| Bsoft 2.0.5 Bernard's software package

src Directory Reference

## Directories
directory | img
directory | mg
directory | model
directory | mol
directory | ps
directory | rwimg
directory | rwmodel
directory | rwmol
directory | rwparam
directory | util

## Files
file | b3v.cpp [code]
| Program to extract 3 orthogonal views from a map.
file | badd.cpp [code]
| Program to catenate image files.
file | baddmask.cpp [code]
| Program to catenate image files.
file | bafm.cpp [code]
| Simulation of AFM experiments.
file | balign.cpp [code]
| Aligns two images.
file | balpha.cpp [code]
| Program to make and analyze alpha helices.
file | bampweigh.cpp [code]
| Program to filter images.
file | bar.cpp [code]
| Program to do simple arithmetic on images.
file | bass.cpp [code]
| Program to assemble molecular components.
file | bbackproj.cpp [code]
| 3D reconstruction by backprojection
file | bbif.cpp [code]
| Program to denoise images by bilateral filtering.
file | bbild.cpp [code]
| Generates BILD output from a model.
file | bcat.cpp [code]
| Program to catenate image files.
file | bcatmol.cpp [code]
| A program to concatenate coordinates from different files.
file | bcatseq.cpp [code]
| A program to concatenate protein sequences from different files.
file | bcc.cpp [code]
| Program for calculating cross-correlations.
file | bclass.cpp [code]
| Classifies raw single particle images with respect to multiple models.
file | bcolour.cpp [code]
| Program to generate nice colour images.
file | bcomplex.cpp [code]
| Program for handing complex images.
file | bconvert.cpp [code]
| Program to catenate image files.
file | bcormut.cpp [code]
| A program to analyze protein sequences for correlated mutations.
file | bcrystal.cpp [code]
| Calculates coordinates for multiple unit cells.
file | bctf.cpp [code]
| A program to determine and correct for the CTF (contrast transfer function) in electron micrographs.
file | bcyl.cpp [code]
| Program to manipulate cylindrical images.
file | bdelta.cpp [code]
| Generating a deltagraph with minimal input parameters.
file | bdens.cpp [code]
| Program to calculate density in selected regions of a map.
file | bdif.cpp [code]
| Analyze diffraction patterns.
file | bdual.cpp [code]
| Program to handle dual tomographic tilt series.
file | bedge.cpp [code]
| A program to float an image in a uniform background.
file | beditimg.cpp [code]
| Segment images into density regions.
file | bfcc.cpp [code]
| Fast cross-correlation search for the best fit of a 3D map to a template.
file | bfft.cpp [code]
| General FFT for n-dimensional data.
file | bfil.cpp [code]
| Extract filaments from a micrograph as straightened filaments or boxed particles.
file | bfile.cpp [code]
| Program to read file contents directly and poke single values.
file | bfilter.cpp [code]
| Program to filter images.
file | bfilwidth.cpp [code]
| Program to calculate moving average images.
file | bfind.cpp [code]
| Searches orientation space for the best fit of a 3D map to a template.
file | bfix.cpp [code]
| Program to fix end-of-line characters in ascii files.
file | bflat.cpp [code]
| Solvent flattening.
file | bflood.cpp [code]
| Segment images into density regions.
file | bftr.cpp [code]
| Program for resizing an image using Fourier transformation.
file | bgex.cpp [code]
| Calculating and comparing atomic models and maps.
file | bgraphseg.cpp [code]
| Segment images into density regions using a nondirected graph.
file | bhead.cpp [code]
| Program to modify image parameters in the header.
file | bheight.cpp [code]
| Projecting a 3D map and calculating comparison statistics of the projections.
file | bhelcross.cpp [code]
| Dealing with images with helical symmetry.
file | bhelix.cpp [code]
| Dealing with images with helical symmetry.
file | bhisto.cpp [code]
| Image histograms.
file | bico.cpp [code]
| Program to analyze icosahedral subtomograms.
file | bimg.cpp [code]
| General image processing program.
file | bint.cpp [code]
| Interpolation of 2D and 3D images.
file | bkernel.cpp [code]
| Program to calculate filter kernels.
file | blevel.cpp [code]
| A program to manipulate level masks.
