14.2 Standard commands
These are the VEGA standard commands:
ADDHYDROG (MCHAR)MolType (MCHAR)HPos
(BOOL)IupacNames (BOOL)ActiveOnly
Add the hydrogens to the molecule. If the hydrogens are already present,
they will be removed before the adding procedure.
Parameters: | ||
MolType |
Molecule type. It must be GEN (generic organic), GENBO (generic organic, bond order method), NA (nucleic acid), NABO (nucleic acid, bond order method), PROT (protein) and PROTBO (protein, bond order method). Use the bond order method if the molecule has a 2D/3D structure having bonds with specified order (e.g. single, partial double, double, triple). The standard method doesn't work properly if the molecule structure is distorted or it have two dimensions only. |
|
HPos |
Hydrogen position in the file. It must be HEAVYATM (the hydrogens are placed after each heavy atom) or RESEND (the hydrogens are placed at the end of each residue). |
|
IupacNames |
If it's true (1), IUPAC hydrogens name convention is used. |
|
ActiveOnly |
If it's true (1), the hydrogens are added to active (visible) atom only. |
Return values:
The number of added hydrogens.
Example:
ADDHYDROG GEN RESEND 1 0
See also:
ADDIONS.
ADDIONS (CHAR)Element (INT)Charge
(UINT)Ions (FLOAT)ExclAtomRad (FLOAT)ExclIonRad
(FLOAT)GridStep (FLOAT)BoxThick
With this command is possible to add one or more counter ions to the active
molecule. For more information about the method, please click
here.
Parameters: | ||
Element | Counter ion element (e.g. Na, K, Mg, Cl, etc). | |
Charge | Ion charge (e.g. 1, 2, -1, etc). | |
Ions | Number of ions to add. | |
ExclAtomRad | Atom-ion closest distance. | |
ExclIonRad | Ion/ion closest distance in order to reduce the electrostatic repulsion. | |
GridStep | Grid step to build the grid used to place the ions. | |
BoxThick | Box thickness surrounding the molecule. |
Return values:
Error code if it fails.
Example:
ADDIONS Na 1 5 6.5
11 0.5 10
See also:
ADDHYDROG.
ASSINGBNDORD (BOOL)ActiveOnly
Assign the bond order (single, partial double, double and triple).
Parameters: | ||
ActiveOnly |
If it's true (1), the command assigns the bond order to active atoms only. |
Return values:
Error code if it fails.
Example:
ASSIGNBNDORD 0
See also:
CONNBUILD, CONNDESTROY.
ATMADD
Add a new atom to the current workspace. The atom is placed at (0, 0, 0)
coordinates, the default element is the carbon (C), the atom name is
C,
the residue name is UNK, the residue number is 1, the atom charge is
0, the atom
type is ?, the color is green. To change these default properties see the
ATMSET
command.
Parameters:
None.
Return values:
If the command fails, 0 is returned, otherwise the atom number is returned.
Example:
ATMADD
See also:
ATMBEGINUPDATE,
ATMBOND, ATMDELETE, ATMGET,
ATMSET, ATMENDUPDATE.
ATMBEGINUPDATE
Notify a massive atom update to the system. This command increase the
performance of the subsequent atom commands.
Parameters:
None.
Return values:
Error code if it fails.
Example:
ATMBEGINUPDATE
See also:
ATMADD, ATMGET,
ATMSET, ATMENDUPDATE.
ATMBOND (UINT)AtomNumber1 (UINT)AtmNumber2
(MCHAR)BondOrder
Bond/unbond two atoms or change the bond order.
Parameters: | ||
AtomNumber1 | Number of the first atom. | |
AtomNumber2 | Number of the second atom. | |
BondOrder |
The bond order could be: NONE (unlink the two atoms), SINGLE, PARDOUBLE (partial double bond, aromatic), DOUBLE and TRIPLE. |
Return values:
If the command fails, 0 (false) is returned, otherwise 1 (true) is returned.
Example:
ATMBOND 1 7 NONE
ATMBOND 4 9 SINGLE
ATMBOND 4 9 DOUBLE
See also:
ATMBEGINUPDATE, ATMADD, ATMGET,
ATMENDUPDATE, ATMSET.
