Yet Another Script Collection or YASC

YASC is a collection of scripts I made to make my computational life easier. Most of the scripts are TINKER-oriented, but some are more generic. The scripts are mainly written in Python, but some of them are written in Perl or Fortran77. Anyway, all are freeware.

Two common "features" for all the YASC scripts are:

  1. the absence of a graphical user interface (GUI);
  2. the absence of common modules;

For many these are more issues than features, but the reasons why things are like that are:

  1. I am not a developer;
  2. a GUI is quite useless if your network does not allow to export the display when you run the software to a remote server;
  3. I have decided to prefer portability over efficiency: if there are not common modules, all the programs are stand-alone and they can be spread on your server as much and as messy you can. The main effort has been to make all the scripts work together, i.e. making a script use as input file directly the output file of another script.

Things may change in a remote future, but if you are willing to create a graphical interface, let me know.

use the software and the scripts in this wiki at your own risk. The software is freeware and it come without any (as in nothing, nada, niente, rien) WARRANTY. Therefore I cannot be responsible for loss of data, time, bad results or anything else deriving by the use of my software.


buildCstruct : CNT/graphite builder (python)
polybuild : polymer builder (python)


molgeom : analyze distances, angles and torsions between atoms (python)

Built for TINKER

modtnkxyz : modify cartesian coordinates in TINKER structures
fixtnkatypes : assign TINKER atom types
tnkfran: optimize and analyze TINKER structures

VMD scripts

VMD is one of the best and more powerful software to visualize and analyze molecular systems, not necessarily bio-stuffs like protein, DNA, drugs, lipids and so on. Plus, it has a TCL console, to allow to write and execute scripts. In the TCL console, you have access to almost all the VMD features available via the graphic interface, and you can combine them with TCL commands to create powerful scripts.

Here all the script I'm making for VMD. As usually, those are free and without any warranty.


fragpdb : split pdb structure in molecular fragments
gls : manipulate gaussian log file


This python script will calculate the number of solvent molecules to have a determined volume of the homogeneous liquid of the molecule at a given density. This script is helpful in particular to properly build a solvent box with the TINKER utility xyzedit.


Xplot is a script I have found on the net (sorry, i don't remember the link, if the author of the script will never read this page, I will be happy to put the give him credit for the script).


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