14.2 Standard commands

In this section, you can find the VEGA ZZ standard commands:

 

 

ADDHYDROG    (MCHAR)MolType   (MCHAR)HPos   (BOOL)IupacNames   (BOOL)ActiveOnly
Add the hydrogens to molecule in the current workspace. If the hydrogens are already present, they are removed before to add the new ones.

Parameters:
MolType   

Molecule type: 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 and defined bond order (e.g. single, partial double, double, triple). The standard method doesn't work properly if the molecule structure is distorted or 2D.

HPos

Hydrogen position in the atom list. 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
Add counter ions to the molecule in the current workspace. For more information about the method, 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 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) to the molecule in the current workspace. This command works properly if all hydrogens are present.

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:
ADDHYDROG, CONNBUILD, CONNDESTROY.


ATMADD
Add a new atom to the current workspace. The atom is placed at (0, 0, 0) coordinates, the default element is 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 ? and the color is green. To change these default properties see 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, ATMENDUPDATE, ATMGET, ATMSET.


ATMBEGINUPDATE
Notify to the system a massive atom update. This command increases the performances of next atom-related commands.

 

Parameters:
None.

 

Return values:
Error code if it fails.

 

Example:
ATMBEGINUPDATE

 

See also:
ATMADD, ATMENDUPDATE, ATMGET, ATMINVCHIRALITY, ATMSET.


ATMBOND   (UINT)AtomNumber1   (UINT)AtmNumber2   (MCHAR)BondOrder
Bind/unbind two atoms or change the bond order if they are already bound.

Parameters:
AtomNumber1    Number of the first atom.
AtomNumber2 Number of the second atom.
BondOrder

The bond order can be: NONE (unlink 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, ATMENDUPDATE, ATMGET, ATMINVCHIRALITY, ATMSET.


ATMDELETE   (UINT)AtomNumber   (UINT)AtomsToDelete
Delete one or more atoms. The identification number of undeleted atoms is automatically renumbered and so the atom IDs could not 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, ATMINVCHIRALITY, ATMSET.


ATMFIND   (MCHAR)Mode   (UINT)FirstAtom   (CHAR)String
Find an atom by element or atom name or 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, ATMINVCHIRALITY.


ATMGET   (UINT)AtomNumber    (MCHAR)Property
Get a property of the specified atom number.

Parameters:
AtomNumber    Atom number.
Property Atom property to obtain.
  
Property Type Value range Size Description
Active BOOL 0-1 1 It it's true (1), the atom is active (visibile), otherwise the atom is inactive (invisible).
Chain CHAR - 1 Chain ID.
Color CHAR - 1-2 Atom color (see COLOR for the color names).
Connect CHAR - 0-6 words It's a string containing from 0 to 6 number corresponding to the connected atoms. If no atom is connected, an empty string is returned.
Coord CHAR - 3 words It's a string containing the three atom coordinates in floating point format.
DrawMode UINT 0-9 1

Atom draw mode. It can be:

DrawMode Description
0 Wireframe.
1 CPK/Van der Waals dotted.
2 CPK/Van der Waals wireframe.
3 CPK/Van der Waals solid.
4 Ball & stick wireframe.
5 Ball & stick solid.
6 Stick wireframe.
7 Stick solid.
8 Tube solid.
9 Trace solid.
Elem CHAR - 1-2 Atomic element.
Fix FLOAT - - Constraint value for MD. For more information, click here.
Flags INT - - Atom flags. They can be combined by OR operator or sum.
Value Description
0 None.
1 HETATM flag.
2 The atom is the last one in the segment.
4 The atom is the last one in the molecule.
8 The atom is a centroid.
16 The atom is a fixed centroid.
32 It's an organic atom.
64 The atom will not considered in the MD trajectory analysis.
Label UINT 0-10 1-2 Label shown. It can be:
Value Description
0 None
1 Atom name
2 Element
3 Atom number
4 Atom type
5 Charge
6 Chirality
7 Constraint value
8 Residue name & number
9 Residue name
10 Residue number
Name CHAR - 1-4 Atom name.
NSost UINT 0-6 1 Number of connected atoms.
ResName CHAR - 1-4 Residue name.
ResSeq CHAR - 1-4 Residue number.
Type CHAR - 1-8 Atom type (force field).

