Bsoft function library

src/img/img_afm.c

img_to_surface Converts a 2D AFM image to a 3D density map.
img_3D_to_height Converts a 3D image to a 2D height image.
afm_generate_tip Generates a rounded conical AFM tip.
afm_simulate Simulates and AFM experiment.
afm_force_to_height Converts an AFM force map into a set of 2D height images at different

src/img/img_align.c

img_align Aligns the second image to the first.
img_sum_two Adds two images together, adjusting for size difference.

src/img/img_ampweigh.c

img_weigh_amplitudes_by_fom Weighs a set of reflections by the figure-of-merit.
img_weigh_amplitudes_with_C_curve Weighs an image's amplitudes with the carbon scattering curve.
img_weigh_amplitudes Weighs an image's amplitudes with the radial power spectrum of another.

src/img/img_background.c

img_calculate_background Calculates the background for each sub-image.
img_calculate_background Calculates the background for each sub-image.
img_correct_background Corrects the background for each sub-image.
img_correct_background Corrects the background for each sub-image.
img_subtract_background Subtracts the background for each sub-image.
img_subtract_background Subtracts the background for each sub-image.
img_shift_background Sets the background for each sub-image to a given value.

src/img/img_backproject.c

project_back_projection Back projects a set of 2D images into a 3D volume.
img_back_project_one Back-projects a 2D image into a 3D volume.
img_weigh_transform Weighs a transform with the FOM.

src/img/img_colour.c

img_one_color Converts a gray-scale image to a single color.
img_color_red Converts a gray-scale image to red.
img_color_green Converts a gray-scale image to green.
img_color_blue Converts a gray-scale image to blue.
img_colorize Colourizes an image from blue to red.
img_red_white_blue Colourizes an image with blue positive and red negative.
img_pure_colour Generates a pure colour image without intensity.
img_color_combine Combines two coloured images.
img_write_phase_colour_wheel Generates a phase color wheel.

src/img/img_combine.c

img_compatibility Check if two images have the same number of channels and data type.
img_add Adds two images together.
img_add_weighed Adds multiple images together with given weights.
img_place Places a small image into a large image.
img_multiply Multiplies two images.
img_multiply_one Multiplies all sub-images of the first with the first sub-image of the second image.
img_divide Divides the first image by the second.
img_largest Selects the largest of each pixel from two images.
img_smallest Selects the smallest of each pixel from two images.
img_linear_fit Linear least squares fit of two images.
img_R_factor Calculates an R factor between two images.
img_one_correlation_coefficient Calculates correlation coefficient between two images.
img_correlation_coefficient Calculates correlation coefficient between two images.
img_correlation_coefficient_radial Calculates the correlation coefficient between two images and
img_correlate Calculates a correlation image and a correlation coefficient between
img_correlate_within_radii Calculates a correlation image and a correlation coefficient between
img_histomatch Fits two images by matching the histogram of the second to the first.
img_mask_with_image Masks the first image with the second at a threshold level of the second.
img_morph_blend Blends the two images, creating a new set of sub-images.

src/img/img_complex.c

img_complex_power Calculates the power in a complex image.
img_complex_product Calculates the complex product of two complex images.
img_complex_conjugate_product Calculates the product of a complex image with the conjugate of a second.
img_complex_apply_mask Applies a mask to a complex image.
img_complex_apply_negative_mask Applies a mask to a complex image.
img_complex_apply_dual_mask Applies a dual mask to a complex image.
img_complex_bandpass Bandpasses a Fourier transform.
img_pack_two_in_complex Packs two real images into one complex image.
img_unpack_combined_transform Unpacks a complex transform obtained from two real images.
img_combined_complex_product Calculates the complex conjugate product of a complex image resulting
img_combined_masked_complex_product Calculates the complex conjugate product of a complex image resulting
img_combined_bandpass_complex_product Calculates the complex conjugate product of a complex image resulting
img_combined_bandpass_masked_complex_product Calculates the complex conjugate product of a complex image resulting
img_merge_amplitudes_and_phases Merges the amplitudes from one map with the phases of another.
img_merge_amplitudes_and_phases Keeps selected phases and replaces amplitudes and other phases from a reference transform.

src/img/img_ctf.c

img_ctf_calculate Calculates a CTF complex image.
img_ctf_apply Applies or corrects for the contrast transfer function (CTF).
img_ctf_radial_average Calculates the power spectrum radial average corrected for astigmatism.
img_ctf_fit Determines the CTF parameters from a power spectrum.
img_ctf_rough_fit Determines the approximate defocus, baseline and envelope.
img_ctf_fit_baseline Fits only the baseline for a given CTF.
img_ctf_fit_envelope Fits only the envelope for a given CTF.
img_ctf_refine_defocus Refines the defocus with a given baseline and envelope.
img_ctf_fit_astigmatism Fits the astigmatism with a given defocus, baseline and envelope.

src/img/img_diffraction.c

img_diffraction_origin Finds the origin of a powder diffraction pattern by cross-correlation.

src/img/img_edit.c

img_delete_within_box Fills a box within an image with a uniform value.
img_delete_within_radius Fills a sphere within an image with a uniform value.
img_add_sphere Adds a sphere of the fill value to an image.
img_add_gaussian_sphere Adds a gaussian sphere of the fill value to an image.
img_delete_within_cylinder Fills a cylinder within an image with a uniform value.
img_delete_range Replaces values in a given range with the fill value.
img_edge_oval Smooths the image edge with a soft oval function.
img_edge_cylinder Smooths the image edge with a soft cylindrical function.
img_edge_rect Smooths the image edge with a soft rectangular function.
img_fill_bar Generates a bar between start and end points.
img_gradient_correction Calculates and corrects for a linear gradient across an image.
img_shell_average Calculates the average density in a shell.
img_extract_tetrahedron Extracts a tetrahedral part of the image.

src/img/img_extract.c

img_extract Extracts part of an image into a new image.
img_extract Extracts part of an image into a new image.
img_extract_shell Extracts a shell from an image into a new image.
img_extract_tiles Extracts a set of tiles from an image into a new image.
img_extract_tiles_at_coords Extracts a set of tiles at specified positions from an image into a new image.
img_extract_orthogonal_slices Extracts orthogonal views around a voxel.
img_extract_show Converts a slice from an image to a 2D plane for display.
img_extract_magnifying Extracts a region from an image to magnify.
img_extract_particles Extracts particles defined by a series of coordinates.
img_extract_filament Extracts a filament defined by a series of coordinates.
img_extract_one_filament Extracts a filament defined by a series of coordinates.

src/img/img_feature.c

img_replace_maxima Replaces maxima above a threshold using local averages.
img_extract_features Finds local minimums in a grey scale image and uses those as features
img_find_features Segments an image into contiguous regions (features).
img_assignAllMyNeighbors Finds all the pixels that are part of the same feature.

src/img/img_filter.c

img_average_kernel Generates a kernel with a uniform non-zero value.
img_gaussian_kernel Generates a gaussian kernel image.
img_laplacian_of_gaussian_kernel Generates a laplacian-of-gaussian kernel.
img_average_filter Applies an averaging filter to an image.
img_median_filter Applies a median filter to an image.
img_peak_filter Finds the peaks in an image.
img_variance Rescales an image based on local variance.
img_convolve Convolves an image with an arbitrary size convolution filter.
img_gradient_filter Calculates the gradient magnitude.
img_laplacian_filter Convolves an image with a 3x3x3 Laplacian filter.
img_bilateral_filter Denoise an image with combined gaussian distance and density difference kernel.
img_denoising_filter Denoise an image with combined gaussian distance and density difference kernel.
img_rolling_ball_filter Apply a rolling ball filter.
img_bandpass_filter Applies a bandpass filter to an image.
img_bandpass_filter Applies a bandpass filter to an image.
img_amplitude_filter Filter the amplitudes of the Fourier transform of an image.
img_phases_only Sets all amplitudes to one.
img_estimate_B_factor Determines the overall B-factor of an image.
img_apply_B_factor Multiplies by a Gaussian curve defined by a B-factor up to a given resolution.
img_apply_ratio_of_gaussians Multiplies by a ratio of Gaussian curves.
img_filter_extremes Filters the extremes out of an image.
img_filter_mg_extremes Filters the extremes out of a micrograph image.

src/img/img_find.c

img_find_density Searches a 2D/3D density map for a template.

src/img/img_fourier.c

fft_setup_plan Sets up a plan for fast Fourier transforms.
fft_destroy_plan Deallocates a plan for fast Fourier transforms.
fft Fast Fourier transforms a data array.
img_fft Fast Fourier transforms an image.
img_fft Fast Fourier transforms an image.
img_fft_complex Fast Fourier transforms an image.
img_fft_complex Fast Fourier transforms an image.
img_fft_times Tests the execution times for a series of image sizes.
img_auto_correlate Calculates an autocorrelation map by Fast Fourier transformation.
img_cross_correlate Calculates a cross-correlation map by Fast Fourier transformation.
img_cross_correlate_two_way Calculates a cross-correlation map by Fast Fourier transformation.
img_cross_correlate_validate Calculates an masked cross-correlation map by Fast Fourier transformation.
img_find_center Finds the center of mass of an image by cross-correlation with its inverse.
img_find_shift Calculates a cross-correlation map to find the shift for the pair of images.
img_find_peak Finds the peak in an image to the nearest voxel.
img_refine_peak Refines the position of a peak to sub-voxel resolution.
img_find_peaks Finds peaks in a map.
img_cc_confidence Calculates a confidence level to associate with a cross-correlation peak.
img_change_transform_size Resizes a "standard" transform.
img_phase_difference Calculates the cosine of the phase difference between two images.
img_average_phase_difference Calculates the average of the cosine of the phase difference between
img_flip_phases Flips the phases of an image based on a phase difference map.

src/img/img_graphseg.c

img_graph_segment Graph-based segmentation of an image.

src/img/img_helix.c

img_helix_symmetrize Symmetrizes an image given helical symmetry parameters.
img_seamed_helix_symmetrize Symmetrizes an image given helical symmetry parameters.
img_find_helix_seam Symmetrizes an image given helical symmetry parameters.
img_convert_to_helix Converts a map to a helix.
img_find_helix_parameters Finds the best helix parameters for helical map.
img_symmetrize_cylinder Calculates a cylindrically symmetrized map.
img_unwrap_cylinder Unwraps an image into a cylindrical projection.

src/img/img_histogram.c

img_histogram Calculates the histogram of an image.
img_calc_histogram Calculates the histogram of an image.
img_percentiles Calculates the percentiles from the histogram of an image.
img_fit_gauss_to_histogram Fits a gaussian function to a histogram of an image.
img_fit_poisson_to_histogram Fits a poisson function to a histogram of an image.

src/img/img_interpolate.c

img_transform Transforms an image by translation, rotation, scaling and skewing.
img_rotate_to_view Rotates an image to a specified view.
img_rotate_using_euler_angles Rotates an image to a specified view.
img_rotate_and_add Rotates an image to a specified view and adds it to another image.
img_invert Inverts each image through its origin.
img_shift Shifts each image as defined in individual shift vectors.
img_shift_with_wrapping Shifts each image to place its origin in the center.
img_center_origin Shifts each image to place its origin in the center.
img_shift_to_origin Shifts each image to place its origin at {0,0,0}.
img_shift_to_zero_origin Shifts each image to place its origin at {0,0,0}.
img_unique_shift_global_rotate Shifts and rotates each image as defined in individual shift vectors.
img_integer_interpolation Interpolates by an integer scale with a density-preserving
img_bin Bins by an integer size.
img_median_bin Bins by an integer size.

