include Directory Reference

Files
file	Bgraphseg.h
	Graph segmentation classes.
file	Bimage.h
	Header file for image class.
file	binomial.h
	Functions to generate and fit binomials.
file	Bplot.h
	Header file for postscript output functions.
file	Bstring.h
	Header file for the string class.
file	Bsuperpixel.h
	Super pixel segmentation.
file	cluster.h
	Header file for clustering functions.
file	Color.h
	Classes for color objects.
file	Complex.h
	Class for complex numbers.
file	ctf.h
	Header file for CTF (contrast transfer function) functions.
file	ctf.inc
file	dose.inc
file	dynamic_programming.h
	Library functions for dynamic programming.
file	Euler.h
	Euler object.
file	fft.h
	General FFT for n-dimensional data.
file	file_util.h
	Header file for file checking functions.
file	FSI_Kernel.h
	Header file for frequency space interpolation kernel.
file	histogram.h
	Header file for calculating and fitting histograms.
file	img_combine.h
	Header file for combining two images in various ways.
file	json.h
file	linked_list.h
	Header file for generalized linked list functions.
file	marker.h
	Header file for image parameter functions.
file	math_util.h
	Header file for general utilities.
file	Matrix.h
	Generalized matrix class.
file	Matrix3.h
	3x3 Matrix manipulation functions
file	matrix_linear.h
	Header file for matrix functions.
file	matrix_util.h
	Utility functions for matrices.
file	mdoc.h
file	mg_align.h
	Header file for functions to align micrographs or coordinates from micrographs and apply the resultant transformation.
file	mg_class.h
	Header file for classification of raw single particle images with respect to multiple models.
file	mg_ctf.h
	Functions for CTF (contrast transfer function) processing.
file	mg_ctf_fit.h
	Header file for CTF (contrast transfer function) functions.
file	mg_ctf_focal.h
	Header file for CTF (contrast transfer function) functions.
file	mg_ctf_sim.h
	Header file for functions to simulate tilted micrographs.
file	mg_extract.h
	Header file for functions to extract particles from micrographs.
file	mg_hand.h
	Author: David Belnap.
file	mg_helix.h
	Header file for functions to process helical data.
file	mg_img_proc.h
	Header file for image processing from micrograph structures.
file	mg_marker.h
	Header file for micrograph marker functions.
file	mg_merge.h
	Header file for functions to merge images.
file	mg_multiple.h
	Selection of single particle parameters from multiple files for classification.
file	mg_multislice.h
	Generates and manipulates projects for multislice calculations.
file	mg_orient.h
	Library routines for single particle analysis.
file	mg_particle_select.h
	Select particles.
file	mg_particles.h
	Manipulates single particle images.
file	mg_pick.h
	Header file for single particle picking functions.
file	mg_processing.h
	Header file for micrograph processing.
file	mg_random.h
	Header file for applying some randomization to parameters.
file	mg_reconstruct.h
	Functions for reconstruction.
file	mg_refine.h
	Reciprocal space refinement of orientation parameters of particle images.
file	mg_select.h
	Header file for micrograph processing.
file	mg_subtomo.h
	Header file for functions finding particles (subtomograms) in a tomogram.
file	mg_tags.h
	All STAR and XML file format tags for micrographs and reconstructions.
file	mg_tomo_rec.h
	Functions to do a tomographic reconstruction.
file	mg_tomo_resol.h
	Functions to assess the resoltion of a tomographic tilt series.
file	mg_tomo_track.h
	Functions to track fiducial markers in a tomographic series of images.
file	mg_tomography.h
	Header file for single particle image processing in Bsoft.
file	mg_xtal.h
	Header file for functions to process crystallographic data.
file	model_color.h
	Functions to color models.
file	model_compare.h
	Functions to compare models and components.
file	model_create.h
	Library routines used for model creation.
file	model_extract_build.h
	Functions to extract subvolumes and build new maps.
file	model_links.h
	Library routines used for model link processing.
file	model_map.h
	Header file for model to map conversions.
file	model_mask.h
	Functions to generate masks from models.
file	model_mechanics.h
	Functions to do molecular mechanics.
file	model_mol.h
	Library routines for processing molecular models.
file	model_multifit.h
	Header file for searching for a template in a map and returning multiple hits in a model.
file	model_neighbors.h
	Functions to manipulate model component neighbors.
file	model_occupancy.h
	Library routines to count components in maps.
file	model_path.h
	Library routines used for model processing.
file	model_plane.h
	Library routines used for plane models.
file	model_poly.h
	Functions to manipulate polyhedral coordinate files.
file	model_poly_delta.h
	Functions to generate deltagraph polyhedra.
