compare
SYNOPSIS
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>
DESCRIPTION
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:
PAIRWISE: each single conformation of file
is best-fitted on the matching conformation of the currently loaded dataset
BLOCK: the file dataset is best-fitted as a whole
rigid body on the currently loaded dataset, and individual RMS distances
between matching conformers are printed
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.
EXAMPLES
# 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