src/img/img_mask.c

img_mask_stats Calculates statistics for a mask.
img_mask_invert Inverts a mask.
img_mask_combine Combines two masks with different operations.
img_thresholded_mask Generates a mask based on an image at a given threshold.
img_variance_mask Calculates a mask based on local variance.
img_mask_collapse Collapse a multi-level mask to a binary mask.
img_mask_select_level Retains the selected levels in a multi-level mask.
img_mask_select_level Retains the selected levels in a multi-level mask.
img_level_mask Converts a mask to a multilevel mask with a given number of voxels per level.
img_min_max_mask Creates a binary mask to exclude extreme pixels.
img_plane_mask Generates a mask on one side of a plane.
img_rectangular_mask Generates a mask along an axis within a 2D image.
img_shell_mask Generates a shell mask within given radii.
img_missing_wedge_mask Generates a mask with a missing wedge.
img_missing_pyramid_mask Generates a mask with a missing pyramid.
img_missing_cone_mask Generates a mask with a missing cone.
img_banded_mask Generate reciprocal space mask based on a specification of bands.
img_composite_mask Generates a composite of multiple masks.
img_multi_mask_compress Compresses a composite mask to remove empty regions.
img_mask_interface_matrix Calculates the interfaces between regions.
img_mask_region_interfaces Reports the whole interface matrix or interfaces for one region only.
img_mask_merge_delete Calculates the interfaces between regions and deletes/merges small ones.
img_apply_binary_mask Applies a binary mask to an image.
img_weigh_with_mask Weighs an image with a floating point mask.
img_mask_difference Calculates the difference mask from two input masks.
img_mask_dilate Dilates a binary mask.
img_mask_erode Erodes a binary mask.
img_mask_open Opens a binary mask.
img_mask_close Closes a binary mask.
img_mask_write Displays a binary mask as an image.

src/img/img_montage.c

img_montage_slices Rearranges a 3D image into a montage of 2D slices for display.
img_montage_images Rearranges a 2D images into a 2D montage.

src/img/img_multislice.c

img_calc_multi_slice Simulates the electron imaging process using a multi-slice approach.
img_calc_wave_propagator Calculates the wave propagation function between slices.
img_calc_potential Calculates the atomic potential.
img_calc_phase_grating Calculates the phase grating approximation from the atomic potential.
img_apply_complex_CTF Applies a complex CTF function to a Fourier transform.
img_impose_MTF Applies a complex MTF function to a Fourier transform.

src/img/img_nad.c

img_nad Denoises a 3D density map by non-linear anisotropic diffusion.

src/img/img_norm.c

img_mass_normalize Normalizes a set of images to a desired average and standard deviation.

src/img/img_pick.c

img_prepare_template Prepares a template for particle picking.
img_pick_particles Picks particles using cross-correlation.

src/img/img_polar.c

img_cartesian_to_spherical Calculates an image with spherical coordinates.
img_cartesian_to_cylindrical Calculates an image with cylindrical coordinates.
img_radial_shells Calculates an image with slices giving the radial shell projections.
img_radial_sections Calculates an image with slices giving the radial section projections.
img_polar_transform Transforms a cartesian image to polar or cylindrical coordinates.
img_polar_power_spectrum Calculates the polar power spectrum from a Fourier transform.
img_polar2D Calculates radial segment averages from an image.

src/img/img_powerspectrum.c

img_power_spectrum Calculates a power spectrum.
img_tiled_powerspectrum Prepares an image for determining CTF parameters.
img_tilt_axis_powerspectrum Prepares an tilted image for determining CTF parameters.
img_colour_power_spectrum Generates a power spectrum with phases coloured according to a colour wheel.

src/img/img_project.c

img_project Projects a 3D image to a 2D image down the z-axis.
img_project_down_axis Projects a 3D image to a 2D image down one of the three major axes.
img_rotate_project Rotates a 3D map and projects it along the z-axis.
img_central_section Calculates a central section of a 3D fourier transform.
img_project_views Calculates a set of projections from a 3D density map.
img_project_views_fourier Calculates a set of projections as central sections from a 3D fourier transform.
img_project_write_views Calculates a set of projections from a 3D density map and write them to separate files.
img_compare_projections Compares a set of projections from a 3D density map.

src/img/img_radial.c

img_radial Calculates the elliptical radial average or volume of an image.
img_radial_average Calculates the radial average of an image.
img_radial_power_spectrum Calculates the radial power spectrum from a Fourier transform.
img_directional_average Calculates the radial average of an image.
img_radial_to_full Generates a full 2D or 3D image from a radial profile in a 1D image.
img_radial_fit Fits a radial profile to a reference radial profile.

src/img/img_random.c

img_random_uniform Generates an image with a uniform random distribution of densities.
img_random_gaussian Generates an image with a gaussian random distribution of densities.
img_random_poisson Press W.H. et al (1992) Numerical Recipes in C.
img_random_logistical Generates an image with a gaussian random distribution of densities.
img_add_gaussian_noise Adds gaussian random noise to an image.
img_add_poisson_noise Adds poisson random noise to an image.

src/img/img_reconstruct.c

img_pack_2D_in_recip_space Packs a 2D Fourier transform into a 3D reciprocal space volume.
part_ft_size Sets the Fourier transform size for 2D particle images for reconstruction.
img_reconstruction_stats Calculates Fourier shell statistics.

src/img/img_reflections.c

img_normalize_reflections Normalizes a set of reflections encoded as a complex image.
img_mirror_reflections Mirrors a set of reflections by negating the phases.
img_select_reflections Selects reflections for output.
img_reflection_profile Calculates a radial profile average.
img_octants Counts the number of reflections in each octant.
img_sfanalyze Analyzes the FOM's of a set of reflections encoded as a complex image.
img_sfscale Scales the input reflections with a second set.
img_sfmerge Merges the input reflections with a second set.

src/img/img_region_stats.c

img_stats_within_radii Calculates the statistics for an image with given radii.
img_stats_in_box Calculates the statistics for an image within the given box.
img_stats_in_poly Calculates the statistics for an image within the given polyhedron.

src/img/img_rescale.c

img_rescale Rescales the image data to a given minimum and maximum.
img_rescale_to_min_max Rescales the image data to a given minimum and maximum.
img_rescale_to_avg_std Rescales the image data to a given average and standard deviation.
img_square Calculates the square of the image.
img_sqrt Calculates the square root of the image.
img_logarithm Calculates the logarithm of the image data.
img_truncate Truncates image data to a given minimum and maximum.
img_truncate_to_min_max Truncates image data to a given minimum and maximum.
img_truncate_to_avg Sets voxels in image data exceeding a given minimum and maximum to
img_truncate_to_background Sets voxels in image data exceeding a given minimum and maximum to
img_limit_levels Converts a full gray scale image to a limited level image.

src/img/img_resize.c

img_resize Resizes without interpolation or rescaling.
img_resize_to_next_power2 Resizes without interpolation or rescaling to the next power of 2.
img_shrink_wrap Shrinks an image to a new size with wrapping of the excluded edges.
img_pad Pads an image to a new size with a given fill value.
img_pad Pads an image to a new size with a given fill value.

src/img/img_resolution.c

img_resolution Calculates resolution measures.
img_resolution_display Calculates the resolution estimates from a plot generated by img_resolution.
xml_resolution Writes one or more XML files from a plot generated by img_resolution.
img_resolution_from_two_images Calculates the resolution from two images.
img_fourier_shell_stats Calculates Fourier shell statistics.
img_spectral_signal_to_power Calculates the spectral signal-to-power ratio.
img_local_resolution Determine the local resolution at each masked voxel in a map.
img_shell_resolution Determine the resolution for each concentric shell in a map.

src/img/img_segment.c

img_blobs Identifies contiguous regions above a given threshold (blobs) and
img_find_threshold Finds the density threshold associated with a particular molecular weight.
img_mass_at_threshold Calculates the mass from the density threshold.
img_internal_volume Finds the density threshold associated with a particular molecular weight.
img_segment_threshold_series Segments a map through a series of thresholds and reports results.
img_flood_fill Creates and expands a feature map from a starting to ending threshold value.
img_flood_peaks Generates a segmented image from peaks above a threshold value.
img_set_second_mask A second level mask is added to a primary mask based on a threshold.
img_check_neighbors Check neighbors in feature map and assign a value if a neighbor is assigned.
img_find_highest_in_kernel Finds the highest value in a kernel excluding the central voxel.
img_excise_feature Finds the density around a voxel associated with a particular feature.
img_excise_all_features Extracts all the features associated with a multi-level mask.

src/img/img_stat_test.c

img_students_t_test Press W.H. et al (1992) Numerical Recipes in C.
img_students_t_test_equal Press W.H. et al (1992) Numerical Recipes in C.
img_students_t_test_unequal Press W.H. et al (1992) Numerical Recipes in C.
img_f_test Press W.H. et al (1992) Numerical Recipes in C.

src/img/img_symmetry.c

img_apply_point_group Applies point group symmetry to an image.
img_check_point_group Checks for the requested symmetries.
img_find_point_group Finds the orientation for an image witha specific a point group symmetry.
img_find_symmetry_equivalent Finds the symmetry equivalent orientation of a particle with respect to a template.
img_find_symmetric_view Finds the view that on symmetrizing fits best to a symmetric template.
img_change_symmetry Changes the symmetry order for cyclic and dihedral maps.
img_add_with_rotation Rotates an image and adds it to the second image.
img_rotate_correlate Rotates a copy of an image and correlates it with the original.
img_mask_asymmetric_units Calculates a multi-level mask to indicate asymmetric units.
img_replicate_asymmetric_unit Calculates a full map from one asymmetric unit.
img_write_symmetry_views Rotates an image to all symmetry-related views and the resultant image.
img_check_space_group Checks the crystal space group symmetry and the shift to a symmetry axis.
img_apply_space_group Applies the necessary shift to superimpose the origin on a symmetry axis.
img_apply_friedel Applies Friedel symmetry.
img_check_friedel Checks Friedel symmetry.
img_check_handedness Checks for the extent of handedness for any symmetric map.

src/img/img_tile_patch.c

img_tile_with_overlap Writes overlapping tiles into new images.
img_pack_into_image Packs a tile with overlap into a new composite image.

src/img/img_tomography.c

img_gold_particle Generates an image representing a gold particle.
img_CC_with_gold Calculates the cross-correlation map with a gold particle image.
img_find_gold_particles Finds gold particles in micrograph images.
img_marker_projection Generates a projection image of the global marker model.
img_stretch Stretches an image to what it should correspond to at 0 degree tilt.
img_clear_extraneous_areas Clears areas from a micrograph not used in a reconstruction.

src/img/img_util.c

img_find_voxel_from_index Calculates the voxel coordinates in an image from an index.
img_density_at_coordinates Returns the average density within a given radius from a voxel.
img_get_recip_resolution Calculates the reciprocal resolution from the resolution field.
img_average Averages images in a multi-image file.
img_catenate Catenates an array of images of the same size into a multi-image structure.
img_catenate Catenates a list of images into a multi-image structure.
img_select Selects a sub-images from a multi-image structure.
img_delete Deletes sub-images from a multi-image structure.
img_translate Shifts an image with or without wrapping.
img_rotate_by_pi Rotates an image by pi.
img_adjust_FOM Adjust the figure-of-merit values to a new range.
img_weigh_by_FOM Weigh the image data by the FOM.
img_fill_upper_triangle Fills the upper triangle of an image with values from the lower triangle.
img_transpose Transposes an image.

src/mg/mg_align.c

mg_align_coordinates Aligns the particle coordinates of a series of micrographs.
mg_align_micrographs Aligns a focal series of micrographs.
mg_align_feature_extraction Calculates the transformation parameters for each set images, by
mg_apply_transform Applies a transformation to particle coordinates in a reference
mg_merge_focal_series Merges corresponding particle images in each focal series.
project_align_series Aligns a series of micrographs by cross-correlation.
project_align_series_seq Aligns a series of micrographs by cross-correlation sequentially.
project_write_aligned_images Calculates aligned micrograph images and write them to a file.

