Rosetta Core  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
core::scoring::electron_density::ElectronDensity Class Reference

#include <ElectronDensity.hh>

Public Member Functions

virtual ~ElectronDensity ()
 Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...
 
 ElectronDensity ()
 constructor More...
 
 ElectronDensity (utility::vector1< core::pose::PoseOP > poses, core::Real reso, core::Real apix)
 calulated density from a vector of poses More...
 
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 (used for debugging only!) More...
 
void init ()
 Initialize map from cmd line options. More...
 
bool readMRCandResize (std::string mapfile, core::Real reso=5.0, core::Real gridSpacing=0.0)
 Load an MRC (="new-CCP4") density map. More...
 
bool readMRCandResize (std::istream &mapin, std::string mapfile, core::Real reso=5.0, core::Real gridSpacing=0.0)
 Load an MRC (="new-CCP4") density map. More...
 
bool writeMRC (std::string mapfilestem, bool writeRhoCalc=false, bool writeRhoMask=false)
 (debugging) Write MRC mapfile More...
 
bool writeMAT (std::string mapfilestem)
 (debugging) Write MATLAB v5 mapfile More...
 
numeric::xyzMatrix< core::RealrotAlign2DPose (core::pose::Pose const &pose, std::string axis)
 Align a pose about a 2D rotation axis. More...
 
core::Real matchCentroidPose (core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=NULL, bool cacheCCs=false)
 Quickly matches a centroid pose into a low-resolution density map by placing a single Gaussian at each CA. More...
 
core::Real matchPose (core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=NULL, bool cacheCCs=false)
 Match a pose into a medium-resolution density map by placing a single Gaussian at each atom. More...
 
void maskDensityMap (poseCoords const &pose, core::Real radius)
 mask the density map (like chimera 'zone' but sigmoidal mask) More...
 
void getResolutionBins (core::Size nbuckets, core::Real maxreso, core::Real minreso, utility::vector1< core::Real > &, utility::vector1< core::Size > &, bool S2_bin=false)
 get resolution bins (informational) More...
 
utility::vector1< core::RealgetIntensities (core::Size nbuckets, core::Real maxreso, core::Real minreso, bool S2_bin=false)
 Compute map intensities. More...
 
utility::vector1< core::RealgetIntensitiesMasked (poseCoords const &pose, core::Size nbuckets, core::Real maxreso, core::Real minreso, bool S2_bin=false)
 Compute map intensities, masked by a pose. More...
 
void getIntensities (poseCoords const &pose, core::Size nbuckets, core::Real maxreso, core::Real minreso, utility::vector1< core::Real > &Imodel, bool S2_bin=false)
 Compute intensities from a pose. More...
 
void getMapMapError (ObjexxFCL::FArray3D< float > const &map2, core::Size nbuckets, core::Real maxreso, core::Real minreso, utility::vector1< core::Real > &FSC, utility::vector1< core::Real > &phaseError, utility::vector1< core::Real > &complexPlaneError, bool S2_bin=false)
 Compute map-map FSC & errors. More...
 
void getModelMapError (poseCoords const &pose, core::Size nbuckets, core::Real maxreso, core::Real minreso, utility::vector1< core::Real > const &mapmapPhaseError, utility::vector1< core::Real > const &mapmapComplexPlaneError, utility::vector1< core::Real > &FSC, utility::vector1< core::Real > &phaseError, core::Real &phaseErrorSum, core::Real &complexPlaneErrorK, core::Real &complexPlaneErrorProb, bool masked=false, bool S2_bin=false, core::Real mask_radius=0)
 Compute model-map FSC & errors. More...
 
void getFSC (poseCoords const &pose, core::Size nbuckets, core::Real maxreso, core::Real minreso, utility::vector1< core::Real > &FSC, bool masked=false, bool S2_bin=false, core::Real mask_radius=0)
 Compute model-map FSC & errors. More...
 
core::Real getRSCC (poseCoords const &pose)
 Compute model-map RSCC. More...
 
core::Real getRSCC (ObjexxFCL::FArray3D< float > const &map2)
 Compute map-map RSCC. More...
 
void scaleIntensities (utility::vector1< core::Real > I_tgt, core::Real maxreso, core::Real minreso, bool S2_bin=false)
 Compute intensities, update density. More...
 
void calcRhoC (poseCoords const &pose)
 
core::Real maxNominalRes ()
 
core::Real matchPoseToPatterson (core::pose::Pose const &pose, bool cacheCCs=false)
 Match a pose to a patterson map. More...
 
core::Real rematchResToPatterson (core::conformation::Residue const &rsd) const
 Rematch the pose to a patterson map, using previous rho_calc with only rsd changed. More...
 
void updateCachedDensity (core::conformation::Residue const &rsd)
 Update cached rho_calc by changing residue 'rsd'. More...
 
core::Real matchRes (int resid, core::conformation::Residue const &rsd, core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP 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. More...
 
core::Real matchResFast (int resid, core::conformation::Residue const &rsd, core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=NULL, bool ignoreBs=false)
 Match a residue's conformation to the density map. Same as matchRes, but using a fast approximation to the match function. More...
 
void compute_symm_rotations (core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=NULL)
 Computes the symmatric rotation matrices. More...
 
core::Real matchPointFast (numeric::xyzVector< core::Real > X)
 access fastdens scoring for a single point More...
 
void dCCdx_PointFast (numeric::xyzVector< core::Real > X, numeric::xyzVector< core::Real > &dCCdx)
 access fastdens scoring for a single point More...
 
