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<section xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink" xml:id="_dir_d44c64559bbebec7f509842c48db8b23">
<title>/Users/bernard/b20/bsoft/include Directory Reference</title>
<indexterm><primary>/Users/bernard/b20/bsoft/include Directory Reference</primary></indexterm>
<simplesect>
    <title>Files    </title>
        <itemizedlist>
            <listitem><para>file <link linkend="__bimage_8h">Bimage.h</link></para>

<para>Header file for image class. </para>
</listitem>
            <listitem><para>file <link linkend="_binomial_8h">binomial.h</link></para>

<para>Functions to generate and fit binomials. </para>
</listitem>
            <listitem><para>file <link linkend="__bplot_8h">Bplot.h</link></para>

<para>Header file for postscript output functions. </para>
</listitem>
            <listitem><para>file <link linkend="__bstring_8h">Bstring.h</link></para>

<para>Header file for the string class. </para>
</listitem>
            <listitem><para>file <link linkend="__bsuperpixel_8h">Bsuperpixel.h</link></para>

<para>Super pixel segmentation. </para>
</listitem>
            <listitem><para>file <link linkend="_cluster_8h">cluster.h</link></para>

<para>Header file for clustering functions. </para>
</listitem>
            <listitem><para>file <link linkend="__color_8h">Color.h</link></para>

<para>Classes for color objects. </para>
</listitem>
            <listitem><para>file <link linkend="__complex_8h">Complex.h</link></para>

<para>Class for complex numbers. </para>
</listitem>
            <listitem><para>file <link linkend="_ctf_8h">ctf.h</link></para>

<para>Header file for CTF (contrast transfer function) functions. </para>
</listitem>
            <listitem><para>file <link linkend="_dynamic__programming_8h">dynamic_programming.h</link></para>

<para>Library functions for dynamic programming. </para>
</listitem>
            <listitem><para>file <link linkend="__euler_8h">Euler.h</link></para>

<para><link linkend="_class_euler">Euler</link> object. </para>
</listitem>
            <listitem><para>file <link linkend="_fft_8h">fft.h</link></para>

<para>General FFT for n-dimensional data. </para>
</listitem>
            <listitem><para>file <link linkend="_file__util_8h">file_util.h</link></para>

<para>Header file for file checking functions. </para>
</listitem>
            <listitem><para>file <link linkend="__f_s_i___kernel_8h">FSI_Kernel.h</link></para>

<para>Header file for frequency space interpolation kernel. </para>
</listitem>
            <listitem><para>file <link linkend="_img__combine_8h">img_combine.h</link></para>

<para>Header file for combining two images in various ways. </para>
</listitem>
            <listitem><para>file <link linkend="_json_8h">json.h</link></para>
</listitem>
            <listitem><para>file <link linkend="_linked__list_8h">linked_list.h</link></para>

<para>Header file for generalized linked list functions. </para>
</listitem>
            <listitem><para>file <link linkend="_marker_8h">marker.h</link></para>

<para>Header file for image parameter functions. </para>
</listitem>
            <listitem><para>file <link linkend="_math__util_8h">math_util.h</link></para>

<para>Header file for general utilities. </para>
</listitem>
            <listitem><para>file <link linkend="__matrix_8h">Matrix.h</link></para>

<para>Generalized matrix class. </para>
</listitem>
            <listitem><para>file <link linkend="__matrix3_8h">Matrix3.h</link></para>

<para>3x3 <link linkend="_class_matrix">Matrix</link> manipulation functions </para>
</listitem>
            <listitem><para>file <link linkend="_matrix__linear_8h">matrix_linear.h</link></para>

<para>Header file for matrix functions. </para>
</listitem>
            <listitem><para>file <link linkend="_matrix__util_8h">matrix_util.h</link></para>

<para>Utility functions for matrices. </para>
</listitem>
            <listitem><para>file <link linkend="_mdoc_8h">mdoc.h</link></para>
</listitem>
            <listitem><para>file <link linkend="_mg__align_8h">mg_align.h</link></para>

<para>Header file for functions to align micrographs or coordinates from micrographs and apply the resultant transformation. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__class_8h">mg_class.h</link></para>

<para>Header file for classification of raw single particle images with respect to multiple models. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__ctf_8h">mg_ctf.h</link></para>

<para>Functions for CTF (contrast transfer function) processing. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__ctf__fit_8h">mg_ctf_fit.h</link></para>

<para>Header file for CTF (contrast transfer function) functions. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__extract_8h">mg_extract.h</link></para>