Return values:
The requested atom property or an error if it fails.

 

Example:
ATMGET   12   COORD

 

See also:
ATMBEGINUPDATE, ATMADD, ATMFIND, ATMINVCHIRALITY, ATMSET, ATMENDUPDATE.


ATMINVCHIRALITY   (UINT)AtomNumber
Invert the chiral center if it's chiral.

Parameters:
AtomNumber    Atom number.

Return values:
None.

 

Example:
ATMINVCHIRALITY   10

 

See also:
ATMBEGINUPDATE, ATMADD, ATMGET, 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 set. For the property list see 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, ATMINVCHIRALITY, ATMENDUPDATE.

 


BUILDPEPT   (CHAR)Sequence    (FLOAT)Phi    (FLOAT)Psi   (FLOAT)Omega   (INT)Flags
Build a peptide from its aminoacidic sequence. If the current workspace is not empty (use GET TotAtm to check it), the current molecule will be lost. To avoid that, check if the current workspace is empty and if it's not true, create a new one (WKSNEW).

Parameters:
Sequence    Aminoacid sequence (single character format).
Phi

Backbone dihedral angles. Use them to specify the secondary structure. For more information about their values, click here.

Psi
Omega  
Flags  

Extra features can be enabled through the following flags that can be combined each others by OR or sum operators:

     
   
Flag Description
1 Add the side chains.
2 Add the hydrogens.
4 Normalize the atom coordinates.

Return values:
Error code if it fails.

 

Example:
BuildPept   AAAAAAA   -57.8   -47.0   180.0   7

 

See also:
SECSTRUCT.


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).

ActiveOnl

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 and 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 most common 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, unbinding all atoms.

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 available. 

Parameters:
FileName    Executable or DLL file name.

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 by 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 by 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 message in standard C format corresponding to the error code.

Parameters:
ErrorCode    Error code.

Return values:
Error string.

 

Example:
ERRMSG    201

 

See also:
MSGERRMODE.

 

 


FINGERPRINT   (MCHAR)Type    (MCHAR)Encoding
Calculate the fingerprint of the molecule in the current workspace.

Parameters:
Type   The fingerprint type. It can be:
      
   
Type Description
Sim Similarity fingerprint, useful for calculating similarity measures.
Sub Substructure fingerprint, useful for substructure screening.
Sub-Res Resonance substructure fingerprint, useful for resonance substructure screening.
Sub-Tau Tautomer substructure fingerprint, useful for tautomer substructure screening.
Full Full fingerprint, which has all the mentioned fingerprint types included.
Encoding   String encoding. It can be: Base64 or Hex (hexadecimal).

Return values:
The molecular fingerprint as hexadecimal string or an empty string if an error occurs.

 

Example:
FINGERPRINT    SIM   HEX

 

See also:
FPSIMILARITY.


FIXAROM   (BOOL)ActiveOnly
Fix the aromatic rings, replacing the conjugated bonds with partial double bonds.

Parameters:
ActiveOnly   If it's true (1), the active (visible) bonds only are fixed.

Return values:
The command returns the number of atoms involved in bond fix. Dividing this value by two, you obtain the number of changed bonds.

 

Example:
FIXAROM    0

 

See also:
None.


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 to the active (visible) atoms only .
Quiet If it's true, no warning messages are shown if a problem is found in the force field assignment.

Return values:
Error code if it fails.

 

Example:
FORCEFIELD    CVFF   0   1

 

See also:
CHARGE, mCalcCharge.


FPSIMILARITY   (CHAR)FingerPrint1   (CHAR)FingerPrint2   (MCHAR)Encoding   (MCHAR)Method   (FLOAT)Alpha   (FLOAT)Beta
Compare two fingerprints and return the similarity index.

Parameters:
FingerPrint1

FingerPrint2

  Fingerprints to compare. They must have the same encoding format and must be calculated in the same way.
Encoding   String encoding. It can be: Base64 or Hex (hexadecimal).
Method   Method used for the similarity index calculation. They can be: Euclid-Sub, Tanimoto and Tversky.
Alpha

Beta

  Coefficients for Tversky method (usual values are Alpha = Beta = 0.5). These parameters are ignored for the other similarity methods.

Return values:
The command returns the similarity index (0-1 range).

