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_arithmetic.c

img_add_constant Adds a constant value to an image.
img_multiply_with_constant Multiplies an image by a constant value.
img_raise_to_power Raises an image to a power.

src/img/img_background.c

img_set_background Sets the background values.
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

img_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_gray2RGB Converts an image from gray scale to RGB (red-green-blue).
img_gray2RGBA Converts an image from gray scale to RGB (red-green-blue-alpha).
img_gray2color Converts an image from gray scale to RGB or RGBA.
img_RGB2gray Converts an image from RGB (red-green-blue) to gray scale.
img_indexed2gray Converts an image from indexed colour map to RGB (red-green-blue).
img_indexed2RGB Converts an image from indexed colour map to RGB (red-green-blue).
img_add_alpha Adds an alpha channel to generate a RGBA (red-green-blue-alpha) image.
img_remove_alpha Removes an alpha channel from a RGBA (red-green-blue-alpha) image.
img_RGB_to_CMYK Converts a RGB image to a CMYK image.
img_CMYK_to_RGB Converts a CMYK image to a RGB image.
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_colour_to_intensity Generates intensity without colour.
img_pure_colour Generates a pure colour image without intensity.
img_color_combine Combines two coloured images.

src/img/img_combine.c

img_compatibility Check if two images have the same number of channels and data type.
add_images Adds two images together.
img_add_weighed Adds multiple images together with given weights.
img_place Places a small image into a large image.
multiply_images Multiplies two images.
largest_img Selects the largest of each pixel from two images.
smallest_img 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
correlate_images Calculates a correlation image and a correlation coefficient between
correlate_images_within_radii Calculates a correlation image and a correlation coefficient between
histomatch_images 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_to_complex_short Converts any data type to a complex short.
img_to_complex_int Converts any data type to a complex integer.
img_to_complex_float Converts any data type to a complex floating point.
img_complex_product Calculates the complex product of two complex images.
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_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_complex2real Gets the real part of a complex floating point image.
img_complex2amplitudes Converts a complex image to an amplitude image.
img_complex2intensities Converts a complex image to an intensity image.
img_complex2phases Converts a complex image to a phase image.
img_complex2signedamplitudes Converts a complex image to a signed amplitude image.
img_merge_amplitudes_and_phases Merges the amplitudes from one map with the phases of another.
img_center_complex_origin Shifts a transform or powerspectrum to center the origin.
img_phase_shift Phase shifts a set of reflections.
img_phase_shift_to_origin Phase shifts a set of reflections to the image origin.
img_phase_shift_to_center Phase shifts a set of reflections to the nominal center of the image origin.
img_colour_power_spectrum Generates a power spectrum with phases coloured according to a colour wheel.

src/img/img_ctf.c

ctf_init Initializes a CTF structure with default values.
ctf_update Updates a CTF structure from another.
electron_wavelength Calculates the wavelength in angstrom from the acceleration voltage.
ctf_calculate Calculates a CTF curve.
ctf_ctf_calculate Calculates a CTF curve.
ctf_baseline_calculate Calculates a baseline value.
ctf_envelope_calculate Calculates an envelope value.
ctf_first_zero Calculates the first zero of a CTF curve in angstrom.
ctf_zeroes Calculates the zeroes of a CTF curve on the spatial frequency scale.
get_defocus_for_first_zero Calculates the defocus for a given first zero reciprocal space distance.
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.
ctf_fit_eman_to_baseline Fits an EMAN-style baseline function.
ctf_fit_gaussian Fits a gaussian function.
ctf_fit_double_gaussian_baseline Fits a double gaussian function.
ctf_fit_double_gaussian_envelope Fits a double gaussian function.

src/img/img_datatypes.c

gettypesize Get the size of a datatype.
getdatatype Get the data type indicated by a single letter code.
get_datatype_from_string Get the data type from a string.
get_string_from_datatype Get the string representation of a datatype.
get_string_from_values Get a formatted string from a pointer to data of a given type.
get_value_from_datatype Get a floating point value from a pointer to data of a given type.
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.
img_to_datatype Convert an image to any new data type.
img_to_bit Converts an image to a bitmap.
img_bit_to_byte Converts an image from a bitmap to a byte type.
img_to_byte Converts an image to character or byte type.
img_to_signed_byte Converts a byte image to signed char.
img_to_unsigned_short Converts an image to signed short or two-byte type.
img_to_short Converts an image to signed short or two-byte type.
img_to_int Converts an image to integer or four-byte type.
img_to_float Converts an image to four-byte floating point type.
img_to_double Converts an image to four-byte floating point type.