<para>Header file for functions to extract particles from micrographs. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__hand_8h">mg_hand.h</link></para>

<para>Author: David Belnap. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__helix_8h">mg_helix.h</link></para>

<para>Header file for functions to process helical data. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__img__proc_8h">mg_img_proc.h</link></para>

<para>Header file for image processing from micrograph structures. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__marker_8h">mg_marker.h</link></para>

<para>Header file for micrograph marker functions. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__merge_8h">mg_merge.h</link></para>

<para>Header file for functions to merge images. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__multiple_8h">mg_multiple.h</link></para>

<para>Selection of single particle parameters from multiple files for classification. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__multislice_8h">mg_multislice.h</link></para>

<para>Generates and manipulates projects for multislice calculations. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__orient_8h">mg_orient.h</link></para>

<para>Library routines for single particle analysis. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__particle__select_8h">mg_particle_select.h</link></para>

<para>Select particles. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__particles_8h">mg_particles.h</link></para>

<para>Manipulates single particle images. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__pick_8h">mg_pick.h</link></para>

<para>Header file for single particle picking functions. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__processing_8h">mg_processing.h</link></para>

<para>Header file for micrograph processing. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__random_8h">mg_random.h</link></para>

<para>Header file for applying some randomization to parameters. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__reconstruct_8h">mg_reconstruct.h</link></para>

<para>Functions for reconstruction. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__refine_8h">mg_refine.h</link></para>

<para>Reciprocal space refinement of orientation parameters of particle images. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__subtomo_8h">mg_subtomo.h</link></para>

<para>Header file for functions finding particles (subtomograms) in a tomogram. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__tags_8h">mg_tags.h</link></para>

<para>All STAR and XML file format tags for micrographs and reconstructions. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__tomo__rec_8h">mg_tomo_rec.h</link></para>

<para>Functions to do a tomographic reconstruction. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__tomo__resol_8h">mg_tomo_resol.h</link></para>

<para>Functions to assess the resoltion of a tomographic tilt series. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__tomo__track_8h">mg_tomo_track.h</link></para>

<para>Functions to track fiducial markers in a tomographic series of images. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__tomography_8h">mg_tomography.h</link></para>

<para>Header file for single particle image processing in Bsoft. </para>
</listitem>
            <listitem><para>file <link linkend="_mg__xtal_8h">mg_xtal.h</link></para>

<para>Header file for functions to process crystallographic data. </para>
</listitem>
            <listitem><para>file <link linkend="_model__color_8h">model_color.h</link></para>

<para>Functions to color models. </para>
</listitem>
            <listitem><para>file <link linkend="_model__compare_8h">model_compare.h</link></para>

<para>Functions to compare models and components. </para>
</listitem>
            <listitem><para>file <link linkend="_model__create_8h">model_create.h</link></para>

<para>Library routines used for model creation. </para>
</listitem>
            <listitem><para>file <link linkend="_model__extract__build_8h">model_extract_build.h</link></para>

<para>Functions to extract subvolumes and build new maps. </para>
</listitem>
            <listitem><para>file <link linkend="_model__links_8h">model_links.h</link></para>

<para>Library routines used for model link processing. </para>
</listitem>
            <listitem><para>file <link linkend="_model__map_8h">model_map.h</link></para>

<para>Header file for model to map conversions. </para>
</listitem>
            <listitem><para>file <link linkend="_model__mask_8h">model_mask.h</link></para>

<para>Functions to generate masks from models. </para>
</listitem>
            <listitem><para>file <link linkend="_model__mechanics_8h">model_mechanics.h</link></para>

<para>Functions to do molecular mechanics. </para>
</listitem>
            <listitem><para>file <link linkend="_model__multifit_8h">model_multifit.h</link></para>

<para>Header file for searching for a template in a map and returning multiple hits in a model. </para>
</listitem>
            <listitem><para>file <link linkend="_model__neighbors_8h">model_neighbors.h</link></para>

<para>Functions to manipulate model component neighbors. </para>
</listitem>
            <listitem><para>file <link linkend="_model__occupancy_8h">model_occupancy.h</link></para>

<para>Library routines to count components in maps. </para>
</listitem>
            <listitem><para>file <link linkend="_model__path_8h">model_path.h</link></para>

<para>Library routines used for model processing. </para>
</listitem>
            <listitem><para>file <link linkend="_model__plane_8h">model_plane.h</link></para>

