Filters (RosettaScripts)

Each filter definition has the following format:

<"filter_name" name="&string" ... confidence=(1 &Real)/>

where "filter_name" 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.

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.

Table of contents

Predefined Filters

TrueFilter

Returns true. Useful for defining a mover without using a filter. Can be explicitly specified with the name "true_filter".

FalseFilter

Always returns false. Can be explicitly specified with the name "false_filter".

Special Filters

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

CompoundStatement filter

This is a special filter that uses previously defined filters to construct a compound logical statement with AND, OR, XOR, NAND and NOR operations. By making compound statements of compound statements, esssentially all logical statements can be defined.

<CompoundStatement name=(&string)>
	<OPERATION filter_name=(true_filter &string)/>
	<....
</CompoundStatement>

where OPERATION is any of the operations defined in CAPS above.Note that the operations are performed in the order that they are defined. No precedence rules are enforced, so that any precedence has to be explicitly written by making compound statements of compound statements.Also note that the first OPERATION is ignored, and the value of the first filter is simply assigned to the filter's results.

CombinedValue filter

This is a special filter that calculates a weighted sum based on previously defined filters.

<CombinedValue name=(&string) threshold=(0.0 &Real)>
	<Add filter_name=(&string) factor=(1.0 &Real) temp=(&Real)/>
	<....
</CombinedValue>

By default, the value is a straight sum of the calculated values (not the logical results) of the listed filters. A multiplicative weighting factor for each filter can be specified with the factor parameter. (As a convenience, temp can be given instead of factor, which will divide the filter value, rather than multiply it.)

For truth value contexts, the filter evaluates to true if the weighted sum if less than or equal to the given threshold.

MoveBeforeFilter

Apply a given mover to the pose before calculating the results from another filter

<MoveBeforeFilter name=(&string) mover=(&string) filter=(&string)/>

Note that, like all filters, MoveBeforeFilter cannot change the input pose - the results of the submover will only be used for the subfilter calculation and then discarded.

Also note that caution must be exercised when using a computationally expensive mover or a mover/filter pair which yields stochastic results. The result of the mover is not cached, and will be recomputed for each call to apply(), report() or report_sm().

ContingentFilter

A special filter that allows movers to set its value (pass/fail). This value can then be used in the protocol together with IfMover to control the flow of execution depending on the success of the mover. Currently, none of the movers uses this filter.

<ContingentFilter name=(&string)/>

General Filters

Torsion

<Torsion name=(&string) lower=(0&Real) upper=(0&Real) resnum=(0&residue number) torsion=("" &string) task_operations=(&comma-delimited list of taskoperations)/>

not setting torsion, will cause the report of both phi and psi. Not specifying resnum will cause a report of all residues. If you want to filter on a given torsion, you have to specify both resnum the torsion and the higher/upper values.

Energy/Score

BindingStrain

Computes the energetic strain in a bound monomer. Automatically respects symmetry

<BindingStrain name=(&string) threshold=(3.0 &Real) task_operations=(comma-delimited list of operations &string) scorefxn=(score12 &string) relax_mover=(null &string) jump=(1 &Int)/>

Dissociates the complex and takes the unbound energy. Then, repacks and calls the relax mover, and measures the unbound relaxed energy. Reports the strain as unbound - unbound_relaxed. Potentially useful to relieve strain in binding.

Delta

Computes the difference in a filter's value compared to the input structure

<Delta name=(&string) upper=(1 &bool) lower=(0 &bool) range=(0 &Real) filter=(&string) unbound=(0 &bool) jump=(see below &Int) relax_mover=(null &string)/>

The filter is evaluated at parsetime and its internal value (through report_sm) is saved. At apply time, the filter's report_sm is called again, and the delta is evaluated.

EnergyPerResidue

Tests the energy of a particular residue. If whole_interface is set to 1, it computes all the energies for the interface residues defined by the jump_number and the interface_distance_cutoff. Helpful for post-design analyses. bb_bb needs to be turn to 1, if one wants to evaluate backbone - backbone hydrogen bonding energies (short and long range).

