reference_fname:
  default: ''
  type: file
  title: Reference structure
  short: Structure to be used when calculating the CAPRI metrics.
  long: Reference tructure to be used when calculating the CAPRI metrics.
    If none is defined then the lowest scoring model is selected by default.
  group: analysis
  explevel: easy

irmsd:
  default: true
  type: boolean
  title: Calculate I-RMSD
  short: Performs Interface RMSD calculations.
  long: Calculates the Interface Root Mean Square Deviation.
    This calculate the RMSD of interface backbone atoms after fitting on the interface backbone atoms.
    The interface is idenfied based on intermolecular contacts shorter than the defined irmsd_cutoff.
  group: analysis
  explevel: easy

fnat:
  default: true
  type: boolean
  title: Calculate FNAT
  short: Performs FNAT calculations.
  long: Calculates the Fraction of Native Contacts. This evaluates how many contacts observed
    in the reference are present in the model. The distance cutoff used to define intermolecular contacts is
    defined by the fnat_cutoff parameter.
  group: analysis
  explevel: easy

lrmsd:
  default: true
  type: boolean
  title: Calculate L-RMSD
  short: Performs Ligand RMSD calculations.
  long: Calculates the Ligand Root Mean Square Deviation. This calculation is done by superimposing
    the receptors (defined by the receptor_chain parameter) and then evaluating the RMSD on the ligands (defined by the ligand_chains parameter). 
    Superposition and RMSD calculations are done on backbone heavy atoms.
  group: analysis
  explevel: easy

ilrmsd:
  default: true
  type: boolean
  title: Calculate I-L-RMSD
  short: Performs Interface Ligand RMSD calculations.
  long: Calculates the Interface Ligand Root Mean Square Deviation. This calculation is done by superimposing the model and the target
        on the interface backbone atoms of the receptor (defined by the receptor_chain parameter) and calculating the RMSD on all heavy atoms 
        of the ligand (defined by the ligand_chains parameter).
  group: analysis
  explevel: easy

dockq:
  default: true
  type: boolean
  title: Calculate DockQ
  short: Evaluate DockQ.
  long: Evaluate DockQ. A single continuous quality measure for protein docked models based on the CAPRI criteria, 
        a combination of i-RMSD, l-RMSD and FNAT value. For details check the DockQ publication `DOI:10.1371/journal.pone.0161879`
  group: analysis
  explevel: easy

global_rmsd:
  default: true
  type: boolean
  title: Calculate global RMSD
  short: Calculate full structure RMSD.
  long: Compute full structure RMSD between reference structure and the model
        after superimposition. Note that a sequence alignment is performed to
        obtain the mapping between the reference and the model. If the one of
        the structure contain a 'small-molecule', we assume that the compared
        structure atoms are in the same order. With default parameters `allatoms = false`, only
        backbone RMSD will be computed.
  group: analysis
  explevel: easy

irmsd_cutoff:
  default: 10.0
  type: float
  min: 3.0
  max: 20.0
  precision: 3
  title: Distance cutoff (Å) used to define interface residues.
  short: Distance cutoff (Å) used to define interface residues based on intermolecular contacts.
  long: Distance cutoff (Å) used to define interface residues based on intermolecular contacts.
  group: analysis
  explevel: easy

fnat_cutoff:
  default: 5.0
  type: float
  min: 3.0
  max: 20.
  precision: 3
  title: Distance cutoff (Å) used to define interface contacts.
  short: Distance cutoff (Å) used to define interface contacts between two interacting molecules.
  long: Distance cutoff (Å) used to define interface contacts between two interacting molecules.
  group: analysis
  explevel: easy

receptor_chain:
  default: A
  type: string
  minchars: 1
  maxchars: 1
  title: Receptor ChainID
  short: Receptor ChainID to be considered for the RMSD calculations.
  long: Receptor ChainID to be considered for the RMSD calculations. This determines which chain will be
    treated as the receptor for the L-RMSD and for I-L-RMSD.
  group: analysis
  explevel: easy

ligand_chains:
  default: []
  type: list
  minitems: 0
  maxitems: 100
  title: Ligand ChainIDs
  short: Ligand ChainIDs to be considered for the RMSD calculations.
  long: Ligand ChainIDs to be considered for the RMSD calculations. This determines which chains will be
    treated as the ligand for the L-RMSD and for I-L-RMSD.
  group: analysis
  explevel: easy

sortby:
  default: score
  type: string
  minchars: 0
  maxchars: 20
  choices:
    - score
    - irmsd
    - lrmsd
    - ilrmsd
    - fnat
    - dockq
  title: Sort the structures/clusters in the output file by this value
  short: Which value should be used to sort the output.
  long: Which value should be used to sort the output, the output table will be sorted accordingly.
  group: analysis
  explevel: easy

sort_ascending:
  default: true
  type: boolean
  title: Sort in ascending order
  short: Sort in ascending order.
  long: Sort in ascending order.
  group: analysis
  explevel: easy

alignment_method:
  default: sequence
  type: string
  minchars: 0
  maxchars: 100
  choices:
    - structure
    - sequence
  title: Alignment method used to match the numbering.
  short: Which alignment method should be used to match the numbering.
  long: Alignment method used to match the numbering. Sequence alignment is haddock3-friendly but might not produce best results
    for structures that are too different, for that use
  group: analysis
  explevel: easy

lovoalign_exec:
  default: ''
  type: string
  minchars: 0
  maxchars: 200
  title: Location (path) of the LovoAlign executable
  short: Location (path) of the LovoAlign executable.
  long: Location (path) of the LovoAlign executable.
  group: analysis
  explevel: easy

clt_threshold:
  default: 4
  type: integer
  min: 1
  max: 1000
  title: Threshold (n) used for the average evaluation in the cluster-based output
  short: Threshold (n) used for the average evaluation in the cluster-based output.
  long: Threshold (n) used for the average evaluation in the cluster-based output.
  group: analysis
  explevel: easy

allatoms:
  default: false
  type: boolean
  title: Atoms to be considered during the analysis.
  short: Atoms to be considered during the analysis.
  long: Atoms to be considered during the analysis. If false (default), only
        backbone atoms will be considered, otherwise all the heavy-atoms.
  group: analysis
  explevel: easy

keep_hetatm:
  default: false
  type: boolean
  title: HETATM to be considered during the analysis.
  short: HETATM to be considered during the analysis.
  long: HETATM to be considered during the analysis. If false (default), only
        ATOM coordinates lines will be used, otherwise the HETATM from reference will also be used.
  group: analysis
  explevel: easy