<para>Library routines used for plane models. </para>
</listitem>
            <listitem><para>file <link linkend="_model__poly_8h">model_poly.h</link></para>

<para>Functions to manipulate polyhedral coordinate files. </para>
</listitem>
            <listitem><para>file <link linkend="_model__poly__delta_8h">model_poly_delta.h</link></para>

<para>Functions to generate deltagraph polyhedra. </para>
</listitem>
            <listitem><para>file <link linkend="_model__poly__spiral_8h">model_poly_spiral.h</link></para>

<para>Functions to generate polyhedra using the spiral algorithm. </para>
</listitem>
            <listitem><para>file <link linkend="_model__select_8h">model_select.h</link></para>

<para>Header file for reading and writing atomic model files. </para>
</listitem>
            <listitem><para>file <link linkend="_model__shell_8h">model_shell.h</link></para>

<para>Library routines used for shell model processing. </para>
</listitem>
            <listitem><para>file <link linkend="_model__symmetry_8h">model_symmetry.h</link></para>

<para>Library routines used for model symmetry operations. </para>
</listitem>
            <listitem><para>file <link linkend="_model__tags_8h">model_tags.h</link></para>

<para>All STAR and XML file format tags for models. </para>
</listitem>
            <listitem><para>file <link linkend="_model__transform_8h">model_transform.h</link></para>

<para>Library routines used for model transformation. </para>
</listitem>
            <listitem><para>file <link linkend="_model__util_8h">model_util.h</link></para>

<para>Library routines used for model processing. </para>
</listitem>
            <listitem><para>file <link linkend="_model__views_8h">model_views.h</link></para>

<para>Library routines used for analysing model component views. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__alpha_8h">mol_alpha.h</link></para>

<para>Header for functions to make and analyze alpha helices. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__bonds_8h">mol_bonds.h</link></para>

<para>Header for molecular dynamics. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__compare_8h">mol_compare.h</link></para>

<para>Library routines used to compare sets of atomic coordinates. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__edit_8h">mol_edit.h</link></para>

<para>Library routines used for atomic coordinates. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__map__energy_8h">mol_map_energy.h</link></para>

<para>Headers of functions to calculate estimates of the fitting of molecules to maps. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__md_8h">mol_md.h</link></para>

<para>Header for molecular dynamics. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__monte_8h">mol_monte.h</link></para>

<para>Headers of functions using a monte carlo metroplis algorithm to energy minimize molecular positions. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__param_8h">mol_param.h</link></para>

<para>Header for functions to extract parameters from coordinate files. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__select_8h">mol_select.h</link></para>

<para>Library routines to select atomic coordinates. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__symmetry_8h">mol_symmetry.h</link></para>

<para>Library routines used for symmetry operations on atomic coordinates. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__tags_8h">mol_tags.h</link></para>

<para>All STAR file format tags for molecules and molecular parameters. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__transform_8h">mol_transform.h</link></para>

<para>Library routines used for atomic coordinate transformations. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__util_8h">mol_util.h</link></para>

<para>Library routines used for atomic coordinates. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__water_8h">mol_water.h</link></para>

<para>Generating and managing water. </para>
</listitem>
            <listitem><para>file <link linkend="_molecule__to__map_8h">molecule_to_map.h</link></para>

<para>Header file for functions to calculate a 3D map from atomic coordinates. </para>
</listitem>
            <listitem><para>file <link linkend="_moving__average_8h">moving_average.h</link></para>

<para>Header file moving average calculations. </para>
</listitem>
            <listitem><para>file <link linkend="_options_8h">options.h</link></para>

<para>Header file for option handlers. </para>
</listitem>
            <listitem><para>file <link linkend="_ps__ctf__plot_8h">ps_ctf_plot.h</link></para>

<para>Header file for postscript output functions. </para>
</listitem>
            <listitem><para>file <link linkend="_ps__marker_8h">ps_marker.h</link></para>

<para>Header file for postscript tools dealing with Bmarkers. </para>
</listitem>
            <listitem><para>file <link linkend="_ps__micrograph_8h">ps_micrograph.h</link></para>

<para>Header file for postscript tools dealing with micrograph particle sets. </para>
</listitem>
            <listitem><para>file <link linkend="_ps__model_8h">ps_model.h</link></para>

<para>Header file for postscript tools dealing with models. </para>
</listitem>
            <listitem><para>file <link linkend="_ps__plot_8h">ps_plot.h</link></para>