file	model_poly_spiral.h
	Functions to generate polyhedra using the spiral algorithm.
file	model_select.h
	Header file for reading and writing atomic model files.
file	model_shell.h
	Library routines used for shell model processing.
file	model_symmetry.h
	Library routines used for model symmetry operations.
file	model_tags.h
	All STAR and XML file format tags for models.
file	model_transform.h
	Library routines used for model transformation.
file	model_util.h
	Library routines used for model processing.
file	model_views.h
	Library routines used for analysing model component views.
file	mol_alpha.h
	Header for functions to make and analyze alpha helices.
file	mol_bonds.h
	Header for molecular dynamics.
file	mol_compare.h
	Library routines used to compare sets of atomic coordinates.
file	mol_edit.h
	Library routines used for atomic coordinates.
file	mol_map_energy.h
	Headers of functions to calculate estimates of the fitting of molecules to maps.
file	mol_md.h
	Header for molecular dynamics.
file	mol_monte.h
	Headers of functions using a monte carlo metroplis algorithm to energy minimize molecular positions.
file	mol_param.h
	Header for functions to extract parameters from coordinate files.
file	mol_select.h
	Library routines to select atomic coordinates.
file	mol_symmetry.h
	Library routines used for symmetry operations on atomic coordinates.
file	mol_tags.h
	All STAR file format tags for molecules and molecular parameters.
file	mol_transform.h
	Library routines used for atomic coordinate transformations.
file	mol_util.h
	Library routines used for atomic coordinates.
file	mol_water.h
	Generating and managing water.
file	molecule_to_map.h
	Header file for functions to calculate a 3D map from atomic coordinates.
file	moving_average.h
	Header file moving average calculations.
file	options.h
	Header file for option handlers.
file	ps_ctf_plot.h
	Header file for postscript output functions.
file	ps_marker.h
	Header file for postscript tools dealing with Bmarkers.
file	ps_micrograph.h
	Header file for postscript tools dealing with micrograph particle sets.
file	ps_model.h
	Header file for postscript tools dealing with models.
file	ps_plot.h
	Header file for postscript output functions.
file	ps_sequence.h
	Header file for postscript output for sequence analysis functions.
file	ps_tree.h
	Header file for writing a tree into a postcsript file.
file	ps_views.h
	Header file for postscript tools dealing with views.
file	qsort_functions.h
	Header file for utility functions for use in qsort calls.
file	Quaternion.h
	Class for quaternions.
file	random_numbers.h
	Header file for functions for creating random images.
file	rwASCII.h
	Header file for reading and writing ASCII files.
file	rwatomprop.h
	Header file for reading atom property files.
file	rwBCR.h
	Header file for reading and writing AFM BCR-STM files.
file	rwBIORAD.h
	Header file for reading and writing BioRad files.
file	rwBRIX.h
	Header file for reading and writing Brix files.
file	rwBrookhavenSTEM.h
	Header file for reading and writing Brookhaven STEM files.
file	rwCCP4.h
	Header file for reading and writing CCP4 files.
file	rwClustal.h
	Header file for reading and writing Clustal sequence files.
file	rwDI.h
	Header file for reading (only) Digital Instruments files.
file	rwDM.h
	Header file for reading and writing DM files.
file	rwDSN6.h
	Header file for reading and writing DSN6 files.
file	rwDX.h
	Header file for reading and writing OpenDX files.
file	rwEER.h
	Header file for reading EER files.
file	rwEM.h
	Header file for reading and writing EM files.
file	rwEMBL.h
	Header file for reading and writing EMBL sequence files.
file	rwFASTA.h
	Header file for reading and writing FASTA sequence files.
file	rwFSC_XML.h
	Library routines to read and write FSC curves.
file	rwGenBank.h
	Header file for reading and writing GenBank sequence files.
file	rwgencode.h
	Header file for reading a genetic code from a file.
file	rwGOODFORD.h
	Header file for reading and writing Peter Goodford's GRID files.
file	rwGRD.h
	Header file for reading and writing Basel GRD files.
file	rwGROMACS.h
	Header file for reading and writing GROMACS coordinate files.
file	rwHKL.h
	Header file for reading and writing HKL reflection files as images.
file	rwIMAGIC.h
	Header file for reading and writing Image Science's Imagic files.
file	rwimg.h
	Header file for 2D and 3D image I/O.
file	rwIP.h
	Header file for reading and writing image plate reader files.
file	rwJPEG.h
	Header file for reading and writing JPEG files.
file	rwkernel.h
	Header file for functions to read and write kernel files.
file	rwmatrix.h
	Header file for reading (and writing) matrices.
file	rwmd.h
	Header to read and write molecular dynamics parameters in STAR format.
