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 |
Syntax:
Atom atomWithBit ( int bit )
Returns the first Atom in the Model which has the specified value of bit (see the relevant accessor above).
Syntax:
void copy ( Model source )
Copy all information from the source Model into this Model.
Syntax:
void addHydrogen ( )
Hydrogen satisfy all atoms in the model. See the addHydrogen command for more details.
Syntax:
double angleEnergy ( )
Calculates and returns the total angle energy for the current model.
Syntax:
void augment ( )
Automatically detect and add multiple bonds in the system. See the augment command for more details.
Syntax:
double bondEnergy ( )
Calculates and returns the total bond energy (including Urey-Bradley contributions) for the current model.
Syntax:
void charge ( )
Assign charges to the model from the current forcefield. See the chargeFF command for more details.
Syntax:
void clearBonds ( )
Remove all bonds from the model. See the clearBonds command for more details.
Syntax:
void clearCharges ( )
Remove al charges from the model, setting them to zero. See the clearCharges command for more details.
Syntax:
void clearSelectedBonds ( )
Remove all bonds from the current atom selection. See the clearSelectedBonds command for more details.
Syntax:
void copy ( )
Copy the current atom selection to the clipboard. See the copy command for more details.
Syntax:
void cut ( )
Cut the current atom selection to the clipboard. See the cut command for more details.
Syntax:
void delete ( )
Delete the current atom selection. See the delete command for more details.
Syntax:
double elecEnergy ( )
Calculates and returns the total electrostatic energy for the current model, using the calculation method specified in the preferences.
Syntax:
void expand ( )
Expand the current atom selection along bonds. See the expand command for more details.
Syntax:
void finalise ( )
Finalise the current model. See the finaliseModel command for more details.
Syntax:
double interEnergy ( )
Calculates and returns the total intermolecular (i.e. combined van der Waals and electrostatic) energy for the current model.
Syntax:
double intraEnergy ( )
Calculates and returns the total intramolecular (i.e. combined bond, angle, and torsion) energy for the current model.
Syntax:
int isPeriodic ( )
Returns 1 if the model has some kind of unit cell, or 0 if it is non-periodic.
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.
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.
Syntax:
void mirrorSelection ( string axis )
Mirror the current atom selection in the model in the specified plane about its geometric centre.
Syntax:
void movePen ( double dx, double dy, double dz )
Move the drawing pen by the specified distances.
Syntax:
void moveToEnd ( )
Move the current atom selection to the bottom (highest IDs) of the atom list. See the moveToEnd command for more details.
Syntax:
void moveToStart ( )
Move the current atom selection to the top (lowest IDs) of the atom list. See the moveToStart command for more details.
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.
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.
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.
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.
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.
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.
Syntax:
Glyph newGlyph ( string style, string options = "" )
Create a new glyph in the model. See the newGlyph command for more details.
Syntax:
Grid newGrid ( string name )
Create a new gridh in the model. See the newGrid command for more details.
Syntax:
void paste ( )
Paste the current clipboard contents into the model. See the paste command for more details.
Syntax:
void rebond ( )
Calculate bonds in the model. See the rebond command for more details.
Syntax:
void rebondPatterns ( )
Calculate bonds within patterns in the model. See the rebondPatterns command for more details.
Syntax:
void rebondSelection ( )
Calculate bonds in the current selection. See the rebondSelection command for more details.
Syntax:
void redo ( )
Redo the last undone change in the model. See the redo command for more details.
Syntax:
void reorder ( )
Reorder atoms so bound atoms have adjacent IDs. See the reorder command for more details.
Syntax:
void resetPen ( )
Resets the pen coordinates for the model to {0,0,0}.
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.
Syntax:
void rotatePenX ( double delta )
Rotate the drawing pen for the current model delta degrees about the X axis.
Syntax:
void rotatePenY ( double delta )
Syntax:
void rotatePenZ ( double delta )
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.
Syntax:
void selectAll ( )
Select all atoms in the model. See the selectAll command for more details.
Syntax:
void selectionAddHydrogen ( )
Hydrogen satisfy all atoms in the current selection. See the selectionAddHydrogen command for more details.
Syntax:
void selectNone ( )
Deselect all atoms in the model. See the selectNone command for more details.
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.
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.
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.
Syntax:
void showAll ( )
Unhides any hidden atoms in the model. See the showAll command for more details.
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.
Syntax:
double torsionEnergy ( )
Calculates and returns the total torsion energy (including improper terms) for the current model.
Syntax:
void transmute ( int|string el )
Transmute all selected atoms to the specified element. See the transmute command for more details.
Syntax:
void undo ( )
Undo the last change made to the model. See the undo command for more details.
Syntax:
double vdwEnergy ( )
Calculates and returns the total van der Waals energy for the current model.