src/mg/mg_class.c

mg_classify Classifies particle images with respect to a series of reference maps.

src/mg/mg_ctf.c

project_ctf Calculates or fits CTF curves to multiple power spectra.
project_merge_CTF_parameters Puts CTF parameters from one project into another.
project_set_defocus Sets the defocus values of all the micrographs.
project_set_volts Sets the acceleration voltage of all the micrographs.
project_set_Cs Sets the spherical aberation constant of all the micrographs.
project_set_amp_fac Sets the amplitude contribution of all the micrographs.
project_set_alpha Sets the beam source size/divergence angle of all the micrographs.
project_set_envelope Sets the envelope equations of all the micrographs.
project_set_coherence_envelope Replaces envelope equations with those based on partial coherence in all micrographs.
project_set_baseline Sets the baseline equations of all the micrographs.
project_update_first_zero Updates the first zero from the defocus average for all the micrographs.
project_plot_ctf Plots the CTF curves.

src/mg/mg_extract.c

particle_setup_filenames Sets up individual particle file names for extraction.
filament_setup_filenames Sets up individual filament file names for extraction.
project_extract_particles Extracts particle images from micrographs defined in a project.
micrograph_extract_particles Extracts particle images from a micrograph.
reconstruction_extract_particles Extracts particle images from a reconstruction.
particle_extract Extracts particle images from an image.
micrograph_extract_gold Extracts gold particle images from a micrograph.
reconstruction_extract_gold Extracts gold particle images from a reconstruction.
marker_extract_gold Extracts gold particle images from an image.
project_extract_filaments Extracts filament images from micrographs defined in a project.
micrograph_extract_filaments Extracts filament images from a micrograph.
reconstruction_extract_filaments Extracts filament images from a micrograph.
filament_extract Extracts filament images from a micrograph.
project_filaments_to_particles Converts filaments to sets of particles.
micrograph_filaments_to_particles Converts filaments to sets of particles.
reconstruction_filaments_to_particles Converts filaments to sets of particles.
filaments_to_particles Converts filaments to sets of particles.
project_mask_filament_particles Masks particles extracted from filaments.
project_rotate_mask_filament_particles Rotates and masks particles extracted from filaments.

src/mg/mg_hand.c

project_get_handedness Determines handedness for all selected particles (sel > 0) in a
hand_get_options_mgselect Gets criteria for selecting micrographs (from a field-of-view) for a
hand_select_consist Sets consistent selection values in all (including unused) micrographs.

src/mg/mg_helix.c

project_filament_powerspectrum Calculates and average power spectrum from filaments.
mg_generate_layer_lines Generates layer lines given the unit cell vectors.
img_mask_layer_lines Masks the image using the list of layer lines.

src/mg/mg_img_proc.c

project_create_from_images Creates a project structure using image file names.
micrograph_get_nominal_origin Gets the nominal origin for a micrograph.
project_set_nominal_mg_origins Sets micrograph origins to the centers of the micrographs.
project_reset_origins Resets particle origins to nominal values.
project_set_part_img_origins Writes particle origins into particle image files.
project_write_particle_classes Writes particles to different stacks based on class.
project_flip_particle_coordinates Reverses one or more particle coordinates.
project_set_views_from_images Gets views from particle images.
project_set_views_in_images Sets views in particle images from the project parameter structure.
project_bin_micrographs Bins all micrographs a project.

src/mg/mg_merge.c

mg_particle_merge_series Aligns and merges (sums) 2D particle images from a focal,
mg_particle_unmerge Gives corresponding particles in a field-of-view the same

src/mg/mg_multiple.c

project_multi_merge Merges multiple projects.
project_multi_select_best_FOM Selects the best particle orientations from multiple parameter files.
project_multi_selection_stats Counts particle assignment distributions using selection arrays.
project_multi_select_low_variance Selects the best particle orientations from multiple parameter files.
project_multi_select_low_difference Selects the best particle orientations from two parameter files.

src/mg/mg_multislice.c

project_generate Generates a project for multislice simulations.
project_generate_asu Generates a project for multislice calculations of an asymmetric unit.
project_generate_potential Generates potential images using a multislice calculation.
project_generate_image Generates final images from a multislice calculation.
project_apply_distortions Applies imaging distortions to the final images from a multislice calculation.

src/mg/mg_orient.c

img_prepare_projections Generate projections if a 3D file, otherwise clean projections.
mg_determine_orientations Find the orientation and origin of every image in a project.
mg_determine_origins Find the origin of every image in a project.
img_align2D_pps Finds the best in-plane alignment for two 2D images using polar power spectra.
img_align2D Finds the best in-plane alignment for two 2D images using polar power spectra.

src/mg/mg_particle_centers.c

project_center_particles Centers single particle images based on the parametric center.
project_set_particle_centers Calculates centers of single particle images by cross-correlation with a reference.
project_find_part_centers_in_mgs Finds the centers of picked particles within a micrograph.
project_find_particle_centers Calculates centers of single particle images.

src/mg/mg_particle_select.c

part_reset_selection Resets selection to all particles.
part_consolidate_selection Consolidates selected particles under one selection number.
part_set_selection Selects one selection number and sets all others to zero.
part_set_FOM Sets the FOM for all particles.
part_deselect_below_cutoff Deselects particles below a given FOM cutoff.
part_set_multi_maps Sets selection for generating multiple maps.
part_set_filament_maps Generates a selection number from the group number for each filament.
part_reselect Reselects particles identified by an input STAR tag and between a minimum and maximum.
part_series_comparison A function to select particles based on comparison of the orientations
part_select_FOM_groups Selects groups of particles based on the FOM.
part_select_percentage Selects a percentage of particles based on the FOM.
part_select_FOM_avg_std Selects particles based on FOM average and standard deviation.
part_select_random Selects particles randomly based on a fraction of the total.
part_select_bootstrap Selects a given number of particles randomly with replacement.
part_select_random_within_view Selects a given number of particles within each view.
part_select_best_within_view Selects the best number of particles within each view.
part_select_group Selects particles with a given group identifier.
part_select_sets Selects sets of particles, each set with the same size.
part_filament_direction Checks the direction of particles associated with filaments.
part_view_select Selects particles based on a distance from a reference view.
part_side_view_select Selects particles based on a distance from a side view.
part_euler_angle_select Selects particles based on Euler angle limits.
part_origin_select Selects particles based on the distance from the nominal origin.
part_set_first_view_in_series Sets all orientation parameters for a particle to the first in the set.
part_set_best_view_in_series Sets all orientation parameters for a particle to the best in the set.
part_select_series Select series where all are already selected.
part_series_from_seed Calculates the locations of particles in a series from a seed.
part_fom_defocus_fit Fits the particle FOMs as a function of the defocus.
part_fom_defocus_fit_deselect Deselects particles below a given FOM cutoff, adjusted for the defocus.
part_select_closest_to_focus Deselects all particles except those from micrographs closest to focus.
part_select_furthest_from_focus Deselects all particles except those from micrographs furthest from focus.

src/mg/mg_pick.c

project_pick_particles Picks particles using cross-correlation.
mg_pick_particles Picks particles using cross-correlation.
mg_find_particles_in_ccmap Finds the peaks in a cross-correlation map corresponding to particles.

src/mg/mg_processing.c

project_init Initializes a micrograph processing project parameter structure.
project_create Creates a micrograph processing project parameter structure.
project_equal_mg_part_files Sets micrograph and particle files to be the same.
field_add Adds a field-of-view parameter structure to a linked list.
field_find_id Finds a field-of-view based on its identifier.
field_find_micrograph Returns a pointer to a specific micrograph in a field-of-view
field_find_micrograph_n Returns a pointer to the nth micrograph in a field-of-view
field_find_micrograph_by_focus Returns a pointer to the micrograph in a field-of-view structure
field_find_micrograph_by_rotang Returns a pointer to the micrograph in a field-of-view structure
field_find_micrograph_by_tiltang Returns a pointer to the micrograph in a field-of-view structure
field_find_zero_tilt_mg Finds the micrograph closest to a zero degree tilt in a series.
field_find_low_tilt_mg_with_markers Finds the micrograph closest to a zero degree tilt in a series with markers.
micrograph_add Adds a micrograph parameter structure to a linked list.
particle_add Adds a particle parameter structure to a linked list.
filament_add Adds a filament parameter structure to a linked list.
filament_node_add Adds a filament node parameter structure to a linked list.
filament_length Calculates the length of a filament.
reconstruction_add Adds a reconstruction parameter structure to a linked list.
project_count_fields Counts all the fields in the project structure.
project_count_micrographs Counts all the micrographs in the project structure.
project_count_mg_selected Counts all the selected micrographs in the project structure.
project_count_reconstructions Counts all the reconstructions in the project structure.
project_count_rec_selected Counts all the selected reconstructions in the project structure.
project_count_mg_particles Counts all the particles in the project structure.
project_count_mg_part_selected Counts the number of particles in a project.
project_count_mg_part_selected Counts the number of particles in a project.
project_count_rec_particles Counts all the particles in the project structure.
project_count_rec_part_selected Counts all the particles in the project structure.
project_count_mg_filaments Counts the number of filaments in a project.
project_count_mg_filament_nodes Counts the number of filament nodes in a project.
project_count_rec_filaments Counts the number of filaments in a project.
project_count_rec_filament_nodes Counts the number of filaments in a project.
field_count Counts the number of fields-of-view in a linked list.
field_count_micrographs Counts all the micrographs in the field-of-view structure.
field_count_particles Counts all the particles in the field-of-view structure.
micrograph_count Counts the number of micrographs in a linked list.
micrograph_count_particles Counts all the particles in the micrograph structure.
particle_count Counts the number of particles in a linked list.
particle_count_selected Counts the number of particles in a linked list.
filament_count Counts the number of filaments in a linked list of filaments.
filament_node_count Counts the number of filament nodes in a linked list of filaments.
project_kill Frees a whole project.
field_kill Frees a whole field-of-view structure.
micrograph_kill Frees a whole micrograph parameter structure.
particle_kill Frees a list of particles.
filament_kill Frees a list of filaments.
reconstruction_kill Frees a whole reconstruction parameter structure.
project_update Updates an existing project with new information.
micrograph_update Updates an existing micrograph with new information.
reconstruction_update Updates an existing reconstruction with new information.
particle_update Updates an existing particle with new information.
project_revert_particle_files Reverts particle file names to what it was in an old project.
project_set_field_id Sets the field id's according to a regular series.
project_show_hierarchy Shows the project hierarchy.
project_show_selection_numbers Shows the selection numbers for the particles in a project.
project_show_selected Shows the selected particles in a project.
project_show_selected_parameters Shows the selected particle parameters in a project.
project_show_fom_histogram Shows a histogram of the FOM values.
project_show_mag_histogram Shows the histogram for magnification values for selected particles.
project_dump Dumps particle info in the project hierarchy.
project_select_field Selects a field from the project and deletes the rest.
project_select_micrograph Selects a micrograph from the project and deletes the rest.
project_set_micrograph_path Sets the path to micrograph files for all the micrographs.
project_set_powerspectrum_path Sets the path to powerspectrum files for all the micrographs.
project_set_particle_path Sets the path to particle files for all the micrographs.
project_set_filament_path Sets the path to filament files for all the micrographs.
project_set_magnification Sets the magnification for all the micrographs.
project_set_scan_sampling Sets the scan sampling for all the micrographs.
project_set_pixel_size Sets the pixel size for all the micrographs.
project_set_tilt Sets the tilt parameters for all the micrographs.
project_set_dose Sets the electron dose of all the micrographs.
project_change_pixel_size Changes all the micrograph fields linked to the pixel size.
project_set_micrograph_origins Sets micrograph origins to the given origin.
project_add_origins_to_coords Adds the particle origins to the micrograph coordinates.
project_renumber_particles Renumbers particles.
project_set_particle_box_radius Sets particle box radius to the given value.
project_set_particle_origins Sets particle origins to given values.
project_set_particle_asu_views Sets particle views within the asymmetric unit.
project_rotate_particle_views Rotates particle views with respect to a reference view.
project_apply_map_magnifications Change particle pixel sizes for particles based on map magnifications.
views_from_project Retrieves the particle views from a project.
get_fom_tag Returns the tag associated with a particular FOM.
get_fom_tag Returns the tag associated with a particular FOM.

