| Bsoft 2.0.5 Bernard's software package

File List
Here is a list of all files with brief descriptions:
[detail level 1 2 3]

► include |
Bimage.h | Header file for image class
binomial.h | Functions to generate and fit binomials
Bplot.h | Header file for postscript output functions
Bstring.h | Header file for the string class
Bsuperpixel.h | Super pixel segmentation
cluster.h | Header file for clustering functions
Color.h | Classes for color objects
Complex.h | Class for complex numbers
ctf.h | Header file for CTF (contrast transfer function) functions
dynamic_programming.h | Library functions for dynamic programming
Euler.h | Euler object
fft.h | General FFT for n-dimensional data
file_util.h | Header file for file checking functions
FSI_Kernel.h | Header file for frequency space interpolation kernel
img_combine.h | Header file for combining two images in various ways
json.h |
linked_list.h | Header file for generalized linked list functions
marker.h | Header file for image parameter functions
math_util.h | Header file for general utilities
Matrix.h | Generalized matrix class
Matrix3.h | 3x3 Matrix manipulation functions
matrix_linear.h | Header file for matrix functions
matrix_util.h | Utility functions for matrices
mdoc.h |
mg_align.h | Header file for functions to align micrographs or coordinates from micrographs and apply the resultant transformation
mg_class.h | Header file for classification of raw single particle images with respect to multiple models
mg_ctf.h | Functions for CTF (contrast transfer function) processing
mg_ctf_fit.h | Header file for CTF (contrast transfer function) functions
mg_extract.h | Header file for functions to extract particles from micrographs
mg_hand.h | Author: David Belnap
mg_helix.h | Header file for functions to process helical data
mg_img_proc.h | Header file for image processing from micrograph structures
mg_marker.h | Header file for micrograph marker functions
mg_merge.h | Header file for functions to merge images
mg_multiple.h | Selection of single particle parameters from multiple files for classification
mg_multislice.h | Generates and manipulates projects for multislice calculations
mg_orient.h | Library routines for single particle analysis
mg_particle_select.h | Select particles
mg_particles.h | Manipulates single particle images
mg_pick.h | Header file for single particle picking functions
mg_processing.h | Header file for micrograph processing
mg_random.h | Header file for applying some randomization to parameters
mg_reconstruct.h | Functions for reconstruction
mg_refine.h | Reciprocal space refinement of orientation parameters of particle images
mg_subtomo.h | Header file for functions finding particles (subtomograms) in a tomogram
mg_tags.h | All STAR and XML file format tags for micrographs and reconstructions
mg_tomo_rec.h | Functions to do a tomographic reconstruction
mg_tomo_resol.h | Functions to assess the resoltion of a tomographic tilt series
mg_tomo_track.h | Functions to track fiducial markers in a tomographic series of images
mg_tomography.h | Header file for single particle image processing in Bsoft
mg_xtal.h | Header file for functions to process crystallographic data
model_color.h | Functions to color models
model_compare.h | Functions to compare models and components
model_create.h | Library routines used for model creation
model_extract_build.h | Functions to extract subvolumes and build new maps
model_links.h | Library routines used for model link processing
model_map.h | Header file for model to map conversions
model_mask.h | Functions to generate masks from models
model_mechanics.h | Functions to do molecular mechanics
model_multifit.h | Header file for searching for a template in a map and returning multiple hits in a model
model_neighbors.h | Functions to manipulate model component neighbors
model_occupancy.h | Library routines to count components in maps
model_path.h | Library routines used for model processing
model_plane.h | Library routines used for plane models
model_poly.h | Functions to manipulate polyhedral coordinate files
model_poly_delta.h | Functions to generate deltagraph polyhedra
model_poly_spiral.h | Functions to generate polyhedra using the spiral algorithm
model_select.h | Header file for reading and writing atomic model files
model_shell.h | Library routines used for shell model processing
model_symmetry.h | Library routines used for model symmetry operations
model_tags.h | All STAR and XML file format tags for models
model_transform.h | Library routines used for model transformation
model_util.h | Library routines used for model processing
model_views.h | Library routines used for analysing model component views
mol_alpha.h | Header for functions to make and analyze alpha helices
mol_bonds.h | Header for molecular dynamics
