Rosetta 3.4
Public Member Functions
core::scoring::electron_density::ElectronDensity Class Reference

#include <ElectronDensity.hh>

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List of all members.

Public Member Functions

 ElectronDensity ()
 constructor
 ElectronDensity (utility::vector1< core::pose::PoseOP > poses, core::Real reso, core::Real apix)
 calulated density from a vector of poses
template<class T >
 ElectronDensity (ObjexxFCL::FArray3D< T > const &map, core::Real apix=1.0, numeric::xyzVector< core::Real > new_origin=numeric::xyzVector< core::Real >(0, 0, 0), bool fftshift=false)
 constructor from an FArray3D (debugging only)
bool readMRCandResize (std::string mapfile, core::Real reso=5.0, core::Real gridSpacing=0.0)
 Load an MRC (="new-CCP4") density map.
bool writeMRC (std::string mapfilestem)
 (debugging) Write MRC mapfile
bool writeMAT (std::string mapfilestem)
 (debugging) Write MATLAB v5 mapfile
numeric::xyzMatrix< core::RealrotAlign2DPose (core::pose::Pose const &pose, std::string axis)
 Align a pose about a 2D rotation axis.
core::Real matchCentroidPose (core::pose::Pose const &pose, const core::conformation::symmetry::SymmetryInfo *symmInfo=NULL, bool cacheCCs=false)
 Quickly matches a centroid pose into a low-resolution density map by placing a single Gaussian at each CA.
core::Real matchPose (core::pose::Pose const &pose, const core::conformation::symmetry::SymmetryInfo *symmInfo=NULL, bool cacheCCs=false)
 Quickly matches a centroid pose into a low-resolution density map by placing a single Gaussian at each atom.
core::Real matchPoseToPatterson (core::pose::Pose const &pose, bool cacheCCs=false)
 Match a pose to a patterson map.
core::Real rematchResToPatterson (core::conformation::Residue const &rsd) const
 Rematch the pose to a patterson map, using previous rho_calc with only rsd changed.
void updateCachedDensity (core::conformation::Residue const &rsd)
 Update cached rho_calc by changing residue 'rsd'.
core::Real matchRes (int resid, core::conformation::Residue const &rsd, core::pose::Pose const &pose, const core::conformation::symmetry::SymmetryInfo *symmInfo=NULL, bool cacheCCs=false)
 Match a residue's conformation to the density map. Backbone atoms from adjacent residues are also used for scoring. Returns the correlation coefficient between map and pose Internally stores per-res CCs, per-atom dCC/dxs.
core::Real matchResFast (int resid, core::conformation::Residue const &rsd, core::pose::Pose const &pose, const core::conformation::symmetry::SymmetryInfo *symmInfo=NULL)
 Match a residue's conformation to the density map. Same as matchRes, but using a fast approximation to the match function.
void compute_symm_rotations (core::pose::Pose const &pose, const core::conformation::symmetry::SymmetryInfo *symmInfo=NULL)
 Computes the symmatric rotation matrices.
void dCCdx_res (int atmid, int resid, numeric::xyzVector< core::Real > const &X, core::conformation::Residue const &rsd, core::pose::Pose const &pose, numeric::xyzVector< core::Real > &gradX)
 Return the gradient of CC w.r.t. atom X's movement Uses information stored from the previous call to matchRes with this resid.
void dCCdx_fastRes (int atmid, int resid, numeric::xyzVector< core::Real > const &X, core::conformation::Residue const &rsd, core::pose::Pose const &pose, numeric::xyzVector< core::Real > &gradX)
 Return the gradient of "fast CC" w.r.t. atom X's movement Uses information stored from the previous call to matchRes with this resid.
void dCCdx_cen (int resid, numeric::xyzVector< core::Real > const &X, core::pose::Pose const &pose, numeric::xyzVector< core::Real > &gradX)
 Return the gradient of CC w.r.t. res X's CA's movement Centroid-mode analogue of dCCdx.
void dCCdx_aacen (int atmid, int resid, numeric::xyzVector< core::Real > const &X, core::pose::Pose const &pose, numeric::xyzVector< core::Real > &gradX)
 Return the gradient of whole-structure-CC w.r.t. atom X's movement non-sliding-window analogue of dCCdx.
void dCCdx_pat (int atmid, int resid, numeric::xyzVector< core::Real > const &X, core::pose::Pose const &pose, numeric::xyzVector< core::Real > &gradX)
 Return the gradient of patterson-CC w.r.t. atom X's movement.
void clear_dCCdx_res_cache (core::pose::Pose const &pose)
 Resets the counters used for derivative computation in sliding-window/fast scoring.
numeric::xyzVector< core::RealgetTransform ()
 Get the transformation from indices to Cartesian coords using 'real' origin.
void set_nres (int nres)
 set # of residues
void showCachedScores (utility::vector1< int > const &reses)
 Print cached CCs.
core::Real getCCs (int resid)
void setUseDensityInMinimizer (bool newVal)
bool getUseDensityInMinimizer () const
void setUseExactDerivatives (bool newVal)
bool getUseExactDerivatives () const
core::Real getNumDerivH () const
core::Real getMean () const
core::Real getMin () const
core::Real getMax () const
core::Real getStdev () const
core::Real getResolution () const
bool isMapLoaded () const
numeric::xyzVector< core::RealgetCoM () const
numeric::xyzVector< core::RealgetOrigin () const
numeric::xyzVector< core::RealgetEffOrigin () const
utility::vector1
< core::kinematics::RT
getsymmOps () const
void maskResidues (int scoring_mask)
void maskResidues (utility::vector1< int > const &scoring_mask)
void clearMask ()
ObjexxFCL::FArray3D< float >
const & 
data () const
void cart2idx (numeric::xyzVector< core::Real > const &cartX, numeric::xyzVector< core::Real > &idxX) const
template<class Q >
void idx2cart (numeric::xyzVector< Q > const &idxX, numeric::xyzVector< core::Real > &cartX) const
template<class Q >
void idxoffset2cart (numeric::xyzVector< Q > const &idxX, numeric::xyzVector< core::Real > &cartX) const
void cart2frac (numeric::xyzVector< core::Real > const &cartX, numeric::xyzVector< core::Real > &fracX) const
void frac2cart (numeric::xyzVector< core::Real > const &fracX, numeric::xyzVector< core::Real > &cartX) const
numeric::xyzVector< core::Realdelt_cart (numeric::xyzVector< core::Real > const &cartX1, numeric::xyzVector< core::Real > const &cartX2)
numeric::xyzVector< core::Realget_cart_unitCell (numeric::xyzVector< core::Real > const &cartX)
numeric::xyzVector< core::Realget_nearest_UC (numeric::xyzVector< core::Real > const &cartX_in, numeric::xyzVector< core::Real > const &cartX_ref)
numeric::xyzVector< core::Realdens_grad (numeric::xyzVector< core::Real > const &idxX) const
void resize (core::Real approxGridSpacing)
 resize the map via FFT
void get_symmMap (int vrtid, utility::vector1< int > &X_map, numeric::xyzMatrix< core::Real > &R)
void get_R (int subunit, numeric::xyzMatrix< core::Real > &R)