 

Example:
Not applicable because the fingerprints lengths are too long to type the command directly in the console. It's only a script command.

 

See also:
FINGERPRINT.


GET   (CHAR)Variable
The command GET returns the value of an internal variable. The argument 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 plug-in (see plugin.h). SendVegaCmd retrieves the result automatically from the clipboard.

 

Standard variables:

Variable Type Description
BMLIPOLE FLOAT Broto & Moreau lipole of the current molecule.
BMLOGP FLOAT Broto & Moreau log P of the current molecule.
CONFIGDIR CHAR Full path of Config directory.
CPUFEATURES INT 32 bit integer containing the CPU features (for x86 CPUs only).
CPUNAME CHAR Installed CPU name.
CPUS UINT Number of installed CPUs.
CPUTYPE CHAR Type, family, model and stepping of installed CPU (for x86 CPUs only).
CPUVENDOR CHAR CPU vendor.
CURDIR CHAR Current directory.
CURLANG CHAR Current language for string localization.
DATADIR CHAR Full 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.
GCLIPOLE FLOAT Ghose & Crippen lipole of the current molecule.
GCLOGP FLOAT Ghose & Crippen log P of the current molecule.
GCMR FLOAT Ghose & Crippen molar refractivity of the current molecule.
ISWOW64 BOOL 1 (true) is VEGA is running on a 64 bit operating system.
HBACC UINT Number of H-bond acceptor atoms (N and O only).
HBDON UINT Number of H-bond donor atoms (H-N and H-O only).
HLBD FLOAT Davies' hydrophilic-lypophilic balance (HLB).
HLBG FLOAT Griffin's hydrophilic-lypophilic balance (HLB).
HLBPSA FLOAT PSA hydrophilic-lypophilic balance (HLB).
INCHI CHAR IUPAC InChI string.
INCHIAUX CHAR IUPAC InChI string + auxiliary data.
ISODIST CHAR

Isotopic distribution. The output is formatted in lines and each line contain the isotopic mass and the probability separated by one space character.

LASTFILENAME CHAR Name of the last file without path and extension.
MASS FLOAT Molecule mass in Daltons.
MASSACT FLOAT Calculate the mass in Daltons of active atoms.
MOL CHAR Obtain the current molecule in IFF format with Base64 encoding.
OS CHAR Operating system (e.g. AmigaOS, Linux, Irix, Unix, Windows 95/98/ME, Windows NT/2000/XP/Vista).
OSFAMILY CHAR Operating system family (e.g. amigaos, unix, windows).
PRFLANG CHAR Preferred language for string localization.
SAVEDIR CHAR Default path to save files.
SEQUENCE CHAR Amino/nucleic acid sequence.
SMILES CHAR SMILES string of the molecule in the current workspace.
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.
TOTBOND UINT Total number of bonds.
TOTCHAIN UINT Total number of chains.
TOTCHIRAL UINT Total number of chiral centres.
TOTEZ UINT Total number of bonds with E/Z geometry.
TOTHEAVYATM UINT Total number of heavy atoms.
TOTHYDROG UINT Total number of hydrogens.
TOTIMP UINT Total number of improper angles.
TOTMOL UINT Total number of molecules. It doesn't perform any seek to find the molecules, but counts the end-of-molecule tags in the atom list. If these tags are missing or misplaced, the number of molecules could be wrong.
TOTREALMOL UINT

Real number of the molecules. It performs the seek to find the molecules, returning the real number of molecules.

TOTREALMOLACT UINT As above, but return the number of the active (visible) molecules. At least one atom must be visible to consider the whole molecule in this count.
TOTRES UINT Total number of residues.
TOTRING UINT Total number of rings.
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 Energy of the best frame of the current MD trajectory.
TRJBESTFRM UINT Number of the best frame of the current MD trajectory.
TRJCURENE FLOAT Energy of the current frame. It returns 0 if the energy is not available.
TRJCURFRM UINT Current frame number selected in the trajectory.
TRJSIMTIME UINT Length of the simulation (ps) of the current MD trajectory.
TRJSTARTTIME UINT Start time of the simulation (ps) of the current MD trajectory.
TRJTEMP UINT Simulation temperature (Kelvin) of the current MD trajectory.
TRJTIMESTEP UINT Time step of the current MD trajectory.
TRJTOTFRM UINT Total number of frames of the current MD trajectory.
TRJWORSEENERGY FLOAT Energy of the worse frame of the current MD trajectory.
TRJWORSEFRM UINT Number of the worse frame of the current MD trajectory.
VEGADIR CHAR Directory path where VEGA ZZ is installed.
VERSION CHAR Full VEGA ZZ version.
VLOGP FLOAT Virtual log P. If an error occurs, an empty value is returned.