<EnergyPerResidue name=(energy_per_res_filter &string) scorefxn=(score12 &string) 
score_type=(total_score &string) pdb_num/res_num(see above) energy_cutoff=(0.0 &float)
whole_interface=(0 &bool) jump_number=(1 &int) interface_distance_cutoff=(8.0 &float) bb_bb=(0, bool)/>

ScoreType

Computes the energy of a particular score type for the entire pose and if that energy is lower than threshold, returns true.

<ScoreType name=(score_type_filter &string) scorefxn=(score12 &string) score_type=(total_score &string) threshold=(&float)/>

Distance

ResidueDistance

What is the distance between two residues? Based on each residue's neighbor atom (usually Cbeta)

<ResidueDistance name=(&string) res1_"res_num/pdb_num see above" res2_"resnum/pdb_num" distance=(8.0 &Real)/>

AtomicContact

Do two residues have any pair of atoms within a cutoff distance? Somewhat more subtle than ResidueDistance (which works by neighbour atoms). Iterates over all atom types of a residue, according to the user specified restrictions (sidechain, backbone, protons)

<AtomicContact name=(&string) residue1=(&integer) residue2=(&integer) sidechain=1 backbone=0 protons=0 distance=(4.0 &integer)/>

Some movers (e.g., PlaceSimultaneously) can set a filter's internal residue on-the-fly during protocol operation. To get this behaviour, do not specify residue2.

AtomicDistance

Are two specified atoms within a cutoff distance? More specific than AtomicContact (which reports if any atom is within the cutoff) or ResidueDistance (which works by neighbor atoms only). Residues can be specified either with pose numbering, or with PDB numbering, with the chain designation (e.g. 34B). One of atomname or atomtype (but not both) needs to be specified for each partner. If atomtype is specified for one or both atoms, the closest distance of all relevant combinations is used.

<AtomicDistance name=(&string) residue1=(&string) atomname1=(&string) atomtype1=(&string) residue2=(&sring) atomname2=(&string) atomtype2=(&string) distance=(4.0 &integer)/>

TerminusDistance

True if all residues in the interface are more than <distance> residues from the N or C terminus. If fails, reports how far failing residue was from the terminus. If passes, returns "1000"

<TerminusDistance name=(&string) jump_number=(1 &integer) distance=(5 &integer)/>

Packing/Connectivity

AverageDegree

What is the average degree connectivity of a subset of residues? Found to be useful for discriminating non-interacting designs from natural complexes. Apparently, many non-interacting designs use surfaces that are poorly embedded in the designed monomer, a feature that can be easily captured by this simple metric. See Fleishman et al. J. Mol. Biol. 414:289

<AverageDegree name=(&string) threshold=(0&Real) distance_threshold=(&10.0) task_operations=(comma-delimited list)/>

InterfaceHoles

Looks for voids at protein/protein interfaces using Will Sheffler's packstat. The number reported is the difference in the holes score between bound/unbound conformations. Be sure to set the -holes:dalphaball option!

<InterfaceHoles name=(&string) jump=(1 &integer) threshold=(200 &integer)/>

ResInInterface

Computes the number of residues in the interface specific by jump_number and if it is above threshold returns true. o/w false. Useful as a quick and ugly filter after docking for making sure that the partners make contact.

<ResInInterface name=(riif &string) residues=(20 &integer) jump_number=(1 &integer)/>

NeighborType

Filter for poses that place a neighbour of the types specified around a target residue in the partner protein.

<NeighborType name=(neighbor_filter &string) "res_num/pdb_num see above" distance=(8.0 &Real)>
        <Neighbor type=(&3-letter aa code)/>
</NeighborType>

SpecificResiduesNearInterface

Filter for poses that have a specific set of residues near the interface. For example, this can be useful for designs that depend on say the N-terminus being close to the interface

<SpecificResiduesNearInterface name=(&string) task_operation=(&string)/>

Burial

Sasa

Computes the interface sasa. If it is **higher** than threshold, it passes. However, it also has the option for an upper_threshold, where it fails if it is above the upper_threshold.

