Rosetta
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@Author Frank Dimaio More...
#include <protocols/cryst/spacegroup.hh>
#include <protocols/cryst/refinable_lattice.hh>
#include <apps/pilot/frank/cryst_reporters.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/io/Remarks.hh>
#include <core/io/CrystInfo.hh>
#include <core/id/AtomID.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/types.hh>
#include <core/pack/task/ResfileReader.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/constraints/ResidueTypeConstraint.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/JobDistributorFactory.hh>
#include <protocols/jd2/util.hh>
#include <protocols/jd2/SilentFileJobOutputter.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/minimization_packing/symmetry/SymPackRotamersMover.hh>
#include <protocols/cryst/cryst_rms.hh>
#include <protocols/relax/FastRelax.hh>
#include <protocols/cryst/util.hh>
#include <utility/vector1.hh>
#include <utility/string_util.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <numeric/random/random.hh>
#include <numeric/fourier/FFT.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/UniformRotationSampler.hh>
#include <numeric/random/random_permutation.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/FArray3D.hh>
#include <utility/excn/Exceptions.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/options/keys/symmetry.OptionKeys.gen.hh>
#include <fstream>
#include <cmath>
#include <string>
#include <queue>
#include <core/optimization/MinimizerOptions.hh>
#include <core/optimization/symmetry/SymAtomTreeMinimizer.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/ResidueLevelTask.hh>
Classes | |
struct | SpacegroupHit |
struct | InterfaceHit |
class | InterfaceHitComparitor |
class | InterfaceHitDatabase |
class | CrystDesign |
class | CrystRelax |
class | CrystCluster |
class | CrystFFTDock |
Macros | |
#define | DEG2RAD 0.0174532925199433 |
#define | RAD2DEG 57.295779513082323 |
Functions | |
double | sign (double x) |
double | norm4 (double a, double b, double c, double d) |
void | adjust_ref_weights (core::scoring::ScoreFunction &scorefxn) |
template<class S > | |
core::Real | interp_linear (ObjexxFCL::FArray3D< S > const &data, numeric::xyzVector< core::Real > const &idxX) |
void | euler2rot (core::Real a, core::Real b, core::Real g, numeric::xyzMatrix< Real > &R) |
numeric::xyzVector< Real > | center_pose_at_origin (Pose &pose) |
void | add_crystinfo_to_pose (Pose &pose, Spacegroup const &sg) |
void * | my_main (void *) |
int | main (int argc, char *argv[]) |
Variables | |
static basic::Tracer | TR ("cryst.design") |
@Author Frank Dimaio
#define DEG2RAD 0.0174532925199433 |
#define RAD2DEG 57.295779513082323 |
void add_crystinfo_to_pose | ( | Pose & | pose, |
Spacegroup const & | sg | ||
) |
References beta_nonlocal::pose.
Referenced by CrystCluster::transform_pdb().
void adjust_ref_weights | ( | core::scoring::ScoreFunction & | scorefxn | ) |
References aa, ObjexxFCL::float_of(), create_a3b_hbs::ii, extract_by_sidechain_sasa_score::l, option, options, runtime_assert, oop_conformations::scorefxn, basic::TR, and basic::options::OptionKeys::inout::dbms::user.
Referenced by CrystDesign::apply(), and main().
numeric::xyzVector<Real> center_pose_at_origin | ( | Pose & | pose | ) |
References count, create_a3b_hbs::i, enumerate_junctions::int, create_a3b_hbs::j, and beta_nonlocal::pose.
Referenced by CrystFFTDock::apply().
void euler2rot | ( | core::Real | a, |
core::Real | b, | ||
core::Real | g, | ||
numeric::xyzMatrix< Real > & | R | ||
) |
References a, compute_difference::b, DEG2RAD, g(), and docking::R.
core::Real interp_linear | ( | ObjexxFCL::FArray3D< S > const & | data, |
numeric::xyzVector< core::Real > const & | idxX | ||
) |
backward interpolation (unrotated->rotated) used to generate grids
References data, test.T009_Exceptions::e, enumerate_junctions::int, and pyrosetta.distributed.cluster.converters::S.
Referenced by CrystFFTDock::resample_maps_and_get_self().
int main | ( | int | argc, |
char * | argv[] | ||
) |
References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::A, adjust_ref_weights(), compute_difference::alpha, argv, basic::options::OptionKeys::corrections::beta, C, basic::options::OptionKeys::corrections::water::cluster_cutoff, basic::options::OptionKeys::msd::debug, test.T009_Exceptions::e, loops::gamma, basic::init(), PREcst::K, SmotifHasher::mode, my_main(), NEW_OPT, basic::options::OptionKeys::mp::mutate_relax::nmodels, and viewer_main().
void* my_main | ( | void * | ) |
References a, compute_difference::b, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::c.
References x.
Referenced by detail::write_float().
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