src/mg/mg_random.c

project_random_defocus Introduces random errors into micrograph defocus averages.
project_random_origins Introduces random errors into particle origins.
project_random_views Replace the original particle orientations by random views.
project_random_helical_views Replace the original particle orientations by random side views for a helix.
project_random_views Introduces random errors into particle views.
project_random_magnification Introduces random errors into particle magnifications.
project_random_symmetry_related_views Replaces the original orientations by symmetry-related views.

src/mg/mg_reconstruct.c

project_fourier_reconstruction Reciprocal space reconstruction from the images in a multi-image file.
project_set_reconstruction_size Sets the reconstruction size for reconstruction from 2D particle images.
project_reconstruct_3D Transforms 3D maps and calculates an average.

src/mg/mg_refine.c

mg_refine_orientations Refine the orientation and origin with respect to a reference map.
part_refine_orientation Refine the orientation and origin of one particle with respect to a reference map.
img_refine_monte Refine the orientation and origin of one particle with respect to a reference map.
img_refine_grid Refine the orientation and origin of one particle with respect to a reference map.

src/mg/mg_resolution.c

mg_determine_resolution Determines the resolution of particle images with respect to several reference maps.

src/mg/mg_tomo_rec.c

project_fourier_reconstruction_slab Reciprocal space reconstruction from the images in a multi-image file.

src/mg/mg_tomo_resol.c

mg_tomo_resolution Estimating the resolution of one micrograph in an aligned tilt series.

src/mg/mg_tomo_track.c

project_find_tilt_axis Finds the tilt axis for a tomographic tilt series.
project_track_markers Aligns markers in a tomographic series.
project_refine_markers Refines marker positions in a tomographic series.
mg_refine_markers Refines marker positions in a tomographic micrograph.
project_refine_tilt_axis Attempt to find the tilt axis from marker movement.
project_refine Refines all the alignment parameters.
project_refine_z Refines the z coordinates of the marker model.
project_refine_origins Refines the micrograph shifts.

src/mg/mg_tomography.c

mg_marker_init Initializes markers from the reference.
mg_marker_update Calculates the predicted positions of markers from the reference.
mg_location_from_3D_model Calculates the 2D location of a marker from a 3D model.
project_tomo_series_from_images Creates a project structure using image file names.
project_mass_normalize Normalizes a set of images in a project to a desired average and standard deviation.
project_sort_markers_by_id Sorts markers for each micrograph by ID number.
project_tomo_residuals Calculates the residuals for an alignment solution.
mg_tomo_residuals Calculates the residuals for an alignment solution of one micrograph.
project_tomo_errors Analyzes marker errors.
project_calculate_model Calculates the z-coordinates of the marker model.
project_generate_markers Generates missing micrograph and model markers.
project_erase_markers Erases or paints markers in micrographs.
mg_reset_model Resets the model x and y coordinates from the zero-tilt micrograph.
mg_find_markers Finds markers in a micrograph.
mg_composite_particle Generates an average particle image from a micrograph.
project_count_markers Counts the markers in a project hierarchy.
project_show_markers Shows the markers in a project hierarchy.
project_show_errors Shows the errors in marker coordinates in a project hierarchy.
project_deselect_markers Deletes selected markers in a project hierarchy.
project_delete_markers Deletes selected markers in a project hierarchy.
project_mg_select Selects micrographs in a project hierarchy.
project_mg_exclude Deselects micrographs in a project hierarchy.
project_set_tilt_axis Sets the tilt axis angle in a project parameter structure.
project_set_tilt_angles Sets the tilt and tilt axis angles in a project parameter structure.
project_mg_marker_select Selects markers.
project_set_marker_radius Sets the marker radius in a project parameter structure.
project_check_markers Checks if the markers in a project parameter structure fall within micrographs.
project_fix_markers Checks if the markers in a project parameter structure fall within micrographs.
project_mg_tilt_to_matrix Sets the matrix from the tilt and axis angles for each micrograph.
project_clear_extraneous_areas Clears areas from a tilt series not used in a reconstruction.
project_marker_rotation_axis Determines the most likely rotation axis location for a tilt series.

src/mg/mg_xtal.c

mg_unitcell_vectors Calculates the unit cell vectors for a 2D crystal.
mg_generate_reflections Generates reflections given the unit cell vectors.
img_mask_reflections Masks the image using the list of reflections.

src/model/model_color.c

model_color_uniformly Colors model components uniformly.
model_color_selected Colors selected model components.
model_color_by_order Colors model components in order from red to blue.
model_color_by_density Colors model components by density.
model_color_by_fom Colors model components by fom.
model_color_selected_types Colors model components by fom.
model_color_curvature Colors model vertices and links as a function of curvature.
model_color_chiral_vertices Colors model vertices as a function of chirality.

src/model/model_create.c

model_platonic Generates a platonic polyhedron.
model_helix Generates a helix model.
model_random Generates components at random non-overlapping locations and with random views.
model_random_gaussian Generates components at random gaussian-distributed locations and with random views.
model_random_shell Generates random components on a shell.
model_create_shell Creates a sphere point model.
model_create_icosahedron Creates an icosahedron point model.
model_create_circle Creates a circle with the given radius, height, and separation.
model_create_ellipse Creates an ellipse with given semiaxes and separation
model_create_ellipsoid Creates an ellipsoid with given semiaxes and separation

src/model/model_extract_build.c

img_density_at_coordinates Calculates the density in a sphere around a coordinate in an image.
img_extract_density Extracts a density associated with a set of coordinates in a model.
img_extract_mask Extracts a transformed mask of a specific size.
model_refine_components Refines component views and positions by cross-correlation.
model_refine_link_positions Refines link positions by cross-correlation.
model_average_component_density Averages the density associated with each component type in a model.
model_extract_component_densities Extracts all densities associated with components in a model.
model_average_link_density Extracts a density associated with each link in a model.
model_build_from_component_density Builds a new map from a densities of components in a model.
model_build_from_link_density Builds a new map from a density of a link in a model.

src/model/model_map.c

img_from_model Calculates a map from model component coordinates.
model_catenate_maps Concatenates all model maps into one multi-image file.
model_shell_fit Fits a shell model as a rigid body to a map.
model_shell_radial_profile Calculates a radial profile from a shell model.
model_shell_power_spectrum Calculates a radial profile from a shell model.

src/model/model_mask.c

model_create_mask Calculates a mask of the components and links of a model structure.
model_create_hull_mask Calculates a mask based on the periphery of a model structure.
model_create_shell_mask Calculates a shell mask covering a model structure.
model_create_level_mask Calculates a mask with one level per model.
img_extract_segments_using_model Extracts segmentss from a multi-level mask around points defined by a model.
img_add_model_to_mask Adds to the mask the component locations.
model_from_multilevel_mask Generates components at the center of mass of each mask level.

src/model/model_mechanics.c

model_mechanics Minimizes the energy of a model.

src/model/model_multifit.c

model_from_densities Searches a 2D/3D density map for a template.
model_from_densities_for_view Searches a 2D/3D density map for a template using a specific view.
model_from_peaks Generates a model from peaks in a map.

src/model/model_occupancy.c

model_occupancy Calculates the occupancy of components in a map.
model_occupancy_distribution Calculates the occupancy distribution of models.
model_refine_comp_for_occupancy Refines component views and positions by cross-correlation.

src/model/model_poly.c

model_poly_faces Generates links between the vertices to define the polyhedron faces.
model_poly_generate Generates polygons based on a vertex network.
model_vertex_types Determines the vertex type based on adjacent polygons.
model_extended_vertex_types Determines the vertex type based on adjacent and opposed polygons.
model_poly_dual Calculates the dual of a polyhedral network.
model_poly_analyze Analyzes a model for polygon regularity and planarity.
model_poly_links Calculates all the model links.
model_poly_angles Calculates all the polygon angles.
model_poly_regularity Analyzes a model for polygon regularity.
model_poly_planarity Analyzes a model for polygon planarity.
model_poly_energy Calculates the different energy terms for all models.
model_poly_pentagon_adjacency Calculates the number of edges shared by pentagons.
model_poly_find_symmetry Finds the symmetry axes associated with polyhedral elements.
model_poly_hand Calculates the polyhedron hand.
model_poly_compare Compares a model with reference models based on the eigenvalues of the adjacency matrix.
model_poly_eigenvalues Generates the eigenvalues of the adjacency matrix for a model.
model_poly_sphere_coor Generates coordinates for components based on the eigenvectors of the adjacency matrix.

src/model/model_poly_delta.c

model_delta_create_tube Generates a new tubular deltagraph.
model_delta_create_tube Generates a new tubular deltagraph.
model_delta_create_cylinder Generates a new deltagraph based on the type.

src/model/model_poly_spiral.c

model_poly_spiral Generates a polyhedron using the spiral algorithm.
model_polyhedron_check Checks a polyhedron for accuracy and completeness.
model_poly_gen_sequence Generates a polyhedron using a given sequence.
model_poly_gen_sequence Generates a polyhedron using a given sequence.
model_poly_gen_permutations All polyhedra are generated for a given number of vertices.
model_poly_gen_cone A cone tip with 5 pentagons and a base with 7 pentagons are use to generate polyhedra.
model_poly_gen_lozenge Two icosahedral tips are set up and polyhedra generated by rotating the 2 tips.
model_poly_gen_coffin An icosahedral tip and a 6-fold base is set up and polyhedra generated by
model_poly_gen_coffin_loose An icosahedral tip and a 6-fold base is set up and polyhedra generated by
model_poly_gen_coffin_jiggle An icosahedral tip and a 6-fold base is set up and polyhedra generated by moving pentagons around.
model_poly_gen_3part Generates several polyhedra by permuting the first and last parts of a three-part sequence.
model_poly_gen_move_pentagons Generates many polyhedrons using a given sequence and moving pentagons around.

src/model/model_select.c

model_select Selects models, components and component types.
model_select_all Resets the selection to all models.
model_select_unknowns Resets the selection to all unknown models.
model_reset_selection Resets the selection to all components.
model_unset_selection Unsets the selection to all components but not models.
model_select_sets Selects sets of components, each set with the same size.
model_select_number_of_components Selects models within a range of the number of components.
model_select_closed Determines if a polyhedron is closed given a rule.
model_select_fullerene Selects fullerene type models.
model_select_non_fullerene Selects non-fullerene type models.
model_select_valence Selects fullerene type models.
model_select_polygons Selects model polygons with a given order.
model_select_first Selects the first number of components.
model_delete Deletes tagged models, components and links.
model_delete_comp_type Deletes components based on their types.
model_delete_non_selected Deletes selected components and associated links from the model.
model_selection_stats Calculates selection statistics.
model_type_from_selection Converts selection numbers to different types.
model_fom_deselect Deselects components based on the FOM.
model_fom_max_fraction_deselect Deselects components based on the FOM relative to the maximum FOM.
model_radius_deselect Deselects components based on the distance from the origin.
model_fom_histogram Selects components based on the FOM.
model_fom_ranking Ranks components based on the FOM.
model_delete_overlapped_components Deletes components that are too close to others.
model_prune_simple Prunes overlapping components based on a distance criterion.
model_prune_fom Deselects components based on overlap distance and the FOM.
model_prune_similar Averages similar components and reduces redundancy.
model_prune_fit Deselects components based on overlap distance and the FOM.
model_prune_large Deselects components based on overlap distance and the FOM.
model_find_overlap Finds the components that overlap with the reference.