<Sasa name=(sasa_filter &string) threshold=(800 &float) upper_threshold=(1000000000000000 &float) hydrophobic=(0&bool) polar=(0&bool) jump=(1 &integer)/>

hydrophobic/polar are computed by discriminating each atom into polar (acceptor/donor or polar hydrogen) or hydrophobic (all else) and summing the delta SASA over each category. Notice that at this point only total sasa can be computed across jumps other than 1. Trying to compute hydrophobic or polar sasa across any other jump will cause an exit during parsing.

ResidueBurial

How many residues are within an interaction distance of target_residue across the interface. When used with neighbors=1 this degenerates to just checking whether or not a residue is at the interface.

<ResidueBurial name=(&string) "res_num/pdb_num see above" distance=(8.0 &Real) neighbors=(1 &Integer) task_operations=(&comma-delimited list of taskoperations)/>

Comparison

RelativePose

Compute a filter's value relative to a different pose's structure. This is useful for cases in which you want to know the effects of a mutation on different poses. An alignment of the pose being read from disk is made to the currently active pose (through the user defined alignment), and applies any sequence changes to the pose read from disk, while repacking a shell around each mutation. It can then apply a relax mover, report a filter's evaluation and dump a scored pose to disk. Works with symmetric poses as well.

<RelativePose name=(&string) pdb_name=(&string) filter=(&string) relax_mover=(null &string) dump_pose=("" &string) alignment=(&string; see below) scorefxn=(score12 &string) packing_shell=(8.0 &Real) thread=(1 &bool) baseline=(1 &bool) unbound=(0 &bool) copy_stretch=(1&bool)>

Rmsd

Calculates the Calpha RMSD over a user-specified set of residues. Superimposition is optional. Selections are additive, so choosing a chain, and individual residue, and span will result in RMSD calculation over all residues selected. If no residues are selected, the filter uses all residues in the pose. Use -in:file:native <filename> to choose an alternate reference pose.

<Rmsd name=(&string) chains=("" &string) threshold=(5 &integer) superimpose=(1 &bool)>
    <residue res/pdb_num=(see above) />
    <span begin_(res/pdb_num)=("" &integer) end_(res/pdb_num)=(""&integer)/>
</Rmsd>

SequenceRecovery

Calculates the fraction sequence recovery of a pose compared to a reference pose. This is similar to the InterfaceRecapitulation mover, but does not require a design mover. Instead, the user can provide a list of task operations that describe which residues are designable in the pose.

<SequenceRecovery name=(&string) rate_threshold=(0.0 &Real) task_operations=(comma-delimited list of task_operations) />

The reference pose against which the recovery rate will be computed can be defined using the -in:file:native command-line flag. If that flag is not defined, the starting pose will be used as a reference.

Bonding

HbondsToResidue

This filter checks whether residues defined by res_num/pdb_num are hbonded with as many hbonds as defined by partners, where each hbond needs to have at most energy_cutoff energy. For backbone-backone hydrogen bonds, turn flag on (bb_bb=1).

<HbondsToResidue name=(hbonds_filter &string) partners="how many hbonding partners are expected &integer" energy_cutoff=(-0.5 &float) backbone=(0 &bool) bb_bb=(0 &bool) sidechain=(1 &bool) res_num/pdb_num=(&string - see above)>

BuriedUnsatHbonds

Maximum number of buried unsatisfied H-bonds allowed. If a jump number is specified (default=1), then this number is calculated across the interface of that jump. If jump_num=0, then the filter is calculated for a monomer. Note that #unsat for monomers is often much higher than 20. Notice that water is not assumed in these calculations.

<BuriedUnsatHbonds name=(&string) jump_number=(1 &Size) cutoff=(20 &Size)/>

DisulfideFilter

Require a disulfide bond between the interfaces to be possible. 'Possible' is taken fairly loosely; a reasonable centroid disulfide score is required (fairly close CB atoms without too much angle strain).

Residues from targets are considered when searching for a disulfide bond. As for DisulfideMover, if no residues are specified from one interface partner all residues on that partner will be considered.

