Summary
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PSSH2 is a collection of tools for creating the sequence-to-structure alignment database PSSH2.

The system has recently seen a huge overhaul, since we have moved to AWS and hhblits3. 

In the src/cloud directory, there are start-up scripts to copy into the user-data on AWS.
These will automatically start processes that run hhblits to generate data for building 
a custom database or to scan structures against that custom database.

hhsuite is now automatically installed from GitHub rather than from any package.

Parameters are collecected in pssh2.conf. Two examples of how that could look like are in
src/pssh2/. Most of the scripts look of a conf file either in a location specified as 
an environment variable (conf_file) or in /etc/pssh2.conf. 



This was the old README:
------------------------

For convenience, the hhsuite, that is used in PSSH2, is also included in this repository. 
The hhsuite is developed and maintained by Soeding and his team at ftp://toolkit.genzentrum.lmu.de/pub/HH-suite/
or as a debian package.

In this repository, the data directory contains all the PSSH2 data that is small enough
to be distributed in a git repository. For the rest, there are just stubs to indicate 
which directories exist at Rostlab.

The src directory contains two main subdirectories, the one for generating and updating pdb_full,
and the one for generating and updating pssh2. 

Setup for pdb_full: Change paths in the scripts if you move to another place! 
(set in the beginning of renew_pdb_full.sh)

Updating pdb_full:
src/pdb_full/renew_pdb_full.sh -u -d <db_name> > & update_pdb_full.log &
Redoing pdb_full from scratch:
src/pdb_full/renew_pdb_full.sh -d <db_name> > & renew_pdb_full.log &

Generating PSSH:
see src/pssh2/pssh2_seq -h
.... TODO