src/model/model_shell.c

model_add_shell Adds a shell to a model using selected components.
model_adjust_shell_to_guide Adjusts a shell model to the faces of a polyhedral guide model.
model_sphericity Calculates how close the model is to a spherical shape.
model_ellipsoidicity Calculates how close the model is to an ellipsoid shape.
model_curvature Calculates the curvature associated with each link.
model_inside_outside Determines if a vector is inside or outside model boundaries.

src/model/model_symmetry.c

model_apply_point_group Applying symmetry to model components.
model_symmetrize Symmetry a model.

src/model/model_transform.c

model_center Shifts all models to their centers of mass.
model_shift Shifts a model.
model_shift_to_center_of_mass Shifts a model.
model_scale Scales a model.
model_reflect Reflects the model through a mirror plane.
model_reflect_and_compare Copies and reflects the model and compares it with the original.
model_rotate Rotates the model.
model_rotate Rotates the model.
model_rotate Rotates the model.
model_rotate Rotates the model.
model_rotate_and_compare Copies and rotates the model and compares it with the original.
model_adjust_for_binning A binned model list is converted back to the unbinned version.
model_align_to_guide A model is oriented to coincide with a guide model.
model_find_transform A model is fitted to a reference model.

src/model/model_util.c

model_list Lists models in table form.
model_component_number_difference Compares the numbers of components in two models.
model_maxnum_components Calculates the largest number of components in a model.
model_replace_components Replaces all components in a model with reference components.
model_merge Merges components from all models into one.
model_rename_components Rename components.
model_mass Calculates the mass of a model from component masses.
model_mass_all Calculates the masses of all the models in the list.
model_center_of_mass Calculates the center-of-mass of a model.
model_gyration_radius Calculates the radius of gyration for a model.
model_principal_axes Calculates the principal axes of a model.
model_radial_distribution Calculates the radial distribution function of a model.
model_compare Compares two models.
model_assemble Concatenates selected molecules into one group.
model_generate_com Calculates the centers-of-mass of molecule group components and generates a new model.
model_update_centers_of_mass Updates the centers-of-mass of molecule group components.
model_invert_views Invert views.
model_find_views Finds the molecule views with respect to a reference.
model_average_components Averages sequential components.
model_reduce_linked Reduces a model to one component per linked set of components.
component_get_array Generates an array of pointers to component structures.
model_adjacency_matrix Constructs the adjacency matrix for a model.
model_distance_matrix Calculates the distance matrix for a model.
model_shortest_path Calculates the shortest path between every pair of vertices.
model_wiener_index Calculates the Wiener index.
model_calculate_views Calculates the views associated with each component.
component_hand Determines the hand of a component.

src/model/model_view_analysis.c

model_view_directions Analyzes view directions in a model.

src/mol/mol_alpha.c

molgroup_generate_alpha_helix Generates an alpha helix of the desired length.
mol_generate_alpha_helix Generates an alpha helix of the desired length.
molgroup_set_alpha_helix Sets a residue range to an alpha helix in all molecules.
molgroup_find_helical_axes Calculates the centers and orientations of all alpha helices.
alpha_find_center Calculates the center of an alpha helix.
alpha_find_orientation Calculates the orientation of an alpha helix.
mol_find_alpha_orientation Calculates the orientation of an alpha helix.
point_on_helix_axis Calculates a point on an alpha helix corresponding to a Ca atom.
molgroup_consolidate_alpha Cluster a set of alpha helices to consolidate helices.

src/mol/mol_bonds.c

md_generate_bond_list Generates a distance-based bond list.
md_generate_molecular_bond_list Generates an intramolecular distance-based bond list.
md_generate_bond_list_with_valence Generates a bond list based on a single valence and the shortest current bond lengths.
md_bond_list_set_parameters Assigns covalent bond lengths to bonds.
md_show_bonds Shows the bonds and bond lengths.
md_show_angles Shows the angles and angular sizes.
md_show_bond_stats Shows the number of bonds and the valency per atom.
md_generate_angle_list Generates an angle list.
md_angle_list_set_parameters Assigns angles from angle types.
md_find_bond_length Finds the reference covalent bond length.
md_find_bond_type Finds the bond type.
md_show_bond_types Shows the bond type composition.
md_angle Calculates the angle between three atoms.
md_find_angle_type Finds the reference angle type between three atoms.
md_find_angle Finds the reference angle between three atoms.
md_calculate_deviations Calculates deviations from the reference bond lengths and angles.
md_calculate_radial_deviation Calculates the radial deviations from the center of the box.

src/mol/mol_compare.c

molgroup_rotate_and_compare Copies and rotates the molecule group and compares it with the original.
molgroup_find_transformation Determines the transformation between two groups of identical molecules.
mol_find_transformation Determines the transformation between two identical molecules.
molgroup_calculate_rmsd Calculates the root-mean-square-deviation between two molecule groups.
mol_calculate_rmsd Calculates the RMSD between two molecules.
molgroup_calc_brute_rmsd Calculates the RMSD based on nearest atoms.

src/mol/mol_edit.c

molgroup_set_atom_types_to_elements Sets atom types to element names.
molgroup_remove_hydrogens Removes all hydrogens from a molecular system.
molgroup_split_into_slices Splits a set of coordinates into slices with a given thickness.
molgroup_insert Inserts one set of molecules into another.
molgroup_randomize Applies random displacements to coordinates.
molgroup_remove_overlapping_atoms Removes overlapping atoms.
molgroup_bond_pseudo_atoms Places pseudo-atoms on bonds.
molgroup_prune_molecules Deletes overlapping molecules.
molgroup_delete_deselected_molecules Deletes deselected molecules.
molgroup_prune_overlapping_atoms Prunes overlapping atoms based on a distance criterion.
molgroup_delete_deselected_atoms Deletes deselected atoms.
molgroup_untangle_molecules Moves overlapping molecules away from each other.
molgroup_untangle_groups Moves overlapping molecules away from each other.

src/mol/mol_map_energy.c

molgroup_map_energy Energy calculation of a molecule fit into a map.
mol_map_energy Energy calculation of a molecule fit into a map.
molgroup_map_correlation Calculation of the fit of a molecule group into a map as a correlation coefficient.
mol_map_correlation Calculation of the fit of a molecule into a map as a correlation coefficient.
molgroup_bond_fit_map_energy Energy calculation of a molecule fit into a map.

src/mol/mol_md.c

md_leapfrog Molecular dynamics using the leapfrog integrator.

src/mol/mol_monte.c

monte_carlo_metropolis Monte Carlo fit of a molecule to a map.
molgroup_generate_masked_grid_list Generates multiple versions of a molecule at different locations.
molgroup_generate_orientation_list Generates multiple versions of a molecule at different locations.
mcm_molecule_list Monte Carlo fit of a molecule to a list of locations and orientations.
mcm_molecule_groups Monte Carlo fit of a set of molecule groups.
molgroup_set_box_to_map_boundaries Sets the box in a molgroup to that defined by the map boundaries.
molgroup_test_if_within_box Tests if a molecule overlaps with a defined box.
monte_rigid_body_fit_energy Calculates the potential energy for rigid body fitting.
monte_atom_fit_energy Calculates the potential energy for fitting atoms to a map.
monte_bond_fit_energy Calculates the potential energy for fitting bonds to a map.
molgroup_atom_overlap Calculates an energy term based on atom overlap.
molgroup_rigid_body_transform Randomly transforms a molecule or molecule group.
molgroup_move_atoms_down_energy Move atoms random distances down the energy gradient.

src/mol/mol_param.c

molgroup_get_atom_types Obtains atomic types from molecule groups.
md_calculate_parameters Calculates atomic parameters from molecule groups.

src/mol/mol_symmetry.c

molgroup_apply_point_group Generates all symmetry-related coordinates.
molgroup_generate_helix Generates a helix from the given parameters.
molgroup_apply_symmetry_from_pdb Generates all symmetry-related coordinates using PDB file matrices.
molgroup_apply_matrices_from_pdb Generates all symmetry-related coordinates using PDB file matrices.
molgroup_find_standard_view Searches for the standard view based on point group symmetry.
molgroup_orient_to_standard_view Searches for the standard view based on point group symmetry.
molgroup_symmetry_RMSD Calculates the RMSD for symmetry in the standard orientation.
molgroup_generate_crystal Generates unit cells from a set of coordinates.

src/mol/mol_transform.c

molgroup_coor_shift Translates a molecule group.
mol_coor_shift Translates a molecule.
molgroup_coor_rotate Rotates and translates a molecule group.
mol_coor_rotate Rotates and translates a molecule.
molgroup_rotate_to_view Rotates a molecule group to a specified view and translates it afterwards.
molgroup_rotate_from_view Rotates a molecule group from a specified view and translates it afterwards.
mol_rotate_to_view Rotates a molecule to a specified view and translates it afterwards.
mol_rotate_from_view Rotates a molecule from a specified view and translates it afterwards.
molgroup_coor_transform Rotates and translates a molecule group.
mol_coor_transform Rotates and translates a molecule.
molgroup_coor_invert Inverts the coordinates of a molecule through a given point.
molgroup_resolve_pbc Recombines coordinates split across periodic box boundaries.
molgroup_pack_in_periodic_box Distributes coordinates across periodic box boundaries.
molgroup_coor_shift_PBC Translates a molecule within a periodic box.
molgroup_coor_shift_rotate_PBC Translates and rotates a molecule within a periodic box.
molgroup_shift_to_center_of_mass Translates a set of coordinates to the center of mass.
mol_shift_to_center_of_mass Translates a set of coordinates to the center of mass.
molgroup_place_at_coordinates Translates a set of coordinates to a defined center-of-mass.

src/mol/mol_util.c

molgroup_select_all Resets selection for all atoms.
molgroup_Bfactors Calculates the average Bfactors for residues in molecules.
molgroup_print_sequence Prints the sequence of a molecule as a single letter code string.
molgroup_coor_select_ring Selects atoms in a ring.
molgroup_coor_select Selects atoms within a box.
molgroup_set_radius Shifts all coordinates to a given radius.
molgroup_rename Renames molecules.
molgroup_residue_renumber Renumbers residues.
molgroup_atom_renumber Renumbers all atoms, disregarding molecule distinction.
molgroup_coor_reset_occupancy Sets occupancies to new values..
molgroup_calculate_weight Calculates the weight of each molecule.
molgroup_center_of_mass Calculates the center of mass of a molecule group.
molgroup_show_center_of_mass Calculates the center of mass of a molecule group.
mol_center_of_mass Calculates the center of mass of a molecule.
mol_show_center_of_mass Calculates the center of mass of a molecule.
molgroup_principal_axes Calculates the principal axes of a molecule group.
mol_principal_axes Calculates the principal axes of a molecule.
molgroup_density Calculates the number and mass density of a molecular system.
molgroup_volume Calculates the volume of a molecular system.
molgroup_composition Calculates the elemental composition of a molecular system.
molgroup_radial_density Calculates a radial distribution function.
molgroup_atom_mesh_lists Generates lists of atoms based on a grid.
atom_get_array Generates an array of pointers to atom structures.

src/mol/mol_water.c

mol_generate_one_water Generates one water molecule at a given location.
molgroup_generate_regular_water Generates a block of water based on a regular lattice.
molgroup_generate_random_water Generates a block of water with random placement.
water_bond_list Generates a bond list for a block of waters.
water_angle_list Generates a bond angle list for a block of waters.
molgroup_calc_water_rdf Calculates a radial distribution function for water molecules.

src/mol/molecule_to_map.c

img_from_molecule Calculates a 3D density map from a set of atomic coordinates.
compare_mol_map Compares reference and calculated maps and calculates an occupancy
img_sf_from_molecule Calculates a 3D set of structure factors from a set of atomic coordinates.
write_scattering_curves Calculates and writes atomic scattering profiles to a file.

