addet ocean-code

README.MD

@@ -1 +1,108 @@
-Placeholder for the source code of the publication "OCEAN: Optimized Cross rEActivity estimatioN"
+OCEAN - Optimized Cross rEActivity estimatioN
+--------
+
+So what is OCEAN?
+--------
+OCEAN is a web-tool for target-prediction of chemical structures which uses ChEMBL as datasource.
+For more details please feel free to read the [paper](http://www.paper.foo).
+
+Software dependencies
+--------
+
+We recommend to use [myChembl20-VM](http://chembl.blogspot.de/2015/07/mychembl-20-has-landed.html) which has almost everything you need to run OCEAN.
+
+Nevertheless here are the core-depencies:
+
+* `RDKit (2015.03.1)` http://www.rdkit.org/
+* `Django (1.7.1)`
+* `numpy (1.9.0)`
+* `sciPy (0.15.1)`
+* `your preferred database-server (Oracle or PostgreSQL, we didn't test MySQL or sqlite but they are supported by Django as well)`
+* `python module for your database-server (cx_oracle for Oracle, psycopg2 for PostgreSQL)`
+
+Optional dependencies
+--------
+
+* `matplotlib (1.3.0)`
+* `pillow (2.6.1)`
+* `images2gif (1.0.1)`
+
+Installation using myCHEMBL-VM
+--------
+Prepare and activate a virtual environment for OCEAN:
+```
+# create a virtualEnv for OCEAN
+virtualenv --system-site-packages ocean_env
+
+# activate ocean_env
+source ocean_env/bin/activate
+
+# install Django 1.7.1
+pip install Django==1.7.1
+```
+Get a clone of OCEAN from the Repo:
+```
+git clone https://www.github.com/rdkit/OCEAN.git
+cd OCEAN
+```
+Create a PostgreSQL-User, the database for OCEAN and fill the OCEAN-DB:
+```
+# create PostgreSQL-User for OCEAN
+# password 'ocean_pw' should be used when asked,
+# according to database-entry in settings.py
+createuser -P -s -d -r -e ocean_user
+
+# create PostgreSQL-Database for OCEAN
+createdb --owner=ocean_user ocean
+```
+If you want to use ChEMBL17-data for OCEAN you should:
+
+
+>change line `CHEMBL_VERSION = "chembl_%d" % (20)` in file `ocean/settings.py` to `CHEMBL_VERSION = "chembl_%d" % (17)`
+
+```
+createdb --owner=ocean_user chembl_17
+
+# create and populate OCEAN-DB (duration <2 min)
+psql chembl_17 < postgres_createOceanDB.sql
+./importOcean17DB.sh
+
+# Chembl17 is not a part of myChembl20-VM, so we need to create and populate
+# a few tables (duration <10 sec)
+psql chembl_17 < postgres_createTargetDict.sql
+./importChembl17Tables.sh
+```
+For ChEMBL20-data you should:
+```
+psql chembl_20 < postgres_createOceanDB.sql
+./importOcean20DB.sh
+```
+It's time to start OCEAN:
+```
+# On first start, you have to sync the django-server to create all missing tables.
+# When asked, you should create a superuser and set a password.
+# This is necessary to have access to the django-admin portal of OCEAN.
+python manage.py syncdb
+
+# Start OCEAN
+python manage.py runserver 0.0.0.0:8080
+```
+The next steps are necessary to create the fingerprints for all structures:
+1. Login to ocean-admin portal http://0.0.0.0:8080/admin
+
+2. Select *CHEMBL* and *6* (section a), press *createFPs* to create Morgan-Fingerprints for all entries. This may take a few minutes. You should see a message at the bottom of the site when the process is done.
+
+The last step is calculating the statistical parameters for OCEAN's scoring-function:
+1. In the Django-Admin portal select *CHEMBL*, *6* and activate Checkbox *rebuild Pairs* (section b), press *recalc Statistics for Fingerprint and Datasource* to calculate statistic-parameters for the scoring-function. This will also take a few minutes. Wait until you see a new message at the bottom of the site.
+
+If you have a MarvinJS licence, you can copy the MarvinJS-folder to `ocean/media/MarvinJS` and change the line `url(r'^$', main_smiles, name='home')` in `ocean/urls.py` to `url(r'^$', main_marvin, name='home')` to use MarvinJS as sketcher.
+
+Now lets try it:
+
+1. Open ocean-website http://0.0.0.0:8080
+
+2. Write a smiles-string into the *smiles*-field or sketch a molecule (if you have MarvinJS) and press Button *Start OCEAN-Search*. You should see the results after a few seconds.
+
+Questions or Problems?
+--------
+If you have any questions or problems with OCEAN please do not hesitate to contact [Paul Czodrowski](mailto:[email protected]) or [Wolf-Guido Bolick](mailto:[email protected]).