Constructor & Destructor Documentation

core::scoring::electron_density::ElectronDensity::ElectronDensity ( )

constructor

null constructor

core::scoring::electron_density::ElectronDensity::ElectronDensity ( utility::vector1< core::pose::PoseOP poses,
core::Real  reso,
core::Real  apix 
)
template<class T >
core::scoring::electron_density::ElectronDensity::ElectronDensity ( ObjexxFCL::FArray3D< T > const &  map,
core::Real  apix = 1.0,
numeric::xyzVector< core::Real new_origin = numeric::xyzVectorcore::Real >(0,0,0),
bool  fftshift = false 
) [inline]

constructor from an FArray3D (debugging only)

References core::scoring::electron_density::pos_mod().


Member Function Documentation

void core::scoring::electron_density::ElectronDensity::cart2frac ( numeric::xyzVector< core::Real > const &  cartX,
numeric::xyzVector< core::Real > &  fracX 
) const [inline]
void core::scoring::electron_density::ElectronDensity::cart2idx ( numeric::xyzVector< core::Real > const &  cartX,
numeric::xyzVector< core::Real > &  idxX 
) const [inline]
void core::scoring::electron_density::ElectronDensity::clear_dCCdx_res_cache ( core::pose::Pose const &  pose)
void core::scoring::electron_density::ElectronDensity::clearMask ( ) [inline]
void core::scoring::electron_density::ElectronDensity::compute_symm_rotations ( core::pose::Pose const &  pose,
const core::conformation::symmetry::SymmetryInfo symmInfo = NULL 
)
ObjexxFCL::FArray3D< float > const& core::scoring::electron_density::ElectronDensity::data ( ) const [inline]
void core::scoring::electron_density::ElectronDensity::dCCdx_aacen ( int  atmid,
int  resid,
numeric::xyzVector< core::Real > const &  X,
core::pose::Pose const &  pose,
numeric::xyzVector< core::Real > &  gradX 
)

Return the gradient of whole-structure-CC w.r.t. atom X's movement non-sliding-window analogue of dCCdx.

References core::scoring::electron_density::getDensityMap(), matchPose(), core::pose::Pose::set_xyz(), and core::scoring::electron_density::TR().