 

OpenGL variables:

Variable Type Description
BACKCOLOR UINT Background color in RGB format.
CONBUFSIZE UINT Console buffer size (lines).
CONDOCKED BOOL 1 (true) if the console is docked.
CONHISTSIZE UINT Maximum number of commands stored in the history buffer.
CONLINES UINT Number of text lines in the console.
CONPOSX UINT X screen position of console window. If the console is docked, the return value is 0.
CONPOSY UINT Y screen position of 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 1 (true) if the console is open.
GLASSWIN BOOL 1 (true) if the glass windows are enabled.
GLZBUFBITS INT Number of bits of OpenGL Z-buffer.
GLRENDERER CHAR OpenGL rendering subsystem (hardware/software).
GLVENDOR CHAR Vendor of installed graphic card.
GLVERSION CHAR OpenGL subsystem version.
GRAPHID UINT ID of the current Graph Editor window.
GRAPHLABELX CHAR X axis label of the current chart.
GRAPHLABELY CHAR Y axis label of the current chart.
GRAPHPOINTS UINT Number of the points  of the current chart.
GRAPHPOSX UINT X screen position of Graph Editor window.
GRAPHPOSY UINT Y screen position of Graph Editor window.
GRAPHSIZEX UINT Width of Graph Editor window.
GRAPHSIZEY UINT Height of Graph Editor window.
GRAPHTITLE CHAR Current chart title.
GRAPHVISIBLE BOOL 1 (true) if the Graph Editor window is open (obsolete, only for backwards compatibility.
ISRUNNING BOOL 1 (true) if a background calculation is running (e.g. Ammp, Mopac, NAMD, etc).
LIGHT BOOL 1 (true) if the light is enabled.
LIGHTAMB BOOL 1 (true) if the ambient light is enabled.
LIGHTAMBCOLOR UINT Ambient light color.
LIGHTCUR UINT Number of the current light sources (from 0 to 3).
LIGHTCURDIFCOL UINT Diffuse color of the current light source.
LIGHTCUREN BOOL 1 (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 VEGA ZZ logo:
Value Position
0 Logo disabled
1 Top left
2 Top center
3 Top right
4 Center left
5 Centered
6 Center right
7 Bottom left
8 Bottom center
9 Bottom right
LOGOSCALE FLOAT Scale factor of VEGA ZZ logo (default 0.5).
MAINSIZEX UINT Width of main window.
MAINSIZEY UINT Height of main window.
MAINPOSX UINT X screen position of main window.
MAINPOSY UINT Y screen position of main window.
MATSHINY UINT Material shininess.
MATSPECULAR UINT Material specularity.
MATVECTSPEC BOOL 1 (true) if the vector specularity is enabled.
MOPACEXE CHAR Full path and file name of Mopac executable.
MSAA UINT Multisample anti-aliasing value (0-16x, 0 = disabled).
PORTNUM UINT Number of communication port.
ROTX FLOAT X rotation of scene (degree).
ROTY FLOAT Y rotation of scene (degree).
ROTZ FLOAT Z rotation of scene (degree).
SCALE FLOAT Visualization scale.
SCREENDEPTH UINT Screen depth in bit per pixel (8, 16, 24, 32).
SCREENX UINT Screen width.
SCREENY UINT Screen height.
SCRIPTSDIR CHAR Scripts directory.
SKYBOXENABLED BOOL 1 (true) if the SkyBox/SkyVision is enabled.
SKYBOXNAME CHAR Name of the current SkyBox.
SKYBOXOFFSETX FLOAT X offset of the current SkyBox.
SKYBOXOFFSETY FLOAT Y offset of the current SkyBox.
SKYBOXROTX FLOAT X rotation (degree) of the current SkyBox.
SKYBOXROTY FLOAT Y rotation (degree) of the current SkyBox.
SKYBOXROTZ FLOAT Z rotation (degree) of the current SkyBox.
SOUNDEFFECTS BOOL 1 (true) if the sound effects are enabled.
SRFALPHA BOOL 1 (true) if the surface alpha blending (transparency) is enabled.
SRFALPHAVAL UINT Alpha value of the current surface (from 0 to 255).
SRFDOTSIZE UINT Dot size of the current surface used for visualization (from 1 to 10). It returns 0 if no surface is available.
SRFVISIBLE BOOL 1 (true) if the current surface is visible.
TOTCTOR UINT Total number of torsions angles (dihedral) usable for a calculation.
TRANSX FLOAT X translation of scene.
TRANSY FLOAT Y translation of scene.
TRANSZ FLOAT Z translation of scene.
WINHANDLE UINT Main window handle.
WKSCURNUM UINT Progressive number (ID) of the current workspace. 0 is the main workspace and it's always present.
WKSCURNAME CHAR Name of the current workspace.
WKSLOCKED BOOL Check if the workspaces are locked (1) or not (0). To lock/unlock workspaces, use WKSLOCK and WKSUNLOCK.
WKSTOT UINT Number of workspaces. It's at least greater or equal to 1.

