Subject: Python code for computational chemistry

From: [email-masked] (Hinsen Konrad)
Date: Tue, 30 Jan 1996 14:48:33 -0500

I have made some Python code for computational chemistry available at
the CCL archive. It can be found via the URLs

  ftp://www.ccl.net:/pub/chemistry/software/SOURCES/PYTHON/HINSEN
  gopher://www.ccl.net:73/11/software/SOURCES/PYTHON/HINSEN

For those who don't know Python, it's a high-level, object-oriented,
interpreted general-purpose programming language. There is a free and
reliable implementation that is being improved constantly by a growing
community of users. There is already an impressive range of extension
modules taking care of applications as diverse as Web browsers,
databases, and numerical calculations. For more information point
your Web browser at http://www.python.org.

Here's a short description of the modules at the CCL archive:

PDB.py

  High-level I/O with PDB files. Allows you to deal with PDB files as if they
  were lists of residues and atoms. Example:
     for residue in PDBConfiguration('protein.pdb'):
         for atom in residue:
             print atom.name, atom.position

Derivatives.py

  Automatic derivatives. Calculates analytical derivatives numerically, given
  only the original function. Example:
     x = DerivVar(1.1,0)
     y = DerivVar(0.44, 1)
     f = exp(x**2+y**2)
     print f
  prints:
     (4.06982499598, [8.95361499116, 3.58144599646])

Potential.py

  Automatic gradient calculation for potential functions (or any function).
  Example:
     def harmonic(k, r1, r2):
          dr = r1-r2
	 return k*dr*dr
     harmonic_g = PotentialWithGradients(harmonic)
     energy, gradients = harmonic_g(100., Vector(0,3,1), Vector(1,2,0)
     print energy, gradients
  prints:
     300.0
     [Vector(-200.0,200.0,200.0), Vector(200.0,-200.0,-200.0)]

Vector.py

  3d-vectors, used by the three other modules.

umath.py

  Simplified substitute for the module "umath" from the
  numerics package. Use it only if you don't have the
  numerics package. This module is used by all the other
  modules in this directory.

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Konrad Hinsen                     | E-Mail: [email-masked]
Departement de chimie             | Tel.: +1-514-343-6111 ext. 3953
Universite de Montreal            | Fax:  +1-514-343-7586
C.P. 6128, succ. Centre-Ville     | Deutsch/Esperanto/English/Nederlands/
Montreal (QC) H3C 3J7             | Francais (phase experimentale)
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