allpy
view README.devel @ 817:835efa2a8c71
optimization of rasmol_homology: keep structure loaded of two sequences only
One of steps of this program is superimposition of all sequences
with main sequence and saving of all structures to pdb file.
Loaded structure of all sequences is not needed to do this.
At every moment only structure of main sequence and of superimposing sequence.
This optimization results in essential memory saving.
Output files should be the same to previous revision.
To implement this optimization methods supeimpose and save_pdb
of alignment were replaced with methods with same names of sequence.
So some code is same as code of methods of alignment.
Note: behaves as before, with superimpose and save_pdb methods of alignment.
Model was returned by these methods but never used while generating spt script.
This can result in collisions of rasmol selections when number of sequences is
greater than max number of chains of one model.
author | boris (kodomo) <bnagaev@gmail.com> |
---|---|
date | Fri, 15 Jul 2011 02:23:27 +0400 |
parents | b87eb91bd929 |
children |
line source
1 Using library in-place
2 ======================
4 To use the library in-place, without installing, you have to add it's
5 directory to PYTHONPATH.
7 e.g, type this in your shell::
9 export PYTHONPATH=`pwd`
11 alternatively, you can type::
13 . ./SETPATH
15 which adds the right path to PYTHONPATH and also adds 'utils' directory
16 to PATH.
18 NEWS file
19 =========
21 NEWS file contains news that are important to the library users, not to the
22 devels. It must contain a word abot every change in any interfaces. It may
23 contain a word about bugfix, if that bugfix was important and could cause users
24 some grief. It must not contain anything else.
26 The file grows upwards (like blog, so that all the most important things are at
27 the top, like)
29 Example file format::
31 1.3.1 (2011-05-01)
32 * bugfix: the Moon was going to fall
34 1.3.0 (2011-04-15)
36 * new: new feature description
37 * new: new feature description
38 * change(!): critical library interface change
39 * change: change in the library interface
40 * bugfix: short bug summary, see #ticket
41 * bugfix: important bug that could destroy the Earth but did not hit trac