Filters (RosettaScripts)

Each filter definition has the following format in the FILTERS block:

<FILTERS>
	<SomeFilterName name="&string" confidence="(1 &Real)" other_option=""/>
</FILTERS>

where "SomeFilterName" belongs to a predefined set of possible filters that the parser recognizes and are listed below, name is a unique identifier for this mover definition and then any number of parameters that the filter needs to be defined.

Filters can be run on arbitrary SimpleMetrics, which will eventually replace some aspects of the Filter system. See the special SimpleMetricFilter for using arbitrary metrics for filtering.

If confidence is 1.0, then the filter is evaluated as in predicate logic (T/F). If the value is less than 0.999, then the filter is evaluated as fuzzy, so that it will return True in (1.0 - confidence) fraction of times it is probed. This should be useful for cases in which experimental data are ambiguous or uncertain.

After the end of the protocols code block, the filters will be run again to report the most up-to-date values to the pose. The run at the end can be avoided, while still retaining filtering, by appending the option: report_at_end=“false”.

Predefined Filters

Simple filter which are available without explicitly defining them.

Filter	Description
TrueFilter	Always passes.
FalseFilter	Never passes.

Special Filters

Filters which are useful for combining, modifying or working with other filters and movers.

Filter	Description
CompoundStatement	Uses previously defined filters with logical operations to construct a compound filter.
CombinedValue	Weighted sum of multiple filters.
CalculatorFilter	Combine multiple filters with a mathematical expression.
ReplicateFilter	Repeat a filter multiple times and average.
Boltzmann	Boltzmann weighted sum of positive/negative filters.
MoveBeforeFilter	Apply a mover before applying the filter.
Operator	Apply a fuzzy logic operation to a set of filters.
Sigmoid	Transform a filter's value according to a sigmoid function.
IfThenFilter	Evaluate to a value contingent on the true/false value of other filters.
ContingentFilter	A special filter that allows movers to set its value (pass/fail).
PoseComment	Test for the existence or the value of a comment in the pose.
Range	Returns true if the value of a given filter is in a given range.

General Filters

Filter	Description
SimpleMetricFilter	Filter based on any arbitrary SimpleMetric

Basic Filters

Filter	Description
ResidueCount	Filter based on the total number of residues.
NetCharge	Filter based on simple sum of protein charge.

Energy/Score

Filter	Description
ScoreType	Filter based on a particular score term.
TaskAwareScoreType (Formerly AverageInterfaceEnergy)	Filter on score of "packable" residues.
BindingStrain	Filter on energetic strain in a bound monomer.
ConstraintScore	Filter that generates a score from a set of constraints generated by ConstraintGenerators
Delta	Compute difference from native of filter value.
EnergyPerResidue	Filter on energy of specific selection (residue(s), interface, protein).
ReadPoseExtraScoreFilter	Extract score previously stored in the pose.
Residue Interaction Energy	Filter on energy of specific residue in the context of an interface or pose.
ResidueSetChainEnergy	Filter on energy of residue set (either in chain or selection).
ScorePoseSegmentFromResidueSelectorFilter	Obtain the score of a requested section of a Pose through a ResidueSelector.

Distance

Filter	Description
ResidueDistance	Filter based on the distance between two residues.
AtomicContact	Are any atoms on two residues within a cutoff distance?
AtomicContactCount	Count number of carbon-carbon contacts.
AtomicDistance	Filter based on the distance between two atoms.
TerminusDistance	Distance in sequence from either terminus to interface.

Sequence analysis

Filter	Description
LongestContinuousPolarSegment	Filter based on length of longest stretch of polar amino acid residues.
LongestContinuousApolarSegment	Filter based on length of longest stretch of apolar amino acid residues.
SequenceDistance	Filter based on the number of mutations between pose sequence and sequence stored in comments in pose.

Alignment analysis

Filter	Description
AlignmentAAFinder	Scans through an alignment, tests all possible amino acids at each position, and generates a file of passing amino acids.
AlignmentGapInserter	Scans through an alignment and inserts gaps where positions in the alignment are not representative of the chemical environment of the pose sequence.

Geometry

Filter	Description
AngleToVector	Filter on angle between two atoms on the first residue of a chain and a given vector.
Torsion	Filter based on the value of a dihedral.
HelixPairing	Filter structures based on the geometry of helix pairings.
SSMotifFinder	Filter structures based on the geometry of loop stems.
SecondaryStructure	Filter structures based on secondary structure.
SecondaryStructureCount	Count number of a single secondary structure element.
SecondaryStructureHasResidue	Count fraction of secondary structure element positions containing specific residue.
HelixKink	Vaguely, filter based on helix topology.
Geometry	Bond geometry and omega angle constraints
HSSTriplet	Evaluate the given helix-strand-strand triplets.
PreProlineFilter	Check for bad torsions in residues before prolines
LoopAnalyzerFilter	Check for bad loop backbone geometries

Packing/Connectivity

Filter	Description
CavityVolume	Always returns true, but calculates intra-protein cavity volume.
AverageDegree	Count number of residues within a distance of another selection of residues.
PackStat	Compute packing statistics.
Holes	Identify voids (holes) in packing
InterfaceHoles	Identify voids at protein-protein interfaces.
NeighborType	Search for residue type within a radius of a target residue.
ResInInterface	Filter based on the total number of residues in the interface.
ShapeComplementarity	Filter on shape complementarity of interface.
SSShapeComplementarity (SecondaryStructureShapeComplementarity)	Filter on secondary structure shape complementarity.
SpecificResiduesNearInterface	Filter on specific residues near interface.

