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.
BUILDDNA (CHAR)Sequence
(MCHAR)Type (INT)Flags
Build a nucleic acid from its nucleotide 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 |
|
Nucleotide sequence (single character format). |
| Type |
|
Type of nuclei acid structure to build:
| Type |
Description |
| ADNA |
Right handed A-DNA (Arnott). |
| ABDNA |
Right handed B-DNA (Arnott). |
| LBDNA |
Right handed B-DNA (Langridge). |
| SBDNA |
Left handed B-DNA (Sasisekharan). |
| ARNA |
Right handed A-RNA (Arnott). |
| APRNA |
Right handed A-PRIME RNA (Arnott). |
|
| Flags |
|
Extra features can be enabled through the following flags that can be
combined each others by OR or sum operators:
| Flag |
Description |
| 1 |
Reserved. |
| 2 |
Add the hydrogens. |
| 4 |
Normalize the atom coordinates. |
| 8 |
Build 3'
5' chain |
| 16 |
Build 5'
3' chain |
By default, it builds both chains (double helix). |
Return values:
Error code if it fails.
Example:
BuildDna ATAG ADNA 0
BuildDna AUCGGGAA ARNA 16
See also:
BUILDPEPT, SECSTRUCT.
BUILDPEPT (CHAR)Sequence (FLOAT)Phi
(FLOAT)Psi (FLOAT)Omega (CHAR)SecStructPattern
(MCHAR)NTermCap (MCHAR)CTermCap (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 |
|
| SecStructPattern |
|
Optional pattern of the secondary structure. By this string, you can set the
secondary structure for each residue according the following scheme:
| Character code |
Description |
| H |
Alpha helix. |
| L |
Left-handed helix. |
| 3 |
3.10 helix. |
| P |
Pi helix. |
| E |
Beta strand. |
| A |
Anti-parallel beta strand. |
| B |
Parallel beta strand |
| U |
User defined |
The pattern string is case insensitive and when you specify U, the
the Phi, Psi and Omega values, specified in the
command, are used. If the length of the pattern string is lower than that of
the residue sequence, it is applied cyclically. |
| NTermCap |
|
Capping on the N-terminus. It can be: H2N-, +H3N-, HCONH-
and CH3CONH- |
| CTermCap |
|
Capping on the N-terminus. It can be: -H, -O-, -OH, -OCH3, -OCH2CH3, -NH2 |
| 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 "" +H3N- -O- 7
BuildPept AAAAAAA -57.8 -47.0
180.0 "HHHHEEE" CH3CONH- -OCH3 7
See also:
BUILDDNA,
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: formal charges (Formal keyword), 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 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 |
| AREA |
FLOAT |
Surface area. |
| ASA |
FLOAT |
Apolar surface area. |
| BMLIPOLE |
FLOAT |
Broto & Moreau lipole of the current molecule. |
| BMLOGP |
FLOAT |
Broto & Moreau log P of the current molecule. |
| CHARGE |
INT |
Total charge of the 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 |
Mass in Daltons. |
| MASSACT |
FLOAT |
Mass in Daltons of active atoms. |
| MASSMI |
FLOAT |
Monoisotopic mass in Daltons. |
| 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/7/8/10). |
| OSFAMILY |
CHAR |
Operating system family (e.g. amigaos, unix, windows). |
| OVALITY |
FLOAT |
Ovality. |
| PRFLANG |
CHAR |
Preferred language for string localization. |
| PSA |
FLOAT |
Polar surface area. |
| SAS |
FLOAT |
Solvent accessible surface area. |
| SAV |
FLOAT |
Solvent accessible volume. |
| 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. |
| VDIAM |
FLOAT |
Volume diameter. |
| VOLUME |
FLOAT |
Volume. |
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. |
| CONRECSTATUS |
UINT |
Console log recording status: 0 = stop, 1 = pause, 2 =
run). |
| 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. |
| ISFULLSCREEN |
BOOL |
1 (true) if the full screen mode is enabled. |
| ISLOCKED |
BOOL |
1 (true) if the session is locked. |
| 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.
MOLDELETE (UINT)ID
Remove a molecule by ID in the current workspace.
| Parameters: |
| ID |
|
ID of the molecule to delete. It is an integer number grater than zero. |
Return values:
Error code if it fails.
Example:
MOLDELETE 2
See also:
SEGDELETE,
mRemoveHydrog, mRemoveInvisAtm,
mRemoveWater.
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:
REMINVATOMS, REMVISATOMS,
SELECT,
mRemoveHydrog, mRemoveInvisAtm,
mRemoveWater.ù
REMINVATOMS
Remove the invisible atoms.
Parameters:
None.
Return values:
The number of removed atoms.
Example:
REMINVATOMS
See also:
REMVISATOMS,
SELECT,
mRemoveHydrog, mRemoveInvisAtm,
mRemoveWater.
REMVISATOMS
Remove the visible atoms.
Parameters:
None.
Return values:
The number of removed atoms.
Example:
REMVISATOMS
See also:
REMVISATOMS,
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 (CHAR)SecStructPattern (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 |
|
| SecStructPattern |
|
Optional pattern of the secondary structure. For more information, see
BUILDPEPT. |
| 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
SecStruct -57.8 -47.0 180.0 "HHHHEEE" 2
See also:
BUILDDNA,
BUILDPEPT.
SEGDELETE (UINT)ID
Remove a segment of a molecule by ID in the current workspace.
| Parameters: |
| ID |
|
ID of the segmant to delete. It is an integer number grater than zero. |
Return values:
Error code if it fails.
Example:
SEGDELETE 3
See also:
MOLDELETE,
mRemoveHydrog, mRemoveInvisAtm,
mRemoveWater.
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 Å. 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 Å, 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, SRFREMOVEALL,
SRFRENAME, 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 Å3 and the volume diameter in Å.
Example:
VOLUME 20 0
See also:
SRFCALC.
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