<para>Header file for postscript output functions. </para>
</listitem>
            <listitem><para>file <link linkend="_ps__sequence_8h">ps_sequence.h</link></para>

<para>Header file for postscript output for sequence analysis functions. </para>
</listitem>
            <listitem><para>file <link linkend="_ps__tree_8h">ps_tree.h</link></para>

<para>Header file for writing a tree into a postcsript file. </para>
</listitem>
            <listitem><para>file <link linkend="_ps__views_8h">ps_views.h</link></para>

<para>Header file for postscript tools dealing with views. </para>
</listitem>
            <listitem><para>file <link linkend="_qsort__functions_8h">qsort_functions.h</link></para>

<para>Header file for utility functions for use in qsort calls. </para>
</listitem>
            <listitem><para>file <link linkend="__quaternion_8h">Quaternion.h</link></para>

<para>Class for quaternions. </para>
</listitem>
            <listitem><para>file <link linkend="_random__numbers_8h">random_numbers.h</link></para>

<para>Header file for functions for creating random images. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_a_s_c_i_i_8h">rwASCII.h</link></para>

<para>Header file for reading and writing ASCII files. </para>
</listitem>
            <listitem><para>file <link linkend="_rwatomprop_8h">rwatomprop.h</link></para>

<para>Header file for reading atom property files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_b_c_r_8h">rwBCR.h</link></para>

<para>Header file for reading and writing AFM BCR-STM files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_b_i_o_r_a_d_8h">rwBIORAD.h</link></para>

<para>Header file for reading and writing BioRad files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_b_r_i_x_8h">rwBRIX.h</link></para>

<para>Header file for reading and writing Brix files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_brookhaven_s_t_e_m_8h">rwBrookhavenSTEM.h</link></para>

<para>Header file for reading and writing Brookhaven STEM files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_c_c_p4_8h">rwCCP4.h</link></para>

<para>Header file for reading and writing CCP4 files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_clustal_8h">rwClustal.h</link></para>

<para>Header file for reading and writing Clustal sequence files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_d_i_8h">rwDI.h</link></para>

<para>Header file for reading (only) Digital Instruments files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_d_m_8h">rwDM.h</link></para>

<para>Header file for reading and writing DM files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_d_s_n6_8h">rwDSN6.h</link></para>

<para>Header file for reading and writing DSN6 files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_d_x_8h">rwDX.h</link></para>

<para>Header file for reading and writing OpenDX files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_e_m_8h">rwEM.h</link></para>

<para>Header file for reading and writing EM files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_e_m_b_l_8h">rwEMBL.h</link></para>

<para>Header file for reading and writing EMBL sequence files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_f_a_s_t_a_8h">rwFASTA.h</link></para>

<para>Header file for reading and writing FASTA sequence files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_f_s_c___x_m_l_8h">rwFSC_XML.h</link></para>

<para>Library routines to read and write FSC curves. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_gen_bank_8h">rwGenBank.h</link></para>

<para>Header file for reading and writing GenBank sequence files. </para>
</listitem>
            <listitem><para>file <link linkend="_rwgencode_8h">rwgencode.h</link></para>

<para>Header file for reading a genetic code from a file. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_g_o_o_d_f_o_r_d_8h">rwGOODFORD.h</link></para>

<para>Header file for reading and writing Peter Goodford&apos;s GRID files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_g_r_d_8h">rwGRD.h</link></para>

<para>Header file for reading and writing Basel GRD files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_g_r_o_m_a_c_s_8h">rwGROMACS.h</link></para>

<para>Header file for reading and writing GROMACS coordinate files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_h_k_l_8h">rwHKL.h</link></para>

<para>Header file for reading and writing HKL reflection files as images. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_i_m_a_g_i_c_8h">rwIMAGIC.h</link></para>

<para>Header file for reading and writing Image Science&apos;s Imagic files. </para>
</listitem>
            <listitem><para>file <link linkend="_rwimg_8h">rwimg.h</link></para>

<para>Header file for 2D and 3D image I/O. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_i_p_8h">rwIP.h</link></para>

<para>Header file for reading and writing image plate reader files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_j_p_e_g_8h">rwJPEG.h</link></para>

<para>Header file for reading and writing JPEG files. </para>
</listitem>
            <listitem><para>file <link linkend="_rwkernel_8h">rwkernel.h</link></para>

<para>Header file for functions to read and write kernel files. </para>
</listitem>
            <listitem><para>file <link linkend="_rwmatrix_8h">rwmatrix.h</link></para>