Burial

Filter	Description
TotalSasa	Filter based on the total solvent accessible surface area of the pose.
Sasa	Filter based on the solvent accessible surface area of an interface.
ResidueBurial	Number of residues within interaction distance across interface of target residue.
BuriedSurfaceArea	Computes the buried surface area for a pose or selection, with an option to consider hydrophobic residues only.
ExposedHydrophobics	Computes the SASA for each hydrophobic residue.

Comparison

Filter	Description
RelativePose	Compute a filter's value relative to a different pose's structure.
Rmsd	Filter based on the C-alpha RMSD to a reference structure.
SidechainRmsd	Compute RMSD for a single sidechain.
IRmsd	Filter based on backbone RMSD over residues in the interface.
RmsdFromResidueSelectorFilter	Similar to the Rmsd. It allows to provide ResidueSelectors for both the query and reference poses.
SequenceRecovery	Calculates the fraction sequence recovery of a pose compared to a reference pose.

Bonding

Filter	Description
ChainBreak	Filter on number of chain breaks in pose.
HbondsToResidue	Filter on number of h-bonding partners to a residue.
SimpleHbondsToAtom	Filter on number of h-bonding partners to an atom(s) with significantly simpler logic than HbondsToAtom.
HbondsToAtom	Filter on number of h-bonding partners to an atom(s).
PeptideInternalHbondsFilter	Filter on the number of hydrogen bonds in a single selection or pose, excluding bonds between residues within a threshold distance of each other in terms of covalent connectivity.
BuriedUnsatHbonds	Filter on maximum number of buried unsatisfied h-bonds.
BuriedUnsatHbonds2	Filter on number of unsatisfied h-bonds at interfaces (different algorithm from filter above).
OversaturatedHbondAcceptorFilter	Filter on number of hydrogen bond acceptors that are receiving hydrogen bonds from more than the allowed number of donors.
DisulfideFilter	Filter based on the presence of a disulfide across an interface.
AveragePathLength	Compute shortest graph path length where residues are nodes and covalent bonds are edges.
DisulfideEntropy	Compute the change in configurational entropy due to disulfide bond formation.

Report Filters

These filters are used primarily for the reports they generate in the log and/or score and silent files, more so than their ability to end a run.

Filter	Description
BundleReporter	Report the helical bundle parameters and energy of a parametrically-generated pose.
DesignableResidues	Report which residues are designable.
Expiry	Filter based on length of simulation (in seconds).
FileExist	Does a file exist on disk?
FileRemove	Remove a file from disk.
RelativeSegmentFilter	Reports the numbers of residues that align with a segment on source pose.
Report	This filter reports the value of another filter with the current job name.
RotamerBoltzmannWeight	Reports the Boltzmann probability for the occurrence of a rotamer.
RotamerBoltzmannWeight2	Reports the Boltzmann probability for the occurrence of the specific rotamers in a given residue subset. Multiple methods for computing probability and scoring are available.
StemFinder	Compare PDBs to template to identify stems for splicing segments.
AlaScan	Reports ddG of alanine scanning.
DdGScan	Reports ddG of alanine scanning on specific residues. This filter used to be named "TaskAwareAlaScanFilter".
FilterScan	Scan all mutations allowed by task_operations and test against a filter.
Time	Report how long a sequence of movers/filters takes.
PeptideDeriver	Derive linear peptide contributing most to binding energy.
PoseInfo	Report basic information about the pose to the tracer.
SaveResfileToDisk	Save resfile to output directory.
SSPrediction	Generate secondary structure predictions from sequence.
ChainCountFilter	Count the number of chains in a Pose.

Special Application Filters

Binding

Filter	Description
Ddg	Filter based on the binding energy.
InterfaceBindingEnergyDensityFilter	Filter based on ddG dived by SASA (using the respective filters).
InterfaceHydrophobicResidueContacts	Filter based on the number of hydrophobic residues on the target that have at least a certain hydrophobic ddG.

Ligand docking and enzyme design

Filter	Description
DSasa	Filter on delta SASA for bound/unbound ligand.
DiffAtomBurial	Compares the DSasa of two specified atoms and checks to see if one is greater or less than other.
LigInterfaceEnergy	Filter based on binding energy of a ligand.
EnzScore	Calculates scores of a pose taking into account (or not) enzdes style cst_energy.
RepackWithoutLigand	Calculates delta_energy or RMSD of protein residues in a protein-ligand interface when the ligand is removed and the interface repacked.

Ligand design

Filter	Description
HeavyAtom	Filter based on the number of heavy atoms in a residue.
CompleteConnections	Filter based on unfulfilled connections.

Hotspot Design

Filter	Description
StubScore	Filter based on if the scaffold is 'feeling' any of the hotspot stub constraints.

MatDes

Filter	Description
OligomericAverageDegree	A version of the AverageDegree filter (see above) that is compatible with oligomeric building blocks.
SymUnsatHbonds	Filter on maximum number of buried unsatisfied H-bonds allowed across an interface.
ClashCheck	Calculate the number of heavy atoms clashing between building blocks.
InterfacePacking	Calculates Will Sheffler's holes score for atoms at inter-building block interfaces.
MutationsFilter	Determines mutated residues in current pose as compared to a reference pose.
GetRBDOFValues	Calculates either the current translation or rotation across a user specified jump.

Backbone Design

Filter	Description
Foldability	Rebuilds a given segment of an input pose a specified number of times using fragment-based assembly.
FragQual	Compare an input pose to a set of fragments.

Cyclic Peptide Design

Filter	Description
CycpepSymmetryFilter	Determines whether a cyclic peptide backbone has a desired cyclic symmetry, and passes if and only if it does. Works with c2, c3, c4, etc. symmetry, as well as with c2/m, c4/m, c6/m, etc. symmetry.