mol_compare.h | Library routines used to compare sets of atomic coordinates
mol_edit.h | Library routines used for atomic coordinates
mol_map_energy.h | Headers of functions to calculate estimates of the fitting of molecules to maps
mol_md.h | Header for molecular dynamics
mol_monte.h | Headers of functions using a monte carlo metroplis algorithm to energy minimize molecular positions
mol_param.h | Header for functions to extract parameters from coordinate files
mol_select.h | Library routines to select atomic coordinates
mol_symmetry.h | Library routines used for symmetry operations on atomic coordinates
mol_tags.h | All STAR file format tags for molecules and molecular parameters
mol_transform.h | Library routines used for atomic coordinate transformations
mol_util.h | Library routines used for atomic coordinates
mol_water.h | Generating and managing water
molecule_to_map.h | Header file for functions to calculate a 3D map from atomic coordinates
moving_average.h | Header file moving average calculations
options.h | Header file for option handlers
ps_ctf_plot.h | Header file for postscript output functions
ps_marker.h | Header file for postscript tools dealing with Bmarkers
ps_micrograph.h | Header file for postscript tools dealing with micrograph particle sets
ps_model.h | Header file for postscript tools dealing with models
ps_plot.h | Header file for postscript output functions
ps_sequence.h | Header file for postscript output for sequence analysis functions
ps_tree.h | Header file for writing a tree into a postcsript file
ps_views.h | Header file for postscript tools dealing with views
qsort_functions.h | Header file for utility functions for use in qsort calls
Quaternion.h | Class for quaternions
random_numbers.h | Header file for functions for creating random images
rwASCII.h | Header file for reading and writing ASCII files
rwatomprop.h | Header file for reading atom property files
rwBCR.h | Header file for reading and writing AFM BCR-STM files
rwBIORAD.h | Header file for reading and writing BioRad files
rwBRIX.h | Header file for reading and writing Brix files
rwBrookhavenSTEM.h | Header file for reading and writing Brookhaven STEM files
rwCCP4.h | Header file for reading and writing CCP4 files
rwClustal.h | Header file for reading and writing Clustal sequence files
rwDI.h | Header file for reading (only) Digital Instruments files
rwDM.h | Header file for reading and writing DM files
rwDSN6.h | Header file for reading and writing DSN6 files
rwDX.h | Header file for reading and writing OpenDX files
rwEM.h | Header file for reading and writing EM files
rwEMBL.h | Header file for reading and writing EMBL sequence files
rwFASTA.h | Header file for reading and writing FASTA sequence files
rwFSC_XML.h | Library routines to read and write FSC curves
rwGenBank.h | Header file for reading and writing GenBank sequence files
rwgencode.h | Header file for reading a genetic code from a file
rwGOODFORD.h | Header file for reading and writing Peter Goodford's GRID files
rwGRD.h | Header file for reading and writing Basel GRD files
rwGROMACS.h | Header file for reading and writing GROMACS coordinate files
rwHKL.h | Header file for reading and writing HKL reflection files as images
rwIMAGIC.h | Header file for reading and writing Image Science's Imagic files
rwimg.h | Header file for 2D and 3D image I/O
rwIP.h | Header file for reading and writing image plate reader files
rwJPEG.h | Header file for reading and writing JPEG files
rwkernel.h | Header file for functions to read and write kernel files
rwmatrix.h | Header file for reading (and writing) matrices
rwmd.h | Header to read and write molecular dynamics parameters in STAR format
rwMFF.h | Header file for reading and writing the What If MFF files
rwmg.h | Header file for reading and writing micrograph parameters
rwmgEMX.h | Reads and writes micrograph exchange files
rwmgIMOD.h | Converts between IMOD files and a micrograph parameter file
rwmgRELION.h | Header file for reading and writing micrograph parameters from and to the RELION STAR format
rwmgSerialEM.h | Converts between SerialEM MDOC files and a micrograph parameter file
rwmgSTAR.h | Header file for reading and writing micrograph parameters from and to the STAR format
rwmgXML.h | Reads and writes micrograph XML files
rwMIFF.h |
rwmodel.h | Header file for reading and writing atomic model files
rwmodel_bild.h | Header file for reading and writing Chimera BILD files
rwmodel_cmm.h | Header file for reading and writing Chimera marker model parameters
rwmodel_mol.h | Header file for reading and writing molecular model parameters
rwmodel_param.h | Header to read and write model dynamics parameters in STAR format
rwmodel_star.h | Header file for reading and writing STAR model parameters