 

Return values:
The value of the specified variable.

 

Example:
GET   TOTATM

 

See also:
PLUGINGET.


IONIZE   (MCHAR)Method   (FLOAT)pH   (FLOAT)pH_Tol   (INT)Flags
Ionize the molecule according to its acid/base groups and the specified pH. If the hydrogens are not already present, you must call ADDHYDROG before this command.

Parameters:
Method    Method used to assign the pKa values to the ionizable groups. At this time, only FAST method is implemented.
pH   Enviroment pH.
pH_Tol   pH tolerance used to discriminate between protonated or non-protonated forms of a given ionizable group (usually 1-2 pH units).
Flags    
      Extra features can be enabled through the following flags that can be combined each other by OR or sum operators:
   
Flag Description
1 Only the active (visible) atoms are considered.
2 If a hydrogen is added, it is paced at the end of each residue).
4 Use IUPAC names when add the hydrogens.

Return values:
Error code if it fails.

 

Example:
IONIZE     FAST   7.4   1   0

 

See also:
ADDHYDROG, ADDIONS.


ISODIST   (CHAR)Formula
Calculate the isotopic distribution of a chemical formula.

Parameters:
Formula    Chemical formula..

Return values:
This command return a multi-line string containing the isotopic distribution. Each line consists of isotopic mass and probability (%) separated by one space character.

 

Example:
ISODIST     C6H12O6

 

180.06338812 100.00000000
181.06674296 6.48943698
181.06760500 0.22855539
181.06966486 0.13801587
182.06763390 1.23299618
182.07009779 0.17546997
182.07095983 0.01483196
182.07182187 0.00021766
182.07301970 0.00895645
182.07388174 0.00031544
183.07098873 0.08001451
183.07185077 0.00234840
183.07345263 0.00253045
183.07391064 0.00170173
183.07431467 0.00040105
183.07637454 0.00024218
184.07187967 0.00633450
184.07434357 0.00216354
184.07520561 0.00015240
184.07726548 0.00011043
185.07523451 0.00041107

See also:

None.


MERGE   (CHAR)FileName   (INT)Flags   (BOOL)ActiveOnly   (BOOL)Force
Merge the molecule in the current workspace with one or more parts of another file. For more information, click here.

Parameters:
FileName    File name of the object (molecule, surface, trajectory) to merge with the molecule in the current workspace.
Flags This argument allows to indicate the molecule fields/elements that will be merged with the atoms in the workspace. The following values can be combined by OR operator or sum:
   
Value Description
1 Atom charges
2 Atom names
4 Atom types
8 Chain IDs
16 Connectivity
32 Atom constraints
64 Atomic coordinates
128 Atom elements
256 Molecule IDs
512 Residue names
1024 Residue numbers
2048 Segments
  
ActiveOnly If it's true (1), the active (visible) atoms are merged only.
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,OPEN, OPENEX, SAVE, mMerge, mNew, mOpen, mSave.


