The Model type contains all the information describing a single model within Aten, including bonds, grid data, measurements, etc..

Member Type RW Description
angles Measurement[] List of current angle measurements in the model
atoms Atom[] Array of atoms in the model
bonds Bond[] Array of bonds defined in the model
cell UnitCell The model’s unit cell
componentDensity double Requested density of the model
componentPartition int The integer index of the partition which this model will be added to in the disordered builder
componentPolicy string Insertion policy for this model
componentPopulation int The number of times this model will be added to the specified partition in the disordered builder
distances Measurement[] List of current distance measurements in the model
eigenvectors Eigenvector[] List of current eigenvectors stored in the model
energy EnergyStore The model’s energy store, containing the total calculated energy and all associated contributions
ff Forcefield Forcefield associated to the model (if any)
ffAngles FFBound[] List of unique forcefield angle terms in the model
ffBonds FFBound[] List of unique forcefield bond terms in the model
ffMass double Forcefield mass of the current model, which can differ from the actual mass if united-atom types have been assigned
ffTorsions FFBound[] List of unique forcefield torsion terms in the model
ffTypes FFAtom[] Array of unique atom types used in the model
frame Model The current frame in the model's trajectory (if it has one)
frames Model[] Array of trajectory frame pointers (only if the trajectory is cached)
glyphs Glyph[] List of glyphs owned by the model
grids Grid[] List of grids owned by the model
id int The index of the model in Aten's internal list of loaded models
mass double Mass of the current model
name string Name of the model
nAngles int Number of angle measurements in the model
nAtoms int Number of atoms in the model
nBasisCartesians int Number of cartesian basis functions defined in stored basis shells
nBasisShells int Number of basis shells defined in the model
nBonds int Number of bonds in the model
nDistances int Number of distance measurements in the model
nFFAngles int Number of unique angle terms used in the model
nFFBonds int Number of unique bond terms used in the model
nFFTorsions int Number of unique torsion terms used in the model
nFFTypes int Number of unique atom types used in the model
nFrames int Number of frames in associated trajectory
nGlyphs int Number of glyphs owned by the model
nGrids int Number of grids owned by the model
nPatterns int Number of patterns defined for the model
nSelected int Number of atoms selected in the model
nTorsions int Number of torsion angle measurements in the model
nUnknown int Number of atoms in the model that are of unknown element
patterns Pattern[] Array of patterns currently defined for the model
selection Atom[] A list of atoms in representing the current atom selection of the model
torsions Measurement[] List of current torsion angle measurements in the model

Model Type Functions

atomWithBit

Syntax:

Atom atomWithBit ( int bit )

Returns the first Atom in the Model which has the specified value of bit (see the relevant accessor above).


copy

Syntax:

void copy ( Model source )

Copy all information from the source Model into this Model.


addHydrogen

Syntax:

void addHydrogen ( )

Hydrogen satisfy all atoms in the model. See the addHydrogen command for more details.


angleEnergy

Syntax:

double angleEnergy ( )

Calculates and returns the total angle energy for the current model.


augment

Syntax:

void augment ( )

Automatically detect and add multiple bonds in the system. See the augment command for more details.


bondEnergy

Syntax:

double bondEnergy ( )

Calculates and returns the total bond energy (including Urey-Bradley contributions) for the current model.


charge

Syntax:

void charge ( )

Assign charges to the model from the current forcefield. See the chargeFF command for more details.


clearBonds

Syntax:

void clearBonds ( )

Remove all bonds from the model. See the clearBonds command for more details.


clearCharges

Syntax:

void clearCharges ( )

Remove al charges from the model, setting them to zero. See the clearCharges command for more details.


clearSelectedBonds

Syntax:

void clearSelectedBonds ( )

Remove all bonds from the current atom selection. See the clearSelectedBonds command for more details.


copy

Syntax:

void copy ( )

Copy the current atom selection to the clipboard. See the copy command for more details.


cut

Syntax:

void cut ( )

Cut the current atom selection to the clipboard. See the cut command for more details.


delete

Syntax:

void delete ( )

Delete the current atom selection. See the delete command for more details.


elecEnergy

Syntax:

double elecEnergy ( )

Calculates and returns the total electrostatic energy for the current model, using the calculation method specified in the preferences.