rwmodel_vega.h | Header file for reading and writing Vega model parameters
rwmodel_xml.h | Read and write models in XML format
rwmol_star.h | Read and write molecules in STAR format
rwmol_text.h | Read and write molecules in plain text
rwmolecule.h | Header file for reading reflection files
rwMRC.h | Header file for reading and writing MRC files
rwPDB.h | Header file for reading and writing PDB coordinate files
rwPhylip.h | Header file for reading and writing Phylip sequence files
rwPIC.h | Header file for reading and writing PIC's BP and BQ files
rwPIF.h | Header file for reading and writing PIF files
rwPIR.h | Header file for reading and writing PIR sequence files
rwPNG.h | Header file for reading and writing PNG files
rwPNM.h | Header file for reading and writing PNM files
rwPostScript.h | Header file for (reading and) writing postscript image files
rwRAW.h | Header file for reading and writing Raw files
rwresprop.h | Header file for reading residue property files
rwSER.h | Header file for reading and writing FEI Ser files
rwSitus.h | Header file for reading and writing Situs files
rwSPE.h | Header file for reading and writing SPE files
rwSPIDER.h | Header file for reading and writing SPIDER files
rwstar.h | A header file for STAR format files
rwSUPRIM.h | Header file for reading and writing SUPRIM files
rwsymop.h | Header file for reading and writing symmetry operators
rwTGA.h | Header file for reading and writing Truevision TGA files
rwTIFF.h | Header file for reading and writing TIFF files
rwtree.h | Header file for reading (and writing) trees
rwWAH.h | Header file for reading and writing Wayne Hendrickson coordinate files
rwxml.h | Reads and writes micrograph XML files
rwXPLOR.h | Header file for reading and writing XPLOR reflection files
seq_align.h | Header file for functions to generate and analyze dot plots
seq_analysis.h | Header file for sequence analysis functions
seq_util.h | Header file for sequence utilities
simplex.h | Nelder and Mead downhill simplex method for generalized parameter fitting
spline.h | Header file for spline interpolation
string_util.h |
sym_tags.h | All STAR file format tags for symmetry parameters
symmetry.h | Header file for general symmetry functions
timer.h | Utilities for timing functions
Transform.h | Class for a generalized transform object
UnitCell.h | Header file for unit cell functions
utilities.h | Header file for general utilities
Vector3.h | Class for 3-value vectors
View.h | View object
► radon |
fft_tool.cpp |
fft_tool.h |
gal_ricoI.cpp |
gal_ricoI.h |
img_radon.cpp | Radon transform functions
img_radon.h |
kernlut.cpp |
kernlut.h |
pocs_tool.cpp |
pocs_tool.h |
proj_tool.cpp |
proj_tool.h |
radon_util.cpp |
radon_util.h |
sin_gal.cpp |
sin_gal.h |
► src |
► img |
Bimage.cpp | Methods for the image class
Bimage_align.cpp | Functions to align images
Bimage_background.cpp | Library routines for manipulating image backgrounds
Bimage_bin.cpp | Library routines for binning images
Bimage_color.cpp | Library routines for mangaing color images
Bimage_combine.cpp | Functions to combine two images in various ways
Bimage_complex.cpp | Routines to convert complex data sets
Bimage_correlate.cpp | Cross correlation functions
Bimage_edit.cpp | Library routines used for editing image contents
Bimage_extract.cpp | Library routines to extract parts of images
Bimage_fft.cpp | General FFT for n-dimensional data
Bimage_filter.cpp | Library routines used for filtering images
Bimage_fspace.cpp | Library routines used for modifying reciprocal space amplitudes
Bimage_helix.cpp | Dealing with images with helical symmetry
Bimage_histogram.cpp | Library routines to calculate histograms for images
Bimage_mask.cpp | Methods for binary mask creation and manipulation
Bimage_montage.cpp | Functions to montage images for display
Bimage_nad.cpp | Denoising by nonlinear anisotropic diffusion: Coherence and edge enhancing diffusion
Bimage_noise.cpp | Functions for generating noise images
Bimage_polar.cpp | Library routines for polar and spherical transformations and calculations
Bimage_powerspectrum.cpp | Functions for calculating and using power spectra in electron micrographs
Bimage_project.cpp | Functions for projections
Bimage_reconstruct.cpp | 2D and 3D reconstruction from single particle images
Bimage_rescale.cpp | Library routines to rescale images
Bimage_resize.cpp | Library routines to resize images
Bimage_resolution.cpp | Library routines to estimate resolution
Bimage_search.cpp | Searches orientation space for the best fit of a 3D map to a template
Bimage_segment.cpp | Methods for segmentation
Bimage_stats.cpp | Functions to calculate statistics on image regions
Bimage_symmetry.cpp | Symmetry function library for crystallography
Bimage_topo.cpp | Functions to convert between 2D topology images to 3D surfaces
