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Fragment replacement for Medicinal Chemistry | ||||
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Fragment replacement for Medicinal Chemistry | ||||
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This section has a series of example Brood command-line executions. Each example is followed by a brief description of its behavior.
In order to execute the following examples as written, the appropriate paths to
the executable file and the database file must be included. In addition, the
file amide.smi will need to be in the working directory. This can be
accomplished with the following command:
prompt> echo ``*C(=O)NC*'' >> amide.smi
This file can now be used as the query for each case below.
prompt> brood amide.smi frags.f50.oeb.gz prompt> brood -query amide.smi -db frag.f50.oeb.gz
These two commands will yield identical results. These execute Brood
with the default parameters. The file amide.smi is opened in SMILES
format as the query, and the file frag.f50.oeb.gz is read in OEBinary
format. The four hitlists will be written to brood.struc.oeb.gz,
brood.color.oeb.gz, brood.elect.oeb.gz and
brood.queryAnalog.oeb.gz, using the default -prefix argument
``brood''. Similarly, the informational output files brood.info,
brood.log, brood.param and brood.rpt will also be written.
prompt> brood -query amide.smi -db frag.f50.oeb.gz -prefix 4dfr
This command is the same as the previous except that the prefix to all of the
output files has been changed from ``brood'' to ``4dfr'' (for example, the log
file will be written to 4dfr.log rather than brood.log).
prompt> brood -prefix 4dfr amide.smi frag.f50.oeb.gz
This command will yield exactly the same results as the example above.
amide.smi will be mapped to the -query flag and
frag.f50.oeb.gz will be mapped to the -db flag.
prompt> brood amide.smi frag.f50.oeb.gz -prefix 4dfr
Though this command-line appears quite similar to the one above, this one will
not work. In the current release of all OpenEye software, all flagged
parameters, such as -prefix, must appear before any keyless parameters,
such as amide.smi on the command line.
prompt> brood -query amide.smi -db frag.f50.oeb.gz -prefix 4dfr -report myRpt
This executes Brood as above, however, the -report argument
over-rides the -prefix argument and the report file is written to the
file ``myRpt'' rather than the file ``4dfr.rpt''.
prompt> brood -param 4dfr.param
This execution of Brood will read all the command-line arguments from the
file ``4dfr.param''. Every time Brood is executed, a param file is
generated that can be used to exactly reproduce the run (vide infra).
prompt> brood -param 4dfr.param -maxHit 2500 prompt> brood -param 4dfr.param -maxHit 5000
The first of these command-lines will execute Brood with the parameters
from ``4dfr.param'', but the -maxHit parameter will be overridden to a
value of 2500. This indicates that 2500 compounds will be stored in each of
the four hitlists. The second command-line shown here will fail to parse
because the -maxHit parameter has an acceptable range of 1-2500.
prompt> brood -query amide.smi -db frag.f50.oeb.gz -oformat sdf -sdtag
This execution will be as before, except now the four hitlist files will be
written in .sdf format. Further, the score of each of the ligands in the file
will be attached to the molecule as SD Tag data.
prompt> brood -query amide.smi -db frag.f50.oeb.gz -dots
The execution will be as before except a single '.' will be written to the
screen every time 25 database fragments are processed. This gives an easy
visual measure of the progress of the execution.
prompt> brood -query amide.smi -db frag.f50.oeb.gz -build mol.smi
The -build flag indicates that the query fragment in amide.smi
will be located in the molecule specified by mol.smi and then each of
the similar fragments in the hitlist will be used to replace that fragment in
the whole molecule to generate a new analog molecule. Since the molecule
specified with the -build flag in this instance is 2D, all of the final
molecules will be generated with 2D coordinates.
prompt> brood -query amide.smi -db frag.f50.oeb.gz -build mol.mol2
This command line acts similarly to the one above. In this case, the molecule
specified by the -build parameter has 3D coordinates. This causes the
query's 3D coordinates to be copies out of the -build molecule
(rather than being generated as a minimized MMFF structure). Further, the
constructed analog molecules will be generated with minimal perturbation to the
3D geometry of the -build molecule.
prompt> brood -query amide.sdf -db frag.f50.oeb.gz -build mol.smi
Again, this execution is similar to the one above. In this case, the query
fragment has 3D structure, but the -build molecule does not. The 3D
query will be carried out with the coordinates specified in the
amide.sdf file, but the built molecules will all be generated with only
2D coordinates.
prompt> brood -query amide.sdf -db frag.f50.oeb.gz -build mol.mol2
In this final example of a -build execution, both the query fragment and
the -build molecule have 3D coordinates. Here, the input 3D coordinates
of the query fragment are discarded and the 3D coordinates that the query
fragment has inside the -build molecule are used to both carry out the
search and to build the analog molecules.
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