Example Commands

This section gives a series of examples of CHOMP command-line executions. Unlike BROOD, CHOMP does not have a GUI and must be accessed from the command line. Each example is followed by a brief description of its behavior.

prompt> chomp -in mymolecules.smi -out myfragDB
prompt> chomp -i mymolecules.smi -o myfragDB
prompt> chomp mymolecules.smi myfragDB

All three of these command lines specify exactly the same thing. In each case, CHOMP will read the molecules in mymolecules.smi and write the BROOD database in the directory myfragDB. This is the most basic and most common CHOMP execution. Since the -dots flag defaults to True, dots will be written to std:cout to indicate the progress of the molecular fragmentation as the job progresses. The myfragDB directory will be filled with just over 40 files that contain all the information critical for efficient 3D BROOD searches.

prompt> chomp -param oldrun.param

This execution of CHOMP will read the command-line parameters from the file oldrun.param. Every time Chomp is executed, a file called chomp.param is written that records the command-line parameters used. This is useful for recalling what was used in a specific execution or for repeating a previous calculation.

prompt> chomp -userFrags myFrags.sdf -out newDB

This reads the molecular fragments from the myFrags.sdf and, bypassing the fragmentation phase, generates 3D conformers and relates precalculated parameters, and writes the database into multiple files in the newDB directory.

prompt> chomp -in myMolecules.sdf -userUnique oldDB -out newDB

This execution of CHOMP behaves the same as the prior execution, except that every fragment generated by the fragmentation of myFrags.sdf will be compared to the fragments in the BROOD database oldDB (generated earlier). Fragments that exist in the old database will not be included in the newDB.

prompt> chomp -in myMolecules.sdf -omega false -out newDB

This reads and fragments the molecules from myMolecules.sdf, then writes all of the fragments (including source information) to the SMILES file newDB.ism. It will not generate conformers nor will it write a BROOD database. The newly generated SMILES file is available for examination and editing. After this partial run, the database preparation can be completed by passing the SMILES newDB.ism into CHOMP using the -userFrags parameter.

prompt> chomp -in myMolecules.sdf -readConfs xtals.sdf -out newDB

This execution of CHOMP reads and fragments the molecules from myMolecules.sdf. Then, rather than using OMEGA to generate conformers for the database, CHOMP uses the conformers read from the structures in xtals.sdf to generate conformers for the fragments. These conformers will be written into the new BROOD database newDB.

prompt> chomp -smarts bondids mymolecules.smi myfrags.oeb.gz
prompt> chomp mymolecules.smi myfrags.oeb.gz -smarts bondids

This example demonstrates two important principles. The first is that the first of these two command lines will work, but the second will result in an error. When specifying a command line with keyless arguments for the -in and -out files, these files must be the final two arguments on the command line.

The second principle involves use of non-default fragmentation patterns. In this example, CHOMP uses the SMARTS patterns in the file bondids to generate fragments rather than the default fragmentation scheme.

prompt> chomp -mpi_np 16 -in mymolecules.sdf -out newDB

In this execution, the mymolecules.sdf is read, the molecules are fragmented, 3D conformers are generated and the database is written to the directory newDB. The fragmentation and the more expensive conformer generation will be carried out on 16 local processors. On modern multicore workstations, this parameter is often a highly efficient means to execute CHOMP.