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. More...
 
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. More...
 
Real dCCdB_fastRes (int atmid, int resid, core::conformation::Residue const &rsd, core::pose::Pose const &pose)
 Gradient of CC w.r.t B factors. More...
 
void dCCdBs (core::pose::Pose const &pose, utility::vector1< core::Real > &dE_dvars)
 calculate all gradients of CC w.r.t B factors (slow more precise version) More...
 
void rescale_fastscoring_temp_bins (core::pose::Pose const &pose, bool init=false)
 
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. More...
 
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. More...
 
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. More...
 
void clear_dCCdx_res_cache (core::pose::Pose const &pose)
 Resets the counters used for derivative computation in sliding-window/fast scoring. More...
 
void compute_rho (core::pose::Pose const &pose, utility::vector1< core::id::AtomID > const &atom_ids, ObjexxFCL::FArray3D< double > &rho_calc, ObjexxFCL::FArray3D< double > &inv_rho_mask)
 compute rho_c based on a list of atoms More...
 
numeric::xyzVector< doublematch_fragment (ObjexxFCL::FArray3D< double > const &rho_calc, ObjexxFCL::FArray3D< double > const &mask, ObjexxFCL::FArray3D< double > const &rho_obs, core::Real radius=6.0)
 
numeric::xyzVector< core::RealgetTransform ()
 Get the transformation from indices to Cartesian coords using 'real' origin. More...
 
void set_nres (int nres)
 set # of residues More...
 
void showCachedScores (utility::vector1< int > const &reses)
 Print cached CCs. More...
 
core::Real getCachedScore (core::Size resid)
 
void setUseDensityInMinimizer (bool newVal)
 
bool getUseDensityInMinimizer () const
 
void setUseExactDerivatives (bool newVal)
 
bool getUseExactDerivatives () const
 
void setSCscaling (core::Real SC_scalingin)
 
core::Real getSCscaling ()
 
void setWindow (core::Size window_in)
 
core::Size getWindow ()
 
void setScoreWindowContext (bool newVal)
 
bool getScoreWindowContext () const
 
bool isMapLoaded () 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
 
numeric::xyzVector< core::RealgetCoM () const
 
numeric::xyzVector< core::RealgetOrigin () const
 
numeric::xyzVector< core::RealgetEffOrigin () const
 
utility::vector1
< core::kinematics::RT
getsymmOps () const
 
core::Real getAtomMask () const
 
void maskResidues (int scoring_mask)
 
void maskResidues (utility::vector1< int > const &scoring_mask)
 
void clearMask ()
 
ObjexxFCL::FArray3D< float >
const & 
data () const
 
void set_data (ObjexxFCL::FArray3D< double > const &density_in)
 
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::xyzMatrix< core::Realget_f2c ()
 
numeric::xyzMatrix< core::Realget_c2f ()
 
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 More...
 
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)
 

Private Member Functions

void density_change_trigger ()
 The function is called everytime the density changes. More...
 
void smooth_intensities (utility::vector1< core::Real > &) const
 
void computeGradients ()
 
void computeStats ()
 
int suggestRadius ()
 
void initializeSymmOps (utility::vector1< std::string > const &symList)
 
void computeCrystParams ()
 
void expandToUnitCell ()
 
void setup_patterson_first_time (core::pose::Pose const &pose)
 Precomputes a bunch of stuff for patterson map scoring. More...
 
void setup_fastscoring_first_time (core::pose::Pose const &pose)
 setup oversampled maps for fast density scoring More...
 
void setup_fastscoring_first_time (Real scalefactor)
 
utility::vector1
< ObjexxFCL::FArray3D
< std::complex< double > > * > 
getFdrhoc (OneGaussianScattering S)
 
double S2 (int h, int k, int l)
 
double voxel_volume ()
 

Private Attributes

bool isLoaded
 
ObjexxFCL::FArray3D< floatdensity
 
ObjexxFCL::FArray3D
< std::complex< double > > 
Fdensity
 
std::map< core::Size, boolscoring_mask_
 
core::Real reso
 
core::Real ATOM_MASK
 
core::Real CA_MASK
 
core::Real force_apix_
 
core::Real SC_scaling_
 
core::Real ATOM_MASK_PADDING
 
core::Size WINDOW_
 
bool score_window_context_
 
bool remap_symm_
 
bool legacy_
 
bool DensScoreInMinimizer
 
bool ExactDerivatives
 
core::Real NUM_DERIV_H
 
core::Real NUM_DERIV_H_CEN
 
core::Real PattersonB
 
core::Real PattersonMinR
 
core::Real PattersonMaxR
 
ObjexxFCL::FArray3D< floatPattersonEpsilon
 
ObjexxFCL::FArray3D< doublep_o
 
double po_bar
 
ObjexxFCL::FArray4D< doublefastdens_score
 
core::Size nkbins_
 
core::Real kmin_
 
core::Real kmax_
 
core::Real kstep_
 
numeric::xyzVector< intfastgrid
 
numeric::xyzVector< core::Realfastorigin
 
ObjexxFCL::FArray3D< doublerho_calc
 TONS OF CACHED STUFF <<< this should live in its own class! More...
 
ObjexxFCL::FArray3D< doublerho_solv
 
ObjexxFCL::FArray3D< doubleinv_rho_mask
 
core::Real rho_calc_sum
 
ObjexxFCL::FArray3D
< std::complex< double > > 
Frho_calc
 
ObjexxFCL::FArray3D
< std::complex< double > > 
Frho_solv
 
utility::vector1< core::Sizebucket_counts
 
ObjexxFCL::FArray3D< core::Sizebucket_id
 
core::Real lowres_cut
 
core::Real hires_cut
 
ObjexxFCL::FArray3D< doubleF_s2
 
ObjexxFCL::FArray3D< doublePcalc
 
utility::vector1< core::RealF2
 
utility::vector1
< ObjexxFCL::FArray3D
< core::Size > > 
symm_ptrs
 
std::map< int,
ObjexxFCL::FArray3D
< std::complex< double > > > 
Fdrhoc_dx
 
std::map< int,
ObjexxFCL::FArray3D
< std::complex< double > > > 
Fdrhoc_dy
 
std::map< int,
ObjexxFCL::FArray3D
< std::complex< double > > > 
Fdrhoc_dz
 
utility::vector1
< utility::vector1
< numeric::xyzVector
< core::Real > > > 
rho_calc_atms
 
utility::vector1
< utility::vector1
< OneGaussianScattering > > 
rho_calc_as
 
core::Real p_sumC
 
core::Real p_sumC2
 
core::Real p_sumO
 
core::Real p_sumO2
 
core::Real p_sumCO
 
core::Real p_vol
 
numeric::xyzVector< core::Reald_min
 
numeric::xyzVector< core::Reald_max
 
numeric::xyzVector< core::Realp_extent
 
numeric::xyzVector< core::Realp_origin
 
numeric::xyzVector< core::Sizep_grid
 
numeric::xyzVector< core::Realp_CoM
 
core::Real minimumB
 
core::Real effectiveB
 
numeric::xyzVector< intgrid
 
numeric::xyzVector< core::Realorigin
 
numeric::xyzVector< core::Realefforigin
 
bool use_altorigin
 
utility::vector1< core::RealCCs
 
core::Real CC_cen
 
core::Real CC_aacen
 
core::Real CC_pat
 
utility::vector1
< numeric::xyzVector
< core::Real > > 
dCCdxs_cen
 
utility::vector1
< utility::vector1
< numeric::xyzVector
< core::Real > > > 
dCCdxs_aacen
 
utility::vector1
< utility::vector1
< numeric::xyzVector
< core::Real > > > 
dCCdxs_res
 
utility::vector1
< utility::vector1
< numeric::xyzVector
< core::Real > > > 
dCCdxs_pat
 
std::map< int, std::pair
< utility::vector1< int >
, numeric::xyzMatrix
< core::Real > > > 
symmap
 SYMMETRY (Rosetta's symmetry, not necessarily crystal symmetry) More...
 
ObjexxFCL::FArray3D< doublecoeff_grad_x
 VISUALIZATION-SPECIFIC. More...
 
ObjexxFCL::FArray3D< doublecoeff_grad_y
 
ObjexxFCL::FArray3D< doublecoeff_grad_z
 
numeric::xyzMatrix< core::Realf2c
 CRYSTAL INFO. More...
 
numeric::xyzMatrix< core::Realc2f
 
numeric::xyzVector< floatcellDimensions
 
numeric::xyzVector< floatcellAngles
 
numeric::xyzVector< floatRcellDimensions
 
numeric::xyzVector< floatcosRcellAngles
 
core::Real V
 
core::Real RV
 
utility::vector1
< core::kinematics::RT
symmOps
 
utility::vector1
< numeric::xyzMatrix
< core::Real > > 
symmRotOps
 
numeric::xyzVector< core::SizeMINMULT
 
numeric::xyzVector< core::RealcenterOfMass
 
core::Real dens_mean
 
core::Real dens_min
 
core::Real dens_max
 
core::Real dens_stdev
 

Constructor & Destructor Documentation

core::scoring::electron_density::ElectronDensity::~ElectronDensity ( )
virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

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

constructor

null constructor

References core::init::init().

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 (used for debugging only!)

References cellAngles, cellDimensions, density, efforigin, grid, init(), isLoaded, origin, and core::scoring::electron_density::pos_mod().

Member Function Documentation

void core::scoring::electron_density::ElectronDensity::calcRhoC ( poseCoords const &  pose)
void core::scoring::electron_density::ElectronDensity::cart2frac ( numeric::xyzVector< core::Real > const &  cartX,
numeric::xyzVector< core::Real > &  fracX 
) const
inline

References c2f.

void core::scoring::electron_density::ElectronDensity::cart2idx ( numeric::xyzVector< core::Real > const &  cartX,
numeric::xyzVector< core::Real > &  idxX 
) const
inline

References c2f, efforigin, and grid.

void core::scoring::electron_density::ElectronDensity::clear_dCCdx_res_cache ( core::pose::Pose const &  pose)
void core::scoring::electron_density::ElectronDensity::clearMask ( )
inline

References scoring_mask_.

void core::scoring::electron_density::ElectronDensity::compute_rho ( core::pose::Pose const &  pose,
utility::vector1< core::id::AtomID > const &  atom_ids,
ObjexxFCL::FArray3D< double > &  rho_calc,
ObjexxFCL::FArray3D< double > &  inv_rho_mask 
)
void core::scoring::electron_density::ElectronDensity::compute_symm_rotations ( core::pose::Pose const &  pose,
core::conformation::symmetry::SymmetryInfoCOP  symmInfo = NULL 
)
void core::scoring::electron_density::ElectronDensity::computeCrystParams ( )
private
void core::scoring::electron_density::ElectronDensity::computeGradients ( )
private
void core::scoring::electron_density::ElectronDensity::computeStats ( )
private
ObjexxFCL::FArray3D< float > const& core::scoring::electron_density::ElectronDensity::data ( ) const
inline

References density.

Real core::scoring::electron_density::ElectronDensity::dCCdB_fastRes ( int  atmid,
int  resid,
core::conformation::Residue const &  rsd,
core::pose::Pose const &  pose 
)
void core::scoring::electron_density::ElectronDensity::dCCdBs ( core::pose::Pose const &  pose,
utility::vector1< core::Real > &  dE_dvars 
)
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 
)
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_PointFast ( numeric::xyzVector< core::Real X,
numeric::xyzVector< core::Real > &  dCCdx 
)
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 
)
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::density_change_trigger ( )
private

The function is called everytime the density changes.

References numeric::xyzVector< class >::clear().

void core::scoring::electron_density::ElectronDensity::expandToUnitCell ( )
private
void core::scoring::electron_density::ElectronDensity::frac2cart ( numeric::xyzVector< core::Real > const &  fracX,
numeric::xyzVector< core::Real > &  cartX 
) const
inline

References f2c.

numeric::xyzMatrix<core::Real> core::scoring::electron_density::ElectronDensity::get_c2f ( )
inline

References c2f.

numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::get_cart_unitCell ( numeric::xyzVector< core::Real > const &  cartX)
numeric::xyzMatrix<core::Real> core::scoring::electron_density::ElectronDensity::get_f2c ( )
inline

References f2c.

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::getAtomMask ( ) const
inline

References ATOM_MASK.

core::Real core::scoring::electron_density::ElectronDensity::getCachedScore ( core::Size  resid)
inline
numeric::xyzVector<core::Real> core::scoring::electron_density::ElectronDensity::getCoM ( ) const
inline

References centerOfMass.

numeric::xyzVector<core::Real> core::scoring::electron_density::ElectronDensity::getEffOrigin ( ) const
inline

References efforigin.

utility::vector1< ObjexxFCL::FArray3D< std::complex< double > > * > core::scoring::electron_density::ElectronDensity::getFdrhoc ( OneGaussianScattering  S)
private
void core::scoring::electron_density::ElectronDensity::getFSC ( poseCoords const &  pose,
core::Size  nbuckets,
core::Real  maxreso,
core::Real  minreso,
utility::vector1< core::Real > &  FSC,
bool  masked = false,
bool  S2_bin = false,
core::Real  mask_radius = 0 
)
inline

Compute model-map FSC & errors.

References getModelMapError().

utility::vector1< core::Real > core::scoring::electron_density::ElectronDensity::getIntensities ( core::Size  nbuckets,
core::Real  maxreso,
core::Real  minreso,
bool  S2_bin = false 
)
void core::scoring::electron_density::ElectronDensity::getIntensities ( poseCoords const &  pose,
core::Size  nbuckets,
core::Real  maxreso,
core::Real  minreso,
utility::vector1< core::Real > &  Imodel,
bool  S2_bin = false 
)
utility::vector1< core::Real > core::scoring::electron_density::ElectronDensity::getIntensitiesMasked ( poseCoords const &  pose,
core::Size  nbuckets,
core::Real  maxreso,
core::Real  minreso,
bool  S2_bin = false 
)

Compute map intensities, masked by a pose.

