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External Files

Input Files

Typically, a user will find it most convenient to generate the BROOD query using the graphical interface. Even if one wants to run BROOD on a cluster or other machine where it isn’t convenient to use the graphical interface, the graphical interface can be used to generate the necessary input and then BROOD can be executed on a different machine after moving the input files. BROOD requires one input file, a query fragment file. With a default installation, the BROOD application can search either one of the default fragment database or a user-generated database (see Database preparation).

Query Files

The entire query is encapsulated into a single query file, typically generated in the GUI. When generated, the GUI names the file brood_1_query.oeb.gz where the 1 is replaced with the next appropriate integer to maintain unique file names. This BROOD query includes the original molecule, the fragment that the user has chosen to replace, the user-edited description of the shape, chemistry and electrostatics of the query. In addition, if the query includes protein structures either for bump-check or selectivity-check, these too will be encapsulated in the query file.

BROOD carries out a 3D search, and a 3D search is required for the search and is usually included in the query file. The BROOD GUI can take either a 2D or a 3D query file. If the original input is 2D, a 3D structure will be generated in the GUI and used during the search.

Fragment Database

As mentioned in the theory section, BROOD comes with a pregenerated, multiconformer fragment database. This database is made from fragments of known molecules that contain 1-15 heavy atoms and 1-3 attachment sites.

BROOD can also search user-generated fragment files. Details on how to create a custom database are included in a later chapter (see Database preparation).

Example Fragment Files

The database file used for BROOD searches is in a highly optimized format with many pre-calculated properties and a complex structure intended to minimize disk access during the time-critical search. These database files can be generated by the CHOMP program included with your BROOD distribution. By default, CHOMP will generate fragments from complete molecules. On the other hand, if a user has their own fragment files they would like to search, these can be loaded directly into the CHOMP program and used to generate a searchable database.

In this case input database fragment for bioisostere searching must be a molecular fragment with one or more “attachment points”. An attachment point represents a bond from the fragment to the rest of the molecule. Inside OEChem, this is represented as a bond to an atom with atomic number 0 (termed a “Dummy Atom”). If it is necessary to uniquely distinguish these dummy atoms, Map Indices can be used via the OEAtomBase::SetMapIdx() and OEAtomBase::GetMapIdx() api.

The input fragment does not need to have 3D coordinates (they can, optionally, be generated on-the-fly). This makes SMILES and 2D SDF file formats the most convenient for query fragment input. On the other hand, the fragment database should contain 3D coordinates with multiple conformers per fragment. In the examples below, a simple amide fragment with generic (amide) and uniquely labeled (amideR) dummy atoms are shown.

SMILES format:

*C(=O)N* amide
[*:1]C(=O)N[*:2] amideR

SDF format:

amide
  -OEChem-01040614232D

  5  4  0     0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 *   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 *   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
M  END
$$$$
amideR
  -OEChem-01040614232D

  5  4  0     0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
M  RGP  2   1   1   5   2
M  END
$$$$

Output Files

BROOD generates seven output files in addition to the hitlist. All of these files begin with the prefix specified by the -prefix flag, that by default is “brood”. The also include an integer to retain unique file names in the working directory (in this example, we will use the integer “1”). These files include:

  1. brood_1.info, the info file
  2. brood_1.log, the log file
  3. brood_1.param, the param file
  4. brood_1.rpt, the report file
  5. brood_1.csv, the spreadsheet file

By default, there is one hitlist and the contents of the hitlist will be determined by the command flags.

  • brood_1.hitlist.oeb.gz

In post-processing of the search, some fragments are removed from the hitlist. These are preserved in the “removed” file.

  • brood_1.removed.oeb.gz

If the -ET flag is used, the hitlist will include molecules electrostatically similar to the query.

Before executing the search, the GUI also writes the encapsulated query into the query file.

