- molecule()
-
Creates a new instance of a molecule object and returns a reference to it.
Note: To obtain object references to molecules already loaded into VIEWMOL
use the
getMolecules
function of the viewmol
module.
- translate(x, y, z)
-
Translates (shifts) molecule by x, y, and z along
the x, y, and z axis, respectively. x, y, and z
have to be integers and are measured in pixels of the screen.
- rotate(x, y, z)
-
Rotates molecule by x, y, and z about x, y, and
z axis, respectively. x, y, and z have to be
integers and are measured in degrees.
- getSpectrum()
-
Creates a new instance of a spectrum object and returns a reference to it
if there is spectral information associated with this molecule.
- getEnergyLevels()
-
Creates a new instance of an energy level object and returns a reference to it
if there is information about energy levels associated with this molecule.
- getHistory()
-
Creates a new instance of a history object and returns a reference to it if
there is information about the optimization history associated with this molecule.
- showForces(status)
-
Sets the display of forces for all molecules to status. status has to
be one of the integer constants
ON
or OFF
defined in the
viewmol
module.
- getAtoms()
-
Returns a list containing references to all atom objects the molecule is composed
off.
- getBonds()
-
Returns a list of tupels describing all bonds in the molecule. The tupels consists
of three integers
(atom1, atom2, order)
where atom1
and atom2
are the indices of the two atoms forming the bond and order
is the bond order.
The bond order can be one of the constants HYDROGENBOND, CONJUGATED, SINGLE, DOUBLE
,
or TRIPLE
for hydrogen/Van der Waals, conjugated, single, double, and triple
bonds, respectively. These constants are defined in the molecule
module.
- getWavenumbers()
-
Returns a list of tupels describing all wave numbers of the molecule. The tupel
consists of four floats and one string
(waveNumber, IRIntensity,
RamanIntensity, INSIntensity, symmetry)
where waveNumber
is the
wave number in cm-1, IRIntensity
, RamanIntensity
,
and INSIntensity
are the IR, Raman, and inelastic neutron scattering intensities in
per cent, and symmetry
is a label describing the symmetry of the mode.
- getMOEnergies()
-
Returns a list of tupels providing information about all molecular orbitals of the
molecule. The tupel consists of two floats, one integer, and one string
(energy, occupation, spin, symmetry)
where energy
is the energy of the molecular orbital in Hartrees, occupation
is the number of electrons in this orbital, spin
in one of the constants
ALPHA+BETA, ALPHA
, or BETA
describing what spin has been assigned
to this orbital, and symmetry
is a label describing the symmetry of the
molecular orbital. The constants are defined in the molecule
module.
- title([title])
-
Sets or returns the title of a molecule. title has to be a string. The
maximum length of the title is limited to 255 characters.
- bondAverage(atom)
-
Returns the average of the lengths of all bonds involving atom atom in
Ångstrøms. atom is an atom object.
- bondLength(atom1, atom2, [length, unit])
-
Returns or sets the length of the bond between atoms atom1 and atom2.
atom1 and atom2 have to be atom objects, the bond length is returned in
Ångstrøms. If length and unit are given, the bond length is set.
length is a double, unit a string containing either
Ang
, au
or
bohr
, or pm
for Ångstrøms, atomic units, or picometers. Everything
else is interpreted as Ångstrøms.
- bondAngle(atom1, atom2, atom3, [angle])
-
Returns or sets the bond angle atom1-atom2-atom3. atom1,
atom2, atom3 are atom objects. If angle is given the bond angle is set.
angle has to be a double and is measured in degrees.
- torsionAngle(atom1, atoms2, atom3, atom4, [torsionAngle])
-
Returns or sets the torsion angle atom1-atom2-atom3-atom4.
atom1, atom2, atom3, atom4 are atom objects. If torsionAngle
is given the torsion angle is set. torsionAngle has to be a double and is measured
in degrees.
- getThermodynamics(property, type)
-
Returns a thermodynamical property of the molecule. property and type are
integers. property can be one of the integer constants
ENTHALPY
, ENTROPY
,
GIBBS_ENERGY
, or HEAT_CAPACITY
defined in the molecule
module.
type can be one of the integer constants TRANSLATION
, PV
, ROTATION
,
VIBRATION
, or TOTAL
also defined in the molecule
module. The
returned thermodynamic property will be in SI units.
- reaction([side])
-
Sets or returns whether the molecule is a reactant or a product in a reaction. side
is an integer and can be set to one of the integer constants
REACTANT
, PRODUCT
,
or ALLREACTIONS
defined in the molecule
module.
- showElectrons(type, [gridResolution, interpolation])
-
Displays wave function related properties of the molecule. type is an integer and can
be set to one of the integer constants
BASIS_FUNCTION
, BASIS_IN_MO
,
MO
, or DENSITY
defined in the molecule
module.
gridResolution is a double specifying the resolution of the grid used to calculate
the isosurface. Larger values for gridResolution result in smoother displays.
interpolation is an optional integer and can be one of the integer constants
IP_NONE
(no interpolation), IP_LINEAR
(linear interpolation), or IP_LOG
(logarithmic interpolation) defined in the molecule
module.
- showGrid(which, [interpolation])
-
Displays a property which has been read as a grid. which is an integer between
1 and the number of grids which have been read for this molecule and identifies the
grid to be shown. interpolation is an optional integer and can be one of the
integer constants
IP_NONE
(no interpolation), IP_LINEAR
(linear
interpolation), or IP_LOG
(logarithmic interpolation) defined in the molecule
module.
- selectBasisfunction(atom, name, count)
-
Selects a basis function for display. atom is an atom object specifying which atom
the basis function belongs to. name is a string specifying what kind of basis
function (s, p, d, etc.) to select. count is an integer specifying which of the
s, p, d, etc. functions to select. Assume atom 1 is a carbon atom in a calculation using
a DZVP basis set. It therefore has three s functions.
selectBasisfunction(1, "s", 1)
would select the 1s function, selectBasisfunction(1, "s", 2)
the first 2s
function, and selectBasisfunction(1, "s", 3)
the second 2s function.
- unitCell(visible, [afac, bfac, cfac])
-
Sets visibility and number of replicas of unit cell. visible has to be one of the
integer constants
ON
or OFF
defined in the viewmol
module to turn
display of the unit cell on or off. afac, bfac, and cfac are doubles
specifying the number of replicas of the unit cell to be displayed along the a, b, and
c axis, respectively. Fractions are allowed for afac, bfac, and cfac.
- millerPlane(visible, [h, k, l])
-
Sets visibility and orientation of Miller plane. visible has to be one of the
integer constants
ON
or OFF
defined in the viewmol
module to
turn display of a Miller plane on or off. h, k, and l are integers
specifying the Miller indices of the plane to display.
- addAtom(symbol, [attach])
-
Adds an atom to the molecule. symbol is a string containing the element symbol
of the atom to add. attach is an atom object specifying the atom the newly added
atom should be attached to. attach can be omitted, but this is only useful for
adding the first atom to a molecule.
Jörg-Rüdiger Hill Fri Oct 31 14:19:21 CET 2003