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_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_delete_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_for_show Converts a slice from an image to a 2D plane for display.
img_extract_for_show_avg Converts a slice from an image to a 2D plane for display.
img_extract_for_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.
img_extract_panels Extracts panels 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_filter Applies an averaging filter to an image.
img_median_filter Applies a median filter to an image.
img_peak_filter Applies a median filter to an image.
img_variance_mask Rescales an image based on local variance.
img_convolution_filter 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_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.
views_within_limits Generates a list of views within an angular distance from the input view.
refine_views Generates a 3x3 grid of views around an input view.

src/img/img_fourier.c

img_fft 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_masked Calculates an masked cross-correlation map by Fast Fourier transformation.
img_cross_correlate_validate Calculates an masked cross-correlation map by Fast Fourier transformation.
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_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_helix.c

img_helix_symmetrize Symmetrizes an image given helical symmetry parameters.
img_convert_to_helix Converts a map to a helix.

src/img/img_histogram.c

img_histogram Calculates the histogram of an image.
img_calc_histogram Calculates 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_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_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_to_mask Converts an image to a mask.
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_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_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_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_ced Denoises a 3D density map by isotropic coherence enhancing diffusion.
img_eed Denoises a 3D density map by anisotropic edge enhancing 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_find_particles Finds particles using a Hough transform with a simple ring.
img_pick_particles Picks particles using cross-correlation and segmentation.
img_find_particles_in_ccmap Finds the peaks in a cross-correlation map corresponding to particles.

src/img/img_polar.c

img_cartesian_to_spherical Calculates an image with spherical coordinates.
img_radial_shells Calculates an image with slices giving the radial shell projections.
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.

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_project_views Calculates a set of projections from a 3D density map.
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_average Calculates the radial average of an image.
img_elliptical_average Calculates the elliptical average of an image.
img_radial_volume Calculates the radial volume above a threshold in 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_fourier_reconstruction Reciprocal space reconstruction from the images in a multi-image file.

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 Analizes 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.
vector3_inside_outside Determines if a vector is inside or outside a polyhedral structure.
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_padAuthors: Dan Krainak and Bernard Heymann

src/img/img_resolution.c

img_resolution Calculates resolution measures.
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_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_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_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_add_with_rotation Rotates an image and adds it to the second image.
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_handedness Checks for the extent of handedness for any symmetric map.

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_get_density Returns the density at a specific voxel.
img_get_recip_resolution Calculates the reciprocal resolution from the resolution field.
img_average Averages images in a multi-image file.
img_select Selects a sub-images from a multi-image structure.
img_delete Deletes sub-images from a multi-image structure.
img_copy_selected Copies a single selected image from a multi-image 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_fill_upper_triangle Fills the upper triangle of an image with values from the lower triangle.
img_transpose Transposes an image.
img_zero_origin Zeroes all the origins in 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_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_random_defocus Introduces random errors into micrograph defocus averages.

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.
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.
mask_filament_particles Masks particles extracted from filaments.

src/mg/mg_hand.c

project_get_handedness Determines handedness for all selected particles (sel > 0) in a
hand_select_consist Sets consistent selection values in all (including unused) micrographs.

src/mg/mg_helix.c

mg_generate_layer_lines Generates reflections given the unit cell vectors.
img_mask_layer_lines Masks the image using the list of layer lines.

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_pimg Finds the best in-plane alignment for two 2D images using polar power spectra.
img_align2D_pimg_masked Finds the best in-plane alignment for two 2D images using polar power spectra.