MSGERRMODE   (MCHAR)Mode
Set the mode used by VEGA ZZ to show 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 error is shown.
Window All errors are shown in a standard window (default for OpenGL operation mode).

Return values:
Error code if it fails.

 

Example:
MSGERRMODE     Console

 

See also:
ERRMSG.


NEW
Clean all objects, removing molecules, surfaces, selections, etc. from the memory, without any 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, OPENEX, MERGE, SAVE, mNew, mOpen, mSave.


OPEN   (CHAR)FileName
Open molecule, surface and trajectory by file name or URL.

Parameters:
FileName    File name or URLof the object to open (molecule, surface, trajectory).

Return values:
Error code if it fails.

 

Example:
OPEN     "C:\Documents\Molecules\MyMolecule.pdb"
OPEN     "http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=2244&disopt=3DSaveSDF"

 

See also:
MERGE, NEW, OPENEX, SAVE, mMerge, mNew, mOpen, mSave.

 


OPENEX   (CHAR)FileName   (INT)Flags
Open molecule, surface and trajectory (extended version) by file name or URL.

Parameters:
FileName    File name or URL of the object to open (molecule, surface, trajectory).
Flags   Flags that can be combined by OR logical operator or sum:
     
     
Flag Description
8 Add the file to the list of the last opened molecules.
16 Don't ask where to place the molecule (add, replace, new workspace).
32 Set the file path as current directory.
64 Don't open the trajectory analysis dialog if you are opening a trajectory.

The flags from 1 to 4 are reserved for future uses.

Return values:
Error code if it fails.

 

Example:
OPENEX     "C:\Documents\Molecules\MyMolecule.pdb"   56

 

See also:
MERGE, NEW, OPEN, SAVE, mMerge, mNew, mOpen, mSave.


REMATOMS   (CHAR)Selection
Remove one or more atoms using pattern matching.

Parameters:
Selection   

Atom selection in standard VEGA format. For more information, see SELECT command. If you want to remove a single atom, you can put the atom number only instead of the standard string selection.

Return values:
The number of removed atoms.

 

Example:
REMATOMS     *:HOH

 

See also:
SELECT, mRemoveHydrog, mRemoveInvisAtm, mRemoveWater.


SAVE   (CHAR)FileName   (CHAR)Format  (CHAR)Compression  (INT)Flags
Save the molecule in the current workspace.

Parameters:
FileName    File name of the output molecule (the file extension is added automatically if it's not present).
Format File format (see -f command line option).
Compression Compression method (NONE, BZIP2, GZIP, POWERPACKER, ZCOMPRESS).
Flags Flags that can be combined by OR logical operator or sum:
  
Flag Description
1 Save the connectivity.
2 Save the constraints if the file format supports them.
4 Don't update the last saved file list in the File menu (VEGA ZZ only).
8 Big endian numeric format. This flag is supported by IFF format only.
16 64 bit. Enable the 64 bit sub-format saving IFF files.
32 Force to add the file extension.

Return values:
Error code if it fails.

 

Example:
SAVE    MyMolecule.pdb   PDB    BZIP2   1

 

See also:
MERGE, NEW, OPEN, OPENEX, mMerge, mNew, mOpen, mSave.


SCORE   (CHAR)ScoreFunctions   (UINT)MolNum    (UFLOAT)Dielectric   (UFLOAT)Cutoff   (BOOL)ActiveOnly
Evaluate the interaction energy of a complex using one or more scoring functions.

Parameters:
ScoreFunctions Scoring functions: CHARMM, CHARMM22, CHARMM36, CVFF, ELECT, ELECTDD, MLPINS, MLPINS2, MLPINS3 and MLPINSF. For more details, see here.
MolNum    Molecule number to identify the ligand. If the molecules are in the same assembly you could need to search them using the Edit Molecules Fix menu item or the mMolFix command.
Dielectric Dielectric constant. It must be greater than or equal to 1.0.
Cutoff Cutoff distance between atom pairs to increase the calculation speed (usually 12.0 Ǻ). Reducing too much this parameter, you can introduce errors in calculation.
ActiveOnly   If it's true (1), the active (visible) atoms are only considered.

Return values:
Error code if it fails.

 

Example:
SCORE   "ELECT   MLPINS   MLPINS2"   2   1.0   12.0   0

 

See also:

mInteractions, mMolFix.


