To build from source, please issue the following commands:
# make install
sdf2xyz2sdf has been successfully built on Windows, Linux, Intel Mac OS X, Solaris x86, FreeBSD using GNU GCC compilers version 4.0 and upper.
sdf2xyz2sdf pre-built binary distributions are provided with all the required dependencies. To use pre-built binary distributions, download and run the installer for your OS (after downloading, you will need to
setup.binfile on Linux, Mac OS X, Solaris and FreeBSD). You will obtain an
open3dtoolsfolder which contains a
binfolder with the
tinkerxyz2sdfexecutables, and a
sdf2xyzs2sdffolder with the license, standard
INSTALLdocumentation and a
If you have not yet installed
openbabel_for_open3dtoolsfor your OS, please download and install them in the same folder where you previously installed sdf2xyz2sdf.
Please note that if you previously installed other Open3DTOOLS, such as Open3DGRID, Open3DALIGN and Open3DQSAR, you should already have installed
openbabel_for_open3dtools, so you need not install them again as long as you install all of the Open3DTOOLS in the same place on your hard disk.
To check that the installation is OK, run the
sdf2xyz2sdf/validation/test.shBASH script (on Windows, run it from a MSYS or Cygwin shell). If TINKER binaries are not in the path, the
TINKER_PATHenvironment variable will have to be set accordingly.
The test consists in the official MMFF94 and MMFF94s validation suites available on CCL.NET.
If everything goes well, all energy values should be in good accordance with literature (deviation < 0.01 kcal/mol), including ionic heteroaromatic rings which could not be assigned proper charges by the original TINKER-MMFF code. Only CYGUAN01 should raise a warning (deviation ~ 0.3 kcal/mol); the reasons of this discrepancy are given by Nicolas Staelens here.