src/mol/seq_align.c

seq_pair_align Aligns two sequences.
seq_find_best_offset Finds the best offset for aligning two sequences without gaps.
seq_dot_plot Calculates a dot plot for two sequences.
seq_dot_plot_mov_avg Calculates a moving average along the diagonals of a dot plot.
seq_dot_plot_interpret .
seq_dot_plot_best_segments .
seq_show_segments Finds the best offset for aligning two sequences without gaps.

src/mol/seq_analysis.c

seq_aligned_identity Calculates the pairwise identities between aligned sequences.
seq_aligned_similarity Calculates the pairwise similarities between aligned sequences.
seq_aligned_profile Generates a PROSITE format profile from an aligned set of sequences.
seq_aligned_information Calculates the sequence logo representation for an alignment.
seq_aligned_hydrophobicity Calculates the average hydrophobicity at every position in an alignment.
seq_frequency_analysis Fourier transforms a vector for frequency analysis.
seq_correlated_mutation Correlated mutation analysis of an alignment.

src/mol/seq_util.c

seq_show Shows all molecular sequences.
seq_complement_all Complements all nucleotide sequences.
seq_translate_all Translates all nucleotide sequences to protein sequences.
seq_find_dna Finds a nucleotide sequence.
seq_find_protein Finds an amino acid sequence.
seq_find_protein_in_dna Finds the coding region for an amino acid sequence.
getcodeindex Obtains the index for a one-letter amino acid designation.
getcode Obtains the one-letter amino acid designation.
getcode3 Converts a one-letter amino acid designation to the three-letter equivalent.
getcode1 Converts a three-letter amino acid designation to the one-letter equivalent.
complement_sequence Complements a nucleotide sequence in place.
get_complement Get the Watson-Crick complement of a nucleotide base.
sequence_translate Translates a nucleotide sequence to a protein sequence.

src/ps/ps_ctf_plot.c

ps_ctf_plot Generates a postscript plot of a contrast transfer function.
ps_ctf_defocus_zeroes Generates a postscript plot of defocus versus zeroes.

src/ps/ps_marker.c

ps_marker_errors Output a postscript file that graphs the deviations of points in a
ps_marker_match Output a postscript file that draws a line between matching features

src/ps/ps_micrograph.c

ps_mg_particle_positions Postscript plot of the positions of particles on micrographs.
ps_particle_views_origins Generates asymmetric unit particle view and origin postscript plots.
ps_origins Generates postscript plot of origins on a square with the size of the box.
ps_part_fom_histogram Postscript plot of the particle FOM histogram.
ps_marker_errors Postscript plot of the errors associated with fiducial markers.
ps_dual_zcompare Generates a PostScript file that displays X by X, Y by Y,

src/ps/ps_model.c

ps_model_views Postscript plot of the distribution of model views.
ps_model_fom_histogram Postscript plot of the model component FOM histogram.
ps_model_occupancy Generates a postscript plot for a model occupancy analysis.

src/ps/ps_plot.c

ps_open_and_init Opens and initializes a postscript file.
ps_open_and_init Opens and initializes a postscript file.
ps_close Closes a postscript file.
ps_plot Generates postscript graphs.
ps_graph Generates postscript graphs.
ps_scale Generates a horizontal scale for a postscript graph.

src/ps/ps_sequence.c

ps_seq_info Generates a postscript plot from an information content analysis of
ps_seq_hydrophob Generates a postscript plot from a hydrophobicity analysis of

src/ps/ps_tree.c

ps_draw_tree Draws a tree into a postscript file.
ps_draw_node Draws a tree node into a postscript file.

src/ps/ps_views.c

ps_views Generates postscript plot of views on the unit sphere.
ps_views Generates postscript plot of views projected as phi and theta.
ps_sets_of_views Postscript plot of the distribution of sets of views.

src/rwimg/Bimage.c

Bsub_image::Bsub_image Initializes a sub-image.
Bimage::Bimage Initializes an image.
Bimage::Bimage Initializes an image.
Bimage::Bimage Initializes an image from an existing data block.
Bimage::Bimage Initializes a generic multi-channel image.
Bimage::~Bimage Image destructor.
Bimage::initialize Image initialization function.
Bimage::check Checks an image for reasonable properties.
Bimage::check_if_same_size Check if two images are the same size.
Bimage::data_alloc Allocate image data.
Bimage::data_alloc Allocate image data with size parameters.
Bimage::data_assign Assign image data.
Bimage::data_delete Deallocates the image data.
Bimage::FOM_find_maximum Calculates the maximum in the FOM block.
Bimage::FOM_initialize Allocates and initializes the FOM block.
Bimage::FOM_delete Deallocates the FOM block.
Bimage::FOM_write Writes the FOM block as an image.
Bimage::operator= Copies an image.
Bimage::operator[] Returns the data value at the given index.
Bimage::get Returns the data value at the given index.
Bimage::complex Returns a complex value at the given index.
Bimage::rgb Returns a color value at the given index.
Bimage::rgba Returns a color value at the given index.
Bimage::cmyk Returns a color value at the given index.
Bimage::set Sets a single value at the given index.
Bimage::set Sets a complex value at the given index.
Bimage::set Sets a color value at the given index.
Bimage::set Sets a color value at the given index.
Bimage::set Sets a color value at the given index.
Bimage::add Adds a value at a given location to neigboring data elements.
Bimage::set_max Sets a value at a given location to neigboring data elements if it is larger.
Bimage::average Averages in the xy plane when scaling is less than 1.
Bimage::interpolate Interpolates using a given location.
Bimage::interpolate_wrap Interpolates using a given location.
Bimage::data_type_size Returns the size of the datatype in bytes.
Bimage::compound_type_size Returns the compound size in number of channels.
Bimage::data_type_min Get the minimum of a datatype.
Bimage::data_type_max Get the maximum of a datatype.
Bimage::data_type_string Get the string representation of a datatype.
Bimage::fix_type Determines the replacement data type.
Bimage::change_type Get the data type indicated by a single letter code.
Bimage::change_type Get the data type from a string.
Bimage::change_type Change the data to the new type.
Bimage::to_mask Change the image to a mask.
Bimage::simple_to_complex A simple image is converted to a complex image.
Bimage::complex_to_real The real part of a complex image is written to a simple image.
Bimage::complex_to_intensities The intensities from a complex image is written to a simple image.
Bimage::complex_to_amplitudes The amplitudes from a complex image is written to a simple image.
Bimage::complex_to_signed_amplitudes The signed amplitudes from a complex image is written to a simple image.
Bimage::complex_to_phases The phases from a complex image is written to a simple image.
Bimage::simple_to_rgb A simple image is converted to a color image.
Bimage::simple_to_rgba A simple image is converted to a color image.
Bimage::color_to_simple A color image is converted to a simple image.
Bimage::rgb_to_rgba An alpha channel is added to a RGB color image.
Bimage::rgb_to_rgba The alpha channel is delete from an RGBA color image.
Bimage::rgb_to_cmyk Converts an RGB color image to CMYK.
Bimage::cmyk_to_rgb Converts a CMYK color image to RGB.
Bimage::zero_fourier_origin Zeroes the first voxel in each image.
Bimage::maximum_included_radius Returns the radius of the largest sphere or circle that will fit
Bimage::slices_to_images Changes the slices in a 3D image into a set of 2D images.
Bimage::images_to_slices Changes the 2D images to slices in a 3D image.
Bimage::statistics Calculates the statistics for an image.
Bimage::information Prints out header information for an image.
Bimage::subimage_information Prints out header information for all sub-images.
Bimage::copy Copies the header information and data of an image into a new image structure.
Bimage::copy_header Copy an image structure into a new one.
Bimage::extract Extracts one sub-image into new image structure.
Bimage::replace Replaces one sub-image in an image structure.
Bimage::invert Inverts the data in the image.
Bimage::reslice Switches axes of an image.
Bimage::add Adds a constant value to an image.
Bimage::multiply Multiplies an image with a constant value.
Bimage::power Calculates the power of an image.
Bimage::square Calculates the square of an image.
Bimage::square_root Calculates the square root of an image.
Bimage::complex_normalize Normalizes the power in a complex image.
Bimage::phase_shift Phase shifts a set of reflections.
Bimage::phase_shift_to_origin Phase shifts a set of reflections to the image origin.
Bimage::phase_shift_to_center Phase shifts a set of reflections to the nominal center of the image origin.

src/rwimg/rwASCII.c

readASCII Reading an ASCII or text image format.
writeASCII Writing an ASCII or text image format.

src/rwimg/rwBIORAD.c

readBIORAD Reading a BioRad image file format.
writeBIORAD Writing a BioRad image file format.

src/rwimg/rwBRIX.c

readBRIX Reading a BRIX image file format.
writeBRIX Writing a BRIX image file format.

src/rwimg/rwBrookhavenSTEM.c

readBrookhavenSTEM Reading a BrookhavenSTEM image file format.
writeBrookhavenSTEM Writing a BrookhavenSTEM image file format.

src/rwimg/rwCCP4.c

set_CCP4_machine_stamp Setting a CCP4 style machine stamp.
readCCP4 Reading a CCP4 map image file format.
writeCCP4 Writing a CCP4 map image file format.

src/rwimg/rwDI.c

readDI Reading a Digital Instruments image file format.

src/rwimg/rwDM.c

readDM Reading a Digital Micrograph image file format.
writeDM Writing a Digital Micrograph map image file format.

src/rwimg/rwDSN6.c

readDSN6 Reading a DSN6 map image file format.
writeDSN6 Writing a DSN6 map image file format.

src/rwimg/rwEM.c

readEM Reading a EM map image file format.
writeEM Writing a EM map image file format.

src/rwimg/rwGOODFORD.c

readGOODFORD Reading Peter Goodford's GRID map image file format.
writeGOODFORD Writing Peter Goodford's GRID map image file format.

src/rwimg/rwGRD.c

readGRD Reading a Basel GRD map image file format.
writeGRD Writing a Basel GRD map image file format.

src/rwimg/rwHKL.c

readHKL Reading a HKL structure factor file format.
writeHKL Writing a HKL structure factor file format.

src/rwimg/rwIMAGIC.c

readIMAGIC Reading an IMAGIC image format.
writeIMAGIC Writing an IMAGIC image format.

src/rwimg/rwimg.c

read_img General driver function to read multiple image formats
img_read_data Read image data in a generalized style.
write_img General driver function to write multiple image formats
write_fom_as_image Converts a FOM block to an image for output
img_write_data Writes a datablock with optional swapping.
img_convert_fourier Converts Fourier transform types.

src/rwimg/rwIP.c

readIP Reading an image plate reader file format.
writeIP Writing an image plate reader file format.

src/rwimg/rwJPEG.c

readJPEG Reading a JPEG image file format.
writeJPEG Writing a JPEG image file format.

src/rwimg/rwkernel.c

readKernel Reads a text kernel file.
writeKernel Writes a text kernel file.

src/rwimg/rwMFF.c

readMFF Reading a MFF image format.
writeMFF Writeing a MFF image format.

src/rwimg/rwMIFF.c

readMIFF Reading an Image Magick map image file format.
writeMIFF Writing an Image Magick map image file format.

src/rwimg/rwMRC.c

readMRC Reading a MRC map image file format.
writeMRC Writing a MRC map image file format.

src/rwimg/rwPIC.c

readPIC Reading a PIC image file format(s).
writePIC Writing a PIC image file format(s).

src/rwimg/rwPIF.c

readPIF Reading a PIF image and structure factor file format.
writePIF Writing a PIF image file format.

src/rwimg/rwPNG.c

readPNG Reading an PNG or text image format.
writePNG Writing an PNG or text image format.

src/rwimg/rwPNM.c

readPNM Reading a PNM type file.
writePNM Writing a PNM type file.