ATMDELETE (UINT)AtomNumber (UINT)AtomsToDelete
Delete one or more atoms. The undeleted atom identification number is
automatically renumbered and so the atom IDs could be be the same before the
deletion.
Parameters: | ||
AtomNumber | Number of the first atom to delete. | |
AtomsToDelete | Total number of atoms to delete. |
Return values:
The command returns the number of deleted atoms.
Example:
ATMDELETE 12 1
ATMDELETE 24 9
See also:
ATMBEGINUPDATE, ATMADD,
ATMENDUPDATE.
ATMENDUPDATE
Notify the end of the atom update.
Parameters:
None.
Return values:
Error code if it fails.
Example:
ATMENDUPDATE
See also:
ATMBEGINUPDATE, ATMADD, ATMGET,
ATMSET.
ATMFIND (MCHAR)Mode
(UINT)FirstAtom (CHAR)String
Find an atom by element, atom name and atom type.
Parameters: | ||
Mode | Search mode: ELEM for atom element, NAME for atom name and ATMTYP for atom type. | |
FirstAtom | The first atom from which the search starts. | |
String | String to find. It could be: atom element (1 one or two characters, case insensitive), selection string (in standard VEGA ZZ format with/without wildcards), and atom type. The atom type search can be used only if the force field is applied to the molecule (see FORCEFIELD). |
Return values:
The command returns the atom number of the first atom that satisfy the search
criteria. If no atom is found, 0 is returned.
Example:
ATMFIND ELEM 1 N
ATMFIND NAME 1 C1
ATMFIND NAME 25 CA:ALA
ATMFIND NAME 1 N*:VAL:*:*:1
ATMFIND ATMTYP 1 cp
See also:
ATMGET.
ATMGET (UINT)AtomNumber (MCHAR)Property
Get a property of the specified atom number.
Parameters: | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AtomNumber | Atom number. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Property | Atom property to obtain. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
Return values:
The requested atom property or an error if it fails.
Example:
ATMGET 12 COORD
See also:
ATMBEGINUPDATE, ATMADD,
ATMFIND, ATMSET,
ATMENDUPDATE.
ATMSET (UINT)AtomNumber (MCHAR)Property
(CHAR)Value
Set a property of the specified atom number.
Parameters: | ||
AtomNumber | Atom number. | |
Property | Atom property to obtain. For the property list see the ATMGET command but remember that Connect and NSost are read-only properties and can't be changed with this command. | |
Value | New property value. |
Return values:
Error code if it fails.
Example:
ATMSET 30 COLOR GREEN
See also:
ATMBEGINUPDATE, ATMADD, ATMGET,
ATMFIND,
ATMENDUPDATE.
CHDIR (CHAR)Directory
Change the current directory. Use CURDIR variable to get it.
Parameters: | ||
Directory |
New directory path. |
Return values:
Error code if it fails.
Example:
CHDIR "C:\My Documents\Molecules"
See also:
None.
CHARGE (CHAR)Method (BOOL)ActiveOnly
Assign the atomic partial charges using the specified method. For more information, click here.
Parameters: | ||
Method |
Method to assign the atomic partial charges. You can choose the Gasteiger-Marsili (Gasteiger keyword) method or the fragment/residue based on a pre-computed database of charges (Charmm22_Char or other keywords). |
|
ActiveOnly |
If it's true (1), the force field is assigned only to the active (visible) atoms. If it's false (0), the force field is assigned to all atoms (visible an invisible). |
Return values:
Error code if it fails.
Example:
CHARGE Gasteiger 0
CHARGE Charmm22_Char 1
See also:
FORCEFIELD, mCalcCharge.
CONNBUILD (UINT)Overlap (BOOL)ActiveOnly
Build the connectivity.
Parameters: | ||
Overlap |
Overlapping percentage of covalent radii to consider two bonded atoms. The usual value is 20. |
|
ActiveOnly | If it's true (1), the command calculates the connectivity to active atoms only. |
Return values:
Error code if it fails.
Example:
CONNBUILD 20 0
See also:
ASSIGNBNDORD, CONNDESTROY.
CONNDESTROY (BOOL)ActiveOnly
Destroy the connectivity.
