show command
**************************************************************************
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
**************************************************************************