#include <AtomicDepth.hh>
core::scoring::atomic_depth::AtomicDepth::AtomicDepth |
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pose::Pose const & |
pose, |
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Real |
probe_radius = 1.4 , |
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bool |
poly_leu_depth = false , |
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Real |
resolution = 0.25 |
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) |
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Constructor for AtomicDepth object If poly_leu_depth is true, mutate pose to poly_leu before depth calculations. The intent is to make this aa independent to avoid surface lysines from adding noise.
References boxlength_, buildboundary(), depty_, fastdistancemap(), fillvoxels(), fixsf_, flagradius_, core::conformation::get_residue_from_name1(), initpara(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::n_non_polymeric_residue_connections(), pheight_, plength_, proberadius_, pwidth_, core::pose::Pose::replace_residue(), core::pose::Pose::residue_type(), scalefactor_, core::conformation::Residue::set_chi(), core::pose::Pose::size(), protocols::kinmatch::str(), core::scoring::TR(), vp_, and widxz_.
void core::scoring::atomic_depth::AtomicDepth::boundingatom |
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pose::Pose const & |
pose | ) |
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private |
References core::conformation::Residue::atom_type(), core::conformation::Residue::atom_type_index(), core::chemical::ResidueTypeBase::atom_type_set(), depty_, core::chemical::AtomType::is_virtual(), core::chemical::AtomTypeSet::n_atomtypes(), core::conformation::Residue::nheavyatoms(), proberadius_, core::pose::Pose::residue(), scalefactor_, core::pose::Pose::size(), core::conformation::Residue::type(), and widxz_.
Referenced by initpara().
void core::scoring::atomic_depth::AtomicDepth::buildboundary |
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References pheight_, plength_, proberadius_, ptran_, pwidth_, scalefactor_, core::conformation::Atom::type(), vp_, core::scoring::atomic_depth::point3d::x, core::conformation::Atom::xyz(), core::scoring::atomic_depth::point3d::y, and core::scoring::atomic_depth::point3d::z.
void core::scoring::atomic_depth::AtomicDepth::fastdistancemap |
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int |
type | ) |
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private |
References cutradis_, core::kinematics::distance(), fastoneshell(), inarray_, outarray_, pheight_, plength_, pwidth_, scalefactor_, totalinnervox_, totalsurfacevox_, and vp_.
Referenced by AtomicDepth().
void core::scoring::atomic_depth::AtomicDepth::fastoneshell |
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int |
innum, |
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int & |
allocout, |
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std::vector< std::vector< std::vector< voxel2 > > > & |
boundpoint, |
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int & |
outnum, |
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int & |
elimi |
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) |
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private |
References core::scoring::atomic_depth::fast_one_shell_cut, core::scoring::atomic_depth::fast_one_shell_highb, core::scoring::atomic_depth::fast_one_shell_lowb, core::scoring::atomic_depth::voxel::ix, core::scoring::atomic_depth::voxel::iy, core::scoring::atomic_depth::voxel::iz, core::scoring::atomic_depth::nb, outarray_, pheight_, plength_, pwidth_, core::chemical::rings::q, totalinnervox_, and vp_.
Referenced by fastdistancemap().
void core::scoring::atomic_depth::AtomicDepth::fill_vp |
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void core::scoring::atomic_depth::AtomicDepth::fillatom |
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conformation::Atom const & |
atom | ) |
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private |
References depty_, pheight_, plength_, ptran_, pwidth_, scalefactor_, core::conformation::Atom::type(), vp_, widxz_, core::scoring::atomic_depth::point3d::x, core::conformation::Atom::xyz(), core::scoring::atomic_depth::point3d::y, and core::scoring::atomic_depth::point3d::z.
Referenced by fillvoxels().
void core::scoring::atomic_depth::AtomicDepth::fillvoxels |
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pose::Pose const & |
pose | ) |
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private |
References core::conformation::Residue::atom(), core::conformation::Residue::atom_type(), fill_vp(), fillatom(), core::chemical::AtomType::is_virtual(), core::conformation::Residue::nheavyatoms(), pheight_, plength_, pwidth_, core::pose::Pose::residue(), core::pose::Pose::size(), and vp_.
Referenced by AtomicDepth().
void core::scoring::atomic_depth::AtomicDepth::initpara |
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pose::Pose const & |
pose | ) |
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private |
References boundbox(), boundingatom(), boxlength_, cutradis_, fixsf_, pheight_, plength_, pmax_, pmin_, proberadius_, ptran_, pwidth_, scalefactor_, vp_, core::scoring::atomic_depth::point3d::x, core::scoring::atomic_depth::point3d::y, and core::scoring::atomic_depth::point3d::z.
Referenced by AtomicDepth().
void core::scoring::atomic_depth::AtomicDepth::visualize_at_depth |
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Real |
depth, |
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std::string const & |
fname, |
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Real |
fraction = 1.0 |
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) |
| const |
References core::conformation::membrane::out, pheight_, plength_, proberadius_, ptran_, pwidth_, scalefactor_, vp_, core::scoring::atomic_depth::point3d::x, core::scoring::atomic_depth::point3d::y, and core::scoring::atomic_depth::point3d::z.
int core::scoring::atomic_depth::AtomicDepth::boxlength_ |
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core::Real core::scoring::atomic_depth::AtomicDepth::cutradis_ |
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std::vector<std::vector<int> > core::scoring::atomic_depth::AtomicDepth::depty_ |
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core::Real core::scoring::atomic_depth::AtomicDepth::fixsf_ |
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bool core::scoring::atomic_depth::AtomicDepth::flagradius_ |
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std::shared_ptr<std::vector<voxel2> > core::scoring::atomic_depth::AtomicDepth::inarray_ |
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std::shared_ptr<std::vector<voxel2> > core::scoring::atomic_depth::AtomicDepth::outarray_ |
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int core::scoring::atomic_depth::AtomicDepth::pheight_ |
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int core::scoring::atomic_depth::AtomicDepth::plength_ |
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point3d core::scoring::atomic_depth::AtomicDepth::pmax_ |
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point3d core::scoring::atomic_depth::AtomicDepth::pmin_ |
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core::Real core::scoring::atomic_depth::AtomicDepth::proberadius_ |
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point3d core::scoring::atomic_depth::AtomicDepth::ptran_ |
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int core::scoring::atomic_depth::AtomicDepth::pwidth_ |
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core::Real core::scoring::atomic_depth::AtomicDepth::scalefactor_ |
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int core::scoring::atomic_depth::AtomicDepth::totalinnervox_ |
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int core::scoring::atomic_depth::AtomicDepth::totalsurfacevox_ |
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std::vector<std::vector<std::vector<volumepixel > > > core::scoring::atomic_depth::AtomicDepth::vp_ |
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std::vector<int> core::scoring::atomic_depth::AtomicDepth::widxz_ |
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private |
The documentation for this class was generated from the following files: