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molinfo


Table 9.3: molinfo set/get 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
name   str N the name of the molecule (usually the name of the file)
filename   str N list of filenames for all files loaded for this molecule
filetype   str N list of file types for this molecule
database   str N list of databases for this molecule
accession   str N list of database accession codes for this molecule
remarks   str N list of freeform remarks for this molecule
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
numvolumedata   int N number of volumetric data sets
frame   int Y current frame number
timesteps   int Y number of elapsed timesteps in an interactive simulation
angles   list Y topology angle types and definitions {type a1 a2 a3}
dihedrals   list Y topology dihedral types and definitions {type a1 a2 a3 a4}
impropers   list Y topology improper types and definitions {type a1 a2 a3 a4}
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
pressure   float Y the simulation pressure
volume   float Y the simulation volume
efield   float Y efield
alpha   float Y unit cell angle alpha in degrees (for the current frame)
beta   float Y unit cell angle beta in degrees (for the current frame)
gamma   float Y unit cell angle gamma in degrees (for the current frame)
a   float Y unit cell length a in Angstroms (for the current frame)
b   float Y unit cell length b in Angstroms (for the current frame)
c   float Y unit cell length c in Angstroms (for the current frame)


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, which is used to determine some parameters, such as the center of view, the data in the animation controls, etc.


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