Referenced by core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative().

void core::scoring::electron_density::ElectronDensity::dCCdx_cen ( int  resid,
numeric::xyzVector< core::Real > const &  X,
core::pose::Pose const &  pose,
numeric::xyzVector< core::Real > &  gradX 
)
void core::scoring::electron_density::ElectronDensity::dCCdx_fastRes ( int  atmid,
int  resid,
numeric::xyzVector< core::Real > const &  X,
core::conformation::Residue const &  rsd,
core::pose::Pose const &  pose,
numeric::xyzVector< core::Real > &  gradX 
)
void core::scoring::electron_density::ElectronDensity::dCCdx_pat ( int  atmid,
int  resid,
numeric::xyzVector< core::Real > const &  X,
core::pose::Pose const &  pose,
numeric::xyzVector< core::Real > &  gradX 
)
void core::scoring::electron_density::ElectronDensity::dCCdx_res ( int  atmid,
int  resid,
numeric::xyzVector< core::Real > const &  X,
core::conformation::Residue const &  rsd,
core::pose::Pose const &  pose,
numeric::xyzVector< core::Real > &  gradX 
)

Return the gradient of CC w.r.t. atom X's movement Uses information stored from the previous call to matchRes with this resid.

References core::conformation::Residue::atom(), core::scoring::electron_density::getDensityMap(), matchRes(), core::scoring::electron_density::TR(), and core::conformation::Atom::xyz().

Referenced by core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative().

numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::delt_cart ( numeric::xyzVector< core::Real > const &  cartX1,
numeric::xyzVector< core::Real > const &  cartX2 
)
numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::dens_grad ( numeric::xyzVector< core::Real > const &  idxX) const
void core::scoring::electron_density::ElectronDensity::frac2cart ( numeric::xyzVector< core::Real > const &  fracX,
numeric::xyzVector< core::Real > &  cartX 
) const [inline]
numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::get_cart_unitCell ( numeric::xyzVector< core::Real > const &  cartX)
numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::get_nearest_UC ( numeric::xyzVector< core::Real > const &  cartX_in,
numeric::xyzVector< core::Real > const &  cartX_ref 
)
void core::scoring::electron_density::ElectronDensity::get_R ( int  subunit,
numeric::xyzMatrix< core::Real > &  R 
) [inline]
void core::scoring::electron_density::ElectronDensity::get_symmMap ( int  vrtid,
utility::vector1< int > &  X_map,
numeric::xyzMatrix< core::Real > &  R 
) [inline]
core::Real core::scoring::electron_density::ElectronDensity::getCCs ( int  resid) [inline]
numeric::xyzVector<core::Real> core::scoring::electron_density::ElectronDensity::getCoM ( ) const [inline]
numeric::xyzVector<core::Real> core::scoring::electron_density::ElectronDensity::getEffOrigin ( ) const [inline]
core::Real core::scoring::electron_density::ElectronDensity::getMax ( ) const [inline]
core::Real core::scoring::electron_density::ElectronDensity::getMean ( ) const [inline]
core::Real core::scoring::electron_density::ElectronDensity::getMin ( ) const [inline]
core::Real core::scoring::electron_density::ElectronDensity::getNumDerivH ( ) const [inline]
numeric::xyzVector<core::Real> core::scoring::electron_density::ElectronDensity::getOrigin ( ) const [inline]
core::Real core::scoring::electron_density::ElectronDensity::getResolution ( ) const [inline]
core::Real core::scoring::electron_density::ElectronDensity::getStdev ( ) const [inline]
utility::vector1< core::kinematics::RT > core::scoring::electron_density::ElectronDensity::getsymmOps ( ) const [inline]
numeric::xyzVector<core::Real> core::scoring::electron_density::ElectronDensity::getTransform ( ) [inline]

Get the transformation from indices to Cartesian coords using 'real' origin.

References idx2cart().

bool core::scoring::electron_density::ElectronDensity::getUseDensityInMinimizer ( ) const [inline]
bool core::scoring::electron_density::ElectronDensity::getUseExactDerivatives ( ) const [inline]
template<class Q >
void core::scoring::electron_density::ElectronDensity::idx2cart ( numeric::xyzVector< Q > const &  idxX,
numeric::xyzVector< core::Real > &  cartX 
) const [inline]

Referenced by getTransform().

