| BsoftDoc 1.9 Bernard's software package

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include Directory Reference

## Files
file | Bimage.h [code]
| Header file for image class.
file | binomial.h [code]
| Functions to generate and fit binomials.
file | Bmatrix.h [code]
| Matrix class.
file | Bstring.h [code]
| Header file for the string class.
file | cluster.h [code]
| Header file for clustering functions.
file | Color.h [code]
| Classes for color objects.
file | Complex.h [code]
| Class for complex numbers.
file | ctf.h [code]
| Header file for CTF (contrast transfer function) functions.
file | datatypes.h [code]
| Functions to check and convert datatypes.
file | dynamic_programming.h [code]
| Library functions for dynamic programming.
file | Euler.h [code]
| Euler object.
file | file_util.h [code]
| Header file for file checking functions.
file | img_afm.h [code]
| Header file for AFM functions.
file | img_align.h [code]
| Header file for functions to align images.
file | img_ampweigh.h [code]
| Header file for image utilities.
file | img_background.h [code]
| Header file for manipulating image backgrounds.
file | img_backproject.h [code]
| Header file for 3D reconstruction by backprojection.
file | img_colour.h [code]
| Functions to handle RGB images.
file | img_combine.h [code]
| Header file for combining two images in various ways.
file | img_complex.h [code]
| Functions to handle complex data sets.
file | img_ctf.h [code]
| Header file for CTF (contrast transfer function) functions.
file | img_diffraction.h [code]
| Library functions for analyzing diffraction patterns.
file | img_edit.h [code]
| Header file for functions for editing image contents.
file | img_extract.h [code]
| Header file for functions to extract parts of images.
file | img_feature.h [code]
| Header file for feature extraction tools.
file | img_filter.h [code]
| Header file for image utilities.
file | img_find.h [code]
| Header file for functions to find a template in an image.
file | img_fourier.h [code]
| General FFT for n-dimensional data.
file | img_graphseg.h [code]
| Header file for segmenting images into density regions using a nondirected graph.
file | img_helix.h [code]
| Dealing with images with helical symmetry.
file | img_histogram.h [code]
| Header file for image utilities.
file | img_interpolate.h [code]
file | img_mask.h [code]
| Header file for mask operation tools.
file | img_montage.h [code]
| Functions to montage images for display.
file | img_multifit.h [code]
| Header file for searching for a template in a map and returning multiple hits in a model.
file | img_multislice.h [code]
| Header file for multi-slice simulation of the electron imaging process.
file | img_nad.h [code]
| Header file for denoising by nonlinear anisotropic diffusion: Coherence and edge enhancing diffusion.
file | img_norm.h [code]
| Function to normalize a set of images based on their histograms.
file | img_pick.h [code]
| Header file for functions to pick particles in images.
file | img_polar.h [code]
| Library routines for polar and spherical transformations and calculations.
file | img_powerspectrum.h [code]
| Header file for calculating and using power spectra.
file | img_project.h [code]
| Header file for projection functions.
file | img_radial.h [code]
| Library routines for radial transformations and calculations.
file | img_random.h [code]
| Header file for functions for creating random images.
file | img_reconstruct.h [code]
| Header file for 2D and 3D reconstruction.
file | img_reflections.h [code]
| Routines to read and write HKL reflection files.
file | img_region_stats.h [code]
| Functions to calculate statistics on image regions.
file | img_rescale.h [code]
| Header file for image utilities.
file | img_resize.h [code]
| Header file for image resizing.
file | img_resolution.h [code]
| Library routines to estimate resolution.
file | img_segment.h [code]
| Header file for image segmenting functions.
file | img_stat_test.h [code]
| Functions for statistical tests.
file | img_symmetry.h [code]
| Header file for symmetry functions.
file | img_tags.h [code]
| All STAR file format tags for images.
file | img_tile_patch.h [code]
| Header file for functions to tile and patch images.
file | img_tomography.h [code]
| Header file for tomographic applications.
file | img_util.h [code]
| Header file for image utilities.
file | kernel.h [code]
| Header file for filter kernel functions.
