13.3 Included scripts
13.3.1 Introduction
The VEGA ZZ package includes some scripts placed in the Scripts directory with the following sub-directory structure:
Scripts | |
_Templates (hidden folder) | |
Ammp | |
Build | |
Calculation | |
Color | |
Common | |
Communication | |
Database | |
Examples | |
File conversion | |
Protein tools | |
Trajectory | |
Utilities |
This folder contains the templates used when a new script is created.
OpenGL.c |
Template for OpenGL C scripts. |
Rebol.r | Template for REBOL scripts. |
Stabdard.c | Template for standard C scripts. |
Window API.c | Template window with close button (Windows API version). |
Window GraphApp.c | Template window with Ok button (GraphApp GUI version). |
The scripts contained in this directory, are useful to control some AMMP jobs in automatic way.
2D to 3D.c |
Convert a structure from 2D to 3D, adding the hydrogens (if needed) and fixing the atom charges with the Gasteiger - Marsili methods if they aren't assigned. The procedure works in several steps:
|
Dipole.c |
Compute the dipole momentum using AMMP. If the charges aren't assigned, they are fixed by the Gasteiger - Marsili method (see AMMP's DIPOLE command). |
Interaction analysis.c |
Evaluate the non-bond interaction energy between two molecules. This calculation requires two molecules in the workspace: the first one must be the receptor and the second one must be the ligand (see AMMP's ANALYZE command). |
Neural network.c |
Use the AMMP's Kohonen neural network to find the 3D space filling curve corresponding to the structure. If the charges aren't assigned, they are fixed by the Gasteiger - Marsili method (see AMMP's KOHONEN command). |
Rigid docking.c |
Perform the genetic algorithm
rigid docking using AMMP. This calculation requires two molecules
in the workspace: the first one must be the receptor and the second one
must be the ligand. This last molecule is moved to obtain the complex.
Both molecules must have the hydrogens and the charges are automatically
fixed (Gasteiger - Marsili method) if they are unassigned. |
With these scripts, it's possible to build complex structures:
Aromaticity fix.c | Fix the bond order in aromatic rings, changing the single and double bonds to partial double bonds. |
Graphite.r | Create one or more graphite planes. |
Nanotube.r |
Generates single-walled carbon nanotube (SWCNT) structures. It's based on VBS code developed by Roberto G. A. Veiga at Instituto de Física - Universidade Federal de Uberlândia (UFU) - Brazil, using using the algorithm described in the work of White et al. (Phys. Rev. B, 1993, Vol. 47, No. 9, pp. 5485-5488). |
Zero coord.c |
Place the atoms at the specified coordinates. Checking Active atoms only, only the visible atoms are moved. |
This directory includes scripts for generic calculations:
Elecrostatic energy.c |
Evaluate the electrostatic energy of the molecule in the current workspace. The default dielectric constant is 1 (vacuum). |
Mopac.r | Perform multiple Mopac jobs for more than one molecule. |
Scripts to color the molecule:
Color RasMol.c | Color the molecule using the RasMol color scheme. |
Color VMD.c |
Color the molecule using the VMD color scheme. |
This directory contains the initialization scripts to include in the REBOL scripts:
Fmod.r | Fmod commands |
Formats.r | File format keywords and other definitions |
Utils.r | Functions for path manipulation |
Vega.r | VEGA ZZ interface (don't change it without any reason) |
Vegadef.r | Default settings used by Vega.r |
Vutils.r | REBOL/View utilities. |
The C header files contained in this directory are hidden and they can't changed directly in the VEGA ZZ environment.
This directory includes communication and Internet-related scripts:
ActiveSync VRML send.c |
Convert the molecule to VRML and send it to the mobile device (e.g. PocketPC) using Microsoft ActiveSync. The molecule can be shown using a pocket VRML viewer (e.g. Parallel Graphics Pocket Cortona). Due to the mobile device hardware limits, don't transfer molecules with complex representation. The script requires Microsoft ActiveSync and it works with all Windows versions. |
E-mail PDB send.c | Save the molecule in PDB format, compress it and attach it to a user-editable e-mail. This script uses the MAPI layer and so it's compatible with MAPI compliant e-mail clients only (e.g. Outlook, Outlook Express, etc). To change the output format or other settings, see the script source code. |
Ftp put.r |
Copy the molecule in the current workspace to a remote host via FTP. |
IrDA VRML send.c |
Convert the molecule to VRML and send it to the mobile device (e.g. PocketPC) over an infrared link. The molecule can be shown using a pocket VRML viewer (e.g. Parallel Graphics Pocket Cortona). Due to the mobile device hardware limits, don't transfer molecules with complex representation. The script requires Windows 2000 or XP or Server 2003. |
Web server.r |
Micro Web server for on-line manual. |
This directory includes scripts to manage the databases:
Database 2D to 3D.c | Convert a database from 2D to 3D SDF format. It uses the graphic user interface to obtain the parameters for the conversion: Input database (2D), Output database (3D), graphic output update and the minimization type (steepest, conjugate, steepest + conjugate). For each minimization type, it's possible to put the number of steps (Steps) and the toler value (Toler). The script is able to add the missing hydrogens, using the more appropriate algorithm and to assign the atom charges with the Gasteiger - Marsili method. Clicking the Convert button, the calculation starts and it can be stopped clicking the Abort button in the progress window. |
Database expander.r | It's a REBOL/View script able to extract the molecules contained in a database into a directory specifying the file format, the compression and the save attributes (connectivity and constraints). |
