**************************************************************************
                             show command
                        Leif Laaksonen CSC 2001
                        Timm Uhlmann       2003
                        Eero Häkkinen  CSC 2005
**************************************************************************

#
# Show used cpu time (not on Windows 95)
#

show   cputime

#
# Show process information (not on Windows)
#

       process

#
# Show current time
#

       time

#
# Show save status (if program needs saving of structure
# before exit)
#

show   savestatus


# These commands return values which can be used as input to new commands.

#
# Return a value showing the user if the graphics is available
# Return value == 0 means no graphics, != 0 means X-Windows is on
#

       graphics

#
# Return redisplay method (returns slow or fast).
#

       redisplay

#
# Return molecule stick display line width
#

       mlinewidth

#
# Return directory where the binary files are
#

       bindirectory

#
# Return directory where the data files are
#

       datadirectory

#
# Return directory where the help files are
#

       helpdirectory

#
# Return login directory
#

       homedirectory

#
# Return background colour as a rgb triplet float float float
#

       bgcolour
       bgcolor

#
# Return colour mapping type. The two types are: "texture" (1D texture) and
# "rainbow".
#

       colourmapping
       colormapping

#
# Return distance to near clipping plane
#

       nearplane   step
                   value

#
# Return distance to far clipping plane
#

       farplane    step
                   value

#
# return perspective projection viewing angle
#

       viewangle

#
# Return drawing buffer (back/front)
#

       drawbuffer

#                    
# Return cylinder quality factor
#

       cylinderquality

#
# Return sphere quality factor
#

       spherequality

#
# Return color type (returns either colour or gray)
#

       colourtype
       colortype

#
# Return color mapping (returns either texture or rainbow)
#

       colourmapping
       colormapping

#
# Return a "rainbow" colour from a scale factor (blue ... green ... red)
#

       rainbow Fvalue

#
# Return number of molecular structures defined
#

       molstructures

#
# Return number of atoms in atom structure Istructure
#

       numatoms         Istructureindex

#
# Return atom number for Seg Res Atm
#

       atomnumber       Seg Res Atm Istruct

#
# Return licorice sphere radius
#

       licosphere

#
# Return licorice cylinder radius
#

       licocylinder

#
# Return number of frames in the trajectory file
#

       numframes

#
# Return number of root mean square fluctuation 
# atoms in the list
#

       rmsfluctuation   length

#
# Return root mean square fluctuation (total,x,y,z) for 
# index Irmsfluctuation
#

                         Irmsfluctuation index

#
# Return real atom index from rmsf list for Irmsfatomindex
#

                         atomindex  Irmsfatomindex

#
# Return the system translation state (translation on or off)
# If on the system will be translated around origo
#

       system           translation

#
# Return structure selection status (= 0 , not selected , = 1 , selected)
#

       status IStructureNumber

#
# Show if the selected coordinates are ative or not (returns on or off)
#

       selection

#
# Show ldp status if the LDP plot is on or off
#

       ldpstatus

#
# Show display list usage status (0 = not in use/1 = in use)
#

       displaylists

#
# Return a display list type name list
#

       displaylists types

#
# Show type specific display list usage status
# (0 = not in use/1 = in use)
#

       displaylists default
       displaylists TypeName

#
# For Iatomindex in Istructureindex:
#
# Return segment, residue and atom names 
#        residue number
#        coordinates (x y z)

       atom   segmentname    Iatomindex Istructureindex
              residuename    Iatomindex Istructureindex
              atomname       Iatomindex Istructureindex
              resnumber      Iatomindex Istructureindex
              coordinates    Iatomindex Istructureindex

# Return atom partial charge
#        nuclear charge
#        covalent radius
#        B value
#        gbasis set

              charge         Iatomindex Istructureindex
              nuclearcharge  Iatomindex Istructureindex
              covar          Iatomindex Istructureindex
              bvalue         Iatomindex Istructureindex
              gbasis         Iatomindex Istructureindex

# Return bond list
#        hydrogen bond list

              connectivity   Iatomindex Istructureindex
              hbconnectivity Iatomindex Istructureindex

# atom display state
#
# Return atom display  state (0 = atom will not be shown, 1 = will be shown)
#        atom cpk      state (0 = cpk not be shown,       1 = will be shown)
#        atom cpk      scale
#        atom licorice state (0 = licorice not be shown,  1 = will be shown)
#        atom colour

              displaystate   Iatomindex Istructureindex
              cpkstate       Iatomindex Istructureindex
              cpkscale       Iatomindex Istructureindex
              licoricestate  Iatomindex Istructureindex
              colour         Iatomindex Istructureindex
              color          Iatomindex Istructureindex