file | linked_list.h [code]
| Header file for generalized linked list functions.
file | marker.h [code]
| Header file for image parameter functions.
file | math_util.h [code]
| Header file for general utilities.
file | matrix.h [code]
| Header file for matrix functions.
file | Matrix3.h [code]
| Class for a 3x3 matrix.
file | matrix_eigen.h [code]
| Header file for eigen analysis.
file | matrix_linear.h [code]
| Header file for matrix functions.
file | matrix_util.h [code]
file | mg_align.h [code]
| Header file for functions to align micrographs or coordinates from micrographs and apply the resultant transformation.
file | mg_class.h [code]
| Header file for classification of raw single particle images with respect to multiple models.
file | mg_ctf.h [code]
| Functions for CTF (contrast transfer function) processing.
file | mg_extract.h [code]
| Header file for functions to extract particles from micrographs.
file | mg_hand.h [code]
| Author: David Belnap.
file | mg_helix.h [code]
| Header file for functions to process helical data.
file | mg_img_proc.h [code]
| Header file for image processing from micrograph structures.
file | mg_merge.h [code]
| Header file for functions to merge images.
file | mg_multiple.h [code]
| Selection of single particle parameters from multiple files for classification.
file | mg_multislice.h [code]
| Generates and manipulates projects for multislice calculations.
file | mg_orient.h [code]
| Library routines for determining single particle orientations with respect tota reference.
file | mg_particle_select.h [code]
| Select particles.
file | mg_particles.h [code]
| Manipulates single particle images.
file | mg_pick.h [code]
| Header file for single particle picking functions.
file | mg_processing.h [code]
| Header file for micrograph processing.
file | mg_random.h [code]
| Header file for applying some randomization to parameters.
file | mg_reconstruct.h [code]
| Functions for reconstruction.
file | mg_refine.h [code]
| Reciprocal space refinement of orientation parameters of particle images.
file | mg_resolution.h [code]
| Library routines to estimate resolution.
file | mg_tags.h [code]
| All STAR and XML file format tags for micrographs and reconstructions.
file | mg_tomo_rec.h [code]
| Functions to do a tomographic reconstruction.
file | mg_tomo_resol.h [code]
| Functions to assess the resoltion of a tomographic tilt series.
file | mg_tomo_track.h [code]
| Functions to track fiducial markers in a tomographic series of images.
file | mg_tomography.h [code]
| Header file for single particle image processing in Bsoft.
file | mg_xtal.h [code]
| Header file for functions to process crystallographic data.
file | model_color.h [code]
| Functions to color models.
file | model_create.h [code]
| Library routines used for model creation.
file | model_extract_build.h [code]
| Functions to extract subvolumes and build new maps.
file | model_links.h [code]
| Library routines used for model link processing.
file | model_map.h [code]
| Header file for model to map conversions.
file | model_mask.h [code]
| Functions to generate masks from models.
file | model_mechanics.h [code]
| Functions to do molecular mechanics.
file | model_multifit.h [code]
| Header file for searching for a template in a map and returning multiple hits in a model.
file | model_neighbors.h [code]
| Functions to manipulate model component neighbors.
file | model_occupancy.h [code]
| Library routines to count components in maps.
file | model_path.h [code]
| Library routines used for model processing.
file | model_plane.h [code]
| Library routines used for plane models.
file | model_poly.h [code]
| Functions to manipulate polyhedral coordinate files.
file | model_poly_delta.h [code]
| Functions to generate deltagraph polyhedra.
file | model_poly_spiral.h [code]
| Functions to generate polyhedra using the spiral algorithm.
file | model_select.h [code]
| Header file for reading and writing atomic model files.
file | model_shell.h [code]
| Library routines used for shell model processing.
file | model_symmetry.h [code]
| Library routines used for model symmetry operations.
file | model_tags.h [code]
| All STAR and XML file format tags for models.
file | model_transform.h [code]
| Library routines used for model transformation.
file | model_util.h [code]
| Library routines used for model processing.
file | model_views.h [code]
| Library routines used for analysing model component views.