Compute intensities from model, applying a mask first.

References density, numeric::fourier::fft3(), grid, core::chemical::element::H, core::chemical::element::K, core::scoring::func::L(), core::scoring::electron_density::pos_mod(), radius, and core::scoring::electron_density::TR.

void core::scoring::electron_density::ElectronDensity::getMapMapError ( ObjexxFCL::FArray3D< float > const &  map2,
core::Size  nbuckets,
core::Real  maxreso,
core::Real  minreso,
utility::vector1< core::Real > &  FSC,
utility::vector1< core::Real > &  phaseError,
utility::vector1< core::Real > &  complexPlaneError,
bool  S2_bin = false 
)
core::Real core::scoring::electron_density::ElectronDensity::getMax ( ) const
inline

References dens_max.

core::Real core::scoring::electron_density::ElectronDensity::getMean ( ) const
inline

References dens_mean.

core::Real core::scoring::electron_density::ElectronDensity::getMin ( ) const
inline

References dens_min.

void core::scoring::electron_density::ElectronDensity::getModelMapError ( poseCoords const &  pose,
core::Size  nbuckets,
core::Real  maxreso,
core::Real  minreso,
utility::vector1< core::Real > const &  mapmapPhaseError,
utility::vector1< core::Real > const &  mapmapComplexPlaneError,
utility::vector1< core::Real > &  FSC,
utility::vector1< core::Real > &  phaseError,
core::Real phaseErrorSum,
core::Real complexPlaneErrorK,
core::Real complexPlaneErrorProb,
bool  masked = false,
bool  S2_bin = false,
core::Real  mask_radius = 0 
)
core::Real core::scoring::electron_density::ElectronDensity::getNumDerivH ( ) const
inline

References NUM_DERIV_H.

numeric::xyzVector<core::Real> core::scoring::electron_density::ElectronDensity::getOrigin ( ) const
inline

References origin.

core::Real core::scoring::electron_density::ElectronDensity::getResolution ( ) const
inline

References reso.

void core::scoring::electron_density::ElectronDensity::getResolutionBins ( core::Size  nbuckets,
core::Real  maxreso,
core::Real  minreso,
utility::vector1< core::Real > &  resbins,
utility::vector1< core::Size > &  counts,
bool  S2_bin = false 
)
core::Real core::scoring::electron_density::ElectronDensity::getRSCC ( poseCoords const &  pose)

Compute model-map RSCC.

References density, and runtime_assert.

core::Real core::scoring::electron_density::ElectronDensity::getRSCC ( ObjexxFCL::FArray3D< float > const &  map2)

Compute map-map RSCC.

References density, and runtime_assert.

bool core::scoring::electron_density::ElectronDensity::getScoreWindowContext ( ) const
inline

References score_window_context_.

core::Real core::scoring::electron_density::ElectronDensity::getSCscaling ( )
inline

References SC_scaling_.

core::Real core::scoring::electron_density::ElectronDensity::getStdev ( ) const
inline

References dens_stdev.

utility::vector1< core::kinematics::RT > core::scoring::electron_density::ElectronDensity::getsymmOps ( ) const
inline

References symmOps.

numeric::xyzVector<core::Real> core::scoring::electron_density::ElectronDensity::getTransform ( )
inline

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

References grid, idx2cart(), and origin.

bool core::scoring::electron_density::ElectronDensity::getUseDensityInMinimizer ( ) const
inline

References DensScoreInMinimizer.

bool core::scoring::electron_density::ElectronDensity::getUseExactDerivatives ( ) const
inline

References ExactDerivatives.

core::Size core::scoring::electron_density::ElectronDensity::getWindow ( )
inline

References WINDOW_.

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

References efforigin, f2c, and grid.

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

References f2c, and grid.

void core::scoring::electron_density::ElectronDensity::init ( void  )
void core::scoring::electron_density::ElectronDensity::initializeSymmOps ( utility::vector1< std::string > const &  symList)
private

also sets MINMULT(XYZ) eventually replace with cctbx

References utility::string_split(), and core::scoring::electron_density::TR.

bool core::scoring::electron_density::ElectronDensity::isMapLoaded ( ) const
inline
void core::scoring::electron_density::ElectronDensity::maskDensityMap ( poseCoords const &  pose,
core::Real  radius 
)

mask the density map (like chimera 'zone' but sigmoidal mask)

References basic::options::OptionKeys::edensity::debug, density, grid, basic::options::option, core::scoring::electron_density::pos_mod(), and writeMRC().

void core::scoring::electron_density::ElectronDensity::maskResidues ( int  scoring_mask)
inline

References scoring_mask_.

void core::scoring::electron_density::ElectronDensity::maskResidues ( utility::vector1< int > const &  scoring_mask)
inline

References scoring_mask_.