SECSTRUCT   (FLOAT)Phi    (FLOAT)Psi   (FLOAT)Omega   (INT)Flags
Change the secondary structure of a peptide.

Parameters:
Phi Backbone dihedral angles. Use them to specify the secondary structure. For more information about their values, click here.
Psi
Omega  
Flags   Extra features can be enabled through the following flags that can be combined each others by OR or sum operators:
     
   
Flag Description
1 Change the secondary structure to active/visible atoms only.
2 Adjust the bond angle that can be distorted by dihedral change.

Return values:
Error code if it fails.

 

Example:
SecStruct   -57.8   -47.0   180.0   2

 

See also:
BUILDPEPT.


SMARTSCOUNT   (CHAR)SmartsString   (INT)Flags
Count the number of recurrences in the current molecule for a given SMARTS query. When you use this command, you must pay attention, because SMARTS language assumes that the bond order is correctly assigned to the molecule. If this condition is not satisfied, you may obtain wrong results.

Parameters:
SmartsSring  SMARTS string of the query.
Flags   If you set this flag to 1, only the visible/active atoms are considered.

Return values:
The number of recurrences found for the SMARTS query.

 

Example:
SMARTSCOUNT   C=O   0

 

See also:

SELSMARTS, UNSELSMARTS.


SMILES   (CHAR)String
Convert a SMILES string to 3D.

Parameters:
Sring   SMILES string.

Return values:
Error code if it fails.

 

Example:
SMILES   c1ccccc1

 

See also:

mSMILES.


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 and the last calculated surface becomes the current.

Parameters:
SurfaceVis Surface visualization mode (DOTS, MESH and SOLID).
SurfaceType    Surface type (DEEP, HBACC, HBDON, ILM, MEP, MLP, PSA and VDW).
ProbeRadius Probe radius in . Usually is 0 or 1.4 for surface accessible to solvent (SAS).
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.

Return values:
The command returns the total surface area in Ų, the surface diameter in , the minimum, the maximum, the average values and the standard deviation of the calculated property. If the SurfaceType is MLP, it returns the Virtual LogP value also, if the SurfaceType is PSA, 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.


SRFSETCUR   (UINT)SurfaceID 
Make 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, SRFRENAME, mOpen, mSurface.


SRFREMOVE
Remove 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, it's set to the previous one.

 

Parameters:
None.

 

Return values:
Error code if it fails.

 

Example:
SRFREMOVE

 

See also:
OPEN, SRFCALC, SRFREMOVEALLSRFRENAME, SRFSETCUR.


SRFREMOVEALL
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, SRFRENAME.


SRFRENAME   (CHAR)SurfaceName
Rename the current surface.

Parameters:
SurfaceName    New name of the current surface.

Return values:
Error code if it fails.

 

Example:
SRFRENAME   "New surface name"

 

See also:
SRFCALC, SRFREMOVE, SRFSETCUR.

 


SRFSAVE   (CHAR)FileName   (UINT)SurfaceID   (MCHAR)Format   (CHAR)Compression
Save the surface in the current workspace.

Parameters:
FileName    Output file name (the file extension is added automatically, if not it's 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 method (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 the trajectory stream and release its resources.

Parameters:
Handle    Trajectory stream handle returned by 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.


TRJCLUSTCOORD   (CHAR)FileName    (MCHAR)Format    (UINT)Compression   (INT)Flags   (FLOAT)Rmsd
Perform the cluster analysis of the conformers included into the current trajectory by their atom coordinates.

Parameters:
FileName    Name of the output file name that will include the lowest energy conformations for each cluster. It's also used to save the energy and cluster population file (*.ene file extension).
Format   For more information, see TRJCREATE.
Compression  
Flags  
Rmsd   Root mean square deviation value used as criterion to collect two conformer in the same cluster.

Return values:
Error code if it fails.

 

Example:
TRJCLUSTCOORD   "MyTrajectory - clust.dcd"   DCD   1   0   3.0

 

See also:
TRJCREATE, TRJCLUSTTOR, TRJCLUSTTORRMS.


 

TRJCLUSTTOR   (CHAR)FileName    (MCHAR)Format    (UINT)Compression   (INT)Flags   (FLOAT)Steps
Perform the cluster analysis of the conformers included into the current trajectory by their values of the torsion angles. The torsion angles to analyze must be defined to do this kind of analysis (use CTORFIND command).