expand

Syntax:

void expand ( )

Expand the current atom selection along bonds. See the expand command for more details.


finalise

Syntax:

void finalise ( )

Finalise the current model. See the finaliseModel command for more details.


interEnergy

Syntax:

double interEnergy ( )

Calculates and returns the total intermolecular (i.e. combined van der Waals and electrostatic) energy for the current model.


intraEnergy

Syntax:

double intraEnergy ( )

Calculates and returns the total intramolecular (i.e. combined bond, angle, and torsion) energy for the current model.


isPeriodic

Syntax:

int isPeriodic ( )

Returns 1 if the model has some kind of unit cell, or 0 if it is non-periodic.


matrixConvertSelection

Syntax:

void matrixConvertSelection ( int _isx, int _jsx, int _isy, int _jsy, int _isz, int _jsz, int _itx, int _jtx, int _ity, int _jty, int _itz, int _jtz )

void matrixConvertSelection ( int _isx, int _jsx, int _isy, int _jsy, int _isz, int _jsz, int _itx, int _jtx, int _ity, int _jty, int _itz, int _jtz, double ox, double oy, double oz )

void matrixConvertSelection ( double _sax, double _say, double _saz, double _sbx, double _sby, double _sbz, double _scx, double _scy, double _scz, double _tax, double _tay, double _taz, double _tbx, double _tby, double _tbz, double _tcx, double _tcy, double _tcz )

void matrixConvertSelection ( double _sax, double _say, double _saz, double _sbx, double _sby, double _sbz, double _scx, double _scy, double _scz, double _tax, double _tay, double _taz, double _tbx, double _tby, double _tbz, double _tcx, double _tcy, double _tcz, double ox, double oy, double oz )

Performs a matrix conversion on the current atom selection of the model. See the matrixConvert() function reference for a full description.


matrixTransformSelection

Syntax:

void matrixTransformSelection ( double ax, double ay, double az, double bx, double by, double bz, double cx, double cy, double cz )

void matrixTransformSelection ( double ax, double ay, double az, double bx, double by, double bz, double cx, double cy, double cz, double ox, double oy, double oz )

Performs a matrix transformation on the current atom selection of the model. See the matrixTransform() function reference for a full description.


mirrorSelection

Syntax:

void mirrorSelection ( string axis )

Mirror the current atom selection in the model in the specified plane about its geometric centre.


movePen

Syntax:

void movePen ( double dx, double dy, double dz )

Move the drawing pen by the specified distances.


moveToEnd

Syntax:

void moveToEnd ( )

Move the current atom selection to the bottom (highest IDs) of the atom list. See the moveToEnd command for more details.


moveToStart

Syntax:

void moveToStart ( )

Move the current atom selection to the top (lowest IDs) of the atom list. See the moveToStart command for more details.


newAtom

Syntax:

Atom newAtom ( int|string el, double x = 0.0, double y = 0.0, double z = 0.0, double vx = 0.0, double vy = 0.0, double vz = 0.0, double fx = 0.0, double fy = 0.0, double fz )

Create a new atom in the model. See the newAtom command for more details.


newAtomFrac

Syntax:

Atom newAtomFrac ( int|string el, double x, double y, double z, double vx = 0.0, double vy = 0.0, double vz = 0.0, double fx = 0.0, double fy = 0.0, double fz )

Create a new atom in the model, in fractional coordinates. See the newAtomFrac command for more details.


newBasisShell

Syntax:

BasisShell newBasisShell ( Atom|int i, string type )

Create a new basis shell definition in the model, centred on the specified atom/id, and of the given shell type. See the newBasisShell command for more details.


newBond

Syntax:

Bond newBond ( Atom|int i, Atom|int j, string|int bondtype = "" )

Create a new bond between atoms in the model. See the newBond command for more details.


newBondId

Syntax:

Bond newBondId ( int _idi, int _idj, string|int bondtype = "" )

Create a new bond between atom IDs in the model. See the newBond command for more details.


newEigenvector

Syntax:

Eigenvector newEigenvector ( int size = (auto) )

Create a new eigenvector in the model of the specified size. If the size is not specified, the vector length is set to match the number of cartesian basis functions store with the current basis shell definitions in the model. See the newEigenvector command for more details.