numeric::xyzVector< double > core::scoring::electron_density::ElectronDensity::match_fragment ( ObjexxFCL::FArray3D< double > const &  rho_calc,
ObjexxFCL::FArray3D< double > const &  mask,
ObjexxFCL::FArray3D< double > const &  rho_obs,
core::Real  radius = 6.0 
)
core::Real core::scoring::electron_density::ElectronDensity::matchCentroidPose ( core::pose::Pose const &  pose,
core::conformation::symmetry::SymmetryInfoCOP  symmInfo = NULL,
bool  cacheCCs = false 
)
core::Real core::scoring::electron_density::ElectronDensity::matchPointFast ( numeric::xyzVector< core::Real X)

access fastdens scoring for a single point

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

References core::scoring::electron_density::interp_spline(), core::scoring::electron_density::pos_mod(), and core::scoring::electron_density::TR.

core::Real core::scoring::electron_density::ElectronDensity::matchPose ( core::pose::Pose const &  pose,
core::conformation::symmetry::SymmetryInfoCOP  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,
core::conformation::symmetry::SymmetryInfoCOP  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::scoring::electron_density::OneGaussianScattering::C(), core::graph::Node::const_edge_list_end(), basic::options::OptionKeys::edensity::debug, density, core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::pose::Pose::fold_tree(), utility::pointer::owning_ptr< T >::get(), core::scoring::electron_density::get_A(), core::graph::Edge::get_first_node_ind(), core::graph::Edge::get_node(), core::graph::Edge::get_second_node_ind(), grid, core::kinematics::FoldTree::is_cutpoint(), core::scoring::electron_density::is_missing_density(), core::scoring::electron_density::OneGaussianScattering::k(), core::conformation::Residue::last_backbone_atom(), core::scoring::electron_density::MAX_FLT, core::conformation::Residue::nheavyatoms(), nres, basic::options::option, core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::scoring::electron_density::TR, basic::options::OptionKeys::edensity::unmask_bb, 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,
core::conformation::symmetry::SymmetryInfoCOP  symmInfo = NULL,
bool  ignoreBs = false 
)
core::Real core::scoring::electron_density::ElectronDensity::maxNominalRes ( )
bool core::scoring::electron_density::ElectronDensity::readMRCandResize ( std::string  mapfile,
core::Real  reso = 5.0,
core::Real  gridSpacing = 0.0 
)

Load an MRC (="new-CCP4") density map.

Referenced by core::scoring::electron_density::getDensityMap_legacy().

bool core::scoring::electron_density::ElectronDensity::readMRCandResize ( std::istream &  mapin,
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::rescale_fastscoring_temp_bins ( core::pose::Pose const &  pose,
bool  init = false 
)
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 
)
double core::scoring::electron_density::ElectronDensity::S2 ( int  h,
int  k,
int  l 
)
inlineprivate

References cosRcellAngles, and RcellDimensions.

void core::scoring::electron_density::ElectronDensity::scaleIntensities ( utility::vector1< core::Real I_tgt,
core::Real  maxreso,
core::Real  minreso,
bool  S2_bin = false 
)
void core::scoring::electron_density::ElectronDensity::set_data ( ObjexxFCL::FArray3D< double > const &  density_in)
inline

References density.

void core::scoring::electron_density::ElectronDensity::set_nres ( int  nres)
inline
void core::scoring::electron_density::ElectronDensity::setScoreWindowContext ( bool  newVal)
inline

References score_window_context_.

void core::scoring::electron_density::ElectronDensity::setSCscaling ( core::Real  SC_scalingin)
inline

References SC_scaling_.

void core::scoring::electron_density::ElectronDensity::setup_fastscoring_first_time ( core::pose::Pose const &  pose)
private
void core::scoring::electron_density::ElectronDensity::setup_fastscoring_first_time ( Real  scalefactor)
private
void core::scoring::electron_density::ElectronDensity::setup_patterson_first_time ( core::pose::Pose const &  pose)
private
void core::scoring::electron_density::ElectronDensity::setUseDensityInMinimizer ( bool  newVal)
inline

References DensScoreInMinimizer.

void core::scoring::electron_density::ElectronDensity::setUseExactDerivatives ( bool  newVal)
inline

References ExactDerivatives.

void core::scoring::electron_density::ElectronDensity::setWindow ( core::Size  window_in)
inline

References WINDOW_.

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::smooth_intensities ( utility::vector1< core::Real > &  Is) const
private
int core::scoring::electron_density::ElectronDensity::suggestRadius ( )
private
void core::scoring::electron_density::ElectronDensity::updateCachedDensity ( core::conformation::Residue const &  rsd)
double core::scoring::electron_density::ElectronDensity::voxel_volume ( )
inlineprivate

References grid, and V.