template<class Q >
void core::scoring::electron_density::ElectronDensity::idxoffset2cart ( numeric::xyzVector< Q > const &  idxX,
numeric::xyzVector< core::Real > &  cartX 
) const [inline]
bool core::scoring::electron_density::ElectronDensity::isMapLoaded ( ) const [inline]
void core::scoring::electron_density::ElectronDensity::maskResidues ( int  scoring_mask) [inline]
void core::scoring::electron_density::ElectronDensity::maskResidues ( utility::vector1< int > const &  scoring_mask) [inline]
core::Real core::scoring::electron_density::ElectronDensity::matchCentroidPose ( core::pose::Pose const &  pose,
const core::conformation::symmetry::SymmetryInfo symmInfo = NULL,
bool  cacheCCs = false 
)
core::Real core::scoring::electron_density::ElectronDensity::matchPose ( core::pose::Pose const &  pose,
const core::conformation::symmetry::SymmetryInfo symmInfo = NULL,
bool  cacheCCs = false 
)
core::Real core::scoring::electron_density::ElectronDensity::matchPoseToPatterson ( core::pose::Pose const &  pose,
bool  cacheCCs = false 
)
core::Real core::scoring::electron_density::ElectronDensity::matchRes ( int  resid,
core::conformation::Residue const &  rsd,
core::pose::Pose const &  pose,
const core::conformation::symmetry::SymmetryInfo symmInfo = NULL,
bool  cacheCCs = false 
)

Match a residue's conformation to the density map. Backbone atoms from adjacent residues are also used for scoring. Returns the correlation coefficient between map and pose Internally stores per-res CCs, per-atom dCC/dxs.

Match a residue to the density map, returning correlation coefficient between map and residue. Caches information about scoring, to be used in derivative computation

References core::conformation::Residue::atom(), core::conformation::Residue::atom_type_index(), core::conformation::Residue::atom_type_set(), core::conformation::symmetry::SymmetryInfo::bb_is_independent(), core::scoring::electron_density::OneGaussianScattering::C(), protocols::forge::build::SegmentInsertConnectionScheme::C, core::pack::interaction_graph::debug, core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), make_table_of_pilot_apps::f, core::pose::Pose::fold_tree(), core::scoring::electron_density::get_A(), core::graph::Edge::get_first_node_ind(), core::graph::Edge::get_second_node_ind(), core::kinematics::FoldTree::is_cutpoint(), core::scoring::electron_density::is_missing_density(), core::conformation::Residue::is_polymer(), core::scoring::electron_density::OneGaussianScattering::k(), core::conformation::Residue::last_backbone_atom(), core::scoring::electron_density::MAX_FLT, core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::scoring::electron_density::TR(), writeMRC(), and core::conformation::Atom::xyz().

Referenced by dCCdx_fastRes(), dCCdx_res(), core::scoring::electron_density::ElecDensEnergy::residue_pair_energy(), and core::scoring::electron_density::ElecDensEnergy::setup_for_derivatives().

core::Real core::scoring::electron_density::ElectronDensity::matchResFast ( int  resid,
core::conformation::Residue const &  rsd,
core::pose::Pose const &  pose,
const core::conformation::symmetry::SymmetryInfo symmInfo = NULL 
)

Match a residue's conformation to the density map. Same as matchRes, but using a fast approximation to the match function.

Match a residue to the density map. Use the fast version of the scoring function

References core::conformation::Residue::atom(), core::conformation::symmetry::SymmetryInfo::bb_is_independent(), core::scoring::electron_density::interp_spline(), core::conformation::Residue::nheavyatoms(), core::scoring::electron_density::TR(), and core::conformation::Atom::xyz().

Referenced by dCCdx_fastRes(), and core::scoring::electron_density::FastDensEnergy::residue_pair_energy().

bool core::scoring::electron_density::ElectronDensity::readMRCandResize ( std::string  mapfile,
core::Real  reso = 5.0,
core::Real  gridSpacing = 0.0 
)
core::Real core::scoring::electron_density::ElectronDensity::rematchResToPatterson ( core::conformation::Residue const &  rsd) const
void core::scoring::electron_density::ElectronDensity::resize ( core::Real  approxGridSpacing)
numeric::xyzMatrix< core::Real > core::scoring::electron_density::ElectronDensity::rotAlign2DPose ( core::pose::Pose const &  pose,
std::string  axis 
)
void core::scoring::electron_density::ElectronDensity::set_nres ( int  nres) [inline]
void core::scoring::electron_density::ElectronDensity::setUseDensityInMinimizer ( bool  newVal) [inline]
void core::scoring::electron_density::ElectronDensity::setUseExactDerivatives ( bool  newVal) [inline]
void core::scoring::electron_density::ElectronDensity::showCachedScores ( utility::vector1< int > const &  reses)

Print cached CCs.

References core::scoring::electron_density::TR().

void core::scoring::electron_density::ElectronDensity::updateCachedDensity ( core::conformation::Residue const &  rsd)
bool core::scoring::electron_density::ElectronDensity::writeMAT ( std::string  mapfilestem)

(debugging) Write MATLAB v5 mapfile

bool core::scoring::electron_density::ElectronDensity::writeMRC ( std::string  mapfilestem)

The documentation for this class was generated from the following files:
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