compare  file=<SDF file containing a set of conformations to be compared to the currently loaded ones>  \
    [type={PAIRWISE | BLOCK}; defaults to PAIRWISE];  \
    [aligned=<SDF file where the fitted conformations may be written>


The compare keyword allows to compare two sets of different conformations of the same dataset, such as those produced by the align keyword. In particular, a set of conformations contained in a file specified through the file parameter is compared to the set of conformations currently loaded by the import command. A table with heavy-atom RMS distances between matching pairs is printed; optionally the best-fitted conformations (that is, the conformations of the file dataset best-fitted on the currently loaded conformations) may be written to an aligned SDF file. The best-fit can be accomplished according to two different paradigms:
By default, the compare module operates in parallel fashion on multiprocessor machines, using all the CPUs available in the system; if one wishes to run the computation on a lower number of CPUs, this may be specified before calling compare with the env n_cpus keyword.


# the following commands performs a pairwise best-fit of file2.sdf on file1.sdf
import  file=file1.sdf
compare  file=file2.sdf

# the following commands performs a block best-fit of file2.sdf on file1.sdf, saving results in file2_aligned_on_file1.sdf
import  file=file1.sdf
compare  type=block  file=file2.sdf  aligned=file2_aligned_on_file1.sdf

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Last update:
May 31. 2015 20:39:55

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