- s -
- SaffOrientationGenerator() : EMAN::SaffOrientationGenerator
- SalIO() : EMAN::SalIO
- save_byteorder_to_dict() : EMAN::EMData
- save_data() : EMAN::Util
- save_pdb_with_helix() : EMAN::PointArray
- save_to_pdb() : EMAN::PDBReader, EMAN::PointArray
- sbasename() : EMAN::Util
- scale() : EMAN::EMData, EMAN::Transform
- ScaleAlignerABS() : EMAN::ScaleAlignerABS
- scaling() : EMAN::Matrix4
- ScreenPoint() : EMAN::ScreenPoint
- ScreenVector() : EMAN::ScreenVector
- SDGDProcessor() : EMAN::SDGDProcessor
- SerIO() : EMAN::SerIO
- set() : EMAN::ImageSort, EMAN::Transform
- set_background() : EMAN::EMAN2Ctf
- set_cmap_data() : EMAN::ColorRGBGenerator
- set_data() : EMAN::ColorRGBGenerator, EMAN::Isosurface, EMAN::MarchingCubes
- set_default() : EMAN::Dict
- set_depth() : EMAN::EMFTGL, EMAN::Region
- set_endian() : EMAN::Gatan::TagTable, EMAN::GatanDM4::TagTable
- set_face_size() : EMAN::EMFTGL
- set_font_file_name() : EMAN::EMFTGL
- set_font_mode() : EMAN::EMFTGL
- set_from() : EMAN::PointArray
- set_from_density_map() : EMAN::PointArray
- set_height() : EMAN::Region
- set_level() : EMAN::Log
- set_log_level() : EMAN::Util
- set_logfile() : EMAN::Log
- set_matrix() : EMAN::Transform
- set_mirror() : EMAN::Transform
- set_mode() : EMAN::BoxingTools
- set_num_images_found() : EMAN::GatanDM4::TagTable
- set_number_points() : EMAN::PDBReader, EMAN::PointArray
- set_origin() : EMAN::Region
- set_param() : EMAN::FactoryBase
- set_params() : EMAN::Aligner, EMAN::AmpweightFourierProcessor, EMAN::Analyzer, EMAN::AreaProcessor, EMAN::Averager, EMAN::Axis0FourierProcessor, EMAN::CircularMaskProcessor, EMAN::Cmp, EMAN::CollapseProcessor, EMAN::CtfCAutoAverager, EMAN::CtfCWautoAverager, EMAN::CtfWtAverager, EMAN::CtfWtFiltAverager, EMAN::DiscritizeProcessor, EMAN::DoGFourierProcessor, EMAN::ExpProcessor, EMAN::FactoryBase, EMAN::FiniteProcessor, EMAN::FixSignProcessor, EMAN::GaussFFTProjector, EMAN::GaussZFourierProcessor, EMAN::KMeansAnalyzer, EMAN::LinearRampProcessor, EMAN::LinearXformProcessor, EMAN::LoGFourierProcessor, EMAN::MaskEdgeMeanProcessor, EMAN::MaskGaussNonuniformProcessor, EMAN::MaskGaussProcessor, EMAN::MaskSharpProcessor, EMAN::MaskSoftProcessor, EMAN::MorphologicalProcessor, EMAN::PaintProcessor, EMAN::PeakOnlyProcessor, EMAN::PolyMaskProcessor, EMAN::Processor, EMAN::Projector, EMAN::RadialProcessor, EMAN::RangeThresholdProcessor, EMAN::RangeZeroProcessor, EMAN::RealPixelProcessor, EMAN::RecipCarefullyProcessor, EMAN::SigmaProcessor, EMAN::SNREvalProcessor, EMAN::SVDAnalyzer, EMAN::Transform, EMAN::ValuePowProcessor, EMAN::Wiener2DAutoAreaProcessor, EMAN::Wiener2DFourierProcessor
- set_params_inverse() : EMAN::Transform
- set_phase() : EMAN::Ctf, EMAN::EMAN1Ctf, EMAN::EMAN2Ctf
- set_points_array() : EMAN::PDBReader, EMAN::PointArray
- set_pre_trans() : EMAN::Transform
- set_progname() : EMAN::TestUtil
- set_radial_non_zero() : EMAN::BoxingTools
- set_randnum_seed() : EMAN::Util
- set_region() : EMAN::BoxingTools
- set_rotation() : EMAN::Transform
- set_sampling() : EMAN::Isosurface, EMAN::MarchingCubes
- set_scale() : EMAN::Transform
- set_seed() : EMAN::Randnum
- set_size() : EMAN::XYData
- set_snr() : EMAN::EMAN2Ctf
- set_state() : EMAN::XYData
- set_surface_value() : EMAN::Isosurface, EMAN::MarchingCubes
- set_thumb_index() : EMAN::Gatan::TagTable, EMAN::GatanDM4::TagTable
- set_trans() : EMAN::Transform
- set_using_display_lists() : EMAN::EMFTGL
- set_value() : EMAN::Vec2< Type >, EMAN::Vec3< Type >, EMAN::Vec4< Type >
- set_value_at() : EMAN::Vec2< Type >, EMAN::Vec3< Type >, EMAN::Vec4< Type >
- set_vector_at() : EMAN::PointArray
- set_verb() : EMAN::TomoSeg
- set_width() : EMAN::Region
- set_x() : EMAN::XYData
- set_xy_list() : EMAN::XYData
- set_xyz_origin() : EMAN::EMData