Database logP.c | Calculate the logP with the Testa's MLP
method for each molecule in the database and export the results in a CSV (Output
file). The input must be a 3D SDF or Zip database (Input database)
and its structures can be pre-processed adding the hydrogens (Add the
hydrogens) applying the geometry method (default) or the bond order
method (Use bond order). This last method is recommended if the
molecules has got the bond order correctly assigned. In the pre-processing
phase, the structures can be optimized using the steepest descend (Steepest
minimization) and/or the conjugate gradients (Conjugate minimization)
methods. For both minimization algorithm, it's possible to put the number of
iterations (Steps), the toler value (Toler) and the dielectric
constant (Dielectric). Checking Update the graphic, the 3D
graphic output is updated every 20 minimization steps. Increasing the Dot
density value, it's possible to make a better prediction of the logP. A
good value is from 10 to 50 dots for Å2. Warning: even if in the theory it's possible to manage a 2D database, adding the hydrogens with the bond order method and optimizing the structures, this procedure is not recommended because the distance geometry optimization is not performed. For this reason, a better choice is the conversion of the database from 2D to 3D (see the Database 2D to 3D.c script) and the resulting database can be used without the pre-processing phase (e.g. hydrogens and optimization) to predict the logP values. |
Database to 0D.c | Convert a 2D or 3D database in a 0D SDF database, placing all atoms at the specified coordinates, usually at (0, 0, 0). |
This directory includes the example scripts:
Benzene.bat | Build a benzene ring using the extended commands. |
Benzene.c | Same of above but written in C. |
Benzene.r | Same of above but written in REBOL. |
Demo.bat | Demo script. |
Demo.r | The same of the above, but written in REBOL. |
Distances.r | This REBOL script explains how to measure the interatomic distances. |
Graph.r | Demo of the extended commands to manage the plots. |
GraphApp demo.r | Demo of the GraphApp GUI library. |
Info.r | Show some information in the VEGA ZZ console. |
Meshload.r | Load & display a 3D rabbit mesh model. |
MP3 player.r | Minimalist mp3 player (fmod demo). |
Requesters.r | Simple demo of the VEGA ZZ built-in requesters. |
VEGA GL.c | Application example of the VEGA GL commands. |
View\VEGA ZZ toolbar.r | Show a REBOL/View toolbar to control the VEGA ZZ main features. |
This directory includes scripts for file format conversion and exportation:
CSSR SOMFA export.c | Export the current molecule in CSSR format readable by SOMFA. |
CSV export.c | Save the molecule in Comma Separated Values (CSV) format. |
Format conversion.r |
This script converts all files placed in a directory using the specified file format/compression. |
Inchi convert.c |
IUPAC InChI converter. The maximum number of supported atoms is 1024. |
This directory includes the visualization scripts:
Aminoacid selector.r |
Show the aminoacid by selection and/or by chemical/physical properties. |
Dump backbone torsions.c | Dump the phi and psi backbone torsions of a protein. |
Fasta to text.r |
Convert a Fasta into a text file. That's is useful to load it into Microsoft Excel. |
HIS protonantion.c |
Find the histidine protonantion state (on NE2 or on ND1) using the CHARMM potential and swap the hydrogens (e.g. H-NE2 to H-ND1) according to the hydrogen bond energy. If the energy difference between the H-NE2 and H-ND1 tautomers is more than 2.0 Kcal/mol the hydrogen is placed on the nitrogen realizing a structure with lower hydrogen bonding energy. The starting structure must contain the hydrogens. |
Move hydrogens to end.c |
Move the hydrogens to the end of the atom list. In this way, you can obtain files split in two parts: the first one containing the heavy atoms and the second one, placed at the end, containing the hydrogens. As an example, that's useful to write mol2 files compatible with the GOLD docking system. |
Remove apolar hydrogens.r |
Remove the apolar hydrogens from the current structure. |
It contains scripts for trajectory management.
Automatic quenching.r | Automatic quenching for dynamics trajectory files. |
Enantiomerizer.r | Convert the trajectory to another format inverting all chiral atoms. It builds the trajectory of the enantiomer. |
Ramachandran.c |
This script perform the Ramachandran analysis for each trajectory frame. Before running it, you must open a trajectory file. For each frame, the Phi and Psi backbone torsion angles are measured and evaluated if they are inside or outside the Ramachandran permission areas. For each frame is calculated the percentage referred to the total number of the residues and these values are visualized in a plot. This calculation is useful to highlight the secondary structure evolution during a MD simulation. If the percentage of the residues (Phi and Psi values) inside the permission areas is decreasing during the simulation, it means that the secondary structure evolves to a worse situation. Vice versa, if the percentage is growing, the secondary structure is improving. |
SDF export.c | Convert the current trajectory in a SDF database. Each structure in the database is equivalent to each frame in the trajectory file. |
Water remover.r |
Remove all water molecules from a trajectory converting it into a PDB multimodel file. This script is obsolete and it's maintained as example only. The same function is now implemented in VEGA ZZ without external scripts. |
This directory includes the generic scripts. Some of these require REBOL/View.
Calculator.r | Simple calculator (script by Ryan S. Cole). |
Calendar.r | Calendar and scheduler (script by Sterling Newton). |
Clock.r | Digital clock (script by Carl Sassenrath). |
Console.r | Open the REBOL console. |
Desktop.r | Open the REBOL desktop. |
Image viewer.r | Image viewer. |