Parameters:
FileName    Name of the output file name that will include the lowest energy conformations for each cluster. It's also used to save the energy and cluster population file (*.ene file extension).
Format   For more information, see TRJCREATE.
Compression  
Flags  
Steps   Number of steps of a round angle used for the classification, e.g.: 6 steps mean cluster differing of 60 degrees each for a complete torsion rotation.

Return values:
Error code if it fails.

 

Example:
TRJCLUSTTOR   "MyTrajectory - clust.xtc"   XTC   3   0   6

 

See also:
CTORFIND, TRJCREATE, TRJCLUSTCOORD, TRJCLUSTTORRMSD.


 

TRJCLUSTTORRMSD   (CHAR)FileName    (MCHAR)Format    (UINT)Compression   (INT)Flags   (FLOAT)Rmsd
Perform the cluster analysis of the conformers included into the current trajectory by RMSD differences of their torsion angles. The torsion angles to analyze must be defined to do this kind of analysis (use CTORFIND command).

Parameters:
FileName    Name of the output file name that will include the lowest energy conformations for each cluster. It's also used to save the energy and cluster population file (*.ene file extension).
Format   For more information, see TRJCREATE.
Compression  
Flags  
Rmsd   Root mean square deviation value of the torsions used as criterion to collect two conformer in the same cluster.

Return values:
Error code if it fails.

 

Example:
TRJCLUSTTORRMSD   "MyTrajectory - clust.iff"   IFF  1   0   60.0

 

See also:
CTORFIND, TRJCREATE, TRJCLUSTCOORD, TRJCLUSTTOR.

 


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

Trajectory file format. It can be: DCD (NAMD/CHARMM DCD), IFF, MOL2 (Sybyl Mol2 multi model), PDB (PDB multi model), TRR (Gromacs TRR) and XTC (Gromacs XTC compressed trajectory).

Compression

This argument has effect with the XTC format only and it's the floating point precision used by XDRF compression. The allowed values are from 1 to 6. For more information, click here.

Flags

Control flags that can be combined by OR logical operator or sum:

  
Flag Value Description
TRJSAVE_ACTONLY 1 Save the active/visible atoms only.
TRJSAVE_SWAPEND 2 Swap the endian (DCD file only). For more information, click here.
TRJSAVE_APPEND 4 Append the trajectory to another one.

Return values:
If no error occurs, the trajectory handle is returned, otherwise the function returns 0.

 

Example:
TRJCREATE    "C:\Temp\MyTrajectory.xtc"  XTC  4  0

 

See also:
TRJCLOSE, TRJWRITE.


TRJOPEN   (CHAR)FileName    (BOOL)OpenDialog
Open a trajectory file to analyze it.

Parameters:
FileName    Trajectory file to analyze.
OpenDialog If it's 1 (true), the analysis dialog box will be 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 to specified format.

Parameters:
FileName    File name of the MD trajectory to save.
Format

The trajectory file format. It can be: DCD (NAMD/CHARMM DCD), PDB (PDB multi model) TRR (Gromacs TRR) 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

Number of frame to skip. Use 0 to disable the frame skipping.

Flags

Control flags that can be combined by OR logical operator or sum:

  
Flag Value Description
TRJSAVE_ACTONLY 1 Save the active/visible atoms only.
TRJSAVE_SWAPEND 2 Swap the endian (DCD file only). For more information, click here.
TRJSAVE_APPEND 4 Append the trajectory to another one.
  
Compression

This argument has effect with the XTC format only and it's the floating point precision used by 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 a trajectory frame by number. The trajectory must be opened by 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 trajectory frame. The trajectory must be opened by 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 trajectory frame. The trajectory must be opened by 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 to the trajectory stream.

Parameters:
Handle    Trajectory stream handle returned by 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 volume of the molecule in the current workspace.

Parameters:
Density    Dot density in Ų for grid calculation. Greater values mean more precise calculation.
SelectedOnly If it's true (1), the visible atoms are considered only.

Return values:
The command returns the volume in 3 and the volume diameter in .

 

Example:
VOLUME   20   0

 

See also:
SRFCALC.


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