Parameters: | ||
ActiveOnly |
If it's true (1), the command removes the connectivity to active atoms only. |
Return values:
Error code if it fails.
Example:
CONNDESTROY 1
See also:
ASSIGNBNDORD, CONNBUILD.
CPUFINDFILE (CHAR)FileName
Check if the specified executable or DLL file exists and return a new file name
if an executable with better performances is present.
Parameters: | ||
FileName |
Method to assign the atomic partial charges. At the present time, the only supported method is Gasteiger. |
Return values:
An empty string if the file doesn't exist or the executable file name optimized
for the installed CPU.
Example:
CPUFINDFILE BioDock.exe
If your system has got an AMD Athlon and the specific executable is installed,
the command returns BioDock_k7.exe.
See also:
None.
ENEPARGET (CHAR)ParameterKey
(BOOL)DefaultValue
Get a parameter used for the molecular mechanics energy evaluation.
Parameters: | ||
ParameterKey | Name of the parameter. | |
DefaultValue | If it's true (1), the default value is returned, otherwise if it's false (0), the current value is returned. |
Return values:
The value associated to the parameter key.
Example:
ENEPARGET AEXP 0
See also:
ENEPARSET.
ENEPARSET (CHAR)ParameterKey
(CHAR)NewValue
Set a parameter used for
the molecular mechanics energy evaluation.
Parameters: | ||
ParameterKey | Name of the parameter. | |
NewValue | New parameter value. It can be an integer or a floating point number. |
Return values:
Error code if it fails.
Example:
ENEPARSET AEXP 4
See also:
ENEPARGET.
ERRMSG (UINT)ErrorCode
Return the error description (standard C format) from the error code.
Parameters: | ||
ErrorCode |
.Error code. |
Return values:
Error string.
Example:
ERRMSG 201
See also:
MSGERRMODE.
FORCEFIELD (CHAR)Template (BOOL)ActiveOnly
(BOOL)Quiet
Assign the atom types using the specified template. For more information, click here.
Parameters: | ||
Template |
Template name used to assign the atom types. |
|
ActiveOnly |
If it's true (1), the force field is assigned only to the active (visible) atoms. If it's false (0), the force field is assigned to all atoms (visible an invisible). |
|
Quiet |
If it's true, no warning messages are shown if a problem was found during the force field attribution. |
Return values:
Error code if it fails.
Example:
FORCEFIELD CVFF 0 1
See also:
CHARGE, mCalcCharge.
GET (CHAR)Variable
The command GET returns the value of a specific internal variable. The argument name
is case-insensitive and the returned value is always a character string. The result can be
read from clipboard or from Result item of VGP_VEGAINFO structure if the
command is sent by a plugin (see plugin.h). SendVegaCmd
retrieves the result automatically from the clipboard.
If you call the GET command from a plug-in, please use PLUGINGET instead of it.
Standard variables:
Variable | Type | Description |
CPUFEATURES | INT | 32 bit integer containing the CPU features (only for x86 CPUs). |
CPUNAME | CHAR | Installed CPU name. |
CPUS | UINT | Number of the installed CPUs. |
CPUTYPE | CHAR | Type, family, model and stepping of the installed CPU (only for x86 CPUs). |
CPUVENDOR | CHAR | CPU vendor. |
CURDIR | CHAR | Current directory. |
CURLANG | CHAR | Current language for string translation. |
DATADIR | CHAR | Directory path of data files (e.g. templates, preferences, etc). |
ERRCODE | UINT | Last error code. |
ERRSTR | CHAR | Last error string. |
FLEXTOR | UINT | Number of flexible torsions. |
FORMULA | CHAR | Molecular formula |
LASTFILENAME | CHAR | Name of the last loaded file without path and extension. |
MASS | FLOAT | Mass of the molecule in Daltons. |
OS | CHAR | Operating system (e.g. AmigaOS, Linux, Irix, Unix, Windows 95/98/ME, Windows NT/2000/XP). |
OSFAMILY | CHAR | Operating system family (e.g. amigaos, unix, windows). |
