molinfo

Table 8.3: 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 is used to get information about a molecule (or loaded file) including the number of loaded atoms, the filename, the graphics selections, and the viewing matrices. It can also be used to return information about the list of loaded molecules.

Each molecule has a unique id, which is assigned to it when it is first loaded. These start at zero and increase by 1 for each new molecule. When a molecule is deleted, the number is not used again. There is one unique molecule, called the top molecule top molecule, which is used to determine some parameters, such as the center of view, the data in the animation form, etc.

• list: Returns a list of all current molecule id's.
• num: Returns the number of loaded molecules.
• top: Returns the id of the top molecule.
• index n: Returns the id of the n'th molecule.
• molecule_id get {list of keywords}
• molecule_id set {list of keywords} {list of values} Access and, in some cases, modify information about a given molecule. The list of recognized keywords is given in Table 8.3.

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