OELoopBuilderOptions

Attention

This API is currently available in C++ and Python.
class OELoopBuilderOptions : public OESystem::OEOptions
This class stores the optional parameter sets for building loops in the OEBuildLoops and OEBuildSingleLoop functions.
Constructors
OELoopBuilderOptions()
OELoopBuilderOptions(const OELoopBuilderOptions &)
Default and copy constructor that constructs a OELoopBuilderOptions object.
operator=
OELoopBuilderOptions &operator=(const OELoopBuilderOptions &)
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 relevant 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.
GetDeleteExistingResidues
bool GetDeleteExistingResidues() const
Returns whether or not to delete residues already present at site where new loops needs to be built.
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 are 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 initial steepest descent 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.

GetRejectClashingLoopsPostMinimization

bool GetRejectClashingLoopsPostMinimization() const

Returns whether or not to reject clashing loops post-minimization.

GetSeqAlignMethod

unsigned GetSeqAlignMethod() const

Returns the sequence alignment method, from the OESeqAlignmentMethod namespace, used to compare the provided sequence and the structure for gaps.

GetSeqAlignGapPenalty

int GetSeqAlignGapPenalty() const

Returns the sequence alignment gap penalty, used to compare the provided sequence and the structure for gaps with the OEGetSimpleAlignment function.

GetSeqAlignExtendPenalty

int GetSeqAlignExtendPenalty() const

Returns the sequence alignment extend penalty, used to compare the provided sequence and the structure for gaps with the OEGetSimpleAlignment function.

GetBuildTails

bool GetBuildTails() const

Returns whether or not to allow building missing tails at the N and C termini.

SetLoopDBFilename

bool SetLoopDBFilename(std::string filename)

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

SetUsePackingResidues

bool SetUsePackingResidues(bool usePackingResidues)

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

SetCropLength

bool 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

bool 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

bool SetStrictProlineMatch(bool strictProline)

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

SetConnectBufferDistance

bool SetConnectBufferDistance(double buffer)

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

SetBackboneClashRejectThreshold

bool 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.

SetDeleteExistingResidues
bool SetDeleteExistingResidues(bool deleteExistingResidues)
Sets whether or not to delete residues already present at site where new loops needs to be built. See also SetRejectClashingLoopsPostMinimization.

SetLoopClashRejectThreshold

bool 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

bool SetOptimizationShell(double optimizationShellRadius)

Set the radius of atoms being considered when minimizing the loops in place. Since multiple loops are 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

bool SetOptimizationTolerance(double optimizationTolerance)

Sets the tolerance used by the optimizer.

SetOptimizationStage1IterMultiplier

bool SetOptimizationStage1IterMultiplier(unsigned stage1multiplier)

Sets the multiplier of optimization steps per residue in the loop used during the initial steepest descent optimization.

SetOptimizationStage2IterMultiplier

bool SetOptimizationStage2IterMultiplier(unsigned stage2multiplier)

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

SetOptimizationUseSolventModel

bool SetOptimizationUseSolventModel(bool useSolventModel)

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

SetOptimizationInclSurfaceAreaTerm

bool SetOptimizationInclSurfaceAreaTerm(bool useSATerm)

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

SetOptimizationMaxLoops

bool 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

bool 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.

SetRejectClashingLoopsPostMinimization

bool GetRejectClashingLoopsPostMinimization() const

Set whether or not to reject clashing loops post-minimization. See also SetDeleteExistingResidues.

SetSeqAlignMethod

bool SetSeqAlignMethod(unsigned seqAlignMethod)

Sets the sequence alignment method, from the OESeqAlignmentMethod namespace, used to compare the provided sequence and the structure for gaps.

SetSeqAlignGapPenalty

bool SetSeqAlignGapPenalty(int gapPenalty)

Set the sequence alignment gap penalty, used to compare the provided sequence and the structure for gaps with the OEGetSimpleAlignment function.

SetSeqAlignExtendPenalty

bool SetSeqAlignExtendPenalty(int extendPenalty)

Set the sequence alignment extend penalty, used to compare the provided sequence and the structure for gaps with the OEGetSimpleAlignment function.

SetBuildTails

bool SetBuildTails(bool BuildTails)
Sets whether or not to allow building missing tails at the C and N termini.