Bimage_transform.cpp | Library routines for transforming images
img_combine.cpp | Functions to combine two images in various ways
► mg |
mg_align.cpp | Functions to align micrographs or coordinates from micrographs and apply the resultant transformation
mg_class.cpp | Classifies raw single particle images with respect to multiple models
mg_ctf.cpp | Functions for CTF (contrast transfer function) processing
mg_ctf_fit.cpp | Functions for CTF (contrast transfer function) processing
mg_extract.cpp | Functions to extract particles from micrographs
mg_hand.cpp | Functions for comparing projections of two oppositely handed reconstructions to images of tilted specimens
mg_helix.cpp | Functions to process helical data
mg_img_proc.cpp | Functions for image processing from micrograph structures
mg_marker.cpp | Functions for dealing with markers and linkers
mg_merge.cpp | Library functions to merge images
mg_multiple.cpp | Selection of single particle parameters from multiple files for classification
mg_multislice.cpp | Generates and manipulates projects for multislice calculations
mg_orient.cpp | Determines orientation angles and x,y origins of single particle images
mg_particle_select.cpp | Select particles
mg_particles.cpp | Calculates centers of single particle images
mg_pick.cpp | Functions for picking single particle images from a micrograph
mg_processing.cpp | Functions for micrograph processing
mg_random.cpp | Functions for applying some randomization to parameters
mg_reconstruct.cpp | Functions for reconstruction
mg_refine.cpp | Reciprocal space refinement of orientation parameters of particle images
mg_subtomo.cpp | Functions to find particles (subtomograms) in a tomographic reconstruction
mg_tomo_rec.cpp | Functions to do a tomographic reconstruction
mg_tomo_resol.cpp | Functions to assess the resoltion of a tomographic tilt series
mg_tomo_track.cpp | Functions to track fiducial markers in a tomographic series of images
mg_tomography.cpp | Functions to manage tomographic series of images
mg_xtal.cpp | Functions to process crystallographic data
► model |
model_color.cpp | Functions to color models
model_compare.cpp | Functions to compare models and components
model_create.cpp | A tool to expand models
model_extract_build.cpp | Functions to extract subvolumes and build new maps
model_links.cpp | Library routines used for model links processing
model_map.cpp | Function to generate a map from a model
model_mask.cpp | Generating a mask from an atomic model
model_mechanics.cpp | Functions to do molecular mechanics
model_multifit.cpp | Searching for a template in a map and returning multiple hits in a model
model_neighbors.cpp | Functions to manipulate model component neighbors
model_occupancy.cpp | Library routines to count components in maps
model_path.cpp | Library routines used for model processing
model_plane.cpp | Library routines used for plane models
model_poly.cpp | Functions to manipulate polyhedral coordinate files
model_poly_delta.cpp | Functions to generate deltagraph polyhedra
model_poly_spiral.cpp | Functions to generate polyhedra using the spiral algorithm
model_select.cpp | Library routines used for model and component selection
model_shell.cpp | Library routines used for shell model processing
model_symmetry.cpp | Library routines used for model symmetry operations
model_transform.cpp | Library routines used for model transformation
model_util.cpp | Library routines used for model processing
model_views.cpp | Library routines used for analyzing the views of components in models
► mol |
mol_alpha.cpp | Functions to make and analyze alpha helices
mol_bonds.cpp | Functions for molecular dynamics
mol_compare.cpp | Library routines used to compare sets of atomic coordinates
mol_edit.cpp | Library routines used for atomic coordinates
mol_map_energy.cpp | Functions to calculate estimates of the fitting of molecules to maps
mol_md.cpp | Functions for molecular dynamics
mol_monte.cpp | Functions for a monte carlo metroplis algorithm to energy minimize molecular positions
mol_param.cpp | Functions to extract parameters from coordinate files
mol_select.cpp | Library routines to select atomic coordinates
mol_symmetry.cpp | Library routines used for symmetry operations on atomic coordinates
mol_transform.cpp | Library routines used for atomic coordinate transformations
mol_util.cpp | Library routines used for atomic coordinates
mol_water.cpp | Generating and managing water
molecule_to_map.cpp | Functions to calculate a 3D map from atomic coordinates
seq_align.cpp | Library routines to generate and analyze dot plots
seq_analysis.cpp | Analysis of protein sequences
seq_util.cpp | Sequence utility functions
► ps |
ps_ctf_plot.cpp | Postscript output functions for calculating CTF parameters
