp}.
+The list of all programs are available from {\tt gmx help}.
 
 \section{File types\swapindexquiet{file}{type}}
 \label{sec:fileformats}
@@ -71,7 +72,4 @@ present on UNIX since they are necessary for NFS support.
 \section{Run Parameters\swapindexquiet{run}{parameter}}
 \input{mdp_opt}
 
-\section{Programs by topic\index{programs by topic}}
-\input{proglist}
-
-% LocalWords:  online html GMXRC MANPATH grompp progman xdr NFS
+% LocalWords:  online html GMXRC MANPATH grompp xdr NFS