file | mol_alpha.h [code]
| Header for functions to make and analyze alpha helices.
file | mol_bonds.h [code]
| Header for molecular dynamics.
file | mol_compare.h [code]
| Library routines used to compare sets of atomic coordinates.
file | mol_edit.h [code]
| Library routines used for atomic coordinates.
file | mol_map_energy.h [code]
| Headers of functions to calculate estimates of the fitting of molecules to maps.
file | mol_md.h [code]
file | mol_monte.h [code]
| Headers of functions using a monte carlo metroplis algorithm to energy minimize molecular positions.
file | mol_param.h [code]
| Header for functions to extract parameters from coordinate files.
file | mol_symmetry.h [code]
| Library routines used for symmetry operations on atomic coordinates.
file | mol_tags.h [code]
| All STAR file format tags for molecules and molecular parameters.
file | mol_transform.h [code]
| Library routines used for atomic coordinate transformations.
file | mol_util.h [code]
| Library routines used for atomic coordinates.
file | mol_water.h [code]
file | molecule_to_map.h [code]
| Header file for functions to calculate a 3D map from atomic coordinates.
file | moving_average.h [code]
| Header file moving average calculations.
file | options.h [code]
| Header file for option handlers.
file | ps_ctf_plot.h [code]
| Header file for postscript output functions.
file | ps_marker.h [code]
| Header file for postscript tools dealing with Bmarkers.
file | ps_micrograph.h [code]
| Header file for postscript tools dealing with micrograph particle sets.
file | ps_model.h [code]
| Header file for postscript tools dealing with models.
file | ps_plot.h [code]
| Header file for postscript output functions.
file | ps_sequence.h [code]
| Header file for postscript output for sequence analysis functions.
file | ps_tree.h [code]
| Header file for writing a tree into a postcsript file.
file | ps_views.h [code]
| Header file for postscript tools dealing with views.
file | qsort_functions.h [code]
| Header file for utility functions for use in qsort calls.
file | Quaternion.h [code]
| Class for quaternions.
file | random_numbers.h [code]
file | rwASCII.h [code]
| Header file for reading and writing ASCII files.
file | rwatomprop.h [code]
| Header file for reading atom property files.
file | rwBIORAD.h [code]
| Header file for reading and writing BioRad files.
file | rwBRIX.h [code]
| Header file for reading and writing Brix files.
file | rwBrookhavenSTEM.h [code]
| Header file for reading and writing Brookhaven STEM files.
file | rwCCP4.h [code]
| Header file for reading and writing CCP4 files.
file | rwClustal.h [code]
| Header file for reading and writing Clustal sequence files.
file | rwDI.h [code]
| Header file for reading (only) Digital Instruments files.
file | rwDM.h [code]
| Header file for reading and writing DM files.
file | rwDSN6.h [code]
| Header file for reading and writing DSN6 files.
file | rwEM.h [code]
| Header file for reading and writing EM files.
file | rwEMBL.h [code]
| Header file for reading and writing EMBL sequence files.
file | rwFASTA.h [code]
| Header file for reading and writing FASTA sequence files.
file | rwFSC_XML.h [code]
| Library routines to read and write FSC curves.
file | rwGenBank.h [code]
| Header file for reading and writing GenBank sequence files.
file | rwgencode.h [code]
| Header file for reading a genetic code from a file.
file | rwGOODFORD.h [code]
| Header file for reading and writing Peter Goodford's GRID files.
file | rwGRD.h [code]
| Header file for reading and writing Basel GRD files.
file | rwGROMACS.h [code]
| Header file for reading and writing GROMACS coordinate files.
file | rwHKL.h [code]
| Header file for reading and writing HKL reflection files as images.
file | rwIMAGIC.h [code]
| Header file for reading and writing Image Science's Imagic files.
file | rwimg.h [code]
| Header file for 2D and 3D image I/O.
file | rwIP.h [code]
| Header file for reading and writing image plate reader files.
file | rwJPEG.h [code]
| Header file for reading and writing JPEG files.
file | rwkernel.h [code]
| Header file for functions to read and write kernel files.
file | rwmatrix.h [code]
| Header file for reading (and writing) matrices.
file | rwmd.h [code]
| Header to read and write molecular dynamics parameters in STAR format.
file | rwMFF.h [code]
| Header file for reading and writing the What If MFF files.
file | rwmg.h [code]
| Header file for reading and writing micrograph parameters.
file | rwmgEMX.h [code]
| Reads and writes micrograph exchange files.
file | rwmgSTAR.h [code]
| Header file for reading and writing micrograph parameters from and to the STAR format.
file | rwmgXML.h [code]
| Reads and writes micrograph XML files.
file | rwMIFF.h [code]
file | rwmodel.h [code]
| Header file for reading and writing atomic model files.
file | rwmodel_bild.h [code]
| Header file for reading and writing Chimera BILD files.
file | rwmodel_cmm.h [code]
| Header file for reading and writing Chimera marker model parameters.
file | rwmodel_mol.h [code]
| Header file for reading and writing molecular model parameters.
file | rwmodel_param.h [code]
| Header to read and write model dynamics parameters in STAR format.
file | rwmodel_star.h [code]
| Header file for reading and writing STAR model parameters.
file | rwmodel_vega.h [code]
| Header file for reading and writing Vega model parameters.
file | rwmodel_xml.h [code]
| Read and write models in XML format.
file | rwmol_star.h [code]
| Read and write molecules in STAR format.
file | rwmol_text.h [code]
| Read and write molecules in plain text.
file | rwmolecule.h [code]
| Header file for reading reflection files.
file | rwMRC.h [code]
| Header file for reading and writing MRC files.
file | rwPDB.h [code]
| Header file for reading and writing PDB coordinate files.
file | rwPhylip.h [code]
| Header file for reading and writing Phylip sequence files.
file | rwPIC.h [code]
| Header file for reading and writing PIC's BP and BQ files.
file | rwPIF.h [code]
| Header file for reading and writing PIF files.
file | rwPIR.h [code]
| Header file for reading and writing PIR sequence files.
file | rwPNG.h [code]
| Header file for reading and writing PNG files.
file | rwPNM.h [code]
| Header file for reading and writing PNM files.
file | rwPostScript.h [code]
| Header file for (reading and) writing postscript image files.
file | rwRAW.h [code]
| Header file for reading and writing Raw files.
file | rwresprop.h [code]
| Header file for reading residue property files.
file | rwSPE.h [code]
| Header file for reading and writing SPE files.
file | rwSPIDER.h [code]
| Header file for reading and writing SPIDER files.
file | rwstar.h [code]
| A header file for STAR format files.
file | rwSUPRIM.h [code]
| Header file for reading and writing SUPRIM files.
file | rwsymop.h [code]
| Header file for reading and writing symmetry operators.
file | rwTIFF.h [code]
| Header file for reading and writing TIFF files.
file | rwtree.h [code]
| Header file for reading (and writing) trees.
file | rwWAH.h [code]
| Header file for reading and writing Wayne Hendrickson coordinate files.
file | rwxml.h [code]
| Reads and writes micrograph XML files.
file | rwXPLOR.h [code]
| Header file for reading and writing XPLOR reflection files.
file | seq_align.h [code]
file | seq_analysis.h [code]
| Header file for sequence analysis functions.
file | seq_util.h [code]
| Header file for sequence utilities.
file | simplex.h [code]
| Nelder and Mead downhill simplex method for generalized parameter fitting.
file | spline.h [code]
| Header file for spline interpolation.
file | sym_tags.h [code]
| All STAR file format tags for symmetry parameters.
file | symmetry.h [code]
| Header file for general symmetry functions.
file | timer.h [code]
| Utilities for timing functions.
file | Transform.h [code]
| Class for a generalized transform object.
file | trigonometry.h [code]
| Header file for trigonometry functions.
file | UnitCell.h [code]
| Header file for unit cell functions.
file | utilities.h [code]
| Header file for general utilities.
file | Vector3.h [code]
| Class for 3-value vectors.
file | View.h [code]
| View object.