PRFLANG | CHAR | Language for string translation in prefs file. |
SAVEDIR | CHAR | Default path for save operations. |
SRFCUR | UINT | Current surface number. |
SRFNAME | CHAR | Name of the current surface. |
SRFTYPE | UINT | Current surface type (0 = dotted/unknown, 1 = mesh, 2 = solid). |
TMPDIR | CHAR | Temporary directory. |
TMPFILE | CHAR | Full path and file name to use as temporary file. |
TOTACTATM | UINT | Total number of active (visible) atoms. |
TOTANG | UINT | Total number of angles. |
TOTATM | UINT | Total number of atoms of the current loaded molecule. |
TOTBOND | UINT | Total number of bonds. |
TOTCHAIN | UINT | Total number of chains. |
TOTIMP | UINT | Total number of improper angles. |
TOTMOL | UINT | Total number of molecules loaded un memory. |
TOTRES | UINT | Total number of residues. |
TOTSEG | UINT | Total number of segments. |
TOTSRF | UINT | Total number of surfaces. |
TOTSRFDOT | UINT | Total number of the current surface dots. |
TOTSRFTRI | UINT | Total number of the current surface triangles. |
TOTTOR | UINT | Total number of torsion angles. |
TRJBESTENERGY | FLOAT | The energy of the best frame in the trajectory file. |
TRJBESTFRM | UINT | The number of the best frame. |
TRJCURFRM | UINT | The current frame number selected in the trajectory. |
TRJSIMTIME | UINT | Length (in ps) of the simulation. |
TRJSTARTTIME | UINT | Start time (ps) of the simulation. |
TRJTEMP | UINT | Simulation temperature (Kelvin). |
TRJTIMESTEP | UINT | Time step. |
TRJTOTFRM | UINT | Total number of frames in the trajectory. |
TRJWORSEENERGY | FLOAT | The energy of the worse frame in the trajectory file. |
TRJWORSEFRM | UINT | The number of the worse frame. |
VEGADIR | CHAR | Directory path where VEGA is installed. |
VERSION | CHAR | Full VEGA version. |
OpenGL variables:
Variable | Type | Description | ||||||||||||||||||||||
BACKCOLOR | UINT | Background color in RGB format. | ||||||||||||||||||||||
CONBUFSIZE | UINT | Console buffer size (lines). | ||||||||||||||||||||||
CONDOCKED | BOOL | True if the console is docked. | ||||||||||||||||||||||
CONHISTSIZE | UINT | Max. number of commands stored in the history buffer. | ||||||||||||||||||||||
CONPOSX | UINT |
X screen position of the console window. If the console is docked, the return value is 0. |
||||||||||||||||||||||
CONPOSY | UINT |
Y screen position of the console window. If the console is docked, the return value is 0. |
||||||||||||||||||||||
CONSIZEX | UINT | Width of the console window. | ||||||||||||||||||||||
CONSIZEY | UINT | Height of the console window. | ||||||||||||||||||||||
CONVISIBLE | BOOL | True if the console is open. | ||||||||||||||||||||||
GLASSWIN | BOOL | True if the glass windows are enabled. | ||||||||||||||||||||||
GLRENDERER | CHAR | OpenGL rendering subsystem (hardware/software). | ||||||||||||||||||||||
GLVENDOR | CHAR | The vendor of the graphic card. | ||||||||||||||||||||||
GLVERSION | CHAR | OpenGL subsystem version. | ||||||||||||||||||||||
GRAPHID | UINT | The ID of the current Graph Editor window | ||||||||||||||||||||||
GRAPHLABELX | CHAR | X axis label. | ||||||||||||||||||||||
GRAPHLABELY | CHAR | Y axis label. | ||||||||||||||||||||||
GRAPHPOINTS | UINT | Number of the points in the current graph. | ||||||||||||||||||||||
GRAPHPOSX | UINT | X screen position of the Graph Editor window. | ||||||||||||||||||||||
GRAPHPOSY | UINT | Y screen position of the Graph Editor window. | ||||||||||||||||||||||
GRAPHSIZEX | UINT | Width of the Graph Editor window. | ||||||||||||||||||||||
GRAPHSIZEY | UINT | Height of the Graph Editor window. | ||||||||||||||||||||||
GRAPHTITLE | CHAR | Chart title. | ||||||||||||||||||||||
GRAPHVISIBLE | BOOL | True if the Graph Editor is open (obsolete, only for backwards compatibility. | ||||||||||||||||||||||
ISRUNNING | BOOL | True if a background calculation is running (e.g. Mopac). | ||||||||||||||||||||||