  • brood_1_query.oeb.gz

Info File

By default, an information file titled brood_1.info is written or updated for every 500 fragments that are processed. Reading this info file allows a user to monitor the progress of the database search while it is occurring and it serves as a record of the performance of that search after the execution is completed. During execution, the GUI uses this file as well as direct communication with the application to keep the user apprised of all information available in the info file.

An example info file is shown below.

*********** Progress Update ***********
Percent of Database Processed    = 100%
Total packets read               = 329
Packets suitable for Processing  = 99
Number of Fragments Overlayed    = 92134
Number of Fragments Eliminated   = 74560
Number of Fragments Processed    = 166694
Number in color hitlist          = 300
  Remove for quick search        = 291
  Remove protein clashes         = 0
  Remove select protein          = 0
  Remove duplicates              = 0
  Remove unstable bonds          = 0
  Remove strained molecules      = 0
Number in final hitlist          = 9
Number of Warnings               = 2
Number of Errors                 = 0
Processed fragments/sec          = 1742
Elapsed Time (sec)               = 95
***************************************

If any warnings or errors are noted in the info file, it is strongly suggested that a user check in the log file to determine the nature of the problem!

Param File

BROOD’s command-line interface can be efficiently run using the -param command line parameter followed by the name of a parameter file. Param files are files that contain one command-line parameter on each line. Every execution of BROOD, including executions started within the GUI, generates a .param file called brood.param. This file contains all of the parameters used by BROOD. Further, this file can be used in subsequent runs with the -param flag either with or without user modifications.

The .param file is particularly useful if you want to use the graphical interface to set up a job, but execute the job on another machine (such as a cluster). The .param file can be moved to a different machine along with the -queryMolecule file it specifies and it can be used to execute exactly the same run as would have been executed from within the graphical interface.

The following is an example of a .param file generated by the GUI (brood_1.param). It can be used to regenerate the run using the command-line below.

This file could be edited or used “as-is” with subsequent runs. In addition, any explicit command-line parameter takes precedent of parameters in the .param file, so this mechanism can be used to execute a series of similar jobs.

prompt> brood -param brood_1.param

prompt> brood -mpi_np 16 -param brood_1.param -prefix brood_mpi1

Listing of brood.param file contents:

#Interface settings

#Execute Options :
  -param  /Users/chemist/data/brood_49.param
  -input_chunksize  10
  -success_chunksize  10
  -failure_chunksize  10

#Brood :

  #Input :
      #-queryFrag (Not set, no default)
      -queryMol  /Users/chemist/data/brood_49_query.oeb.gz
      -db  /Users/chemist/data/db/chembl17
      #-prot (Not set, no default)
      #-select (Not set, no default)
      #-noqueryprot  false
      #-cpddb  none
      #-param (Not set, no default)

  #Output :
      -prefix  brood_49
      -dots  true
      #-log (Not set, no default)
      #-info (Not set, no default)
      #-report (Not set, no default)
      -format  oeb.gz
      -csv  true
      -idea  true
      -neutralpH  true
      -tautomer  true
      -hitlistProt  true

  #Control parameters :
      -quickLook  true
      -ringOnly  true
      -ET  false
      -linkOnly  false
      -sdTag  verbose
      -checkBond  true
      #-maxHit  1000
      #-title (Not set, no default)
      -attachColor  false
      #-attachFrag  true

  #Advanced parameters :
      #-bondOrder  true
      -attachmentCutoff  0.78
      -shapeCutoff  0.6
      -attachmentScale  1.5
      -checkGeometry  true
      -fromCT  false
      -fileChrg  false
      -interval  5000
      -hitinterval  1000
      #-maxFrag  0
      -rangeSize  6
      -rangeOffset  0
      -bumpRadius  2.25

  #Property Selection :
      -property  false
      #-maxMolWt  500.0
      #-minMolWt  100.0
      #-maxlogp  5.0
      #-minlogp  -1.0
      #-maxpsa  150
      #-minpsa  60
      #-maxRotBond  13
      #-minRotBond  0
      #-maxHvyAtom  35
      #-minHvyAtom  7
      #-maxLipinskiDon  8
      #-minLipinskiDon  1
      #-maxLipinskiAcc  11
      #-minLipinskiAcc  2