# atom parameter file data connected to an atom
#
# Return atom type number
#        bonding radius
#        van der Waals spheres radius
#        sphere radius
#        value used in global search for bonds
#        value (emin,rmin) used in the calculation of
#          van der Waals and electrostatic energy
#        atom polarizabilities
#        hydrogen bond identity
#          acceptor            (A)
#          donor               (D,E)
#          not hydrogen bonded (N)
#        CHARMm atom type

              type           Iatomindex Istructureindex
              bnd            Iatomindex Istructureindex
              vdw            Iatomindex Istructureindex
              plu            Iatomindex Istructureindex
              global         Iatomindex Istructureindex
              rmin           Iatomindex Istructureindex
              emin           Iatomindex Istructureindex
              patom          Iatomindex Istructureindex
              mass           Iatomindex Istructureindex
              cnct           Iatomindex Istructureindex
              hbond          Iatomindex Istructureindex
              atype          Iatomindex Istructureindex

# Return atom force
#        atom velocity

              force          Iatomindex Istructureindex
              velocity       Iatomindex Istructureindex

# general data
#
# Return cross length used for atom display
#        atom neighbour search window in atoms
#        atom selection mode (residue/atom)
#        atom reconnectivity
#          0 = bonds are not recalculated between frames
#          1 = bonds are recalculated between frames
#        atom hydrogen bond reconnectivity
#        maximum number of connections (bonds) an atom can have

              cross
              window
              selection
              reconnectivity
              hbreconnectivity
              maxconnectivity

# Return list of atom symbol name, element index, colour,
# basis set and covar radius.

              info           AtomName


#
# show atom identify stage on/off (1/0)
#

              identify

#
# Show atom structure related information
#
# Return number of atom structures
# For Istructureindex,
# return number of atom in the structure
#        structure filename
#        strucrure name
#        

              structure define
                        atoms    Istructureindex
                        filename Istructureindex
                        name     Istructureindex
#
# show bond style (smooth/half)
#

       bondstyle

#
# Show various contour related information
#
# Return number of contours
# For Icontourindex,
# return contour file name
#        contour name
#        header information (xdim ydim zdim xmin xmax ymin ymax zmin zmax)
#        cell dimension (xmin xmax ymin ymax zmin zmax xdim ydim zdim)
#          where the xdim, ydim and zdim are the number of points in
#          the x, y and z direction.
#        number of levels
#        contour type
#        contour transparency
#        minimum and maximum values for the contour data
#        show display state
#        smoothing state (1 = on , 0 = off)
#        structure the contour is combined (glued) to
#        mapping
#          {ContourName 0} if not mapped
#          {ContourName n min_1 max_1 min_2 max_2 ... min_n max_n}
#          where n is the number of levels if mapped
#  

       contour          defined
                        filename     Icontourindex
                        name         Icontourindex
                        header       Icontourindex
                        cube         Icontourindex
                        cell         Icontourindex
                        levels       Icontourindex
                        type         Icontourindex
                        transparency Icontourindex
                        minimum      Icontourindex
                        maximum      Icontourindex
                        display      Icontourindex
                        smooth       Icontourindex
                        structure    Icontourindex
                        mapping      Icontourindex

#
# Return contour level cullface state (on, off)
#                      value (value red green blue)
#

                        values       IContour IContourLevel
                        cullface     IContour IContourLevel

#
# Show a direction of clip plane normal of a line type contour.
# Can be x, y or z.
# Show a position of clip plane of a line type contour on the axis.
#

                         clipplane direction IContour IContourLevel
                                   position  IContour IContourLevel

#
# It is possible to extract the polygon data from the last
# displayed surface(s) using the polygon command.
# The first command gives the number of polygons (triangles)
# and the second gives:
# x1,y1,z1,nx1,ny1,nz1,x2,y2,z2,nx2,ny2,nz2,x3,y3,z3,nx3,ny3,nz3,
# c1,c2,c3
# where xi,yi,zi are the corned points of the triangle,
# nxi,nyi,nzi are the surface normals at the corners and
# c1, c2 and c3 are a colour value between 0.0 and 1.0,
# which goes from blue to red through green. The entry number
# EntryIndex is the index to the data structure.
# The method option gives either direct or save
# where direct means that the polygons are are not saved
# and save means that the polygons are saved to be retried
# using the data option 
#

                         polygon   entries         IContourLevel IContour
                                   data     IEntry IContourLevel IContour
                                   method

#
# Show cutplane properties
#
# shows cutplane smoothing for the yz, xz and xy planes
#                damping or the constant with which the value between 0.0 and 1.0 
#                is multiplied
#                type returns the current type for the yz, xz and xy planes.
#                The return value can be 2d or 3d.
#                xyzN return xyz clipping plane state
#

       cutplane         smooth   yz
                                 xz
                                 xy
                        damping
                        type
                        xyz1
                        xyz2
                        xyz3

#
# Return cell colour
#             dimensions (a b c alpha beta gamma)
#             line width in pixels
#             translation or position (x y z)
#

       cell              colour
                         color
                         dimensions
                         linewidth
                         translation
                         position