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

(debugging) Write MATLAB v5 mapfile

References density, and out.

bool core::scoring::electron_density::ElectronDensity::writeMRC ( std::string  mapfilestem,
bool  writeRhoCalc = false,
bool  writeRhoMask = false 
)

Member Data Documentation

core::Real core::scoring::electron_density::ElectronDensity::ATOM_MASK
private

Referenced by getAtomMask().

core::Real core::scoring::electron_density::ElectronDensity::ATOM_MASK_PADDING
private
utility::vector1<core::Size> core::scoring::electron_density::ElectronDensity::bucket_counts
private
ObjexxFCL::FArray3D< core::Size > core::scoring::electron_density::ElectronDensity::bucket_id
private
numeric::xyzMatrix<core::Real> core::scoring::electron_density::ElectronDensity::c2f
private

Referenced by cart2frac(), cart2idx(), and get_c2f().

core::Real core::scoring::electron_density::ElectronDensity::CA_MASK
private
core::Real core::scoring::electron_density::ElectronDensity::CC_aacen
private
core::Real core::scoring::electron_density::ElectronDensity::CC_cen
private
core::Real core::scoring::electron_density::ElectronDensity::CC_pat
private
utility::vector1<core::Real> core::scoring::electron_density::ElectronDensity::CCs
private

Referenced by getCachedScore(), and set_nres().

numeric::xyzVector<float> core::scoring::electron_density::ElectronDensity::cellAngles
private

Referenced by ElectronDensity().

numeric::xyzVector<float> core::scoring::electron_density::ElectronDensity::cellDimensions
private

Referenced by ElectronDensity().

numeric::xyzVector<core::Real> core::scoring::electron_density::ElectronDensity::centerOfMass
private

Referenced by getCoM().

ObjexxFCL::FArray3D< double > core::scoring::electron_density::ElectronDensity::coeff_grad_x
mutableprivate

VISUALIZATION-SPECIFIC.

ObjexxFCL::FArray3D< double > core::scoring::electron_density::ElectronDensity::coeff_grad_y
mutableprivate
ObjexxFCL::FArray3D< double > core::scoring::electron_density::ElectronDensity::coeff_grad_z
mutableprivate
numeric::xyzVector<float> core::scoring::electron_density::ElectronDensity::cosRcellAngles
private

Referenced by S2().

numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::d_max
private
numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::d_min
private
utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > core::scoring::electron_density::ElectronDensity::dCCdxs_aacen
private

Referenced by set_nres().

utility::vector1< numeric::xyzVector< core::Real > > core::scoring::electron_density::ElectronDensity::dCCdxs_cen
private

Referenced by set_nres().

utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > core::scoring::electron_density::ElectronDensity::dCCdxs_pat
private

Referenced by set_nres().

utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > core::scoring::electron_density::ElectronDensity::dCCdxs_res
private

Referenced by set_nres().

core::Real core::scoring::electron_density::ElectronDensity::dens_max
private

Referenced by getMax().

core::Real core::scoring::electron_density::ElectronDensity::dens_mean
private

Referenced by getMean().

core::Real core::scoring::electron_density::ElectronDensity::dens_min
private

Referenced by getMin().

core::Real core::scoring::electron_density::ElectronDensity::dens_stdev
private

Referenced by getStdev().

ObjexxFCL::FArray3D< float > core::scoring::electron_density::ElectronDensity::density
private

Referenced by data(), ElectronDensity(), and set_data().

bool core::scoring::electron_density::ElectronDensity::DensScoreInMinimizer
private
core::Real core::scoring::electron_density::ElectronDensity::effectiveB
private
numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::efforigin
private
bool core::scoring::electron_density::ElectronDensity::ExactDerivatives
private
utility::vector1<core::Real> core::scoring::electron_density::ElectronDensity::F2
private
numeric::xyzMatrix<core::Real> core::scoring::electron_density::ElectronDensity::f2c
private

CRYSTAL INFO.

Referenced by frac2cart(), get_f2c(), idx2cart(), and idxoffset2cart().

ObjexxFCL::FArray3D< double > core::scoring::electron_density::ElectronDensity::F_s2
private
ObjexxFCL::FArray4D< double > core::scoring::electron_density::ElectronDensity::fastdens_score
private
numeric::xyzVector< int > core::scoring::electron_density::ElectronDensity::fastgrid
private
numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::fastorigin
private
ObjexxFCL::FArray3D< std::complex<double> > core::scoring::electron_density::ElectronDensity::Fdensity
private
std::map< int , ObjexxFCL::FArray3D< std::complex<double> > > core::scoring::electron_density::ElectronDensity::Fdrhoc_dx
private
std::map< int , ObjexxFCL::FArray3D< std::complex<double> > > core::scoring::electron_density::ElectronDensity::Fdrhoc_dy
private
std::map< int , ObjexxFCL::FArray3D< std::complex<double> > > core::scoring::electron_density::ElectronDensity::Fdrhoc_dz
private
core::Real core::scoring::electron_density::ElectronDensity::force_apix_
private
ObjexxFCL::FArray3D< std::complex<double> > core::scoring::electron_density::ElectronDensity::Frho_calc
private
ObjexxFCL::FArray3D< std::complex<double> > core::scoring::electron_density::ElectronDensity::Frho_solv
private
numeric::xyzVector< int > core::scoring::electron_density::ElectronDensity::grid
private
core::Real core::scoring::electron_density::ElectronDensity::hires_cut
private
ObjexxFCL::FArray3D< double > core::scoring::electron_density::ElectronDensity::inv_rho_mask
private
bool core::scoring::electron_density::ElectronDensity::isLoaded
private

