FLYNN

Previous: 3. Using Flynn Up: 3. Using Flynn Next: 3.2 Example Executions

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• 3.1.1 Required Parameters
• 3.1.2 Molecular File Formats
• 3.1.3 Map File Formats
• 3.1.4 Basic Parameters
• 3.1.5 MTZ File parameters
• 3.1.6 Advanced Parameters
• 3.1.7 3D Construction Parameters and Torsion Driving Parameters

 
3.1 Command Line Interface

Executing flynn with no arguments will result in:

prompt> flynn
          :jGf:
        :jGDDDDf:
      ,fDDDGjLDDDf,            F L Y N N
    ,fDDLt:   :iLDDL;          i i o e o
  ;fDLt:         :tfDG;        t g u e w
,jft:   ,ijfffji,   :iff       t a   d
     .jGDDDDDDDDDGt.           i n
    ;GDDGt:''':tDDDG,          n d
   .DDDG:       :GDDG.         g s
   ;DDDj         tDDDi
   ,DDDf         fDDD,         Copyright (c) 2008
    LDDDt.     .fDDDj          OpenEye Scientific Software, Inc.
    .tDDDDfjtjfDDDGt
      :ifGDDDDDGfi.            Version: 1.1
          .:::.
  ......................       OEChem version: 1.6.0 20080514
  DDDDDDDDDDDDDDDDDDDDDD       Platform: osx-10.5-g++4.0-x86
  DDDDDDDDDDDDDDDDDDDDDD


No argument specified on the command line
Required parameters:
    -map : Input density grid used to fit against
    -in : Input filename used to generate conformations
    -out : Output filename outputs final poses
For more help type:
  ./flynn --help

For the rest of this document, the OpenEye banner will be omitted.

A description of the command line interface can be obtained by executing flynn with the -help option.

prompt> flynn --help

  ./flynn --help simple      : Get a list of simple parameters
  ./flynn --help all         : Get a complete list of parameters
  ./flynn --help defaults    : List the defaults for all parameters
  ./flynn --help <parameter> : Get detailed help on a parameter
  ./flynn --help html        : Create an html help file for this program

If you desire to see all of the command-line options use -help all.

prompt> flynn --help all

will generate the following output:

Complete parameter list
    File Options
      -in : Input filename used to generate conformations
      -map : Input density grid used to fit against
      -out : Output filename outputs final poses
      -param : Flynn control parameter file
      -prot : Optional protein used to mask input grid
      -verbose : Triggers copious logging output

    Basic Parameters
      -blobsThenBox : If a blob isn't found, use the box
      -box : Input a molecule to use as a bounding box for the density
      -boxpad : Pad supplied box (in angstroms)
      -densityAsIs : Don't attempt to find the ligand density, use the density
                     as is.
      -distance : Reject blobs whose average distance to the protein is greater
                  than this value.
      -ligandAsIs : Don't generate conformers from the input ligands (use ligand
                    as is)
      -reportfile : Filename for report file.
      -resname : Set the output residue name.
      -sortAllChiral : If true, when multiple chiralities are enumerated, sort
                       all chiralities from best to worst per blob, otherwise sort
                       chiral structures independently (Note: This may interleave
                       chiral structures)

    MTZ File parameters
      -Fc : Column to use for Fc.
      -Fdelwt : Column to use for Fdelwt or difference map amplitudes
      -Fobs : Column to use for FObs.
      -Fwt : Column to use for Fwt or regular map amplitudes.
      -Phic : Column to use for Phic.
      -Phidelwt : Column to use for Phdelwt or difference map phases.
      -Phiwt : Column to use for Phwt or regular map phases.
      -autoMTZ : Automatically try to open the mtz file using the DELWT and
                 FDELWT columns from REFMAC5 mtz files.
      -mtype : The map type to use for fitting. Fo-Fc, Fc, 2Fo-Fc, 3Fo-Fc, Fwt,
               Fdelwt...