<DisulfideFilter name="&string" targets=(&string)/>

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.


Boltzmann

Returns the Boltzmann weighted sum of a set of positive and negative filters. The fitness is actually defined as -F with [-1-0] range (-1 most optimal, 0 least).

<Boltzmann name=(&string) fitness_threshold=(0&real) temperature=(0.6 &real) positive_filters=(&comma delimited list) negative_filters=(&comma delimited list) anchors=(&comma delimited list of floats)/>

Useful for balancing counteracting objectives.

DesignableResidues

Reports to tracers which residues are repackable/designable according to use-defined task_operations. Useful for automatic interface detection (use the ProteinInterfaceDesign task operation for that). The residue number that are reported are pdb numbering.

<DesignableResidues name=(&string) task_operations=(comma-separated list) designable=(1 &bool) packable=(0 &bool)/>

RelativeSegmentFilter

Reports the numbers of residues that align with a segment on source pose.

<RelativeSegment name=(&string) source_pose=(&string) start_res=(&string) stop_res=(&string)/>

Taskoperation RestrictToAlignedSegments supersedes this filter as it allows more than one segment to be defined. Use that taskoperation and feed it to DesignableResidues filter to find aligned residues in the input pose.

RotamerBoltzmannWeight

Approximates the Boltzmann probability for the occurrence of a rotamer. The method, usage examples, and analysis scripts are published in Fleishman et al. (2011) Protein Sci. 20:753.

Residues to be tested are defined using a task_factory (set all inert residues to no repack). A first-pass alanine scan looks at which residues contribute substantially to binding affinity. Then, the rotamer set for each of these residues is taken, each rotamer is imposed on the pose, the surrounding shell is repacked and minimized and the energy is summed to produce a Boltzmann probability. Can be computed in both the bound and unbound state.

This is apparently a good discriminator between designs and natives, with many designs showing high probabilities for their highly contributing rotamers in both the bound and unbound states.

The filter also reports a modified value for the complex ddG. It computes the starting ddG and then reduces from this energy a fraction of the interaction energy of each residue the rotamer probability of which is below a certain threshold. The interaction energy is computed only for the residue under study and its contacts with residues on another chain.

<RotamerBoltzmannWeight name=(&string) task_operations=(comma-delimited list) radius=(6.0 &Real) jump=(1 &Integer) unbound=(1 &bool) ddG_threshold=(1.5 &Real) scorefxn=(score12 &string) temperature=(0.8 &Real) energy_reduction_factor=(0.5 &Real) repack=(1&bool) skip_ala_scan=(0 &bool)>
   <??? threshold_probability=(&Real)/>
   .
   .
   .
</RotamerBoltzmannWeight>

AlaScan

Substitutes Ala for each interface position separately and measures the difference in ddg compared to the starting structure. The filter always returns true. The output is only placed in the .report file. Repeats causes multiple ddg calculations to be averaged, giving better converged values.

<AlaScan name=(&string) scorefxn=(score12 &string) jump=(1 &Integer) interface_distance_cutoff=(8.0 &Real) partner1=(0 &bool) partner2=(1 &bool) repeats=(1 &Integer) repack=(1 &bool)/>

FilterScan

Scan all mutations allowed by task_operations and test against a filter. Produces a report on the filter's values for each mutation as well as a resfile that says which mutations are allowed. The filter can work with symmetry poses; simply use SetupForSymmetry and run. It will figure out that it needs to do symmetric packing for itself.

<FilterScan name=(&string) scorefxn=(score12 &string) task_operations=(comma separated list) triage_filter=(true_filter &string) dump_pdb=(0 &bool) filter=(&string) report_all=(0 &bool) relax_mover=(null &string) resfile_name=(<PDB>.resfile &string) resfile_general_property=("nataa" &string) delta=(0 &bool) unbound=(0 &bool) jump=(1 &int) rtmin=(0&bool)/>

To compute a baseline, the entire pose is first repacked (with include current, no design, initialized from the comandline, but ignoring the taskoperations), and relax_mover is called. This can be useful to get the pose's energy down.