  #Synthetic Properties :
      #-maxComplexity  1.0
      #-minComplexity  0.0
      #-maxFreq  100
      #-minFreq  1

  #Derived Property Selection :
      #-maxLipinski  1
      #-minLipinski  0
      #-maxMartin  1.0
      #-minMartin  0.2
      #-eganEgg  true
      #-veber  false
      #-maxFsp3C  1.0
      #-minFsp3C  0.3
      #-maxAromFJCt  5
      #-minAromFJCt  0
prompt> brood -param brood.param

This would result in exactly the same execution as the one which generated the file above.

Log File

The log file contains all of the critical information about the execution in one place. It begins with a copy of the param file and it finishes with the final info file output. In between, it contains all the warnings and errors that might have occurred during execution. The log file gives a user a single place they can check to determine what job was run, if it executed properly and how long it took.

Report File

The report file contains a detailed listing of the similarity scores for every molecule in the database that was sufficiently similar to warrant a 3D overlay. By default, the file is titled brood_1.rpt and contains 1 line for the column titles and 1 line for each molecule in the database (tab separated columns). The report file contains columns for

  • database fragment SMILES
  • database fragment title
  • query SMILES
  • number of attachment bonds
  • structural rms value
  • attachment score
  • shape Tanimoto
  • color Tanimoto
  • combo score (shape + color)
  • et attachment score
  • et shape Tanimoto
  • electrostatic Tanimoto
  • et combo score (shape + et)
  • a comment regarding the disposition of the fragment (if and why it failed to be scored)

If a particular score was not calculated for any given fragment, “-” will be found in the report file under the corresponding column. Since all the data for a fragment is contained in a single line, there is only one report file regardless of the number or type of the number or type of hitlists generated. This file is in tab separated format and can easily be imported into a spreadsheet program for further analysis of the results.

Hitlist File

As discussed above, a hitlist is generated for each execution of BROOD. All of the hitlists are written in the file format specified by -format, which defaults to gzipped OEB format .oeb.gz. If the -queryMolecule flag is specified, the hitlist will contain complete molecules, otherwise it will contain fragments. The first entry in the hitlist is the query molecule or query fragment. Each subsequent analog molecule (fragment) in the hitlist is oriented in the optimum overlay on the query molecule (fragment). For the “struc” hitlist, this overlay is the optimum overlay of the attachment point atoms. In addition, by default, the similarity scores and physical property data for each molecule (fragment) are attached as SDTags (OEB and SD format only). In the case when the queryMolecule is not specified, but the -ET flag is set, in the hitlist, the attachment vectors of the fragments are replaced by methyl groups. This facilitates easy calculation of electrostatic potentials in data visualization programs such as VIDA.

By default, the hitlist files are written periodically while the search is being carried out (see -hitinterval). This allows a user to examine results at intermediate stages without waiting for the entire search to complete.

If the -queryMolecule flag specified a 2D input molecule, then all of the analog molecules in the hitlist will likewise be in 2D format, though the fragment similarity search will have been carried out in 3D. When using the graphical interface with a 2D input molecule, a 3D molecule is generated prior to processing and the output format will always be 3D.

Removed File

At the end of the primary fragment search, a complete hitlist is generated. In post-processing, the fragments are build into whole molecules and tested for strain, the newly formed bonds are examined for chemical stability, potential duplicates in the hitlist are removed, the new molecules are checked for bumps with the protein environment and against the optional selectivity protein. At any of these stages fragments that are similar according to the primary search criteria may be removed from the hitlist for these secondary criteria. In rare cases, few fragments may remain in the final hitlist and the user may want to examine the removed fragments without needing to re-run the entire search. For this reason, any fragment removed at the post-processing stage is written to the removed hitlist brood_1.removed.oeb.gz.