    Advanced Parameters
      -dumps : Dump the intermediate data such as surfaces and grids
      -flipper : Enumerate all stereochemistry, otherwise enumerate all missing
                 stereochemistry.
      -gscale : Scale for the input grid (larger means coarser)
      -mmff94s : Use the mmff94s variant of the MMFF94 forcefield ( this uses
                 planar aniline nitrogens).
      -overlays : Number of initial Shape overlays to use for MMFF/Shape fits.
      -precheck : Perform a precheck on the inputs for basic validity.
      -reporthtml : Output html report after a successful run (requires
                    -precheck flag).
      -residues : comma seperated list of residues (<residuenumber><chainid> to
                  compute distance to). Example: 120C,134C
      -rms : Compute rms distance to input ligand (for validation only)
      -split : Split up the results into seperate files
      -suppressH : Suppress the output hydrogens in output poses.

    3D Construction Parameters
      -addfraglib : File(s) containing fragments used for 3D construction, in
                    addtion to built-in fraglib.
      -setfraglib : File(s) containing fragments used for 3D construction.
                    Replaces built-in fraglib

    Torsion Driving Parameters
      -ewindow : Energy window used for conformer selection
      -fraglib : File(s) containing fragments used for 3D construction
      -maxconfgen : Maximum number of conformations to be generated
      -maxconfs : Maximum number of conformations to be saved
      -torlib : Input name of torsion rules file

3.1.1 Required Parameters

-in

File containing one or more molecular connection tables to be processed by flynn as ligands. File format types are discussed in section 3.1.2.

-out

File to write ligand poses generated by flynn. File formats are discussed in section 3.1.2.

-map

The file containing the map containing the density. Map file format types are discussed in .

-param

The argument for this flag is the name of a file containing control parameters. The control parameter file acts to either replace or augment the command line interface. All parameters necessary for program execution may be provided in the control parameter file, although any command given explicitly on the command line will supercede options found in the parameter file. Flynn generates a new parameter file containing the full set of execution parameters upon every execution. The name of the parameter file written by Flynn is created by combining the prefix base name (see -prefix) with the '.parm' extension.

-prot

The optional file containing the protein model used to build the input map. This model is used to mask away density where the ligand should not be placed. While the protein is not required, it is highly recommended.

-verbose

This is a boolean flag that controls the level of detail written to the log file. By default flynn will only write minimal information to the console. Verbose logging will cause more information to be written to the log file in order to follow behavior during program execution. [default = false]

 
3.1.2 Molecular File Formats

Flynn can read and write a variety of molecular file formats. The file format is automatically interpreted from the filename suffix.

Old OEBinary format can be read but not written by Flynn. Gzipped OEBinary version 2 (.oeb.gz) is the recommended output format.

Flynn is also capable of piping formatted input and output. The simple "-" can be used in place of a file name to indicate std::cin or std::cout with the default SMILES format.

prompt> flynn -in - -out -

This execution will run Flynn with std::cin as the input with SMILES format. It will also open std::cout with SMILES format as output. However, the use of "-" does not allow control of the file format.

To control the format of std::cin and std::cout one may use the file extensions without a preceeding filename.

prompt> flynn -in .ism -out .oeb.gz

This executes Flynn with the input from std::cin formated in isomeric SMILES and the output sent to std::cout in gzipped OEBinary version 2 format.

 
3.1.3 Map File Formats

Flynn can read and write a variety of map file formats. The file format is automatically interpreted from the filename suffix.

The MTZ format, in particular, requires that the amplitude column the phase column and the map types be specfied. OpenEye does provide a facility to open the most common MTZ formats automatically as output by REFMAC5.

The only map file types that can be written are ASCII, Grasp and OpenEye grid files.

 
3.1.4 Basic Parameters

-blobsThenBox

Search for correctly sized blobs inside the given bounding box. If no blobs are found, use the bounding box as is for placing the ligand. [default = false]

-box

Use the extents of the supplied molecule as a bounding box for density. For example, if you already have a partially fit ligand, you can use it to define the bounding box.

-boxpad

Take the input bounding box and pad it with the specified amount in angstroms. For example, if you have a 2x2x2 box and pad it with 1.0 you will end up with a 4x4x4 box. [default = 0]

-densityAsIs

Use the input density as is, do not search for blobs of density roughly the same size of the ligand. Note that the supplied density has to be pretty close to the actual ligand density for this to work [default = false].

