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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.


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