# proteinprep interface file

!BRIEF <inmol> [<outcplx> [<outlig>]]

!CATEGORY "input/output options :" 1
   !PARAMETER -in 1
      !ALIAS -i
      !TYPE string
      !BRIEF Input molecule filename (must have 3D coordinates)
      !SIMPLE true
      !REQUIRED true
      !KEYLESS 1
   !END

   !PARAMETER -cplxout 2
      !ALIAS -p
      !TYPE string
      !DEFAULT proteinprep.oeb.gz
      !BRIEF Output complex filename
      !SIMPLE true
      !REQUIRED false
      !KEYLESS 2
   !END

   !PARAMETER -ligout 3
      !ALIAS -l
      !TYPE string
      !BRIEF Output ligand filename
      !SIMPLE true
      !REQUIRED false
      !KEYLESS 3
   !END
!END

!CATEGORY "Calculation options :" 2
    !PARAMETER -alts 1
       !TYPE string
       !LEGAL_VALUE occupancy
       !LEGAL_VALUE a
       !LEGAL_VALUE ignore
       !LEGAL_VALUE compare
       !DEFAULT occupancy
       !BRIEF Alternate location atom handling (affects atom:atom interactions)
       !SIMPLE true
       !REQUIRED false
       !DETAIL
         occupancy - keep just the highest average occupancy for each alt group
         a - keep only loc code A (and blank)
         ignore - assume alts already selected appropriately
         compare - keep all alts but only interact if same loc code (or blank)
    !END

    !PARAMETER -placehydrogens 2
       !TYPE bool
       !DEFAULT true
       !BRIEF If false, hydrogens will not be added
       !SIMPLE true
       !REQUIRED false
    !END

    !PARAMETER -waterprocessing 3
       !TYPE string
       !LEGAL_VALUE ignore
       !LEGAL_VALUE focused
       !LEGAL_VALUE fullsearch
       !DEFAULT fullsearch
       !BRIEF How waters are processed
       !SIMPLE true
       !REQUIRED false
       !DETAIL
         ignore - leave water hydrogens in a random orientation
         focused - search orientations based on neighboring polar groups
         fullsearch - do an extensive search of water orientations
    !END

    !PARAMETER -standardizehyd 4
       !ALIAS -stdhyd
       !TYPE bool
       !DEFAULT true
       !BRIEF If false, bonds for hydrogens are not adjusted to standard lengths
       !SIMPLE false
       !REQUIRED false
    !END

    !PARAMETER -clashcutoff 5
        !TYPE double
        !DEFAULT 0.4
        !BRIEF Van der Waals overlap (in Angstroms) defined to be a bad clash
        !SIMPLE false
        !REQUIRED false
    !END

    !PARAMETER -flipbias 6
        !TYPE double
        !DEFAULT 1.0
        !BRIEF Scale factor for the bias against flipping sidechains such as HIS
        !SIMPLE false
        !REQUIRED false
    !END

    !PARAMETER -maxsubstates 7
        !TYPE double
        !DEFAULT 1.0e8
        !BRIEF Maximum number of substates in a single step of hydrogen placement optimization
        !SIMPLE false
        !REQUIRED false
    !END
!END

!CATEGORY "Display options :" 9
   !PARAMETER -verbose 1
      !ALIAS -v
      !TYPE bool
      !DEFAULT false
      !BRIEF Display more information about the process
      !SIMPLE true
      !REQUIRED false
   !END
!END