newGlyph

Syntax:

Glyph newGlyph ( string style, string options = "" )

Create a new glyph in the model. See the newGlyph command for more details.


newGrid

Syntax:

Grid newGrid ( string name )

Create a new gridh in the model. See the newGrid command for more details.


paste

Syntax:

void paste ( )

Paste the current clipboard contents into the model. See the paste command for more details.


rebond

Syntax:

void rebond ( )

Calculate bonds in the model. See the rebond command for more details.


rebondPatterns

Syntax:

void rebondPatterns ( )

Calculate bonds within patterns in the model. See the rebondPatterns command for more details.

rebondSelection

Syntax:

void rebondSelection ( )

Calculate bonds in the current selection. See the rebondSelection command for more details.


redo

Syntax:

void redo ( )

Redo the last undone change in the model. See the redo command for more details.


reorder

Syntax:

void reorder ( )

Reorder atoms so bound atoms have adjacent IDs. See the reorder command for more details.


resetPen

Syntax:

void resetPen ( )

Resets the pen coordinates for the model to {0,0,0}.


reorientSelection

Syntax:

void reorientSelection ( Atom|int _isx, Atom|int _jsx, Atom|int _isy, Atom|int _jsy, Atom|int _isz, Atom|int _jsz, double _tax, double _tay, double _taz, double _tbx, double _tby, double _tbz, double _tcx, double _tcy, double _tcz )

void reorientSelection ( Atom|int _isx, Atom|int _jsx, Atom|int _isy, Atom|int _jsy, Atom|int _isz, Atom|int _jsz, double _tax, double _tay, double _taz, double _tbx, double _tby, double _tbz, double _tcx, double _tcy, double _tcz, double ox, double oy, double oz )

Operates in exactly the same manner as matrixTransformSelection() except that the source matrix is defined from atoms (or their IDs) and the destination matrix is provided as a matrix.


rotatePenX

Syntax:

void rotatePenX ( double delta )

Rotate the drawing pen for the current model delta degrees about the X axis.


rotatePenY

Syntax:

void rotatePenY ( double delta )

Rotate the drawing pen for the current model delta degrees about the Y axis.

rotatePenZ

Syntax:

void rotatePenZ ( double delta )

Rotate the drawing pen for the current model delta degrees about the Z axis.

saveBitmap

Syntax:

void saveBitmap ( string format, string filename, int width = (auto), int height = (auto), int quality = 100 )

Save a bitmap image of the current model view. See the saveBitmap command for more details.


selectAll

Syntax:

void selectAll ( )

Select all atoms in the model. See the selectAll command for more details.


selectionAddHydrogen

Syntax:

void selectionAddHydrogen ( )

Hydrogen satisfy all atoms in the current selection. See the selectionAddHydrogen command for more details.


selectNone

Syntax:

void selectNone ( )

Deselect all atoms in the model. See the selectNone command for more details.


selectTree

Syntax:

int selectTree ( Atom i, Bond exclude = NULL )

Select all atoms from atom i reachable by following any number of chemical bonds. See the selectNone command for more details.


shiftDown

Syntax:

void shiftDown ( int n = 1 )

Shift the current atom selection down one (or more) places in the atom list (towards higher IDs). See the shiftDown command for more details.


shiftUp

Syntax:

void shiftUp ( int n = 1 )

Shift the current atom selection up one (or more) places in the atom list (towards lower IDs). See the shiftUp command for more details.


showAll

Syntax:

void showAll ( )

Unhides any hidden atoms in the model. See the showAll command for more details.


toAngstroms

Syntax:

void toAngstroms ( )

Converts cell specification and atomic coordinates in the model from (assumed units of) Bohr into Angstroms. No changes to associated trajectory frames or grid data is made.


torsionEnergy

Syntax:

double torsionEnergy ( )

Calculates and returns the total torsion energy (including improper terms) for the current model.


transmute

Syntax:

void transmute ( int|string el )

Transmute all selected atoms to the specified element. See the transmute command for more details.


undo

Syntax:

void undo ( )

Undo the last change made to the model. See the undo command for more details.


vdwEnergy

Syntax:

double vdwEnergy ( )

Calculates and returns the total van der Waals energy for the current model.