LIGHT | BOOL | True if the light is enabled. | ||||||||||||||||||||||
LIGHTAMB | BOOL | True if the ambient light is enabled. | ||||||||||||||||||||||
LIGHTAMBCOLOR | UINT | Ambient light color. | ||||||||||||||||||||||
LIGHTCUR | UINT | Number of the current light source (from 0 to 3). | ||||||||||||||||||||||
LIGHTCURDIFCOL | UINT | Diffuse color of the current light source. | ||||||||||||||||||||||
LIGHTCUREN | BOOL | True if the current light source is enabled. | ||||||||||||||||||||||
LIGHTCURSPECCOL | UINT | Specular color of the current light source. | ||||||||||||||||||||||
LIGHTCURPOS | CHAR | Position of the current light source. It's a string containing a vector (X, Y, Z coordinates). | ||||||||||||||||||||||
LOGOPOS | UINT | Position of the VEGA ZZ superimposed logo:
|
||||||||||||||||||||||
LOGOSCALE | FLOAT | Scale factor of the VEGA ZZ superimposed logo (default 0.5). | ||||||||||||||||||||||
MAINSIZEX | UINT | Width of the main window. | ||||||||||||||||||||||
MAINSIZEY | UINT | Height of the main window. | ||||||||||||||||||||||
MAINPOSX | UINT | X screen position of the main window. | ||||||||||||||||||||||
MAINPOSY | UINT | Y screen position of the main window. | ||||||||||||||||||||||
MATSHINY | UINT | Material shininess. | ||||||||||||||||||||||
MATSPECULAR | UINT | Material specularity. | ||||||||||||||||||||||
MATVECTSPEC | BOOL | True if the vector specularity is enabled. | ||||||||||||||||||||||
MSAA | UINT | Current multisample anti-aliasing value (0-16x, 0 = disabled). | ||||||||||||||||||||||
PORTNUM | UINT | Communication port number. | ||||||||||||||||||||||
ROTX | FLOAT | X rotation of the scene (degree). | ||||||||||||||||||||||
ROTY | FLOAT | Y rotation of the scene (degree). | ||||||||||||||||||||||
ROTZ | FLOAT | Z rotation of the scene (degree). | ||||||||||||||||||||||
SCALE | FLOAT | Visualization scale. | ||||||||||||||||||||||
SCREENDEPTH | UINT | Screen depth in bit per pixel. | ||||||||||||||||||||||
SCREENX | UINT | Screen width. | ||||||||||||||||||||||
SCREENY | UINT | Screen height. | ||||||||||||||||||||||
SKYBOXENABLED | BOOL | True if the SkyBox/SkyVision is enabled. | ||||||||||||||||||||||
SKYBOXNAME | CHAR | Name of the current SkyBox. | ||||||||||||||||||||||
SKYBOXOFFSETX | FLOAT | SkyBox X offset. | ||||||||||||||||||||||
SKYBOXOFFSETY | FLOAT | SkyBox Y offset. | ||||||||||||||||||||||
SKYBOXROTX | FLOAT | SkyBox X rotation (degree). | ||||||||||||||||||||||
SKYBOXROTY | FLOAT | SkyBox Y rotation (degree). | ||||||||||||||||||||||
SKYBOXROTZ | FLOAT | SkyBox Z rotation (degree). | ||||||||||||||||||||||
SOUNDEFFECTS | BOOL | True if the sound effects are enabled. | ||||||||||||||||||||||
SRFALPHA | BOOL | Check if the current surface alpha blending is active (1) or not (0). | ||||||||||||||||||||||
SRFALPHAVAL | UINT | Alpha value of the current surface (from 0 to 255). | ||||||||||||||||||||||
SRFDOTSIZE | UINT | Dot size of the current surface used for the visualization (from 1 to 10). It returns 0 if no surfaces are available. | ||||||||||||||||||||||
SRFVISIBLE | BOOL | Check if the current surface is visible (1) or not (0). | ||||||||||||||||||||||
TRANSX | FLOAT | X translation of the scene. | ||||||||||||||||||||||
TRANSY | FLOAT | Y translation of the scene. | ||||||||||||||||||||||
TRANSZ | FLOAT | Z translation of the scene. | ||||||||||||||||||||||
WINHANDLE | UINT | Main window handle. | ||||||||||||||||||||||
WKSCURNUM | UINT |
Progressive number of the current workspace. 0 is the main workspace and it's always present. |
||||||||||||||||||||||
WKSCURNAME | CHAR | Name of the current workspace. | ||||||||||||||||||||||
WKSTOT | UINT | Number of the workspaces. It's at least greater or equal to 1. |
Return values:
The value of the specified variable.