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_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.
part_set_multi_maps Sets selection for generating multiple maps.
part_set_filament_maps Generates a selection 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 particles randomly with replacement.
part_select_group Selects particles with a given group identifier.
part_select_sets Selects sets of particles, each with the same size.
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_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_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.

src/mg/mg_pick.c

project_find_particles Finds particles in micrographs.
mg_pick_particles Picks particles from micrographs based on micrograph coordinates.
mg_find_particle_centers Finds the centers of picked particles within a micrograph.

src/mg/mg_processing.c

project_init Initializes a micrograph processing project parameter structure.
project_create Creates a micrograph processing project parameter structure.
project_create_from_images Creates a project structure using image file names.
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.
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_micrographs_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_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 micrograph with new information.
particle_update Updates an existing particle with new information.
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_particle_path Sets the path to particle 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.
micrograph_get_nominal_origin Gets the nominal origin for a micrograph.
project_set_micrograph_origins Sets micrograph origins to the given origin.
project_set_nominal_mg_origins Sets micrograph origins to the centers of the micrographs.
project_add_origins_to_coords Adds the particle origins to the micrograph coordinates.
project_renumber_particles Renumbers particles.
project_set_particle_origins Sets particle origins to given values.
project_reset_origins Resets particle origins to nominal values.
project_flip_particle_coordinates Reverses one or more particle coordinates.
project_random_origins Introduces random errors into particle origins.
project_random_views Introduces random errors into particle views.
project_random_magnification Introduces random errors into particle magnifications.
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.
project_apply_map_magnifications Change particle pixel sizes for particles based on map magnifications.
views_from_project Retrieves the particle views from a project.

src/mg/mg_tomo_rec.c

img_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 in an aligned tilt series.

src/mg/mg_tomo_track.c

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.
mg_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.
project_refine_scales Refines the micrograph scales.
project_refine_views Refines the views from the marker positions and marker model.
mg_marker_shift Finds the shift of a micrograph wrt the reference using markers.
mg_marker_z_search Refines the z-coordinate of a global marker model.
mg_z_matrix_update Updates the z-coordinate of a global marker model.
mg_marker_init Initializes markers from the reference.
mg_marker_update Calculates the predicted positions of markers from the reference.

src/mg/mg_tomography.c

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_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.
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_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.

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_by_order Colors model components in order from red to blue.
model_color_valency Colors model components with a given valency.
model_color_polygons Colors model polygons with a given order.
model_color_curvature Colors model vertices and links as a function of curvature.

src/model/model_mask.c

model_inside_outside Determines if a vector is inside or outside model boundaries.
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.

src/model/model_poly.c

poly_get_connectivity Generates polygons based on a vertex network.
model_poly_generate Generates polygons based on a vertex network.
model_vertex_types Determines the vertex type based on adjacent polygons.
model_poly_dual Calculates the dual of a polyhedral network.
model_poly_analyze Analyzes a model for polygon regularity and planarity.
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_find_symmetry Finds the symmetry axes associated with polyhedral elements.
model_distance_energy Calculates the energy based on the distances between components.
model_morse_energy Calculates the energy based on the distances between components.
model_link_energy Calculates the model link energy.
model_angle_energy Calculates the link angular forces and energy.
model_polygon_energy Calculates the polygon regularity.
model_polygon_plane_energy Calculates the polygon planarity.
model_point_force Calculates the forces and energy resulting from a single point force.
model_zero_forces Zeroes the component forces.
model_move_components_down_energy Move components random distances down the energy gradient.
model_calculate_deviations Calculates the deviations from regularity in a polyhedral model.
model_regularize Regularizes a model.

