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 TODO List
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Notes on features that we might want to add in the future. If you are
willing to work on any of those projects and want to contribute ideas
or code then please get in touch with us (see README/AUTHORS for
contact details or http://mdanalysis.cooglecode.com)

Feature requests and pertinent bugs
===================================
(see also http://code.google.com/p/mdanalysis/issues/list )

* hydrogen bond analysis

* possibly use VMD's molfile plugins for reading?

* robust guessing of masses

* build a bonds list from a structure

* introduce new Residue classes such as AminoAcid(Residue) or
  NucleicAcid(Residue) with specific methods (e.g. phi/psi dihedrals);
  Bio.PDB has something like this

* add density data and enhance selections so that one can select
  molecules that are within a certain region


Streamline AtomGroup

- make the following methods properties:

    bfactors  (already attribute but scheduled to be a method in 0.8)
    charges
    indices
    masses
    names
    radii
    resids
    resnames
    resnums
    segids
    
    velocities
    coordinates

- for simple numerical values or strings return numpy arrays instead
  of lists

Improve topology handling

- create a Topology class that becomes part of Universe as
  Universe.topology: Universe is supposed to bind Topology and
  Trajectory together.

  Topology will then have methods to add/delete/copy
  atoms/residues/segments --- basically just add/delete Atom instances
  and then rerun build_residues()/build_segments().

  However, we could also use Andyi's PSFGEN port and use the VMD
  topology structure (in C) as our topology.

- move/mirror AtomGroup setters to topology??


Installation
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* intel compiler does not work (at least Ubuntu 8.04 Linux) 
  
