Install from source

Building Open3DALIGN is very straightforward. Open3DALIGN can be built without effort on virtually any platform which supports GNU Autotools (i.e., Autoconf and Automake). Interestingly, a native Windows executable which does not depend on any third party DLLs can be obtained using only MinGW and MSYS.

Open3DALIGN depends on BLAS and LAPACK math libraries, which exist under both open-source and vendor implementations. A very efficient, freely available implementation is the ATLAS library, which can be easily built for all platforms; building and installation of this library are described in great detail in the ATLAS website and are also summarized here. Alternatively, an excellent vendor implementation is the one included in the Sun Studio compiler suite, which is available to Linux and Solaris users for free. Another BLAS/LAPACK implementation is the one provided by the Intel Math Kernel Library, which is available at no cost for Linux non-commercial developers, while a license has to be purchased for Windows and Mac OS X versions.

Open3DALIGN has been successfully built on the following platforms:

  Windows

  Linux

  Intel Mac OS X

  Solaris x86

  FreeBSD

Each hyperlink points to detailed compilation/installation instructions for the different operating systems.

Please note that Open3DALIGN has a number of dependencies, namely:

• Open3DQSAR
  Open3DALIGN depends on the Open3DQSAR library libo3q.a; therefore, prior to installing Open3DALIGN, you should install Open3DQSAR
  as described in the Open3DQSAR website.

• OpenBabel
  The latest CVS OpenBabel version can be downloaded from the OpenBabel website. and installed as per the OpenBabel website instructions. Alternatively, you may download the openbabel_for_open3dtools self-installing package for your OS from the binary downloads page.
  

• Pharao
  Pharao is an open source program for generation and alignment of pharmacophores released under the GPL by Silicos. It depends on OpenBabel and its installation is very straightforward following the instructions reported in the documentation. On some platforms (e.g., Windows) you might need to include the directory containing the Pharao binary to the executable path setting the PATH environment variable appropriately. Alternatively, before executing Open3DALIGN you may point the O3_PHARAO environment variable (or alternatively use the env pharao keyword in your Open3DALIGN script) to the Pharao executable.

• TINKER
  The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics. It can be obtained from the TINKER webpage both as source code and as pre-built binaries for Windows, Linux and Mac OS X. You might need to include the directory containing TINKER binaries to the executable path setting the PATH environment variable appropriately. Alternatively, before executing Open3DALIGN you may point the O3_TINKER_PATH environment variable (or alternatively use the env tinker_path keyword in your Open3DALIGN script) to the directory which contains TINKER binaries.