Example:
GET TOTATM
See also:
PLUGINGET.
MERGE (CHAR)FileName (INT)Flags
(BOOL)ActiveOnly (BOOL)Force
Merge the loaded molecule with one or more parts of another molecule. For more
information click here.
Parameters: | ||||||||||||||||||||||||||||
FileName |
File name of the object to load (molecule, surface, trajectory). |
|||||||||||||||||||||||||||
Flags |
This argument allows to specify the molecule fields/elements that are merged with the atoms already in memory. The following values can be combined through the "or" operator (or addition): |
|||||||||||||||||||||||||||
|
||||||||||||||||||||||||||||
ActiveOnly |
If it's true (1), it merges the molecule with the active (visible) atoms only, otherwise (false, 0) it merges the molecule with all atoms in memory. |
|||||||||||||||||||||||||||
Force |
If it's true (1) and the molecules are different (but with the same number of atoms), the merging is forced. |
Return values:
Error code if it fails.
Example:
MERGE "C:\Documents\Molecules\MyMolecule.pdb"
10 0
See also:
NEW, SAVE, mMerge, mNew, mOpen, mSave.
MSGERRMODE (MCHAR)Mode
This command sets the mode used by VEGA to show the error messages.
Parameters: | ||||
Mode |
Error message mode. It can be: |
|||
Console | Shows the errors in the console window (default for command line operation mode). | |||
Quiet | No errors are shown. | |||
Window | All errors are shown in a standard request window (default for OpenGL operation mode). |
Return values:
Error code if it fails.
Example:
MSGERRMODE Console
See also:
ERRMSG.
NEW
It cleans all objects, removing molecules, surfaces, selections, etc from the memory,
without confirm. Use mNew if you want that this operation must be confirmed.
Parameters:
None.
Return values:
Error code if it fails.
Example:
NEW
See also:
OPEN, MERGE, SAVE,
mNew, mOpen, mSave.
OPEN (CHAR)FileName
Open a molecule or a surface or a trajectory file.
Parameters: | ||
FileName |
File name of the object to load (molecule, surface, trajectory). |
Return values:
Error code if it fails.
Example:
OPEN "C:\Documents\Molecules\MyMolecule.pdb"
See also:
MERGE, NEW, SAVE,
mMerge, mNew, mOpen, mSave.
REMATOMS (CHAR)Selection
Remove one or more atoms using the pattern matching.
Parameters: | ||
Selection |
It's the atom selection in standard VEGA format. For more information, see the SELECT command. Please remember that if you want remove a single atom, you can put the atom number only instead of the standard string selection. |
Return values:
The number of the removed atoms.
Example:
REMATOMS *:HOH
See also:
SELECT, mRemoveHydrog,
mRemoveInvisAtm, mRemoveWater.
SAVE (CHAR)FileName (CHAR)Format
(CHAR)Compression (BOOL)Flags
This command saves the current molecule or assembly.
Parameters: | ||||||||||||||
FileName | File name of the output molecule (the file extension is added automatically if not present). | |||||||||||||
Format | File format (see -f command line option). | |||||||||||||
Compression | Compression mode (NONE, BZIP2, GZIP, POWERPACKER, ZCOMPRESS). | |||||||||||||
Flags | Special flags that can be combined through the OR logical operator (or addition): | |||||||||||||
|
Return values:
Error code if it fails.