Filter and triage_filter are potentially confusing. You can use the same filter for both. Triage_filter can be more involved, including compound filter statements, whereas the filter option is reserved to filters that have meaningful report_sm methods (ddG, energy...).

The reported values from filter will appear in a Tracer called ResidueScan, so -mute all -unmute ResidueScan will only output the necessary information

Use the unbound option only on a Prepacked structure with jump_number=1, o/w the reference energy (baseline) won't make any sense.

Time

Simple filter for reporting the time a sequence of movers/filters takes.

<Time name=(&string)/>

Within the protocol, you need to call time at least twice, once, when you want to start the timer, and then, when you want to stop. The reported time is that between the first and last calls.

Special Application Filters

Binding

Ddg

Computes the binding energy for the complex and if it is below the threshold returns true. o/w false. Useful for identifying complexes that have poor binding energy and killing their trajectory.

<Ddg name=(ddg &string) scorefxn=(score12 &string) threshold=(-15 &float) jump=(1 &Integer) repeats=(1 &Integer) repack=(true &bool) relax_mover=(&string)/>

Ligand docking and enzyme design

DSasa

(Formerly known as LigDSasa)

Computes the fractional interface delta_sasa for a ligand on a ligand-protein interface and checks to see if it is *between* the lower and upper threshold. A DSasa of 1 means ligand is totally buried (loses all it's accessible surface area), 0 means totally accessible (loses none upon interface formation).

<DSasa name=(&string) lower_threshold=(0.0 &float) upper_threshold=(1.0 &float)/>

DiffAtomBurial

Compares the DSasa of two specified atoms and checks to see if one is greater or less than other. This is useful for figuring out whether a ligand is oritented in the correct way (i.e. whether in the designed interface one atom is more/less exposed than another)

<DiffAtomBurial name=(&string)  res1_res_num/res1_pdb_num=(0, see res_num/pdb_num convention) res2_res_num/res2_pdb_num=(0, see convention) atomname1=(&string) atomname2=(&string) sample_type=(&string)/>


LigInterfaceEnergy

Calculates interface energy across a ligand-protein interface taking into account (or not) enzdes style cst_energy.

<LigInterfaceEnergy name=(&string)  scorefxn=(&string) include_cstE=(0 &bool) jump_number=(last_jump &integer) energy_cutoff=(0.0 &float)/>

include_cstE=1 will *not* subtract out the cst energy from interface energy. jump_number defaults to last jump in the pose (assumed to be associated with ligand). energy should be less than energy_cutoff to pass.


EnzScore

Calculates scores of a pose e.g. a ligand-protein interface taking into account (or not) enzdes style cst_energy. Residues can be accessed by res_num/pdb_num or their constraint id. One and only one of res/pdb_num, cstid, and whole_pose tags can be specified. energy should be less than cutoff to pass.

<EnzScore name=(&string)  scorefxn=(&string, score12) whole_pose= (&bool,0) score_type = (&string) res_num/pdb_num = (see convetion) cstid =  (&string) energy_cutoff=(0.0 &float)/>


RepackWithoutLigand

Calculates delta_energy or RMSD of protein residues in a protein-ligand interface when the ligand is removed and the interface repacked. RMSD of a subset of these repacked residues (such as catalytic residues) can be accessed by setting the appropriate tags.

<RepackWithoutLigand name=(&string)  scorefxn=(&string, score12) target_res = (&string) target_cstids =  (&string) energy_threshold=(0.0 &float) rms_threshold=(0.5 &float)/>

Ligand design

HeavyAtom

<HeavyAtom name="&string" chain="&string" heavy_atom_limit=(&int)/>

Stop growing this designed ligand once we reach this heavy atom limit

CompleteConnections

<CompleteConnections name="&string" chain="&string"/>

Are there any connections left to fulfill? If not, stop growing ligand

Hotspot Design

StubScore

See Movers (RosettaScripts)#StubScore

Currently Undocumented

The following Filters are available through RosettaScripts, but are not currently documented. See the code (particularly the respective parse_my_tag() and apply() functions) for details. (Some may be undocumented as they are experimental/not fully functional.)