Using molinfo to access information about a molecule

The molinfo command can also be used to access and, in some cases, modify information specific to a given molecule. A query is in the form:

• molinfo molecule_id get {list of keywords}

and the result is a list of elements, one for each keyword.

Examples:
vmd > molinfo top get numatoms
Info) 568
vmd > molinfo 0 get {source filename}
Info) File /home/dalke/pdb/pti.pdb

This next example is a bit more complicated. It loops through all the graphical representation (numreps) and, for each one, gets the representation used (rep), the selection text (selection), and the coloring method (color).

vmd > for {set i 0} {$i < [molinfo top get numreps]} {incr i} {
? lassign [molinfo top get "{rep $i} {selection $i} {color $i}"] a b c
? puts "view $i:"
? puts " representation: $a"
? puts " selection: $b"
? puts " coloring method: $c"
? }
view 0:
 representation: Tube 0.300000 8.000000
 selection: protein backbone
 coloring: method Structure
view 1:
 representation: Lines 2.000000
 selection: same residue as name "S.*"
 coloring: method ResName
view 2:
 representation: VDW 1.000000 6.000000
 selection: name "S.*"
 coloring: method Name

A similar behavior can be achieved by using mol list top , in which case, however, there is no direct access to the data. A complete list of keywords is given in Table 12.1.2.

Table 12.1: molinfo keywords

Keyword	Aliases	Arg	Set	Description
id		int	N	molecular id
index		int	N	index on the molecule list
numatoms		int	N	number of atoms
source		str	N	one of File, Graphics, Remote, or Sigma
name		str	N	the name of the molecule (usually the name of the file)
filename		str	N	full filename (if two files, the topology file)
filetype		str	N	corresponding file type (PSF, PDB, XYZ, ...)
filename2		str	N	full filename of coordinate file (if two files)
filetype2		str	N	corresponding file type (DCD, PDB, XTC, ...)
active		bool	Y	is/make the molecule active
drawn	displayed	bool	Y	is/make the molecule drawn
fixed		bool	Y	is/make the molecule fixed
top		bool	Y	is/make the molecule top
center		vector	Y	get/set the coordinate used as the center
center_matrix		matrix	Y	get/set the centering matrix
rotate_matrix		matrix	Y	get/set the rotation matrix
scale_matrix		matrix	Y	get/set the scaling matrix
global_matrix		matrix	Y	get/set the global (rotation/scaling) matrix
view_matrix		matrix	N	get/set the overall viewing matrix
numreps		int	N	the number of representations
selection i		string	N	the string for the i'th selection
rep i		string	N	the string for the i'th representation
color i	colour	string	N	the string for the i'th coloring method
numframes		int	N	number of animation frames
frame		int	Y	current frame number
bond		float	N	the bond energy (for the current frame)
angle		float	N	the angle energy
dihedral		float	N	the dihedral energy
improper		float	N	the improper energy
vdw		float	N	the van der Waal energy
electrostatic	elec	float	N	the electrostatic energy
hbond		float	N	the hydrogen bond energy
kinetic		float	N	the total kinetic energy
potential		float	N	the total potential energy
energy		float	N	the total energy
temperature	temp	float	N	the overall temperature

The molinfo command, contrary to its name, can also be used to set some keyword values, such as the current frame number and the display state flags. This duplicates some of the functionality of the mol command, though there are distinct differences in the implementation. Specifically, the mol command uses the internal command queue which, among other things, notifies the appropriate forms that a change occured, redraws the graphics, and logs the commands to the log file, of logging is enabled. In future versions of VMD there will be only one command; for now we suggest only using the molinfo command to get information and to set the frame value and the various viewing matrices.

Examples:

Two functions, one to save the current view position, the other to restore it. The position of the axis is not changed by these operations.

proc save_viewpoint {} {
   global viewpoints
   if [info exists viewpoints] {unset viewpoints}
   # get the current matricies
   foreach mol [molinfo list] {
      set viewpoints($mol) [molinfo $mol get {
	center_matrix rotate_matrix scale_matrix global_matrix}]
   }
}
proc restore_viewpoint {} {
   global viewpoints
   foreach mol [molinfo list] {
      puts "Trying $mol"
      if [info exists viewpoints($mol)] {
         molinfo $mol set {center_matrix rotate_matrix scale_matrix
	   global_matrix} $viewpoints($mol)
      }
   }
}

Cycle through the list of displayed molecules, turning each one on one at a time. At the end, return the display flags to their original state.

# save the current display state
foreach mol [molinfo list] {
  set disp($mol) [molinfo $mol get drawn]
}
# turn everything off
mol off all
# turn each molecule on then off again
foreach mol [molinfo list] {
  if $disp($mol) {
     mol on $mol
     sleep 1
     mol off $mol
  }
}
# turn the original ones back on
foreach mol [molinfo list] {
  if $disp($mol) {mol on $mol }
}

The last loop, which turns the originally drawn molecules back on, doesn't turn them on at the same time. That's because some commands (those which use the command queue) redraw the graphics when they are used. This can be disabled with the display update (see section §  for more information). Using this, the final loop becomes

#turn the original ones back on
display update off
foreach mol [molinfo list] {
  if $disp($mol) {mol on $mol }
}
display update on

Alternatively, since the drawn option is settable, you could do:

foreach mol [molinfo list] {
  if $disp($mol) {molinfo $mol set drawn 1}
}

However, that won't set the flag to redraw the scene so you need to force a redraw with display redraw.