Awesome

reduce

Reduce - tool for adding and correcting hydrogens in PDB files

Deprecation notice

This version of reduce is being replaced by reduce2, which is integrated into the CCTBX project as described at https://github.com/cctbx/cctbx_project/tree/master/mmtbx/reduce with additional development being done there. The reduce2 program handle native CIF file input and is being maintained with ongoing file-format and other changes. Reduce2 is slower than reduce and there are a few corner-case files where it does not work, but it produces more accurate results in most cases.

Building

Makefile

The original Makefile-based build can be used on Unix-like operating systems. To use it, you run make in the root directory. It will build libraries in the libtbx, toolclasses, and reduce_src directories and place the reduce executable in the reduce_src subdirectory.

Once the code has been installed, run sudo make install to install it in /usr/local/bin and the required files in /usr/local.

CMake

A CMakeLists.txt file has been created to support cross-platform building use CMake. This supports building on Windows in addition to Unix-like platforms.

This approach supports out-of-source builds, where the build is done in a directory other than the source directory, so that build artifacts do not clutter the source tree (and in particular, to avoid clobbering the original Makefile files).

If the source has been checked out in ~/src/reduce then the following is one approach to doing a CMake-based build:

mkdir -p ~/build/reduce
cd ~/build/reduce
cmake ~/src/reduce
make
sudo make install

This will install the executable by default in /usr/local/bin and the required files in /usr/local. As with other CMake projects, the you can set the CMAKE_INSTALL_PREFIX variable and it will put the executable there under the bin/ directory and the HET dictionary in the prefix directory, telling the program where to find it.

Running

Once installed, if /usr/local/bin is on your PATH, reduce can be run using reduce. Use reduce -help for more information about the arguments and behavior of the program.

Installation using package manager

Ueno, M. (github ID eunos-1128) has graciously made the original (now deprecated) version of reduce available through standard installation channels as described below.

Conda

You can install reduce using conda package manager.

conda install reduce -c bioconda

Homebrew/Linuxbrew

You can also install reduce using homebrew (or linuxbrew).

brew tap brewsci/bio
brew install reduce