ps_marker.cpp | Methods for postscript tools dealing with markers
ps_micrograph.cpp | Postscript output for micrographs
ps_model.cpp | Postscript output for models
ps_plot.cpp | Postscript output functions
ps_sequence.cpp | Postscript output for sequence analysis functions
ps_tree.cpp | Postscript tree output functions
ps_views.cpp | Postscript output for views
► rwimg |
rwASCII.cpp | Functions for reading and writing ASCII files
rwBCR.cpp | Functions for reading and writing AFM BCR-STM files
rwBIORAD.cpp | Functions for reading and writing BioRad confocal files
rwBRIX.cpp | Functions for reading and writing BRIX files
rwBrookhavenSTEM.cpp | Functions for reading and writing Brookhaven STEM files
rwCCP4.cpp | Functions for reading and writing CCP4 files
rwDI.cpp | Functions for reading (only) Digital Instruments files
rwDM.cpp | Functions for reading and writing Digital Micrograph files
rwDSN6.cpp | Functions for reading and writing DSN6 files
rwDX.cpp | Functions for reading and writing OpenDX files
rwEM.cpp | Functions for reading and writing EM files
rwGOODFORD.cpp | Functions for reading and writing Peter Goodford's GRID files
rwGRD.cpp | Functions for reading and writing GRD files
rwHKL.cpp | Routines to read and write HKL reflection files
rwIMAGIC.cpp | Functions for reading and writing Image Science's Imagic files
rwimg.cpp | Library for 2D and 3D image I/O
rwIP.cpp | Functions for reading and writing image plate reader files
rwJPEG.cpp | Functions for reading and writing JPEG files
rwkernel.cpp | Library routines to read and write kernel files
rwMFF.cpp | Functions for reading and writing What If MFF files
rwMIFF.cpp | Functions for reading and writing ImageMagick MIFF files
rwMRC.cpp | Functions for reading and writing MRC files
rwPIC.cpp | Functions for reading and writing PIC BP and BQ files
rwPIF.cpp | Functions for reading and writing PIF files
rwPNG.cpp | Functions for reading and writing PNG files
rwPNM.cpp | Functions for reading and writing PBM, PGM and PPM files
rwPostScript.cpp | Functions for (reading and) writing postscript image files
rwRAW.cpp | Functions for reading and writing RAW files
rwSER.cpp | Reading FEI SER files
rwSitus.cpp | Functions for reading and writing Situs files
rwSPE.cpp | Functions for reading and writing SPE CCD files
rwSPIDER.cpp | Functions for reading and writing SPIDER files
rwSUPRIM.cpp | Functions for reading and writing SUPRIM files
rwTGA.cpp | Functions for reading and writing Truevision TGA files
rwTIFF.cpp | Functions for reading and writing TIFF files
rwXPLOR.cpp | Routines to read and write XPLOR reflection files
► rwmodel |
rwmodel.cpp | Library routines to read and write atomic model parameters
rwmodel_bild.cpp | Library routines to read and write Chimera BILD model parameters
rwmodel_cmm.cpp | Library routines to read and write Chimera marker model parameters
rwmodel_mol.cpp | Library routines to read and write atomic model parameters
rwmodel_star.cpp | Library routines to read and write STAR model parameters
rwmodel_vega.cpp | Library routines to read and write Vega model parameters
rwmodel_xml.cpp | Library routines to read and write XML model parameters
► rwmol |
rwClustal.cpp | Library routines to read and write Clustal sequence files
rwEMBL.cpp | Library routines to read and write EMBL sequence files
rwFASTA.cpp | Library routines to read and write FASTA sequence files
rwGenBank.cpp | Library routines to read and write GenBank sequence files
rwGROMACS.cpp | Library routines to read and write GROMACS coordinate files
rwmol_star.cpp | Library routines to read and write molecule files in STAR format
rwmol_text.cpp | Library routines to read and write molecule files in plain text
rwmolecule.cpp | Library routines to read and write molecule file, including sequences and coordinates
rwPDB.cpp | Library routines to read and write PDB coordinate files
rwPhylip.cpp | Library routines to read and write Phylip sequence files
rwPIR.cpp | Library routines to read and write PIR sequence files
rwWAH.cpp | Library routines to read and write Wayne Hendrickson coordinate files
► rwparam |
rwatomprop.cpp | Library routines to read and write atom properties
rwFSC_XML.cpp | Library routines to read and write FSC curves
rwgencode.cpp | Library routines to read and write genetic codes
rwmd.cpp | Library routines to read and write molecular dynamics parameters in STAR format
rwmg.cpp | Library routines to read and write micrograph parameters
rwmgEMX.cpp | Reads and writes micrograph exchange files
rwmgIMOD.cpp | Converts between IMOD files and a micrograph parameter file
rwmgRELION.cpp | Library routines to read and write micrograph parameters in RELION STAR format
rwmgSerialEM.cpp | Converts between a SerialEM MDOC file and a micrograph parameter file