file	rwMFF.h
	Header file for reading and writing the What If MFF files.
file	rwmg.h
	Header file for reading and writing micrograph parameters.
file	rwmgEMX.h
	Reads and writes micrograph exchange files.
file	rwmgIMOD.h
	Converts between IMOD files and a micrograph parameter file.
file	rwmgRELION.h
	Header file for reading and writing micrograph parameters from and to the RELION STAR format.
file	rwmgSerialEM.h
	Converts between SerialEM MDOC files and a micrograph parameter file.
file	rwmgSTAR.h
	Header file for reading and writing micrograph parameters from and to the STAR format.
file	rwmgXML.h
	Reads and writes micrograph XML files.
file	rwMIFF.h
file	rwmodel.h
	Header file for reading and writing atomic model files.
file	rwmodel_bild.h
	Header file for reading and writing Chimera BILD files.
file	rwmodel_cif.h
	Read and write molecules in CIF format.
file	rwmodel_cmm.h
	Header file for reading and writing Chimera marker model parameters.
file	rwmodel_mol.h
	Header file for reading and writing molecular model parameters.
file	rwmodel_param.h
	Header to read and write model dynamics parameters in STAR format.
file	rwmodel_pdb.h
	Header file for reading and writing molecular model parameters.
file	rwmodel_star.h
	Header file for reading and writing STAR model parameters.
file	rwmodel_vega.h
	Header file for reading and writing Vega model parameters.
file	rwmodel_xml.h
	Read and write models in XML format.
file	rwmodel_xyz.h
	Header file for reading and writing Kirkland's xyz atomic model parameters.
file	rwmol_star.h
	Read and write molecules in STAR format.
file	rwmol_text.h
	Read and write molecules in plain text.
file	rwmolecule.h
	Header file for reading reflection files.
file	rwMRC.h
	Header file for reading and writing MRC files.
file	rwND2.h
	Header file for reading Nikon ND2 files.
file	rwPDB.h
	Header file for reading and writing PDB coordinate files.
file	rwPhylip.h
	Header file for reading and writing Phylip sequence files.
file	rwPIC.h
	Header file for reading and writing PIC's BP and BQ files.
file	rwPIF.h
	Header file for reading and writing PIF files.
file	rwPIR.h
	Header file for reading and writing PIR sequence files.
file	rwPNG.h
	Header file for reading and writing PNG files.
file	rwPNM.h
	Header file for reading and writing PNM files.
file	rwPostScript.h
	Header file for (reading and) writing postscript image files.
file	rwRAW.h
	Header file for reading and writing Raw files.
file	rwresprop.h
	Header file for reading residue property files.
file	rwSER.h
	Header file for reading and writing FEI Ser files.
file	rwSitus.h
	Header file for reading and writing Situs files.
file	rwSPE.h
	Header file for reading and writing SPE files.
file	rwSPIDER.h
	Header file for reading and writing SPIDER files.
file	rwstar.h
	A header file for STAR format files.
file	rwSUPRIM.h
	Header file for reading and writing SUPRIM files.
file	rwsymop.h
	Header file for reading and writing symmetry operators.
file	rwTGA.h
	Header file for reading and writing Truevision TGA files.
file	rwTIFF.h
	Header file for reading and writing TIFF files.
file	rwtree.h
	Header file for reading (and writing) trees.
file	rwWAH.h
	Header file for reading and writing Wayne Hendrickson coordinate files.
file	rwxml.h
	Reads and writes micrograph XML files.
file	rwXPLOR.h
	Header file for reading and writing XPLOR reflection files.
file	scatter.h
	Functions for calculating electron scattering profiles.
file	seq_align.h
	Header file for functions to generate and analyze dot plots.
file	seq_analysis.h
	Header file for sequence analysis functions.
file	seq_util.h
	Header file for sequence utilities.
file	simplex.h
	Nelder and Mead downhill simplex method for generalized parameter fitting.
file	spline.h
	Header file for spline interpolation.
file	star.h
file	string_util.h
file	sym_tags.h
	All STAR file format tags for symmetry parameters.
file	symmetry.h
	Header file for general symmetry functions.
file	timer.h
	Utilities for timing functions.
file	Transform.h
	Class for a generalized transform object.
file	TrigLUT.h
	Trigonometric look-up tables.
file	UnitCell.h
	Header file for unit cell functions.
file	use_ctf.inc
file	use_dose.inc
file	utilities.h
	Header file for general utilities.
file	Vector3.h
	Class for 3-value vectors.
file	versions.h
	Library functions to encode versions of all included packages.
file	View.h
	View object.
file	View2.h
file	zernike.h
	A class for handling Zernike polynomials.