Example:
SAVE MyMolecule.pdb PDB
BZIP2 1
See also:
MERGE, NEW, OPEN,
mMerge, mNew, mOpen, mSave.
SRFCALC (MCHAR)SurfaceVis (MCHAR)SurfaceType
(UFLOAT)ProbeRadius (UINT/UFLOAT)Density/MeshSize
(BOOL)SelectedOnly
Calculate and show (in OpenGL mode) the molecular surface. The MLP, MEP and ILM
calculations ignore the ProbeRadius. Please remember that the last
calculated surface becomes the current.
Parameters: | ||
SurfaceVis | Surface visualization mode (DOTS, MESH, SOLID). | |
SurfaceType | Surface type (DEEP, HBACC, HBDON, ILM, MEP, MLP, PSA and VDW). | |
ProbeRadius | Probe radius in Å. | |
Density/MeshSize | Dot density in Ų for dotted surface or mesh size for mesh and solid surface. | |
SelectedOnly | If it's true (1), the visible atoms only will be considered, otherwise if it's false (0), the the surface is calculated for all atoms. |
Return values:
The command returns the total surface area in Ų, the surface
diameter in Å, the minium value and the maximum value of the calculated
property. If the SurfaceType
is ILM, it returns the Virtual LogP value also, if the SurfaceType is
PSA and it returns the positive and the negative surface areas in Ų.
If it fails, the error code is returned.
Example:
SRFCALC SOLID PSA 1.4
1.0 0
See also:
OPEN,
SRFSAVE, mOpen, mSurface.
SRFCUR (UINT)SurfaceID
It makes current the specified surface.
Parameters: | ||
SurfaceID |
Surface identification number (1 for the first, 2 for the second and so on). |
Return values:
Error code if it fails.
Example:
SRFSETCUR 2
See also:
OPEN, SRFCALC, SRFCOLOR,
SRFCOLORBY, mOpen, mSurface.
SRFREMOVE
It removes the current surfaces from the current workspace. The current surface
is set to the next surface in the surface list, but if the removed surface is
the last, the it's set to the previous.
Parameters:
None.
Return values:
Error code if it fails.
Example:
SRFREMOVE
See also:
OPEN, SRFCUR, SRFREMOVEALL, SRFCALC.
SRFREMOVEALL
This command removes all surfaces from the current workspace. The surfaces in
the other workspaces are kept.
Parameters:
None.
Return values:
Error code if it fails.
Example:
SRFREMOVEALL
See also:
OPEN, SRFREMOVE, SRFCALC.
SRFSAVE (CHAR)FileName (UINT)SurfaceID
(MCHAR)Format
(CHAR)Compression
This command saves the surface.
Parameters: | ||
FileName | Output file name (the file extension is added automatically if not present). | |
SurfaceID | Surface identification number (0 for the first, 1 for the second and so on). | |
Format | Surface format (CSV, INSIGHT, QUANTA, Raw, VrmlDotted, VrmlSolid). | |
Compression | Compression mode (NONE, BZIP2, GZIP, POWERPACKER, ZCOMPRESS) |
Return values:
Error code if it fails.
Example:
SRFSAVE "Molecules\MySurface" 0 QUANTA NONE
See also:
OPEN, SRFCALC, SRFCOLOR,
SRFCOLORBY, mOpen, mSurface.
TRJCLOSE
(UINT)Handle
Close a trajectory stream and release its resources.
Parameters: | ||
Handle |
It's the trajectory stream handle returned by the TrjCreate command. |
Return values:
If it fails (e.g. the stream is already closed or the handle is invalid), 0
(false) is returned, otherwise 1 (true) is set.
Example:
TRJCLOSE 23567
See also:
TRJCREATE, TRJWRITE.
TRJCREATE (CHAR)FileName (MCHAR)Format
(UINT)Compression (INT)Flags
Create a new trajectory stream.