-distance

Reject blobs whose average distance to the protein is greater than this value. [default = 4 ]

-ligandAsIs

Use the input ligands as is, do not perform a conformational search. [default = false]

-reportfile

Generate a comma separated file containing the results. Example output:

Smiles,Blob,Stereo Variant,Conformer,Tanimoto Shape,Tanimoto MMFF/SHAPE,Local Strain
CC(=O)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CCC4=CC(=O)CC[C@]34C)C,1,,,0.4110,  0.4296
CC(=O)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CCC4=CC(=O)CC[C@]34C)C,1,,,0.313,  0.3704
CC(=O)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CCC4=CC(=O)CC[C@]34C)C,1,,,0.3265,  0.3628

-resname

Set the output residue name. For example -resname LIG will set all residues in the output ligands to be ``LIG''. The default is the leave the residue names that are already on the ligand.

-sortAllChiral

If multiple stereochemistries are generated, this sorts the chiralities by best fit when fitting to a blob. For example, if two blobs are found, then the output will have all chiral structures sorted from best fit to worst fit for the first blob, and then all chiral structures sorted from best fit to worst fit for the second blobs. Note that the second blob may contain better fits than the first. [default = true]

 
3.1.5 MTZ File parameters

-autoMTZ

This flag enables automatically opening mtz files that have been generated from REFMAC5 or standard packages. The appropriate FWT and DELFWT (or FOFCWT and 2FOFCWT) columns are created and used for making the Fwt or Fdelwt maps. [default = true]

-Fobs

Use this MTZ column as the observed amplitude column. [default = F]

-Fc

Use this MTZ column as the calculated amplitude column. Note, to load arbitrary columns, you can use the ``-Fc'' and ``-Phic'' columns and the ``Fc'' maptype. [default = FC]

-Phic

Use this MTZ column as the calculated phase column [default = PHIC]

-Fdelwt

Column to use for Fdelwt or difference map amplitudes.

-Fwt

Column to use for Fwt or regular map amplitudes.

-Phic

Column to use for Phic.

-Phidelwt

Column to use for Phdelwt or difference map phases.

-Phiwt

Column to use for Phwt or regular map phases.

-mtype

This argument indicates what type of map will be used for the ligand placement. Available options are Fc, 2Fo-Fc, 3Fo-Fc, 5Fo-3Fc, 2Fo-Fc (SigmaA), Fo-Fc (SigmaA), Fwt, Fdelwt [default = 2Fo-Fc]

3.1.6 Advanced Parameters

-flipper

Force enumeration of all sterochemical centers. Otherwise, only missing stereo chemistry will be enumerated. [default = false]

-mmff94s

Use the mmff94s variant of the MMFF94 forcefield ( this uses planar aniline nitrogens). [default = false]

-overlays

Set the number of initial rigidly fit overlays to optimize into density. [default = 10]

-precheck

Perform only a preliminary check of the data to see if fitting is possible. (This flag is meaningless without the -reporthtml flag). [default = false]

-reporthtml

Generate an html report of the fitting process. This is a useful first step to verify the data. It also includes a 2D image of the ligand that is being fit in order to verify bond orders. All output of flynn will be captured in the specified html file.

-residues

Comma separated list of residues to use as distance constraints. If residues are specified, the -distance flag will use the residues to reject blobs that are too far away. Note that with a residue list, the distance computed is a minimum distance, not an average distance. Residues must be specified as <residue number><chain id>. For example: 120C,134C

-rms

If the input ligand has 3D coordinates, this calculates the RMS distance to the ligand and records it in the molecule. If -split is on, it also records it in the file name. [default = false]

-split

Split the result into different files. Each filename is annotated with the resulting shape score so that when the output directory is listed alphabetically, the best scores will be displayed in order. In the case where the output format is pdb the ligand fitting results are written in REMARK statements at the top of the file. [default = false]

-suppressH

By default flynn does outputs hydrogens of the resulting poses. Setting this to false will not output hydrogens. [default = false]

3.1.7 3D Construction Parameters and Torsion Driving Parameters

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				FLYNN

Previous: 3. Using Flynn Up: 3. Using Flynn Next: 3.2 Example Executions

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Documentation released on July 24, 2008.