rwmgSTAR.cpp | Library routines to read and write micrograph parameters in STAR format
rwmgXML.cpp | Reads and writes micrograph XML files
rwmodel_param.cpp | Library routines to read and write model dynamics parameters in STAR format
rwresprop.cpp | Library routines to read and write residue properties
rwstar.cpp | Parse and interpret STAR format files
rwsymop.cpp | Library routines to read and write symmetry operators
rwtree.cpp | Functions for reading (and writing) trees
rwxml.cpp | Reads to and writes from XML structures
► util |
binomial.cpp | Functions to generate and fit binomials
Bplot.cpp | Postscript output functions
Bstring.cpp | Functions in the string class
cluster.cpp | Clustering functions
ctf.cpp | Functions to manage CTF (contrast transfer function) parameters
dynamic_programming.cpp | Library functions for dynamic programming
fft.cpp | General FFT for n-dimensional data
file_util.cpp | Library functions for file checking
json.cpp |
linked_list.cpp | Generalized linked list functions
marker.cpp | Functions for dealing with markers and linkers
math_util.cpp | Mathematics utility functions
matrix.cpp | Matrix manipulation functions
Matrix3.cpp | Matrix manipulation functions
matrix_linear.cpp | Solving sets of linear equations through matrix algebra
matrix_util.cpp | Utility functions for matrices
moving_average.cpp | Functions for moving average calculations
options.cpp | Functions to handle general options
qsort_functions.cpp | Library utility functions for use in qsort calls
Quaternion.cpp | Quaternion functions
random_numbers.cpp | Functions for generating random sequences
simplex.cpp | Nelder and Mead downhill simplex method for generalized parameter fitting
spline.cpp | Functions to calculate spline curves
string_util.cpp |
symmetry.cpp | General symmetry functions
timer.cpp | Utilities for timing functions
Transform.cpp | Transform manipulation functions
UnitCell.cpp | Unit cell functions
utilities.cpp | Library functions useful in all the package
View.cpp | View functions
b3v.cpp | Program to extract 3 orthogonal views from a map
badd.cpp | Program to catenate image files
baddmask.cpp | Program to catenate image files
bafm.cpp | Simulation of AFM experiments
balign.cpp | Aligns two images
balpha.cpp | Program to make and analyze alpha helices
bampweigh.cpp | Program to filter images
bar.cpp | Program to do simple arithmetic on images
bass.cpp | Program to assemble molecular components
bbackproj.cpp | 3D reconstruction by backprojection
bbif.cpp | Program to denoise images by bilateral filtering
bbild.cpp | Generates BILD output from a model
bcat.cpp | Program to catenate image files
bcatmol.cpp | A program to concatenate coordinates from different files
bcatseq.cpp | A program to concatenate protein sequences from different files
bcc.cpp | Program for calculating cross-correlations
bclass.cpp | Classifies raw single particle images with respect to multiple models
bcolour.cpp | Program to generate nice colour images
bcomplex.cpp | Program for handing complex images
bconvert.cpp | Program to catenate image files
bcormut.cpp | A program to analyze protein sequences for correlated mutations
bcrystal.cpp | Calculates coordinates for multiple unit cells
bctf.cpp | A program to determine and correct for the CTF (contrast transfer function) in electron micrographs
bcyl.cpp | Program to manipulate cylindrical images
bdelta.cpp | Generating a deltagraph with minimal input parameters
bdens.cpp | Program to calculate density in selected regions of a map
bdif.cpp | Analyze diffraction patterns
bdual.cpp | Program to handle dual tomographic tilt series
bedge.cpp | A program to float an image in a uniform background
beditimg.cpp | Segment images into density regions
bfcc.cpp | Fast cross-correlation search for the best fit of a 3D map to a template
bfft.cpp | General FFT for n-dimensional data
bfil.cpp | Extract filaments from a micrograph as straightened filaments or boxed particles
bfile.cpp | Program to read file contents directly and poke single values
bfilter.cpp | Program to filter images
bfilwidth.cpp | Program to calculate moving average images
bfind.cpp | Searches orientation space for the best fit of a 3D map to a template
bfix.cpp | Program to fix end-of-line characters in ascii files
bflat.cpp | Solvent flattening
bflood.cpp | Segment images into density regions
bftr.cpp | Program for resizing an image using Fourier transformation
bgex.cpp | Calculating and comparing atomic models and maps
bgraphseg.cpp | Segment images into density regions using a nondirected graph
bhead.cpp | Program to modify image parameters in the header
bheight.cpp | Projecting a 3D map and calculating comparison statistics of the projections
bhelcross.cpp | Dealing with images with helical symmetry
bhelix.cpp | Dealing with images with helical symmetry