Parameters: | ||||||||||||||
FileName | File name of the MD trajectory to create. | |||||||||||||
Format | The trajectory file format. It should be: DCD (NAMD/CHARMM DCD), IFF, PDB (PDB multi model) and XTC (Gromacs XTC compressed trajectory). | |||||||||||||
Compression | This argument has effect with the XTC format only and it's the floating point precision used in the XDRF compression. The allowed values are from 1 to 6. For more information about it, click here. | |||||||||||||
Flags | Control flags that can be combined with the "or" operator (or addition): | |||||||||||||
|
Return values:
If no errors are found, the handle is returned, otherwise the function returns 0.
Example:
TRJCREATE "C:\Temp\mytrajectory.dcd" XTC 4 0
TRJOPEN (CHAR)FileName (BOOL)OpenDialog
Open a trajectory file to analyze it.
Parameters: | ||
FileName | Trajectory file to analyze. | |
OpenDialog | If 1 (true), the analysis dialog box is opened. |
Return values:
Error code if it fails.
Example:
TRJOPEN "Simul.DCD" 1
See also:
OPEN, TRJSAVE, TRJSEL, TRJSELFIRST,
TRJSELLAST, TRJSELLAST,
mOpen, mSaveTraj, mAnalysis.
TRJSAVE (CHAR)FileName (MCHAR)Format
(UINT)StartFrm (UINT)EndFrm (UINT)SkipFrm
(INT)Flags (UINT)Compression
Save the current MD trajectory converting it in the specified format.
Parameters: | ||||||||||||||
FileName | File name of the MD trajectory to save. | |||||||||||||
Format | The trajectory file format. It should be: DCD (NAMD/CHARMM DCD), PDB (PDB multi model) and XTC (Gromacs XTC compressed trajectory). | |||||||||||||
StarFrm | Starting frame number. | |||||||||||||
EndFrm | Ending frame number. To obtain the total number of trajectory frames, use GET TRJTOTFRM. | |||||||||||||
SkipFrm | The number of frame to skip. Use 0 to skip nothing. | |||||||||||||
Flags | Control flags that can be combined with the "or" operator (or addition): | |||||||||||||
|
||||||||||||||
Compression |
This argument has effect with the XTC format only and it's the floating point precision used in the XDRF compression. The allowed values are from 1 to 6. For more information about it, click here. |
Return values:
Error code if it fails.
Example:
TRJSAVE "C:\Temp\mytrajectory.dcd" DCD 1 100 0 0 1
See also:
OPEN, TRJOPEN, mOpen, mSaveTraj,
mAnalysis.
TRJSEL (UINT)Number
Select the frame by number. The trajectory must be opened with TRJOPEN command.
Parameters: | ||
Number |
Frame number .(0 < Number <= LastFrameNumber) |
Return values:
Error code if it fails.
Example:
TRJSEL 25
See also:
OPEN, TRJOPEN, TRJSELFIRST,
TRJSELLAST, TRJSELLAST,
mOpen, mAnalysis.
TRJSELFIRST
Select the first frame of the trajectory. The trajectory must be opened with TRJOPEN
command.
Parameters:
None.
Return values:
Error code if it fails.
Example:
TRJSELFIRST
See also:
OPEN, TRJOPEN, TRJSEL, TRJSELLAST, TRJSELLAST, mOpen, mAnalysis.
TRJSELLAST
Select the last frame of the trajectory. The trajectory must be opened with TRJOPEN
command.
Parameters:
None.
Return values:
Error code if it fails.
Example:
TRJSELFIRST
See also:
OPEN, TRJOPEN, TRJSEL, TRJSELFIRST, mOpen, mAnalysis.
TRJWRITE
(UINT)Handle
Write the current conformation into a trajectory stream.
Parameters: | ||
Handle |
It's the trajectory stream handle returned by the TrjCreate command. |
Return values:
If it fails, 0
(false) is returned, otherwise 1 (true) is set.
Example:
TRJWRITE 23567
See also:
TRJCREATE, TRJCLOSE.
VOLUME
(UINT)Density (BOOL)SelectedOnly
Calculate the molecular volume.
Parameters: | ||
Density | Dot density in Ų for the grid calculation. Greater values mean more precise calculation. | |
SelectedOnly | If it's true (1), the visible atoms only will be considered. |
Return values:
The command returns the volume in Å3 and the volume diameter in Å.
Example:
VOLUME 20 0
See also:
SRFCALC.