filter  [type={INTRA | INTER; defaults to INTRA}]}  \
    [level={degree of similarity above which duplicate conformers are discarded (0.0-1.0); defaults to 0.7}]}  \
    [object_list=<comma/hyphen separated list or ALL>; defaults to ALL]}; defaults to INCLUDE_LIST]  \
    [hybrid={YES | NO; defaults to NO}]  \
    [merge={YES | NO; defaults to NO}]  \
    [template_conf_dir=<directory from which SDF conformational databases are retrieved>; defaults to qmd_dir, if defined]  \
    [filter_conf_dir=<directory in which filtered SDF conformational databases are stored>]


The filter keyword is used to reduce the number of conformers available in a conformational database associated to a dataset to the truly diverse ones, in order to reduce the number of multi-template alignments to be computed.
To this purpose, pharmacophores are extracted by Pharao from the initial pool of available template conformations. Subsequently, pairwise comparisons are made between pharmacophores, assessing the value of two similarity indexes computed by Pharao namely Tanimoto and Tversky scores, both ranging from 0 to 1. The filtration can be carried out within the conformational database associated with each template molecule (type=INTRA), or among all available template conformational databases (type=INTER).
Usually, the two filtering steps are carried out sequentially, picking the conformations for the type=INTER step from the filtered database generated by the type=INTRA step carried out previously.


# the following command performs intra-database filtration merging nearby compatible pharmacophores into a single pharmacophore, not using hybrid pharmacophores, using the default 0.7 similarity threshold, picking initial conformational databases from the initial_folder directory and putting filtered databases in the intra_filtered_folder directory; all available objects are filtered
filter  hybrid=y  merge=y  template_conf_dir=initial_folder  \
    filter_conf_dir=intra_filtered_folder  type=intra  pool=include_list  object_list=ALL

# the following command performs inter-database filtration with the same settings as before, picking as initial conformational databases those previously filtered with type=INTRA, and putting the further filtered databases in the inter_filtered_folder directory
filter  hybrid=y  merge=y  template_conf_dir=intra_filtered_folder  \
    filter_conf_dir=inter_filtered_folder  type=inter  pool=include_list  object_list=ALL

Print version
Mailing list

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

Powered by
CMSimple - CMSimple-Styles

Get Open3DALIGN at Fast, secure and Free Open Source software downloads

Would you like to test your
alignment in a 3D-QSAR
model? Try Open3DQSAR
Just wish to compute a MIF?
Try Open3DGRID