Unpacking the distribution files

The rDock source files and test suite files are provided as independent gzipped tar (.tar.gz) distributions. Depending on your requirements, the two distributions can be unpacked to entirely separate locations, or can be unpacked under the same location. In this example they are unpacked under the same location.

Table 2 rDock distribution files

File

Description

rDock_[CODELINE]_src.tar.gz

rDock source distribution

[TEST]_rDock_TestSet.tar.gz

Test suite data files and scripts

Here [CODELINE], and [TEST] will vary depending on the release and test set. [CODELINE] represents the major version string (for example, 2013.1) and [TEST] represents the given dataset (ASTEX, RNA or DUD).

Example unpacking procedure

Create a new directory for building rDock.

$ mkdir ~/dev

The directory you created is referred to as [BUILDDIR] in the subsequent steps.

Copy or download the distribution files to [BUILDDIR].

$ cp ~/mydownloads/rDock_2013.1_src.tar.gz ~/dev/

Extract the distributions.

$ cd ~/dev/
$ tar -xvzf rdock_2013.1_src.tar.gz

The distributions contain files with relative path names, and you should find the following subdirectories created under rDock_[CODELINE]_src. Note that the ./rDock_2013.1_src subdirectory may have a different name depending on the major version string (see above).

$ find . -type d
.
./fw
./src
./src/daylight
./src/lib
./src/exe
./src/GP
./build
./build/test
./build/test/RBT_HOME
./build/tmakelib
./build/tmakelib/linux-pathCC-64
./build/tmakelib/linux-g++-64
./build/tmakelib/linux-g++
./build/tmakelib/unix
./data
./data/filters
./data/sf
./data/pmf
./data/pmf/smoothed
./data/scripts
./lib
./import
./import/tnt
./import/tnt/include
./import/simplex
./import/simplex/src
./import/simplex/include
./docs
./docs/images
./docs/newDocs
./include
./include/GP
./bin

Make a note of the following locations for later use.

The rDock root directory is [BUILDDIR]/rDock_[CODELINE]_src and will be referred to as [RBT_ROOT] in later instructions. In this example, [RBT_ROOT] is ~/dev/rDock_2013.1_src/.