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
OELoopBuilderOptions(arg2: OELoopBuilderOptions) -> OELoopBuilderOptions
Default and copy constructor that constructs a OELoopBuilderOptions object.
GetLoopDBFilename
GetLoopDBFilename() -> str
Returns the filename of the loop database used when searching for compatible loops.
GetUsePackingResidues
GetUsePackingResidues() -> bool
Returns the boolean whether or not to use crystal packing residues during loop modeling (if available).
GetCropLength
GetCropLength() -> int
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
GetTransformThreshold() -> int
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
GetStrictProlineMatch() -> bool
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
GetConnectBufferDistance() -> float
Returns the buffer distance allowed between the anchor atoms (connection points) when searching for fuzzy sequence matches.
GetBackboneClashRejectThreshold
GetBackboneClashRejectThreshold() -> float
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
GetDeleteExistingResidues() -> bool
Returns whether or not to delete residues already present at site where new loops needs to be built.
GetLoopClashRejectThreshold
GetLoopClashRejectThreshold() -> float
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
GetOptimizationShell() -> float
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
GetOptimizationTolerance() -> float
Returns the tolerance used by the optimizer.
GetOptimizationStage1IterMultiplier
GetOptimizationStage1IterMultiplier() -> int
Returns the multiplier of optimization steps per residue in the loop used during the initial steepest descent optimization.

GetOptimizationStage2IterMultiplier

GetOptimizationStage2IterMultiplier() -> int

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

GetOptimizationUseSolventModel

GetOptimizationUseSolventModel() -> bool

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

GetOptimizationInclSurfaceAreaTerm

GetOptimizationInclSurfaceAreaTerm() -> bool

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

GetOptimizationMaxLoops

GetOptimizationMaxLoops() -> int

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

GetAllowBuildDisulfideBridges

GetAllowBuildDisulfideBridges() -> bool

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

GetRejectClashingLoopsPostMinimization

GetRejectClashingLoopsPostMinimization() -> bool

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

GetSeqAlignMethod

GetSeqAlignMethod() -> int

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

GetSeqAlignGapPenalty

GetSeqAlignGapPenalty() -> int

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

GetSeqAlignExtendPenalty

GetSeqAlignExtendPenalty() -> int

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

GetBuildTails

GetBuildTails() -> bool

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

SetLoopDBFilename

SetLoopDBFilename(value: str) -> bool

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

SetUsePackingResidues

SetUsePackingResidues(value: bool) -> bool

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

SetCropLength

SetCropLength(value: int) -> bool

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

SetTransformThreshold(value: int) -> bool

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

SetStrictProlineMatch(value: bool) -> bool

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

SetConnectBufferDistance(value: float) -> bool

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

SetBackboneClashRejectThreshold

SetBackboneClashRejectThreshold(value: float) -> bool

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

SetLoopClashRejectThreshold

SetLoopClashRejectThreshold(value: float) -> bool

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

SetOptimizationShell(value: float) -> bool

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

SetOptimizationTolerance(value: float) -> bool

Sets the tolerance used by the optimizer.

SetOptimizationStage1IterMultiplier

SetOptimizationStage1IterMultiplier(value: int) -> bool

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

SetOptimizationStage2IterMultiplier

SetOptimizationStage2IterMultiplier(value: int) -> bool

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

SetOptimizationUseSolventModel

SetOptimizationUseSolventModel(value: bool) -> bool

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

SetOptimizationInclSurfaceAreaTerm

SetOptimizationInclSurfaceAreaTerm(value: bool) -> bool

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

SetOptimizationMaxLoops

SetOptimizationMaxLoops(value: int) -> bool

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

SetAllowBuildDisulfideBridges

SetAllowBuildDisulfideBridges(value: bool) -> bool

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

SetRejectClashingLoopsPostMinimization

SetRejectClashingLoopsPostMinimization(value: bool) -> bool

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

SetSeqAlignMethod

SetSeqAlignMethod(value: int) -> bool

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

SetSeqAlignGapPenalty

SetSeqAlignGapPenalty(value: int) -> bool

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

SetSeqAlignExtendPenalty

SetSeqAlignExtendPenalty(value: int) -> bool

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

SetBuildTails

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