Output Options

Here is a list of common used output options.

Misc

-out:overwrite 		         Ignore 'CHECKPOINT' file and the overwrite the PDB file(s).
                           [Boolean]
-out:nstruct		           Number of times to process each input PDB", default="1"
			                     [Integer]
-out:prefix		             Prefix for output structure names, like old -series code",
			                     Default="". [String]
-out:suffix                Suffix for output structure names
                           Default="". [String]
-out:pdb_gz                Compress (gzip) output pdbs", default="false". [Boolean]
-out:pdb                   Output PDBs", default="false". [Boolean]
-out:nooutput              Surpress outputfiles. Default="false". [Boolean]
-out:output                Force outputfiles. Default="false". [Boolean]
-out:show_accessed_options At the end of the run show options that has been accessed
                           Default="false". [Boolean]
-out:user_tag              Add this tag to structure tags: e.g., a process id.
                           Default="". [String]

Tracer related options.

User can dynamically, in run time specify command line options to mute/unmute specific/all channels and to change level of output.

-mute                      Mute specified chanels, specify 'all' to mute all chanels.
                           Defaule="false" [StringVector]
-unmute                    UnMute specified chanels. Default="false" [StringVector]

Controlling Tracer output from command line. For Example:

# unmute all channels - default behavior, the same as just './a.out'
./a.out -unmute all

# mute all channels, unmute ChannelA and ChannelB
./a.out -mute all -unmute ChannelA ChannelB

# mute ChannelA and  ChannelB
./a.out -mute ChannelA ChannelB

# Set priority of output messages to be between 0 and 10
./a.out -out:level 10

# disable output of channels names
./a.out -chname off

Files related output options

-out:file:o               Output file name. [String]
-out:file:silent          Use silent file output, use filename after this flag.
                          Default="default.out" [String]
-out:file:scorefile       Write a scorefile to the provided filename.
                          Default = "default.sc [String]
-out:file:fullatom        Enable full-atom output of PDB or centroid structures.
                          Default = "fault" [Boolean]

Path related output options

-out:path:pdb             PDB file output path. [Path]
-out:path:score           Score file output path. [Path]

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