file | blocfilt.cpp [code]
| Local resolution analysis.
file | blocres.cpp [code]
| Local resolution analysis.
file | bmapdist.cpp [code]
| Calculates a distance criterion between a set of 2D images or 3D maps.
file | bmark.cpp [code]
| Program to generate symmetry axes for mark group symmetries.
file | bmask.cpp [code]
| Generating and manipulating masks.
file | bmaskmod.cpp [code]
| Generating a model from a mask.
file | bmatch.cpp [code]
| Program to search an image with multiple projections and orient them.
file | bmatrix.cpp [code]
| Program to process matrices.
file | bmaxpow.cpp [code]
| Determining orientations by maximum power of 3D reconstruction from single particle images.
file | bmd.cpp [code]
| Molecular dynamics - humble beginnings.
file | bmedian.cpp [code]
| Program to filter images.
file | bmg.cpp [code]
| Manipulating project and micrograph structures.
file | bmg2imod.cpp [code]
| Converts between IMOD files and a micrograph parameter file.
file | bmgalign.cpp [code]
| Aligns micrographs specified in parameter files.
file | bmgconvert.cpp [code]
| Convert between micrograph parameter formats.
file | bmgft.cpp [code]
| Disk-based 3D reconstruction for a tomography series.
file | bmgtransfer.cpp [code]
| Transfer pieces of information between micrograph paramater files.
file | bmissing.cpp [code]
| Generating and manipulating masks.
file | bmm.cpp [code]
| A program to do model mechanics.
file | bmod2part.cpp [code]
| Converting from a pseudo-atomic model to particle parameters.
file | bmodcol.cpp [code]
| A tool to color models.
file | bmodcomp.cpp [code]
| A tool to compare polyhedra.
file | bmodedit.cpp [code]
| A tool to create and edit models.
file | bmodel.cpp [code]
| Manipulates models.
file | bmodmap.cpp [code]
| A tool to genrate a map from a model.
file | bmodmask.cpp [code]
| Generating a mask from an atomic model.
file | bmodsel.cpp [code]
| Manipulates selections from sets of components as solutions of fits.
file | bmodsym.cpp [code]
| Deals with model and component symmetries.
file | bmodview.cpp [code]
| Manipulates models.
file | bmol.cpp [code]
| A tool to edit and analyze coordinate files.
file | bmoledit.cpp [code]
| A tool to edit coordinate files.
file | bmolhel.cpp [code]
| A program to perform helical symmetry operations on coordinate files.
file | bmolsym.cpp [code]
| A tool to perform symmetry operations on coordinate files.
file | bmontage.cpp [code]
| A program to generate a montage from a 3D image or a set of 2D images.
file | bmonte.cpp [code]
| Program to use a monte carlo metroplis algorithm to energy minimize molecular positions.
file | bmultifit.cpp [code]
| Searching for a template in a map and returning multiple hits in a model.
file | bmultimask.cpp [code]
| Generating and manipulating composite masks.
file | bmultislice.cpp [code]
| Multi-slice simulation of the electron imaging process.
file | bnad.cpp [code]
| Image denoising by nonlinear anisotropic diffusion: Coherence and edge enhancing diffusion.
file | bnorm.cpp [code]
| Program to normalize a set of images based on their histograms.
file | bop.cpp [code]
| A program to operate on image pairs.
file | borient.cpp [code]
| Determines orientation angles and x,y origins of single particle images.
file | bparam.cpp [code]
| A tool to extract parameters from coordinate files.
file | bpart.cpp [code]
| Calculates centers of single particle images.
file | bpartmulti.cpp [code]
| Selection of single particle parameters from multiple files for classification.
file | bpartsel.cpp [code]
| Selection of single particles for 3D reconstruction.
file | bpatch.cpp [code]
| Program to patch tiled image files.
file | bpath.cpp [code]
| A program to analyze paths and cycles in a model.
file | bphase.cpp [code]
| A program to examine phase differences between image pairs.
file | bpick.cpp [code]
| Pick particles in a micrograph given the particle coordinates, or pick particles in a focal series of micrographs with alignment of the micrographs.
file | bplane.cpp [code]
| A tool to expand models.