<para>Header file for reading (and writing) matrices. </para>
</listitem>
            <listitem><para>file <link linkend="_rwmd_8h">rwmd.h</link></para>

<para>Header to read and write molecular dynamics parameters in STAR format. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_m_f_f_8h">rwMFF.h</link></para>

<para>Header file for reading and writing the What If MFF files. </para>
</listitem>
            <listitem><para>file <link linkend="_rwmg_8h">rwmg.h</link></para>

<para>Header file for reading and writing micrograph parameters. </para>
</listitem>
            <listitem><para>file <link linkend="_rwmg_e_m_x_8h">rwmgEMX.h</link></para>

<para>Reads and writes micrograph exchange files. </para>
</listitem>
            <listitem><para>file <link linkend="_rwmg_i_m_o_d_8h">rwmgIMOD.h</link></para>

<para>Converts between <link linkend="_struct_i_m_o_d">IMOD</link> files and a micrograph parameter file. </para>
</listitem>
            <listitem><para>file <link linkend="_rwmg_r_e_l_i_o_n_8h">rwmgRELION.h</link></para>

<para>Header file for reading and writing micrograph parameters from and to the RELION STAR format. </para>
</listitem>
            <listitem><para>file <link linkend="_rwmg_serial_e_m_8h">rwmgSerialEM.h</link></para>

<para>Converts between SerialEM MDOC files and a micrograph parameter file. </para>
</listitem>
            <listitem><para>file <link linkend="_rwmg_s_t_a_r_8h">rwmgSTAR.h</link></para>

<para>Header file for reading and writing micrograph parameters from and to the STAR format. </para>
</listitem>
            <listitem><para>file <link linkend="_rwmg_x_m_l_8h">rwmgXML.h</link></para>

<para>Reads and writes micrograph XML files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_m_i_f_f_8h">rwMIFF.h</link></para>
</listitem>
            <listitem><para>file <link linkend="_rwmodel_8h">rwmodel.h</link></para>

<para>Header file for reading and writing atomic model files. </para>
</listitem>
            <listitem><para>file <link linkend="_rwmodel__bild_8h">rwmodel_bild.h</link></para>

<para>Header file for reading and writing Chimera BILD files. </para>
</listitem>
            <listitem><para>file <link linkend="_rwmodel__cmm_8h">rwmodel_cmm.h</link></para>

<para>Header file for reading and writing Chimera marker model parameters. </para>
</listitem>
            <listitem><para>file <link linkend="_rwmodel__mol_8h">rwmodel_mol.h</link></para>

<para>Header file for reading and writing molecular model parameters. </para>
</listitem>
            <listitem><para>file <link linkend="_rwmodel__param_8h">rwmodel_param.h</link></para>

<para>Header to read and write model dynamics parameters in STAR format. </para>
</listitem>
            <listitem><para>file <link linkend="_rwmodel__star_8h">rwmodel_star.h</link></para>

<para>Header file for reading and writing STAR model parameters. </para>
</listitem>
            <listitem><para>file <link linkend="_rwmodel__vega_8h">rwmodel_vega.h</link></para>

<para>Header file for reading and writing Vega model parameters. </para>
</listitem>
            <listitem><para>file <link linkend="_rwmodel__xml_8h">rwmodel_xml.h</link></para>

<para>Read and write models in XML format. </para>
</listitem>
            <listitem><para>file <link linkend="_rwmol__star_8h">rwmol_star.h</link></para>

<para>Read and write molecules in STAR format. </para>
</listitem>
            <listitem><para>file <link linkend="_rwmol__text_8h">rwmol_text.h</link></para>

<para>Read and write molecules in plain text. </para>
</listitem>
            <listitem><para>file <link linkend="_rwmolecule_8h">rwmolecule.h</link></para>

<para>Header file for reading reflection files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_m_r_c_8h">rwMRC.h</link></para>

<para>Header file for reading and writing MRC files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_p_d_b_8h">rwPDB.h</link></para>

<para>Header file for reading and writing PDB coordinate files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_phylip_8h">rwPhylip.h</link></para>

<para>Header file for reading and writing Phylip sequence files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_p_i_c_8h">rwPIC.h</link></para>

<para>Header file for reading and writing PIC&apos;s BP and BQ files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_p_i_f_8h">rwPIF.h</link></para>

<para>Header file for reading and writing PIF files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_p_i_r_8h">rwPIR.h</link></para>

<para>Header file for reading and writing PIR sequence files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_p_n_g_8h">rwPNG.h</link></para>

