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Saturday, December 17, 2005
You can find the list my ports hear. There are some programs which can be helpful for chemists: OpenBabel, EasyChem, Molden, ViewMol, ChemTool, gChemPaint and Povray. The last one can be also useful for others. I also added Polish dictionary for aspell, it have alt(ernative) in the name, but it is the official dictionary now. There are also my version of Gajim (with speller), Mutt with sidebr patch and WmCalClock (fixed problems with download). Recently, I added nice tool to creating static html image galleries - igal.
Tuesday, December 06, 2005
I created the filter which allow to load files with Cartesian geometry into viewmol. These files have a number of atoms in the first line and comments in the second one. Next description of all atoms goes. In each line there are: symbol of element and location of atom (x,y and z vectors). You can obtained this kind of files i.e. from molden program. The filter script is written in python:
#!/usr/bin/python from sys import * def change(a,linia): return float(linia.split()[a]) def reading (file_inp): factor=1 a_number=int(file_inp.readline()) file_inp.readline() for i in range (a_number): linia=file_inp.readline() atom.append(linia.split()) x.append(change(1,linia)*factor) y.append(change(2,linia)*factor) z.append(change(3,linia)*factor) file_inp.close return(atom,x,y,z,a_number) atom= x= y= z= atom,x,y,z,a_number=reading(open(argv)) print('$title') print(argv) print('$coord') for n in range(a_number): print('%14.4f %10.4f %10.4f %7c'% (x[n],y[n],z[n],atom[n])) print('$end')To use it you have to copy xyz.py file into your $VIEWMOLPATH (usually in /usr/lib/viewmol), and modify your viewmolrc file (it should be located in your $VIEWMOLPATH). You have to add one line :
option xyz $VIEWMOLPATH/xyz.py '%s' "SCF Done"Now you can read your xyz file into viewmol using commandline option:
viewmol -xyz name_of_file