file | bpoly.cpp [code]
| A tool to manipulate polyhedral coordinate files.
file | bproject.cpp [code]
| Projecting a 3D map and calculating comparison statistics of the projections.
file | bradial.cpp [code]
| Polar images and radial averages.
file | bradsec.cpp [code]
| Generates radial sections from 3D images.
file | brandom.cpp [code]
| Program to generate random images.
file | brecadd.cpp [code]
| Program to average selected reconstructions.
file | brecmod.cpp [code]
| A tool to merge data from micrograph reconstruction and model files.
file | breconstruct.cpp [code]
| 3D reconstruction from single particle images
file | brefine.cpp [code]
| Reciprocal space refinement of orientation parameters of particle images.
file | bresolve.cpp [code]
| Calculate resolution estimates and Fourier shell statistics.
file | bscale.cpp [code]
| Program to find the scaling of map with respect to a reference.
file | bsegment.cpp [code]
| Segment images into density regions.
file | bseq.cpp [code]
| A program to manipulate DNA and protein sequences.
file | bseqaln.cpp [code]
| A program to analyze aligned protein sequences.
file | bseries.cpp [code]
| Program to align and analyze series of images.
file | bsf.cpp [code]
| Calculating structure factors from atomic models.
file | bshell.cpp [code]
| Generates a shell point component model.
file | bsim.cpp [code]
| A tool to generate a project with random orientations for a molecule and to simulate TEM images from given orientations.
file | bspiral.cpp [code]
| A tool to generate polyhedra using the spiral algorithm.
file | bsplit.cpp [code]
| Program to seperate a multi-image file into individual image files.
file | bsplitmol.cpp [code]
| A program to concatenate coordinates from different files.
file | bspr.cpp [code]
| 3D reconstruction from single particle images
file | bstar.cpp [code]
| Examines STAR format files.
file | bsupix.cpp [code]
| Segment images.
file | bsurf.cpp [code]
| AFM image analysis and reconstruction.
file | bsym.cpp [code]
| Program to generate symmetry axes for point group symmetries.
file | bsymcomp.cpp [code]
| Finds the best orientation that fits a symmetrized template.
file | btile.cpp [code]
| Program to split an image into overlapping tiles.
file | btomaln.cpp [code]
| Program to do fiducialless alignment of a tilt series.
file | btomo.cpp [code]
| Program to process tomographic series of images.
file | btompart.cpp [code]
| Program to extract single particle images from a tilt series and generate individual reconstructions.
file | btomrec.cpp [code]
| Disk-based 3D reconstruction for a tomography series.
file | btomres.cpp [code]
| Program to determine the resolution of a tilt series.
file | btrack.cpp [code]
| Program to track fiducial markers in a tomographic series of images.
file | btree.cpp [code]
| Program to process trees.
file | btube.cpp [code]
| Symmetrizes helical tubes with hexagonal lattices.
file | bwater.cpp [code]
| Molecular dynamics - humble beginnings.
file | bxb.cpp [code]
| Extracting a part of a density map and building a new map.
file | bxml.cpp [code]
| Reads, writes and validates XML files.
file | bzfft.cpp [code]
| Disk-based z-line transforms for big reconstructions.
file | dcount.cpp [code]
| A program to determine the occupancy of components in models.
file | dhand.cpp [code]
| Compare projections of two oppositely handed reconstructions to images of tilted specimens.
file | dimgstats.cpp [code]
| Calculates statistical measures within a set of images or between sets of images.
file | dmerge.cpp [code]
| Merge images in a defocal or other series, align images before adding together.
file | emgrand.cpp [code]
| Generate random values for micrograph parameters.
file | jave.cpp [code]
| Program to average files and weigh the average in Real/Fourier space.
file | jpartdif.cpp [code]
| Analysis of particle differences between two starfiles.
file | jsubtomo.cpp [code]
| Finds particles (subtomograms) in a tomographic reconstruction and refines their origins and orientations.
file | jviews.cpp [code]
| Generates views covering an asymmetric unit or all symmetry related views.
file | radon.cpp [code]
| Program to do radon transforms.
file | radonrecon.cpp [code]
| Program to do radon transforms.