src/rwimg/rwPostScript.c

writePostScriptImage Writing a postscript image format.

src/rwimg/rwRAW.c

readRAW Reading a raw block of data in a file.
writeRAW Writing a raw block of data in a file.

src/rwimg/rwSPE.c

readSPE Reading a SPE image file format.
writeSPE Writing a SPE image file format.

src/rwimg/rwSPIDER.c

readSPIDER Reading a SPIDER image file format.
writeSPIDER Writing a SPIDER image file format.

src/rwimg/rwSUPRIM.c

readSUPRIM Reading a SUPRIM map image file format.
writeSUPRIM Writing a SUPRIM map image file format.

src/rwimg/rwTIFF.c

readTIFF Reading a TIFF image file format.
writeTIFF Writing a TIFF image file format.

src/rwimg/rwXPLOR.c

readXPLOR Reading a XPLOR map or structure factor file format.
writeXPLOR Writing a XPLOR map or structure factor file format.

src/rwmodel/rwmodel.c

read_model Reads model parameters.
write_model Writes model parameters.
model_init Initializes a model structure.
model_add Adds a model to a linked list.
component_type_add Adds a component type to a linked list.
component_add Adds a component to a linked list.
link_add Adds a component link to a linked list.
link_index Returns the index of a linked component.
model_set_map_filenames Sets all the map file names of selected models.
model_add_type_by_id Add a type to a model if the identifier does not exist already.
model_add_type_by_filename Add a type to a model if the type with the given file name does not exist already.
model_add_type_by_id_and_filename Add a type to a model if the type with the given id and file name does not exist already.
model_get_type Return the type corresponding to an identifier.
model_set_type Reset the component types.
model_count_component_types Counts the number of components for each type.
model_check Checks model properties.
model_component_count Counts the total number of components.
model_list_setup_links Set up the link list for each component.
model_setup_links Set up the link list for each component.
model_list_copy Copies a model.
model_copy Copies a model.
component_type_copy Copies all elements from one component to another.
component_copy Copies all elements from one component to another.
component_find Finds a component in a component list.
component_kill Deallocates memory for one component.
component_list_kill Deallocates memory for a list of components.
comp_type_kill Deallocates memory for one component type.
comp_type_list_kill Deallocates memory for a list of component types.
model_link_list_kill Deallocates memory for a list of component links.
link_kill Deletes a link.
link_kill Deletes a link.
poly_list_kill Deallocates memory for a list of polygons.
comp_associated_links_kill Deallocates memory for links associated with a component.
model_kill Deallocates all memory in the list.
model_update_comment Puts a set of strings and time in the comment of a model.
model_associate Associates a model file with a component type.
model_associate_mass Associates a mass with a component type.
model_set_comptype_filenames Sets the filenames of all selected component types to the given string.
model_link_list_generate Generates a link list for a model based on vertex separation.
model_set_link_length Sets the reference link lengths.
model_set_component_radius Set the display radius for all components to a specific value.
model_set_link_radius Set the display radius for all links to a specific value.
model_set_density Set the density of selected components to a specific value.
model_set_fom Set the FOM of selected components to a specific value.

src/rwmodel/rwmodel_cmm.c

read_model_chimera Reads Chimera marker model parameters.
write_model_chimera Writes Chimera marker model parameters.

src/rwmodel/rwmodel_mol.c

read_model_molecule Reads molecular model parameters.
write_model_molecule Writes molecular model parameters.

src/rwmodel/rwmodel_star.c

read_model_star Reads STAR model parameters.
write_model_star Writes STAR model parameters.

src/rwmodel/rwmodel_vega.c

read_model_vega Reads Vega model parameters.
write_model_vega Writes Vega model parameters.

src/rwmodel/rwmodel_xml.c

read_model_xml Reads XML model parameters.
write_model_xml Writes XML model parameters.

src/rwmol/rwClustal.c

readClustal Reads Clustal format sequence files.
writeClustal Writes Clustal format sequence files.

src/rwmol/rwEMBL.c

readEMBL Reads EMBL format sequence files.
writeEMBL Writes EMBL format sequence files.

src/rwmol/rwFASTA.c

readFASTA Reads FASTA format sequence files.
writeFASTA Writes FASTA format sequence files.

src/rwmol/rwGenBank.c

readGenBank Reads GenBank format sequence files.
writeGenBank Writes GenBank format sequence files.

src/rwmol/rwGROMACS.c

readGROMACS Reads a Gromacs coordinate file.
writeGROMACS Writes a Gromacs coordinate file.

src/rwmol/rwmol_star.c

read_mol_star Reads a molecule group from a STAR format file.
write_mol_star Writes a molecule group to a STAR format file.

src/rwmol/rwmol_text.c

read_mol_text Reads a molecule group from a text file.
write_mol_text Writes a molecule group to a text file.

src/rwmol/rwmolecule.c

molgroup_init Initializes and allocates a new molecule group.
molecule_add Adds a molecule to a linked list.
residue_add Adds a residue to a linked list.
atom_add Adds an atom to a linked list.
residue_count Counts the number of residues in a molecule group.
atom_count Counts the number of atoms in a molecule group.
atom_clean_type Cleans up the type string and assigns an element code to an atom.
bond_add Adds a bond to a linked list.
angle_add Adds an angle to a linked list.
molgroup_list_kill Destroys a molecule group linked list.
molgroup_kill Destroys a molecule group.
molecule_kill Destroys a molecule.
residue_kill Destroys a residue.
bond_kill Dealocates a list of bonds.
angle_kill Dealocates a list of angles.
molgroup_list_copy Copies a molecule group list.
molgroup_copy Copies a molecule group.
molecule_copy Copies a molecule.
mol_copy_and_add_to_molgroup Copies a molecule and assign to a new pointer in the molgroup.
molgroup_bond_list_copy Copies a bond list.
molgroup_from_molgroup_list Converts a molecule group list to a single molecule group.
read_molecule The generalized function for reading molecular files.
write_molecule Writes a molecule group.
molgroup_list_write Writes a molecule group list.
molgroup_count_molecules Counts the total number of molecules in a molecule group.
molgroup_count_residues Counts the total number of residues in a molecule group.
mol_count_residues Counts the total number of residues in a molecule.
molgroup_count_atoms Counts the total number of atoms in a molecule group.
mol_count_atoms Counts the total number of atoms in a molecule.
molgroup_consolidate_gaps Removes redundant gaps from an alignment.
molgroup_stats Calculates the statistics of a molecule group.
mol_stats Calculates the statistics of a molecule.
molecule_update_comment Puts a set of strings and time in the main comment of a molecule group.
molecule_get_masses Gets atomic masses from a parameter file.
molgroup_bond_list_generate Generates a bond list based on atom separation.

src/rwmol/rwPDB.c

readPDB Reads a PDB format coordinate file.

src/rwmol/rwPhylip.c

readPhylip Reads Phylip format sequence files.
writePhylip Writes Phylip format sequence files.

src/rwmol/rwPIR.c

readPIR Reads PIR format sequence files.
writePIR Writes PIR format sequence files.

src/rwmol/rwWAH.c

readWAH Reads a Wayne Hendrickson coordinate file.
writeWAH Writes a Wayne Hendrickson coordinate file.

src/rwparam/rwatomprop.c

get_atom_properties Reading atomic properties from parameter files.
write_atom_properties Writing atomic properties from parameter files.
atom_type_add Adds an atom type structure to a linked list.
atom_type_kill Destroys an atom type.

src/rwparam/rwgencode.c

get_genetic_code Gets the genetic code from a parameter file.
write_genetic_code Writing genetic code.
index_from_codon Gets the index associated with a specific codon.

src/rwparam/rwmatrix.c

read_matrix Reads a matrix file.
write_matrix Writes a matrix file.

src/rwparam/rwmd.c

md_init Initializes a molecular dynamics structure.
md_init_with_types Initializes a molecular dynamics structure.
read_md_parameters Reading molecular dynamics parameters from STAR files.
write_md_parameters Writing molecular dynamics parameters to a STAR file.
md_kill Deallocates a molecular dynamics structure.

src/rwparam/rwmg.c

read_project Reading micrograph parameters from files.
write_project Writing micrograph parameters to a file.
project_update_comment Puts a set of strings and time in the main comment of a project.

src/rwparam/rwmgSTAR.c

read_project_star Reading micrograph parameters from STAR files.
write_project_star Writing micrograph parameters to a STAR file.
mg_star_update_tags Replacing old STAR tags with new ones.

src/rwparam/rwmgXML.c

read_project_xml Reading micrograph parameters from XML files.
write_project_xml Writing micrograph parameters to a XML file.

src/rwparam/rwmodel_param.c

model_param_init Initializes a model parameter structure and allocates memory.
model_param_kill Deallocates memory for a model parameter structure.
model_param_read Reads a model parameter file.
model_param_write Writes a model parameter file.
model_param_display Displays a model parameter in the shell.
model_param_generate Generates a model parameter file from a model.
model_param_set_type_indices Sets the component type indices from the model parameters.

src/rwparam/rwresprop.c

get_residue_properties Reading residue properties from parameter files.
write_residue_properties Writing residue properties from a parameter file.
get_residue_matrix Reading a residue matrix from a file.
residue_matrix_kill Deallocating a residue matrix.

src/rwparam/rwstar.c

init_star Creates a STAR data base.
kill_star Destroys a STAR data base.
kill_block Destroys a STAR data block.
kill_item Destroys an item in a data block in a STAR data base.
read_star Reads paramaters and data into a STAR data base from a list of files.
read_block Reads paramaters and data into a STAR data block from an open file.
read_single_item Reads a single-valued item or comment line into a STAR data block
read_loop_items Reads a loop structure with multiple items into a STAR data block
write_star Writes a STAR data base to one or more STAR format files.
write_block Writes paramaters and data from a STAR data block into an open file.
star_update_comment Puts a set of strings and time in the main comment of the STAR data base.
star_set_string_lengths Sets the maximum string lengths for each item in each block.
item_change_tag Replaces one tag with another in the STAR data base.
show_tags Prints the list of tags in the STAR data base.
item_index Gets the STAR item associated with a tag in a STAR data block.
block_find_with_tag Gets the first block associated with a tag in a STAR data base.
item_find Gets the STAR item associated with a tag in a STAR data block.
item_find_or_make Gets the STAR item associated with a tag in a STAR data block.

src/rwparam/rwsymop.c

read_symat Reading crystallographic symmetry operators.
read_symop Reading crystallographic symmetry operators.
write_symat Writing crystallographic symmetry operators.
write_pointgroup Writing point group symmetry operators.

src/rwparam/rwtree.c

read_tree Reads a phylip format tree file.
tree_read_node Reads a node into a tree structure.
tree_calculate_angle Calculates an angle for each node for plotting.
tree_delete_node Deletes a node with all daughter nodes.
tree_rotate Adds an angle to all nodes.
tree_show Shows a node with all daughter nodes.

src/rwparam/rwxml.c

xml_check_for_node Checks for an XML node.
xml_check_for_node_in_tree Checks recursively for an XML node in a tree.
xml_copy_string Copies a string value associated with an XML tag.
xml_get_string Returns a string value associated with an XML tag.
xml_get_integer Gets a integer value associated with an XML tag.
xml_get_float Gets a floating point value associated with an XML tag.
xml_set_integer_attribute Sets an integer value associated with an XML attribute tag.
xml_set_integer Sets an integer value associated with an XML tag.
xml_set_float Sets a floating point value associated with an XML tag.

src/util/binomial.c

Bnpk Calculates the probability of k occurrences in n cases.
binomial_fit Fits a distribution to one or more binomial distributions.

src/util/Bmatrix.c

matrix_show Displays the matrix contents.
img_from_matrix Converts a matrix to an image.
matrix_random Generates a matrix with random values.
matrix_rearrange Rearranges a matrix with a given order.