#
# Return Gaussian basis sets
#                 tag name for Ivalue index
#                 entry    for Ivalue index
#

       gbasis           sets
                        tag       Ivalue
                        entry     Ivalue

#
# Display information about plumbers.
#  Show total number of plumbers
#  Show plumber display state (0 = off, 1 = on)
#  Show plumber colour (three floats, red, green and blue)
#  Show index of structure to which the plumber is tied to
#  Show indeces of plumber atoms (comma separated range list, empty
#      list for unglued plumbers)
#  Show plumber type (one of ribbon, tube, fhelix, shelix, arrow,
#      strand, trace)
#

       plumber           count
                         dislaystate
                         colour       IPlumber
                         color        IPlumber
                         structure    IPlumber
                         atoms        IPlumber
                         type         IPlumber

#
# Return material specular
# Return material shininess
#

       material         specular   red
                                   green
                                   blue
                        shininess

#
# Return light diffuse
# Return light position (result will be one of c, n, ne, e, se, s, sw, w, nw)
#

       light            diffuse   red
                                  green
                                  blue
                        position

#
# Return monitor distance state 
#                         colour for Index
#        list of atoms defining the list
#        number of distance time series
#
 
       monitor          distance  state
                                  colour Index
                                  color  Index
                                  type    Index
                                  list
                                  timeseries

#
# Return monitor angle    state 
#                         colour for Index
#        list of atoms defining the list
#        number of distance time series
#

       monitor          angle     state
                                  colour Index
                                  color  Index
                                  type    Index
                                  list
                                  timeseries

#
# Return monitor torsion  state 
#                         colour for Index
#        list of atoms defining the list
#        number of distance time series
#

       monitor          torsion   state
                                  colour Index
                                  color  Index
                                  type    Index
                                  list
                                  timeseries

#
# Display text stack containing all printed messages.
#

       output

#
# Return radial distribution function
# calculate and return average from collected entries
# return number of discrete observations (bins)
# return status

       rdf               average
                         observations
                         points
                         status

#
# Return number of trajectory frames
# return status value to see if there is a trajectory defined
# return trajectory file name
# return trajectory file type string
# return trajectory display parameters (first frame, last frame, step frame)
# return number of current displayed frame
# display frame number (on) or turn frame number display off
# return fast (0) or slow (1) retrieve mode for formatted trajectory files
#

       trajectory       frames
                        defined
                        filename                         
                        type
                        display
                        current
                        fid
                        action

#
# Return the Gromos96 coordinate amplifier with which the coordinate
# values will be multiplied
#

       gromos96          coordamplifier

#
# Return number of trace sets defined
#

       traces

#
# Return rotations state
#

       rotation         state

#
# Return translation array (x, y , z) and state  (1 == on , 0 == off)
#

       translation      array
                        state 

#
# Return scaling type applied. It is possible to scale local
# objects and thus break the chemistry/physics. This can be used purely
# for display purposes. 
# The scaling states are: "global" apply same scaling to all objects
#                         "local" the scaling is applied only on 
#                         the selected objects
#

       scaling           type

#
# Show the used projection method
# 0 = perspective
# 1 = orthographic
#

        projection

#
# Show window style. Result is either single or multi.
# Show window defined. Result is currently active/defined number of windows.
# Show window redraw/update method. Result is either automatic or manual.
# Show window parameters for window WinID.
# Returns a four item list of the window location (x, y) and
# window width and height.
#

        window    style
                  defined
                  redraw
                  update
                  parameters WinID

#
# Show pairwise (crossedeye stereo) parameters
# status returns either "on" or "off" depending on if the display is on or off
# angle returnes the angle in which the pair is "tilted"
# distance gives the distance with which the pair is translated to each other
#

       spair      angle
                  distance
                  state

#
# Hardware stereo is currently available only on a small number
# of display devices. Inside gOpenMol it's called quadstereo.
#
# Angle is the half angle with which the structures are tilted.
# State gives the status of the quadstereo. The return values are
# "on" and "off".
# Available gives a value "1" if hardware stereo is availabel and 
# "0" if it is not.
# 

       quadstereo angle
                  state
                  available

#
#
# show global text string
#

       gtext

#
# show gopenmol release
#

       release

#
# show gopenmol version
#

       version

#
# show operating system name
#

       os

#
# display output in widget
#

       output


#
#
#
#

       status struct


#
# 
# show colorscale
#

        cscale     bins
                   mininum
                   maximum
                   state


#
#
# current transformation type (local/global)
#

       transformation    type

#
#
# show atom stack
#

         atom            stack

#
#
# show residue stack
#

         residue         stack

#
#
# show segment stack
#

          segment        stack

#
# show vector info
#

        vector

#
# show cluster status
#

        cluster status

#
# show size of the system
#

        sizeofsystem


**************************************************************************
LUL/2005
**************************************************************************