Xmipp
v3.23.11-Nereus
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Classes | |
class | ProgNmaAlignmentVol |
class | ObjFunc_nma_alignment_vol |
double ProgNmaAlignmentVol::computeFitness | ( | Matrix1D< double > & | trial | ) | const |
Computes the fitness of a set of trial parameters
FileName ProgNmaAlignmentVol::createDeformedPDB | ( | ) | const |
Create deformed PDB
Definition at line 164 of file nma_alignment_vol.cpp.
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inlineprotectedvirtual |
Definition at line 183 of file nma_alignment_vol.h.
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virtual |
Define params.
Reimplemented from XmippMetadataProgram.
Definition at line 46 of file nma_alignment_vol.cpp.
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virtual |
Implements ObjectiveFunction.
Definition at line 210 of file nma_alignment_vol.cpp.
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virtual |
Write the final parameters.
Reimplemented from XmippMetadataProgram.
Definition at line 148 of file nma_alignment_vol.cpp.
ObjFunc_nma_alignment_vol::ObjFunc_nma_alignment_vol | ( | int | _t, |
int | _n = 0 |
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) |
Definition at line 277 of file nma_alignment_vol.cpp.
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virtual |
Produce side info. An exception is thrown if any of the files is not found
Reimplemented from XmippMetadataProgram.
Definition at line 130 of file nma_alignment_vol.cpp.
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virtual |
Assign NMA and Alignment parameters to a volume
Implements XmippMetadataProgram.
Definition at line 280 of file nma_alignment_vol.cpp.
ProgNmaAlignmentVol::ProgNmaAlignmentVol | ( | ) |
Empty constructor.
Definition at line 31 of file nma_alignment_vol.cpp.
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virtual |
Read arguments from command line.
Reimplemented from XmippMetadataProgram.
Definition at line 79 of file nma_alignment_vol.cpp.
void ProgNmaAlignmentVol::show | ( | ) |
Show.
Definition at line 111 of file nma_alignment_vol.cpp.
bool ProgNmaAlignmentVol::updateBestFit | ( | double | fitness | ) |
Update the best fitness and the corresponding best trial
Definition at line 200 of file nma_alignment_vol.cpp.
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virtual |
Write the parameters found for one image
Definition at line 321 of file nma_alignment_vol.cpp.
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inline |
Definition at line 203 of file nma_alignment_vol.h.
ProgNmaAlignmentVol::~ProgNmaAlignmentVol | ( | ) |
Destructor.
Definition at line 41 of file nma_alignment_vol.cpp.
bool ProgNmaAlignmentVol::alignVolumes |
Align volumes.
Definition at line 82 of file nma_alignment_vol.h.
FILE* ProgNmaAlignmentVol::AnglesShiftsAndScore |
Definition at line 137 of file nma_alignment_vol.h.
float ProgNmaAlignmentVol::Best_Angles_Shifts[6] |
Definition at line 138 of file nma_alignment_vol.h.
FileName ProgNmaAlignmentVol::currentVolName |
Definition at line 122 of file nma_alignment_vol.h.
double ProgNmaAlignmentVol::cutoff_LPfilter |
Low-pass cut-off frequency.
Definition at line 73 of file nma_alignment_vol.h.
bool ProgNmaAlignmentVol::do_centerPDB |
Center the PDB structure.
Definition at line 67 of file nma_alignment_vol.h.
bool ProgNmaAlignmentVol::do_FilterPDBVol |
Low-pass filter the volume from PDB.
Definition at line 70 of file nma_alignment_vol.h.
float ProgNmaAlignmentVol::fit_value |
Definition at line 139 of file nma_alignment_vol.h.
double ProgNmaAlignmentVol::fitness_min |
Definition at line 113 of file nma_alignment_vol.h.
bool ProgNmaAlignmentVol::flip = false |
Definition at line 142 of file nma_alignment_vol.h.
FileName ProgNmaAlignmentVol::fnmask |
Mask file for 2D masking of the projections of the deformed volume.
Definition at line 64 of file nma_alignment_vol.h.
FileName ProgNmaAlignmentVol::fnModeList |
File with a list of mode filenames.
Definition at line 58 of file nma_alignment_vol.h.
FileName ProgNmaAlignmentVol::fnOutDir |
Output directory.
Definition at line 55 of file nma_alignment_vol.h.
FileName ProgNmaAlignmentVol::fnOutPDB |
Output PDB.
Definition at line 52 of file nma_alignment_vol.h.
FileName ProgNmaAlignmentVol::fnPDB |
Reference atomic or pseudo-atomic structure in PDB format.
Definition at line 49 of file nma_alignment_vol.h.
double ProgNmaAlignmentVol::frm_freq |
Definition at line 94 of file nma_alignment_vol.h.
int ProgNmaAlignmentVol::frm_shift |
Definition at line 95 of file nma_alignment_vol.h.
int ProgNmaAlignmentVol::imgSize |
Definition at line 119 of file nma_alignment_vol.h.
MultidimArray<int> ProgNmaAlignmentVol::mask |
Definition at line 134 of file nma_alignment_vol.h.
bool ProgNmaAlignmentVol::MPIversion |
MPI version
Definition at line 43 of file nma_alignment_vol.h.
char ProgNmaAlignmentVol::nameTemplate[256] |
Definition at line 125 of file nma_alignment_vol.h.
int ProgNmaAlignmentVol::niter |
Definition at line 88 of file nma_alignment_vol.h.
int ProgNmaAlignmentVol::numberOfModes |
Definition at line 116 of file nma_alignment_vol.h.
Matrix1D<double> ProgNmaAlignmentVol::parameters |
Definition at line 104 of file nma_alignment_vol.h.
ProgPdbConverter* ProgNmaAlignmentVol::progVolumeFromPDB |
Definition at line 128 of file nma_alignment_vol.h.
int ProgNmaAlignmentVol::rangen |
Definition at line 101 of file nma_alignment_vol.h.
bool ProgNmaAlignmentVol::resume |
Resume computations
Definition at line 46 of file nma_alignment_vol.h.
double ProgNmaAlignmentVol::rhoEndBase |
Definition at line 87 of file nma_alignment_vol.h.
double ProgNmaAlignmentVol::rhoStartBase |
Definition at line 86 of file nma_alignment_vol.h.
double ProgNmaAlignmentVol::sampling_rate |
Pixel size in Angstroms.
Definition at line 61 of file nma_alignment_vol.h.
double ProgNmaAlignmentVol::sigmaGaussian |
Gaussian standard deviation for pseudo-atoms.
Definition at line 79 of file nma_alignment_vol.h.
int ProgNmaAlignmentVol::tilt0 |
Definition at line 91 of file nma_alignment_vol.h.
int ProgNmaAlignmentVol::tiltF |
Definition at line 91 of file nma_alignment_vol.h.
Matrix1D<double> ProgNmaAlignmentVol::trial |
Definition at line 107 of file nma_alignment_vol.h.
Matrix1D<double> ProgNmaAlignmentVol::trial_best |
Definition at line 110 of file nma_alignment_vol.h.
double ProgNmaAlignmentVol::trustradius_scale |
Parameters required from the CONDOR optimization.
Definition at line 85 of file nma_alignment_vol.h.
bool ProgNmaAlignmentVol::useFixedGaussian |
Use pseudo-atoms instead of atoms.
Definition at line 76 of file nma_alignment_vol.h.
Image<double> ProgNmaAlignmentVol::V |
Definition at line 131 of file nma_alignment_vol.h.
Image<double> ProgNmaAlignmentVol::Vdeformed |
Definition at line 131 of file nma_alignment_vol.h.