src/util/Bstring.c

string_add Adds a string to a linked list.
string_kill Kills a string linked list.
parameter_file_path Finds the parameter file path.
string_sort Sorts a list of strings in ascending (descending) lexical or value order.

src/util/cluster.c

affin_prop_clustering Generate clusters from a similarity matrix usinf affinity propagation.

src/util/ctf.c

CTFparam::CTFparam Initializes a CTF structure with default values.
CTFparam::update Updates a CTF structure from another.
CTFparam::calculate Calculates a CTF curve.
CTFparam::zeroes Calculates the zeroes of a CTF curve on the spatial frequency scale.
CTFparam::baseline_equation Generates a baseline equation string from 4 or 5 coefficients.
CTFparam::envelope_equation Generates an envelope equation string from 4 coefficients.
CTFparam::parse_baseline_equation Extracts the coefficients from the baseline string.
CTFparam::parse_envelope_equation Extracts the coefficients from the envelope string.
electron_wavelength Calculates the wavelength in angstrom from the acceleration voltage.
get_defocus_for_first_zero Calculates the defocus for a given first zero reciprocal space distance.

src/util/datatypes.c

gettypesize Get the size of a datatype.
getdatatype Get the data type indicated by a single letter code.
set_value_datatype Set a pointer to a value with a given data type.
set_value_with_datatype Set a pointer to a value with a given data type.

src/util/dynamic_programming.c

dp_matrix_scoring Calculates the scoring matrix in dynamic programming.
dp_matrix_backtrace Backtraces the scoring matrix in dynamic programming.

src/util/file_util.c

find_file Searches for a file within or without the given path.
file_type Checks the file type using the extension and contents.
fread_large Reads blocks of memeory no larger than 1Gb.
detect_and_fix_carriage_return Detects carriage returns in text files and converts them to new-lines.

src/util/kernel.c

kernel_mean Generates a kernel with a uniform non-zero value.
kernel_gaussian Generates a gaussian kernel.
kernel_laplacian_of_gaussian Generates a laplacian-of-gaussian kernel.
RSI_Kernel::RSI_Kernel Calculates a reciprocal space interpolation lookup table.
RSI_Kernel::interpolate Calculates the complex value at an image location by kernel-based interpolation.

src/util/linked_list.c

add_item Adds an item to a linked list.
copy_item Copies an item to an existing item without changing the link.
remove_item Finds the given item and deletes it from the linked list.
copy_list Generates a complete copy of a linked list.
kill_list Frees all the items in a linked list.
count_list Counts the number of items in a linked list.
reverse_list Reverse the order of items in a linked list.

src/util/marker.c

marker_stats Calculating image parameter statistics.
markers_copy Copies a set of markers.
markers_delete_non_selected Deletes markers not selected.
marker_shift Shifting markers.
marker_transform Transforming markers.
marker_find_matrix Determines the rotation matrix between two sets of markers.
marker_find_transform Determines the rotation matrix between two sets of markers.
markers_find_rottrans Finds the rotation and shift between two sets of vectors.
markers_map_and_find_transform This function finds the transform parameters between sets of
markers_limit This method constricts a marker set to target_num points.
model_from_markers Convert markers to a model.
marker_plane Fits a plane to a set of markers.
markers_sort_by_id Sorts a set of markers by ID number.
markers_renumber Renumbers a set of markers.
markers_center Centers a set of markers.
marker_sets_to_bild Generates a bild file with the two marker sets.

src/util/math_util.c

bfloor Truncates a value to a specified number of decimal places.
bround Rounds a value to a specified number of decimal places.
factorial Press W.H. et al (1992) Numerical Recipes in C.
number_of_combinations Press W.H. et al (1992) Numerical Recipes in C.
partition Determines the index k'th value in the array.
prime_factors Finds all the prime factor for the input number.
smallest_prime Finds the smallest prime number factor of the input number.
next_permutation Produces the next permutation in lexical order.
fishers_z_transform Calculates Fisher's z-transform.
betacf Press W.H. et al (1992) Numerical Recipes in C.
betai Press W.H. et al (1992) Numerical Recipes in C.

src/util/matrix.c

show_matrix Print out a matrix.
show_matrix Print out a matrix.
matrix_vector_multiply Multiplies a square matrix by a vector.
matrix_vector_multiply_in_place Multiplies a square matrix by a vector.

src/util/Matrix3.c

matrix3_show Print out a matrix.
matrix3_show_hp Print out a matrix.
matrix3_from_tilt_and_axis Calculates a 3x3 rotation matrix from given tilt and axis angles (2D).
matrix3_rotation_between_two_matrices Calculates the rotation between two matrices.
matrix3_singular_value_decomposition Inverts a 3x3 matrix using singular value decomposition.

src/util/matrix_eigen.c

jacobian_rotation Press W.H. et al (1992) Numerical Recipes in C.
eigen_sort Press W.H. et al (1992) Numerical Recipes in C.
principal_axes Calculates the principal axes of 3D coordinates.

src/util/matrix_linear.c

linear_least_squares Does a linear least squares fit between two vectors.
fit_polynomial Fits a data set to a polynomial function.
matrix_LU_decomposition Press W.H. et al (1992) Numerical Recipes in C.
matrix_singular_value_decomposition Press W.H. et al (1992) Numerical Recipes in C.

src/util/matrix_util.c

matrix_log_1_R Calculates the logarithmic derivative of an R-factor in a matrix.
matrix_find_linear_sequence Finds a linear sequence of elements based on a pairwise matrix.
matrix_permute Permutes the order of a pairwise matrix and calculate a distance criterion.
matrix_calc_dist_fit Calculates an R-factor for a specific order of elements in a pairwise matrix.

src/util/moving_average.c

moving_average Calculates a moving average over an array of data.
moving_average_complex Calculates a moving average over an array of complex data.

src/util/options.c

get_option_list Parses command line arguments based on a template.
option_kill Deallocates a linked list of option structures.
get_option_verbose Sets the verbose option.
get_option_string Sets the desired output data type for images.
get_option_filename Sets the desired output data type for images.
get_option_datatype Sets the desired output data type for images.
get_option_size Sets the 3D size for an image.
get_option_origin Gets the 3D origin for an image.
get_option_sampling Sets the sampling or voxel size for an image.
get_option_vector3 Gets a 3-value vector.
get_option_normalized_vector3 Gets a normalized 3-value vector.
get_option_view Gets a view vector and the rotation angle around it.
get_option_fill_value Sets the fill value for various operations involving adding or replacing data.
get_option_symmetry Sets the symmetry point group string.
get_option_unit_cell Gets crystal unit cell parameters.
get_option_ctf_action Gets the type of CTF operation.
get_option_mass Returns the adjusted mass based on the added character.

src/util/qsort_functions.c

QsortSmallToLargeFloat Utility function for sorting floating point values in qsort.
QsortLargeToSmallFloat Utility function for sorting floating point values in qsort.
QsortSmallToLargeDouble Utility function for sorting double precision floating point values in qsort.
QsortLargeToSmallDouble Utility function for sorting double precision floating point values in qsort.
QsortSmallToLargeIntFloat Utility function for sorting int float pairs in qsort.
QsortLargeToSmallIntFloat Utility function for sorting int float pairs in qsort.

src/util/Quaternion.c


src/util/random_numbers.c

get_rand_max Finds the maximum random number for a system.
random_array_uniform Generates a series with a uniform random distribution.
random_gaussian Generates a value with a gaussian random distribution.
random_array_gaussian Generates a series with a gaussian random distribution of values.
random_poisson Press W.H. et al (1992) Numerical Recipes in C.
random_array_poisson Press W.H. et al (1992) Numerical Recipes in C.
random_logistical Generates a value with a logistical random distribution.
random_array_logistical Generates an array with a logistical random distribution.
vector3_random_unit_sphere Generates a random vector on the unit sphere.
vector3_random Generates a random vector within a defined cube.
vector3_random Generates a random vector within a defined cube.
vector3_random Generates a random vector within a defined sphere.
vector3_random_gaussian Generates a random vector within a random gaussian-distributed length.
vector3_xy_random_gaussian Generates a random vector within a random gaussian-distributed length in the xy plane.

src/util/simplex.c

simplex Press W.H. et al (1992) Numerical Recipes in C.
init_simplex Initializes a Bsimplex structure.
kill_simplex Frees all memory associated with a Bsimplex structure.

src/util/spline.c

vector3_catmull_rom_spline Calculates a 2D/3D spline curve using the Catmull-Rom algorithm.

src/util/symmetry.c

init_point_group_symmetry Sets up a symmetry structure from a string identifier.
kill_symmetry Deallocates a symmetry structure.
symmetry_clean_pointgroup Corrects an existing point group string.
symmetry_order Returns the symmetry order.
symmetry_get_axes Get all symmetry axes.
symmetry_get_all_views Get all symmetry-related views of one given view.
symmetry_get_all_matrices Get all symmetry-related views of one given view.
asymmetric_unit_views Initializes a well-distributed set of views in an asymmetric unit.
side_views Initializes a set of views around the z-axis for helical projection.
change_views_to_asymmetric_unit Change the views to those in the asymmetric unit.
find_asymmetric_unit_view Finds the corresponding view in the asymmetric unit.
reference_asymmetric_unit_views Returns a reference view for each asymmetric unit.
test_asymmetric_unit_view Returns an asymmetric unit index number.
sym_matrices_from_text_list Calculates symmetry matrices from a list of strings.
sym_show_matrices Show symmetry matrices.
sym_show_operational_matrices Show symmetry matrices associated with each symmetry operator.

src/util/timer.c

getwalltime Returns the current time.
getcputime Returns the clock time.
timer_start Starts timer and prints the time.
timer_report Reports the time elapsed since a given time.

src/util/Transform.c

transform_matrix_solve Solves a 3D geometry fit matrix.
transform_find Determines the transformation between two sets of vectors.

src/util/trigonometry.c

bcos Avoid non-zero values for cos(PI/2) and cos(-PI/2).
bsin Avoid non-zero values for sin(PI) and sin(-PI).
btan Avoid non-zero values for tan(PI) and tan(-PI).
bacos Wrapper to avoid NaN's returned from acos.
basin Wrapper to avoid NaN's returned from asin.
batan2 Sets small values to zero before calling atan2.

src/util/UnitCell.c

calc_skew_matrix Calculates the skew matrix from the unit cell parameters.

src/util/utilities.c

get_cmd_line Returns the command line as a string.
command_line_time Returns a set of strings and time in a string.
usage Prints usage information.
systype Finds the system type - mostly just for byte order.
bexit Exit function for cleanup and debugging.
select_numbers Converts a string with a selection specification into an integer array.
findNextPowerOf Finds the next greatest number that is a power of a given number.
get_integer Converts a defined length string into an integer.
get_float Converts a defined length string into a floating point number.
swapbytes Swaps bytes.
swapbytes Swaps bytes.
vax2ieee Converts VAX floating point format to IEEE floating point format.
angle_set_negPI_to_PI Returns an angle between -PI and PI.
remove_negative_zeros Prevent a negative sign from being placed in front of zero value in
get_chunk_size Returns the chunk size per thread.
error_show Displays the error with file and line reference.

src/util/View.c

show_views Displays a linked list of views.
view_from_tilt_and_axis Calculates a view from given tilt and axis angles (2D).
view_from_angle_and_axis3 Calculates a view from a given axis and angle.
tilt_views Initializes a set of views tilted around the y axis.
random_view Calculates a random view.
random_views Calculates a set of random views.
views_within_limits Generates a list of views within an angular distance from the input view.
views_for_refinement Generates a 3x3 grid of views around an input view.
view_list_expand_angles Expands each view to several views with different rotation angles.
view_list_subset Replaces a view list with a subset of it.
matrix3_random_reslice Generates a random reslicing 3x3 rotation matrix.


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