Subsections

5.7 Complete list of output files

This is a complete list of all output files FRED can write during a run. Some of these files may not be written depending upon user input.

<prefix>_setup.txt: : Setup File
<prefix>_status.txt: : Status file
<prefix>_info_log.txt: : Information message log
<prefix>_info_log.txt: : Warning log
<prefix>_receptor.oeb.gz: : Protein file
<prefix>_<scoring function>_scores.txt: : Score File
<prefix>_<scoring function>_docked.<file ext>: : Docked Structure File
<prefix>_<scoring function>_alt_scores.txt: : Alternate Score File
<prefix>_<scoring function>_alt_docked.<file ext>: : Alternate Docked Structure File
<prefix>_consensus_scores.txt: : Non-masc consensus hitlist scores.
<prefix>_consensus_docked.<file ext>: : Non-masc consensus hitlist docked structures.
<prefix>_masc_consensus_scores.txt: : MASC consensus hitlist scores.
<prefix>_masc_consensus_docked.<file ext>: : MASC consensus hitlist docked structures.
<prefix>_undocked_<return code>.smi: Smiles file listing the molecules FRED could not dock.

where <prefix> is the setting of the -prefix flag and <file ext> is the setting of the -oformat flag which also determines the molecular format used. <scoring function> is the name of one of the selected scoring functions (see section 7.5). In the case where more than one scoring function is used a separate file is written for each scoring function.

5.7.1 Setup File

<prefix>_setup.txt

This file is automatically written at the beginning of each FRED run. This file lists the settings of every parameter used during the FRED run (this includes the default setting of parameters that were not explicitly set by the user). This file can be used as a parameter file to duplicate the original FRED run that generated the file (provided all of the required files are still present).

5.7.2 Status File

<prefix>_status.txt

This file is written during at the beginning of a run and updated every few seconds during the course of the run. It lists information about the status of the current FRED run.

5.7.3 Information message log

<prefix>_info_log.txt

This file contains informational messages that are sent during the run. It is primarily used by FRED during a multiprocessor run to report the progress of the slaves.

5.7.4 Warning log

<prefix>_warning_log.txt

This file contains a log of any warnings issued during the run. The first time a warning is issued FRED will splash a message to stderr indicating that a warning log is being created. All subsequent warning will be redirected to the warning log, and a 'W' character will be inserted into the screen output to indicate that a new warning was issued.

5.7.5 Receptor file

<prefix>_receptor.oeb.gz

This file contains a copy of the receptor file FRED used (or created).

5.7.6 Score Files

<prefix>_<scoring function>_scores.txt

A separate score file will be written for each of the selected scoring functions. The format of the file is a tab separated text file, which contains the name, score, score components and a smiles representation of each ligand in the hitlist (one per line). The number and ordering of ligands in this file depends upon the setting of the -serial and -hitlist_size flags as follows.

If the -serial is false (the default setting) the ligands will be sorted by score and the maximum number of ligand appearing in the list will be specified by the -hitlist_size flag, which defaults to 1000.

If the -serial flag is true every ligand that FRED successfully docks will appear in the score file. If FRED is not being run in PVM mode the order of molecules in the output file will be the order they appear in the input file. Information for each ligand will be written as the ligand is docked, rather than at the end of the docking run, as occurs when -serial is false.

5.7.7 Docked Structure Files

<prefix>_<scoring function>_docked.<file ext>

Docked structure files will only be written if the -output_structs flag is true (true is the default setting). A separate docked structure file will be written for each of the selected scoring functions. The top scoring pose of each ligand will appear in the file. The format of the file and <file ext> is determined by the -oformat flag. Which ligands are listed in the file depends upon the setting of the -serial and -hitlist_size flags.

If the -serial flag is true every ligand that FRED successfully docks will appear in the docked structure file. If FRED is not being run in PVM mode the order of molecules in the output file will be the order they appear in the input file. The structure of each ligand will be written to the file as the ligand is docked, rather than at the end of the docking run.

With certain file formats (see the -oformat flag), scores are stored within the molecule record. This is independent of, and in addition to, the the output of the scores in the score and alternate score files. See appendix H.

5.7.8 Alternate Score Files

<prefix>_<scoring function>_alt_scores.txt

Alternate score file will only be written if the flag -num_alt_poses is set to a non-zero value. The format of this file is a tab separated text file, that contains the ligand name, pose number, score, score components and a smiles representation of poses. Poses of the same ligand will be grouped together. Ordering of ligands is the same as the standard score text file (see section 5.7.6).

5.7.9 Alternate Docked Structure Files

<prefix>_<scoring function>_alt_docked.<file ext>

Alternate docked structure files will only be written if -num_alt_poses is set to a non-zero value. The file contains the structure of different possible poses of each ligand in the active site. Poses of the same ligand are grouped together. Ligand ordering is the same as the standard docked structure file (see section 5.7.7).

5.7.10 Consensus Hitlist

<prefix>_consensus_scores.txt
<prefix>_consensus_docked.<file ext>

These files will be written if the following conditions are met:

-serial is false (the default value).
-consensus is true (the default value).
More than one non-masc scoring function has been selected.

The scores.txt file contains the names of the top ranked molecules by consensus score of the non-masc variant scoring functions, as well as its rank in each of the individual scoring functions and overall consensus score.

The docked file contains the top consensus structure pose of each of the top ranked ligands rank by consensus score. The order will be the same as the scores.txt file.

5.7.11 MASC Consensus Hitlists

<prefix>_MASC_consensus_scores.txt
<prefix>_MASC_consensus_docked.<file ext>

These files will be written if the following conditions are met:

-serial is false (the default value)
-consensus is true (the default value)
More than one MASC scoring function has been selected.

The scores file contains the names of the top ranked molecules by consensus score of the Non-MASC variant scoring functions, as well as its rank in each of the individual scoring functions and overall consensus score.

The docked file contains the top consensus structure pose of each of the top ranked ligands rank by consensus score. The order will be the same as the scores file.

5.7.12 Undocked Ligand Files

undocked_code<return code>.smi

These smiles files contain all the molecules that FRED read in but could not dock. <return code> is an integer value that specifies why FRED could not dock the ligands listed in the particular file. See section 4.4.2 for the meaning of individual return codes.

				FRED Fast Rigid Exhaustive Docking

				FRED Fast Rigid Exhaustive Docking