Referenced by ElectronDensity(), and isMapLoaded().

core::Real core::scoring::electron_density::ElectronDensity::kmax_
private
core::Real core::scoring::electron_density::ElectronDensity::kmin_
private
core::Real core::scoring::electron_density::ElectronDensity::kstep_
private
bool core::scoring::electron_density::ElectronDensity::legacy_
private
core::Real core::scoring::electron_density::ElectronDensity::lowres_cut
private
core::Real core::scoring::electron_density::ElectronDensity::minimumB
private
numeric::xyzVector<core::Size> core::scoring::electron_density::ElectronDensity::MINMULT
private
core::Size core::scoring::electron_density::ElectronDensity::nkbins_
private
core::Real core::scoring::electron_density::ElectronDensity::NUM_DERIV_H
private

Referenced by getNumDerivH().

core::Real core::scoring::electron_density::ElectronDensity::NUM_DERIV_H_CEN
private
numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::origin
private
numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::p_CoM
private
numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::p_extent
private
numeric::xyzVector< core::Size > core::scoring::electron_density::ElectronDensity::p_grid
private
ObjexxFCL::FArray3D< double > core::scoring::electron_density::ElectronDensity::p_o
private
numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::p_origin
private
core::Real core::scoring::electron_density::ElectronDensity::p_sumC
private
core::Real core::scoring::electron_density::ElectronDensity::p_sumC2
private
core::Real core::scoring::electron_density::ElectronDensity::p_sumCO
private
core::Real core::scoring::electron_density::ElectronDensity::p_sumO
private
core::Real core::scoring::electron_density::ElectronDensity::p_sumO2
private
core::Real core::scoring::electron_density::ElectronDensity::p_vol
private
core::Real core::scoring::electron_density::ElectronDensity::PattersonB
private
ObjexxFCL::FArray3D< float > core::scoring::electron_density::ElectronDensity::PattersonEpsilon
private
core::Real core::scoring::electron_density::ElectronDensity::PattersonMaxR
private
core::Real core::scoring::electron_density::ElectronDensity::PattersonMinR
private
ObjexxFCL::FArray3D< double > core::scoring::electron_density::ElectronDensity::Pcalc
private
double core::scoring::electron_density::ElectronDensity::po_bar
private
numeric::xyzVector<float> core::scoring::electron_density::ElectronDensity::RcellDimensions
private

Referenced by S2().

bool core::scoring::electron_density::ElectronDensity::remap_symm_
private
core::Real core::scoring::electron_density::ElectronDensity::reso
private

Referenced by getResolution().

ObjexxFCL::FArray3D< double > core::scoring::electron_density::ElectronDensity::rho_calc
private

TONS OF CACHED STUFF <<< this should live in its own class!

utility::vector1< utility::vector1< OneGaussianScattering > > core::scoring::electron_density::ElectronDensity::rho_calc_as
private
utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > core::scoring::electron_density::ElectronDensity::rho_calc_atms
private
core::Real core::scoring::electron_density::ElectronDensity::rho_calc_sum
private
ObjexxFCL::FArray3D< double > core::scoring::electron_density::ElectronDensity::rho_solv
private
core::Real core::scoring::electron_density::ElectronDensity::RV
private
core::Real core::scoring::electron_density::ElectronDensity::SC_scaling_
private

Referenced by getSCscaling(), and setSCscaling().

bool core::scoring::electron_density::ElectronDensity::score_window_context_
private
std::map< core::Size, bool > core::scoring::electron_density::ElectronDensity::scoring_mask_
private

Referenced by clearMask(), and maskResidues().

utility::vector1< ObjexxFCL::FArray3D< core::Size > > core::scoring::electron_density::ElectronDensity::symm_ptrs
private
std::map< int , std::pair< utility::vector1<int> , numeric::xyzMatrix<core::Real> > > core::scoring::electron_density::ElectronDensity::symmap
private

SYMMETRY (Rosetta's symmetry, not necessarily crystal symmetry)

Referenced by get_R(), get_symmMap(), and set_nres().

utility::vector1< core::kinematics::RT > core::scoring::electron_density::ElectronDensity::symmOps
private

Referenced by getsymmOps().

utility::vector1< numeric::xyzMatrix<core::Real> > core::scoring::electron_density::ElectronDensity::symmRotOps
private
bool core::scoring::electron_density::ElectronDensity::use_altorigin
private
core::Real core::scoring::electron_density::ElectronDensity::V
private

Referenced by voxel_volume().

core::Size core::scoring::electron_density::ElectronDensity::WINDOW_
private

Referenced by getWindow(), and setWindow().


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