OELoopBuilderOptions

Attention

PRELIMINARY-IMAGE This is a preliminary API until Spring 2021 and may be improved based on user feedback. It is currently available in C++ and Python.

class OELoopBuilderOptions

This class stores the optional parameter sets for building loops OEBuildLoops and OEBuildSingleLoop functions.

Constructors

OELoopBuilderOptions()=default
OELoopBuilderOptions(const OELoopBuilderOptions &)=default

Default and copy constructor that constructs a OELoopBuilderOptions object.

operator=

OELoopBuilderOptions &operator=(const OELoopBuilderOptions &)=default

Assignment operator.

GetLoopDBFilename

std::string GetLoopDBFilename() const

Returns the filename of the loop database used when searching for compatible loops.

GetUsePackingResidues

bool GetUsePackingResidues() const

Returns the boolean whether or not to use crystal packing residues during loop modeling (if available).

GetCropLength

unsigned GetCropLength() const

Returns the number of residues on either side of a gap to remove, since these are known to sometimes be poorly resolved and therefore have configurations that make it difficult to build loops.

GetTransformThreshold

unsigned GetTransformThreshold() const

Returns the number of loops from the database to transform, meaning mutate from their database sequence to target sequence, if they are not 100% sequence matching. Structures with 100% sequence match are not affected by this threshold.

GetStrictProlineMatch

bool GetStrictProlineMatch() const

Returns the boolean of whether or not fuzzy sequence matches have to have proline residues in the correct position. This can be relavant since they have a different backbone conformation than other amino acid residues.

GetConnectBufferDistance

double GetConnectBufferDistance() const

Returns the buffer distance allowed between the anchor atoms (connection points) when searching for fuzzy sequence matches.

GetBackboneClashRejectThreshold

double GetBackboneClashRejectThreshold() const

Returns the threshold of clashing backbone atoms. If the clash level is above this threshold a loop from the database is rejected, and is not processed further.

GetLoopClashRejectThreshold

double GetLoopClashRejectThreshold() const

Returns the threshold of clashing loops atoms. This threshold excludes already considered clashing backbone atoms. If the clash level is above this threshold a loop from the database is rejected, and is not processed further.

GetOptimizationShell

double GetOptimizationShell() const

Returns the radius of atoms being considered when minimizing the loops in place. Since multiple loops can being optimized, it is the union of atoms inside the radius around each starting loop configuration that is considered. This allows comparison of the energies between each loop conformation as the systems are of identical size.

GetOptimizationTolerance

double GetOptimizationTolerance() const

Returns the tolerance used by the optimizer.

GetOptimizationStage1IterMultiplier

unsigned GetOptimizationStage1IterMultiplier() const

Returns the multiplier of optimization steps per residue in the loop used during the intial steepest decent optimization.

GetOptimizationStage2IterMultiplier

unsigned GetOptimizationStage2IterMultiplier() const

Returns the multiplier of optimization steps per residue in the loop used during the secondary BFGS optimization.

GetOptimizationUseSolventModel

bool GetOptimizationUseSolventModel() const

Returns whether or not to use a simplistic solvent model during the loop optimization.

GetOptimizationInclSurfaceAreaTerm

bool GetOptimizationInclSurfaceAreaTerm() const

Returns whether or not to include the surface area term when scoring the loops after optimization.

GetOptimizationMaxLoops

unsigned GetOptimizationMaxLoops() const

Returns the number of loops to optimize, the higher the number the longer the calculation will take, but also includes more structural diversity.

GetAllowBuildDisulfideBridges

bool GetAllowBuildDisulfideBridges() const

Returns whether or not to allow building disulfide bridges between the loop and the protein if possible, requires cystine residues in proximity.


SetLoopDBFilename

void SetLoopDBFilename(std::string filename)

Sets the filename of the loop database to use when searching for compatible loops.

SetUsePackingResidues

boid SetUsePackingResidues(bool usePackingResidues)

Sets whether or not to use crystal packing residues during loop modeling (if available).

SetCropLength

void SetCropLength(unsigned cropLength)

Returns the number of residues on either side of a gap to remove, since these are known to sometimes be poorly resolved and therefore have configurations that make it difficult to build loops.

SetTransformThreshold

void SetTransformThreshold(unsigned transformThreshold)

Sets the number of loops from the database to transform, meaning mutate from their database sequence to target sequence, if they are not 100% sequence matching. Structures with 100% sequence match are not affected by this threshold.

SetStrictProlineMatch

void SetStrictProlineMatch(bool strictProline)

Sets whether or not fuzzy sequence matches have to have proline residues in the correct position. This can be relavant since they have a different backbone conformation than other amino acid residues.

SetConnectBufferDistance

void SetConnectBufferDistance(double buffer)

Sets the buffer distance allowed between the anchor atoms (connection points) when searching for fuzzy sequence matches.

SetBackboneClashRejectThreshold

void SetBackboneClashRejectThreshold(double bbClashThreshold)

Sets the threshold of clashing backbone atoms. If the clash level is above this threshold a loop from the database is rejected, and is not processed further.

SetLoopClashRejectThreshold

void SetLoopClashRejectThreshold(double loopClashThreshold)

Sets the threshold of clashing loops atoms. This threshold excludes already considered clashing backbone atoms. If the clash level is above this threshold a loop from the database is rejected, and is not processed further.

SetOptimizationShell

void SetOptimizationShell(double optimizationShellRadius)

Set the radius of atoms being considered when minimizing the loops in place. Since multiple loops can being optimized, it is the union of atoms inside the radius around each starting loop configuration that is considered. This allows comparison of the energies between each loop conformation as the systems are of identical size.

SetOptimizationTolerance

void SetOptimizationTolerance(double optimizationTolerance)

Sets the tolerance used by the optimizer.

SetOptimizationStage1IterMultiplier

void SetOptimizationStage1IterMultiplier(unsigned stage1multiplier)

Sets the multiplier of optimization steps per residue in the loop used during the intial steepest decent optimization.

SetOptimizationStage2IterMultiplier

void SetOptimizationStage2IterMultiplier(unsigned stage2multiplier)

Sets the multiplier of optimization steps per residue in the loop used during the secondary BFGS optimization.

SetOptimizationUseSolventModel

void SetOptimizationUseSolventModel(bool useSolvetModel)

Sets whether or not to use a simplistic solvent model during the loop optimization.

SetOptimizationInclSurfaceAreaTerm

void SetOptimizationInclSurfaceAreaTerm(bool useSATerm)

Sets whether or not to include the surface area term when scoring the loops after optimization.

SetOptimizationMaxLoops

void SetOptimizationMaxLoops(unsigned maxOptLoops)

Sets the number of loops to optimize, the higher the number the longer the calculation will take, but also includes more structural diversity.

SetAllowBuildDisulfideBridges

void SetAllowBuildDisulfideBridges(bool allowBuildDisulfideBridges)

Sets whether or not to allow building disulfide bridges between the loop and the protein if possible, requires cystine residues in proximity.

See also