bhisto.cpp | Image histograms
bico.cpp | Program to analyze icosahedral subtomograms
bimg.cpp | General image processing program
bint.cpp | Interpolation of 2D and 3D images
bkernel.cpp | Program to calculate filter kernels
blevel.cpp | A program to manipulate level masks
blocfilt.cpp | Local resolution analysis
blocres.cpp | Local resolution analysis
bmapdist.cpp | Calculates a distance criterion between a set of 2D images or 3D maps
bmark.cpp | Program to generate symmetry axes for mark group symmetries
bmask.cpp | Generating and manipulating masks
bmaskmod.cpp | Generating a model from a mask
bmatch.cpp | Program to search an image with multiple projections and orient them
bmatrix.cpp | Program to process matrices
bmaxpow.cpp | Determining orientations by maximum power of 3D reconstruction from single particle images
bmd.cpp | Molecular dynamics - humble beginnings
bmedian.cpp | Program to filter images
bmg.cpp | Manipulating project and micrograph structures
bmg2imod.cpp | Converts between IMOD files and a micrograph parameter file
bmgalign.cpp | Aligns micrographs specified in parameter files
bmgconvert.cpp | Convert between micrograph parameter formats
bmgft.cpp | Disk-based 3D reconstruction for a tomography series
bmgtransfer.cpp | Transfer pieces of information between micrograph paramater files
bmissing.cpp | Generating and manipulating masks
bmm.cpp | A program to do model mechanics
bmod2part.cpp | Converting from a pseudo-atomic model to particle parameters
bmodcol.cpp | A tool to color models
bmodcomp.cpp | A tool to compare polyhedra
bmodedit.cpp | A tool to create and edit models
bmodel.cpp | Manipulates models
bmodmap.cpp | A tool to genrate a map from a model
bmodmask.cpp | Generating a mask from an atomic model
bmodsel.cpp | Manipulates selections from sets of components as solutions of fits
bmodsym.cpp | Deals with model and component symmetries
bmodview.cpp | Manipulates models
bmol.cpp | A tool to edit and analyze coordinate files
bmoledit.cpp | A tool to edit coordinate files
bmolhel.cpp | A program to perform helical symmetry operations on coordinate files
bmolsym.cpp | A tool to perform symmetry operations on coordinate files
bmontage.cpp | A program to generate a montage from a 3D image or a set of 2D images
bmonte.cpp | Program to use a monte carlo metroplis algorithm to energy minimize molecular positions
bmultifit.cpp | Searching for a template in a map and returning multiple hits in a model
bmultimask.cpp | Generating and manipulating composite masks
bmultislice.cpp | Multi-slice simulation of the electron imaging process
bnad.cpp | Image denoising by nonlinear anisotropic diffusion: Coherence and edge enhancing diffusion
bnorm.cpp | Program to normalize a set of images based on their histograms
bop.cpp | A program to operate on image pairs
borient.cpp | Determines orientation angles and x,y origins of single particle images
bparam.cpp | A tool to extract parameters from coordinate files
bpart.cpp | Calculates centers of single particle images
bpartmulti.cpp | Selection of single particle parameters from multiple files for classification
bpartsel.cpp | Selection of single particles for 3D reconstruction
bpatch.cpp | Program to patch tiled image files
bpath.cpp | A program to analyze paths and cycles in a model
bphase.cpp | A program to examine phase differences between image pairs
bpick.cpp | Pick particles in a micrograph given the particle coordinates, or pick particles in a focal series of micrographs with alignment of the micrographs
bplane.cpp | A tool to expand models
bpoly.cpp | A tool to manipulate polyhedral coordinate files
bproject.cpp | Projecting a 3D map and calculating comparison statistics of the projections
bradial.cpp | Polar images and radial averages
bradsec.cpp | Generates radial sections from 3D images
brandom.cpp | Program to generate random images
brecadd.cpp | Program to average selected reconstructions
brecmod.cpp | A tool to merge data from micrograph reconstruction and model files
breconstruct.cpp | 3D reconstruction from single particle images
brefine.cpp | Reciprocal space refinement of orientation parameters of particle images
bresolve.cpp | Calculate resolution estimates and Fourier shell statistics
bscale.cpp | Program to find the scaling of map with respect to a reference
bsegment.cpp | Segment images into density regions
bseq.cpp | A program to manipulate DNA and protein sequences
bseqaln.cpp | A program to analyze aligned protein sequences
bseries.cpp | Program to align and analyze series of images
bsf.cpp | Calculating structure factors from atomic models
bshell.cpp | Generates a shell point component model
bsim.cpp | A tool to generate a project with random orientations for a molecule and to simulate TEM images from given orientations