- set_y() : EMAN::XYData
- setCmapData() : EMAN::Isosurface, EMAN::MarchingCubes
- setCmapMinMax() : EMAN::Isosurface, EMAN::MarchingCubes
- setDataAt() : wustl_mm::SkeletonMaker::Volume
- SetDataAt() : wustl_mm::SkeletonMaker::VolumeData
- setDims() : EMAN::BoxSVDClassifier
- setdm() : EMAN::ChaoProjector
- setMinMax() : EMAN::ColorRGBGenerator
- setNeedToRecolor() : EMAN::ColorRGBGenerator
- setOrigin() : EMAN::ColorRGBGenerator, wustl_mm::SkeletonMaker::Volume
- SetOrigin() : wustl_mm::SkeletonMaker::VolumeData
- setRGBmode() : EMAN::ColorRGBGenerator, EMAN::Isosurface, EMAN::MarchingCubes
- setRGBorigin() : EMAN::Isosurface, EMAN::MarchingCubes
- setRGBscale() : EMAN::Isosurface, EMAN::MarchingCubes
- setScale() : EMAN::ColorRGBGenerator
- SetSize() : wustl_mm::SkeletonMaker::VolumeData
- setSpacing() : wustl_mm::SkeletonMaker::Volume
- SetSpacing() : wustl_mm::SkeletonMaker::VolumeData
- setup() : EMAN::BackProjectionReconstructor, EMAN::CUDA_Aligner, EMAN::CUDA_multiref_aligner, EMAN::FourierIterReconstructor, EMAN::FourierReconstructor, EMAN::FourierReconstructorSimple2D, EMAN::nn4_ctf_rectReconstructor, EMAN::nn4_ctfReconstructor, EMAN::nn4_ctfwReconstructor, EMAN::nn4_ctfwsReconstructor, EMAN::nn4_rectReconstructor, EMAN::nn4Reconstructor, EMAN::nnSSNR_ctfReconstructor, EMAN::nnSSNR_Reconstructor, EMAN::RealMedianReconstructor, EMAN::Reconstructor, EMAN::XYZReconstructor
- setup4slice() : EMAN::EMData
- setup_params() : EMAN::CUDA_multiref_aligner
- setup_seed() : EMAN::FourierIterReconstructor, EMAN::FourierReconstructor, EMAN::Reconstructor
- setup_seedandweights() : EMAN::FourierIterReconstructor, EMAN::FourierReconstructor, EMAN::Reconstructor
- sfopen() : EMAN::ImageIO
- sgn() : EMAN::Util
- ShapeAnalyzer() : EMAN::ShapeAnalyzer
- SigmaAverager() : EMAN::SigmaAverager
- sim_add_point_double() : EMAN::PointArray
- sim_add_point_one() : EMAN::PointArray
- sim_descent() : EMAN::PointArray
- sim_minstep() : EMAN::PointArray
- sim_minstep_seq() : EMAN::PointArray
- sim_pointpotential() : EMAN::PointArray
- sim_potential() : EMAN::PointArray
- sim_potentiald() : EMAN::PointArray
- sim_potentialdxyz() : EMAN::PointArray
- sim_printstat() : EMAN::PointArray
- sim_rescale() : EMAN::PointArray
- sim_set_pot_parms() : EMAN::PointArray
- sim_updategeom() : EMAN::PointArray
- SingleOrientationGenerator() : EMAN::SingleOrientationGenerator
- SingleSpiderIO() : EMAN::SingleSpiderIO
- SitusIO() : EMAN::SitusIO
- size() : EMAN::Dict, EMAN::ImageSort, EMAN::TypeDict
- size_of_in_bytes() : EMAN::U3DWriter
- skeleton() : wustl_mm::SkeletonMaker::Volume
- sort() : EMAN::ImageSort, wustl_mm::SkeletonMaker::GridQueue
- sort_by_axis() : EMAN::PointArray
- sort_mat() : EMAN::Util
- sph2cb() : EMAN::ChaoProjector
- SpiderIO() : EMAN::SpiderIO
- SqEuclideanCmp() : EMAN::SqEuclideanCmp
- square() : EMAN::Util
- square_sum() : EMAN::Util
- squared_length() : EMAN::Vec2< Type >, EMAN::Vec3< Type >
- sstrncmp() : EMAN::Util
- static_get_param_types() : EMAN::RotateFlipAligner, EMAN::RotateFlipAlignerIterative, EMAN::RotateTranslateFlipAligner, EMAN::RotateTranslateFlipAlignerIterative
- stos2() : EMAN::EMAN2Ctf
- str_to_lower() : EMAN::Util
- sum_oe() : EMAN::CUDA_Aligner
- surface_face_z() : EMAN::MarchingCubes
- surfaceSkeletonPres() : wustl_mm::SkeletonMaker::Volume
- SVDAnalyzer() : EMAN::SVDAnalyzer
- svdcmp() : EMAN::Util
- swap() : wustl_mm::SkeletonMaker::GridQueue2
- swap_bytes() : EMAN::ByteOrder
- swap_central_slices_180() : EMAN::Phase180Processor
- swap_corners_180() : EMAN::Phase180Processor
- swap_data() : EMAN::SpiderIO
- swap_header() : EMAN::ImagicIO2, EMAN::ImagicIO, EMAN::MrcIO, EMAN::SpiderIO
- swapEle() : wustl_mm::SkeletonMaker::GridQueue
- Symmetry3D() : EMAN::Symmetry3D