cryst

Bindings for core::scoring::cryst namespace

class pyrosetta.rosetta.core.scoring.cryst.PhenixInterface

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface, : pyrosetta.rosetta.core.scoring.cryst.PhenixInterface) → pyrosetta.rosetta.core.scoring.cryst.PhenixInterface

C++: core::scoring::cryst::PhenixInterface::operator=(const class core::scoring::cryst::PhenixInterface &) –> class core::scoring::cryst::PhenixInterface &

calculateDensityMap(*args, **kwargs)

Overloaded function.

1. calculateDensityMap(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface, pose: pyrosetta.rosetta.core.pose.Pose) -> str

2. calculateDensityMap(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface, pose: pyrosetta.rosetta.core.pose.Pose, no_sidechain: bool) -> str

use pose to rephase data; calculate a new density map; return map file name

C++: core::scoring::cryst::PhenixInterface::calculateDensityMap(class core::pose::Pose &, bool) –> std::string

fitBfactors(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface, pose: pyrosetta.rosetta.core.pose.Pose) → None

fit bfactors

C++: core::scoring::cryst::PhenixInterface::fitBfactors(class core::pose::Pose &) –> void

getInfoLine(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface) → str

dump r and rfree to a string for informational purposes

C++: core::scoring::cryst::PhenixInterface::getInfoLine() –> std::string

getR(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface) → float

dump r and rfree

C++: core::scoring::cryst::PhenixInterface::getR() –> double

getRfree(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface) → float

C++: core::scoring::cryst::PhenixInterface::getRfree() –> double

getScore(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface, pose: pyrosetta.rosetta.core.pose.Pose) → float

score a structure

C++: core::scoring::cryst::PhenixInterface::getScore(const class core::pose::Pose &) –> double

getScoreAndDerivs(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface, pose: pyrosetta.rosetta.core.pose.Pose, grads: pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t) → float

score a structure with derivatives

C++: core::scoring::cryst::PhenixInterface::getScoreAndDerivs(const class core::pose::Pose &, class utility::vector1<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >, class std::allocator<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > > > &) –> double

optimizeSolvParams(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface) → None

explicitly recompute ksol/bsol

C++: core::scoring::cryst::PhenixInterface::optimizeSolvParams() –> void

optimizeSolvParamsAndMask(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface) → None

explicitly recompute ksol/bsol and fmask

C++: core::scoring::cryst::PhenixInterface::optimizeSolvParamsAndMask() –> void

optimizeSolventMask(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface) → None

optimize fmask

C++: core::scoring::cryst::PhenixInterface::optimizeSolventMask() –> void

setAlgorithm(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface, twin_law: str) → None

set sf calculation algorithm

C++: core::scoring::cryst::PhenixInterface::setAlgorithm(std::string) –> void

setResLimits(*args, **kwargs)

Overloaded function.

1. setResLimits(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface) -> None

2. setResLimits(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface, res_high: float) -> None

3. setResLimits(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface, res_high: float, res_low: float) -> None

set the res limits

C++: core::scoring::cryst::PhenixInterface::setResLimits(double, double) –> void

setTwinLaw(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface, twin_law: str) → None

set twin law

C++: core::scoring::cryst::PhenixInterface::setTwinLaw(std::string) –> void

set_adp_strategy(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface, adp_strat: str) → None

set strategy for adp refinement

C++: core::scoring::cryst::PhenixInterface::set_adp_strategy(std::string) –> void

set_cif_files(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface, cif_in: pyrosetta.rosetta.utility.vector1_std_string) → None

set cif files (ligand refinement)

C++: core::scoring::cryst::PhenixInterface::set_cif_files(class utility::vector1<std::string, class std::allocator<std::string > >) –> void

set_map_type(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface, map_type: str) → None

set target function

C++: core::scoring::cryst::PhenixInterface::set_map_type(std::string) –> void

set_sharpen_b(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface, sharpen_b: float) → None

set b sharpen value

C++: core::scoring::cryst::PhenixInterface::set_sharpen_b(double) –> void

set_target_function(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface, tgt_val: str) → None

set target function

C++: core::scoring::cryst::PhenixInterface::set_target_function(std::string) –> void

updateFcalc(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface) → None

update fcalc

C++: core::scoring::cryst::PhenixInterface::updateFcalc() –> void

updateSolventMask(*args, **kwargs)

Overloaded function.

1. updateSolventMask(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface) -> None

update mask

C++: core::scoring::cryst::PhenixInterface::updateSolventMask() –> void

2. updateSolventMask(self: pyrosetta.rosetta.core.scoring.cryst.PhenixInterface, pose: pyrosetta.rosetta.core.pose.Pose) -> None

update mask

C++: core::scoring::cryst::PhenixInterface::updateSolventMask(const class core::pose::Pose &) –> void

pyrosetta.rosetta.core.scoring.cryst.fix_bfactorsH(: pyrosetta.rosetta.core.pose.Pose) → None

fix the hydrogen bfactors in the pose

C++: core::scoring::cryst::fix_bfactorsH(class core::pose::Pose &) –> void

pyrosetta.rosetta.core.scoring.cryst.fix_bfactorsMissing(pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::scoring::cryst::fix_bfactorsMissing(class core::pose::Pose &) –> void

pyrosetta.rosetta.core.scoring.cryst.getPhenixInterface() → pyrosetta.rosetta.core.scoring.cryst.PhenixInterface

The EDM instance

C++: core::scoring::cryst::getPhenixInterface() –> class core::scoring::cryst::PhenixInterface &