<para>Header file for reading and writing PNG files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_p_n_m_8h">rwPNM.h</link></para>

<para>Header file for reading and writing PNM files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_post_script_8h">rwPostScript.h</link></para>

<para>Header file for (reading and) writing postscript image files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_r_a_w_8h">rwRAW.h</link></para>

<para>Header file for reading and writing Raw files. </para>
</listitem>
            <listitem><para>file <link linkend="_rwresprop_8h">rwresprop.h</link></para>

<para>Header file for reading residue property files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_s_e_r_8h">rwSER.h</link></para>

<para>Header file for reading and writing FEI Ser files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_situs_8h">rwSitus.h</link></para>

<para>Header file for reading and writing Situs files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_s_p_e_8h">rwSPE.h</link></para>

<para>Header file for reading and writing SPE files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_s_p_i_d_e_r_8h">rwSPIDER.h</link></para>

<para>Header file for reading and writing SPIDER files. </para>
</listitem>
            <listitem><para>file <link linkend="_rwstar_8h">rwstar.h</link></para>

<para>A header file for STAR format files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_s_u_p_r_i_m_8h">rwSUPRIM.h</link></para>

<para>Header file for reading and writing SUPRIM files. </para>
</listitem>
            <listitem><para>file <link linkend="_rwsymop_8h">rwsymop.h</link></para>

<para>Header file for reading and writing symmetry operators. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_t_g_a_8h">rwTGA.h</link></para>

<para>Header file for reading and writing Truevision TGA files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_t_i_f_f_8h">rwTIFF.h</link></para>

<para>Header file for reading and writing TIFF files. </para>
</listitem>
            <listitem><para>file <link linkend="_rwtree_8h">rwtree.h</link></para>

<para>Header file for reading (and writing) trees. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_w_a_h_8h">rwWAH.h</link></para>

<para>Header file for reading and writing Wayne Hendrickson coordinate files. </para>
</listitem>
            <listitem><para>file <link linkend="_rwxml_8h">rwxml.h</link></para>

<para>Reads and writes micrograph XML files. </para>
</listitem>
            <listitem><para>file <link linkend="_rw_x_p_l_o_r_8h">rwXPLOR.h</link></para>

<para>Header file for reading and writing XPLOR reflection files. </para>
</listitem>
            <listitem><para>file <link linkend="_seq__align_8h">seq_align.h</link></para>

<para>Header file for functions to generate and analyze dot plots. </para>
</listitem>
            <listitem><para>file <link linkend="_seq__analysis_8h">seq_analysis.h</link></para>

<para>Header file for sequence analysis functions. </para>
</listitem>
            <listitem><para>file <link linkend="_seq__util_8h">seq_util.h</link></para>

<para>Header file for sequence utilities. </para>
</listitem>
            <listitem><para>file <link linkend="_simplex_8h">simplex.h</link></para>

<para>Nelder and Mead downhill simplex method for generalized parameter fitting. </para>
</listitem>
            <listitem><para>file <link linkend="_spline_8h">spline.h</link></para>

<para>Header file for spline interpolation. </para>
</listitem>
            <listitem><para>file <link linkend="_string__util_8h">string_util.h</link></para>
</listitem>
            <listitem><para>file <link linkend="_sym__tags_8h">sym_tags.h</link></para>

<para>All STAR file format tags for symmetry parameters. </para>
</listitem>
            <listitem><para>file <link linkend="_symmetry_8h">symmetry.h</link></para>

<para>Header file for general symmetry functions. </para>
</listitem>
            <listitem><para>file <link linkend="_timer_8h">timer.h</link></para>

<para>Utilities for timing functions. </para>
</listitem>
            <listitem><para>file <link linkend="__transform_8h">Transform.h</link></para>

<para>Class for a generalized transform object. </para>
</listitem>
            <listitem><para>file <link linkend="__unit_cell_8h">UnitCell.h</link></para>

<para>Header file for unit cell functions. </para>
</listitem>
            <listitem><para>file <link linkend="_utilities_8h">utilities.h</link></para>

<para>Header file for general utilities. </para>
</listitem>
            <listitem><para>file <link linkend="__vector3_8h">Vector3.h</link></para>

<para>Class for 3-value vectors. </para>
</listitem>
            <listitem><para>file <link linkend="__view_8h">View.h</link></para>

<para><link linkend="_class_view">View</link> object. </para>
</listitem>
        </itemizedlist>
</simplesect>
</section>
