Install



To build from source, please issue the following commands:

$ ./bootstrap
$ ./configure
$ make
# 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 chmod +x the setup.bin file on Linux, Mac OS X, Solaris and FreeBSD). You will obtain an open3dtools folder which contains a bin folder with the sdf2tinkerxyz and tinkerxyz2sdf executables, and a sdf2xyzs2sdf folder with the license, standard README and INSTALL documentation and a validation suite.

If you have not yet installed openbabel_for_open3dtools for 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.sh BASH script (on Windows, run it from a MSYS or Cygwin shell). If TINKER binaries are not in the path, the TINKER_PATH environment 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.

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Last update:
June 21. 2014 20:28:23

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