| 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 |