Getting Started

Build Documentation

Rosetta Basics

Application Documentation

Scripting Interfaces

Development Documentation

Internal Documentation

How to Write Documentation

FAQ

Glossary

Options list

FragmentScoreFilter

Autogenerated Tag Syntax Documentation:

Filter based on any score that can be calculated in fragment_picker.

<FragmentScoreFilter name="(&string;)" scoretype="(FragmentCrmsd &string;)"
        threshold="(6 &real;)" direction="(- &string;)"
        compute="(average &string;)" fragment_size="(3 &non_negative_integer;)"
        sort_by="(FragmentCrmsd &string;)" outputs_folder="(&string;)"
        outputs_name="(pose &string;)" csblast="(&string;)"
        blast_pgp="(&string;)" placeholder_seqs="(&string;)"
        sparks-x="(&string;)" sparks-x_query="(&string;)" psipred="(&string;)"
        vall_path="(/home/benchmark/rosetta/database//sampling/vall.jul19.2011.gz &string;)"
        frags_scoring_config="(&string;)" n_frags="(200 &non_negative_integer;)"
        n_candidates="(1000 &non_negative_integer;)"
        print_to_pdb="(false &xs:boolean;)"
        start_res="(&refpose_enabled_residue_number;)"
        end_res="(&refpose_enabled_residue_number;)"
        task_operations="(&task_operation_comma_separated_list;)"
        packer_palette="(&named_packer_palette;)" confidence="(1.0 &real;)" />
  • scoretype: Which attribute to filter on. See FragmentScoreManager::register_score_maker for options.
  • threshold: Filter threshold.
  • direction: Choose whether you want outputs to be greater or less than the threshold. Right now the only options are greater than ('+') or less than ('-'); if you put anything else, all will pass.
  • compute: How to calculate filter value. Right now the options are average, maximum, or minimum of the scores collected.
  • fragment_size: Size of fragments to be computed (default 3)
  • sort_by: Choose how to pick the best fragment from the final list of candidates at each position. Default is by FragmentCrmsd, and RamaScore, SecondarySimilarity, and TotalScore are enabled by default. You can use any other fragment score if you include it via a weights file by using the command line option "-frags::scoring::config"
  • outputs_folder: Folder where you would like external files to go, such as secondary structure prediction and blast checkpoint files. If not set, files will be placed in current working directory.
  • outputs_name: Base name of intermediate files, i.e. the name of your design.
  • csblast: Directory of csblast program, ex. software/csblast-2.2.3_linux64
  • blast_pgp: Path to blastpgp for creating psipred file.
  • placeholder_seqs: Path to placeholder sequence database for creating psipred file.
  • sparks-x: Path to sparks-x directory
  • sparks-x_query: Path to sparks-x script, "buildinp_query.sh"
  • psipred: Path to runpsipred_single script.
  • vall_path: Path to vall database.
  • frags_scoring_config: Path to scoring config file (required).
  • n_frags: Number of fragments to be picked (default 200)
  • n_candidates: Number of candidates per position (default 1000)
  • print_to_pdb: Prints scores for all residues analyzed to the pdb.
  • start_res: The N-terminal residue of the piece of backbone to be analyzed.
  • end_res: The C-terminal residue of the piece of backbone to be analyzed.
  • task_operations: A comma-separated list of TaskOperations to use.
  • packer_palette: A previously-defined PackerPalette to use, which specifies the set of residue types with which to design (to be pruned with TaskOperations).
  • confidence: Probability that the pose will be filtered out if it does not pass this Filter