src/model/model_poly_delta.c

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

polygon_add Adds a polygon to a model based on the spiral algorithm.
model_poly_spiral Generates a polyhedron using the spiral algorithm.
model_poly_sphere_coor Generates coordinates for components based on the eigenvectors of the adjacency matrix.
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_all Resets the selection to all models.
model_reset_selection Resets the selection to all components.
model_select_closed Determines if a polyhedron is closed given a rule.
model_select_fullerene Selects fullerene type models.
model_select Selects components based on their types.
model_select_first Selects the first number of components.
model_delete 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_fom_deselect Deselects components based on the FOM.
model_fom_histogram Selects components based on the FOM.
model_remove_deselected Trims a set of solutions to the selected ones.

src/model/model_util.c

model_set_type Reset the component types.
model_rename_components Rename components.
model_center_of_mass Calculates the center-of-mass of a model.
model_center Shifts all models to their centers of mass.
model_principle_axes Calculates the principle axes of a model.
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_and_compare Copies and rotates the model and compares it with the original.
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_find_views Finds the molecule views with respect to a reference.
model_apply_point_group Applying symmetry to model components.
model_prune_overlapping_components Prunes overlapping components based on a distance criterion.
model_average_components Averages sequential components.
component_get_array Generates an array of pointers to component structures.
model_adjacency_matrix Constructs the adjacency matrix for a model.
model_shortest_path Calculates the shortest path between every pair of vertices.
model_wiener_index Calculates the Wiener index.
model_poly_eigen Eigenanalysis of the adjacency matrix.
model_calculate_views Calculates the views associated with each component.
model_curvature Calculates the curvature associated with each link.

src/mol/md.c

md_leapfrog Molecular dynamics using the leapfrog integrator.

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_bondlist_get_top Finds the top shortest bonds.
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_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_symmetry.c

molgroup_apply_point_group Generates all symmetry-related coordinates.
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_principle_axes Calculates the principle axes of a molecule group.
mol_principle_axes Calculates the principle 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.
mol_to_image 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.
mol_to_structure_factors Calculates a 3D set of structure factors from a set of atomic coordinates.

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_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.
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_coord.c

ps_coord_dev Output a postscript file that graphs the deviations of points in a
ps_coord_match Output a postscript file that draws a line between matching features
ps_PickedPartImg Output a postscript file that numbers and circles the particles

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_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_views Generates postscript plot of views on the unit sphere.
ps_origins Generates postscript plot of origins on a square with the size of the box.
ps_marker_errors Postscript plot of the errors associated with fiducial markers.
ps_part_fom_histogram Postscript plot of the particle FOM historgram.

src/ps/ps_plot.c

ps_open_and_init Opens and initializes a postscript file.
ps_graph Generates postscript graphs.
ps_scale Generates a horizontal scale for a postscript graph.
ps_resolution Generates one postscript page with graphs of resolution curves.

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/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

init_img General image structure initialization.
init_img_header General image header structure initialization.
init_img_with_parameters General image structure initialization with data memory allocation.
img_init_fom Initializes the FOM block.
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
write_data_block_as_image Converts a data block to an image for output.
img_write_data Writes a datablock with optional swapping.
copy_img_header Copy an image structure into a new one.
copy_img Copies the header information and data of an image into a new image structure.
move_img Moves an image from one pointer to another.
img_slices_to_images Changes the slices in a 3D image into a set of 2D images.
img_images_to_slices Changes the 2D images to slices in a 3D image.
kill_img General image structure destruction.
kill_all_but_main_img Deallocate all pointers in an image structure.
img_clear_data Sets the data block to zero.
img_fill_data Sets the data block to a given value.
img_check_param Checks an image structure for badly set parameters.
img_set_origin Sets the origins (offsets from the first voxel) in an image header.
img_set_sampling Sets the sampling values (voxel size) in an image header.
img_set_isotropic_sampling Sets the sampling values (voxel size) in an image header.
img_max_radius Returns the radius of the largest sphere or circle that will fit
img_stats Calculates the statistics for an image.
img_convert_fourier Converts Fourier transform types.
img_reslice Rotates an image by multiples of pi/2.
img_invert_data Inverts the image density data.
img_check_if_same_size Check if two images are the same size.
img_info Prints out header information for an image.
sub_img_info Prints out header information for all sub-images.

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/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.
writeMI