bspiral.cpp | A tool to generate polyhedra using the spiral algorithm
bsplit.cpp | Program to seperate a multi-image file into individual image files
bsplitmol.cpp | A program to concatenate coordinates from different files
bspr.cpp | 3D reconstruction from single particle images
bstar.cpp | Examines STAR format files
bsupix.cpp | Segment images
bsurf.cpp | AFM image analysis and reconstruction
bsym.cpp | Program to generate symmetry axes for point group symmetries
bsymcomp.cpp | Finds the best orientation that fits a symmetrized template
btile.cpp | Program to split an image into overlapping tiles
btomaln.cpp | Program to do fiducialless alignment of a tilt series
btomo.cpp | Program to process tomographic series of images
btompart.cpp | Program to extract single particle images from a tilt series and generate individual reconstructions
btomrec.cpp | Disk-based 3D reconstruction for a tomography series
btomres.cpp | Program to determine the resolution of a tilt series
btrack.cpp | Program to track fiducial markers in a tomographic series of images
btree.cpp | Program to process trees
btube.cpp | Symmetrizes helical tubes with hexagonal lattices
bwater.cpp | Molecular dynamics - humble beginnings
bxb.cpp | Extracting a part of a density map and building a new map
bxml.cpp | Reads, writes and validates XML files
bzfft.cpp | Disk-based z-line transforms for big reconstructions
dcount.cpp | A program to determine the occupancy of components in models
dhand.cpp | Compare projections of two oppositely handed reconstructions to images of tilted specimens
dimgstats.cpp | Calculates statistical measures within a set of images or between sets of images
dmerge.cpp | Merge images in a defocal or other series, align images before adding together
emgrand.cpp | Generate random values for micrograph parameters
jave.cpp | Program to average files and weigh the average in Real/Fourier space
jpartdif.cpp | Analysis of particle differences between two starfiles
jsubtomo.cpp | Finds particles (subtomograms) in a tomographic reconstruction and refines their origins and orientations
jviews.cpp | Generates views covering an asymmetric unit or all symmetry related views
radon.cpp | Program to do radon transforms
radonrecon.cpp | Program to do radon transforms
► tcltk |
brun_panel.tcl | Panel to construct and run Bsoft command lines
bshow.cpp | A shared object to load Bsoft image files in TCL/Tk
bshow_boxes.tcl | Procedures to create, move and destroy particle boxes
bshow_ctf.tcl | Procedures to do CTF fitting
bshow_diffraction.tcl | Procedures to analyze diffraction patterns
bshow_filament.tcl | Procedures to create, move and destroy filament selections
bshow_file.tcl | Procedures to manage file I/O
bshow_getinfo.tcl | Procedures to show image information
bshow_graph.tcl | Procedures to draw graphs in Bshow
bshow_helix.tcl | Procedures to manage helical diffraction patterns
bshow_histogram.tcl | Procedures to draw a histogram in Bshow
bshow_image.tcl | Procedures for manipulating images in Bshow
bshow_magnify.tcl | Procedures for rendering the magnifying window in Bshow
bshow_misc.tcl | Miscellaneous procedures for Bshow and other scripts
bshow_model.tcl | Procedures to create and destroy model components and links in images
bshow_param.tcl | Procedures to read and write parameter files
bshow_scales.tcl | Procedures to manage scales for image display
bshow_select.tcl | Procedures to draw selections in Bshow
bshow_tomo.tcl | Procedures to manage tomographic images
bshow_tools.tcl | The toolbox window
bshow_voxels.tcl | Procedures to record voxel values in Bshow
bshow_xtal.tcl | Procedures to manage crystallographic images
bsoft_tcl.cpp | A stub function to interface the Bsoft library within TCL/Tk
btext.tcl | Window to show text information
tcltk_bbox.cpp | A shared object to manage micrograph parameter files in TCL/Tk
tcltk_bbox.h |
tcltk_bfil.cpp | A shared object to manage micrograph parameter files in TCL/Tk
tcltk_bfil.h |
tcltk_bhelix.cpp | A shared object to manage micrograph parameter files in TCL/Tk
tcltk_bhelix.h |
tcltk_bimage.cpp | A shared object to load Bsoft image files in TCL/Tk
tcltk_bimage.h | A shared object to load Bsoft image files in TCL/Tk
tcltk_bmarker.cpp | A shared object to manage markers in micrograph parameter files in TCL/Tk
tcltk_bmarker.h | A shared object to manage markers in micrograph parameter files in TCL/Tk
tcltk_bmg.cpp | A shared object to manage micrograph parameter files in TCL/Tk
tcltk_bmg.h | A shared object to manage boxes in micrograph parameter files in TCL/Tk
tcltk_bmodel.cpp | A shared object to load Bsoft model files in TCL/Tk
tcltk_bmodel.h | A shared object to manage model parameter files in TCL/Tk
tcltk_bxtal.cpp | A shared object to manage micrograph parameter files in TCL/Tk
tcltk_bxtal.h |
bsoft.js |