from .align import align, align_principal_axis, superpose
from .correlation import acorr, timecorr, velocity_autocorrelation, xcorr
from .crank import crank
from .dssp import dssp, dssp_allatoms, dssp_allresidues
from .energy_analysis import energy_analysis, ene_decomp, esander, lie
from .gist import gist, GistConfig, GistResult
from .infraredspec import infraredspec
from .lipidscd import lipidscd
from .fluct import atomicfluct, bfactors, rmsf
from .matrix import correl, covar, dist, mwcovar
from .structure import get_average_frame, mean_structure, make_structure, strip, radgyr_tensor
from .velocity import get_velocity
from .wavelet import wavelet
from .rmsd import distance_rmsd
from .pairwise import pairwise_rmsd
from .clustering import cluster_trajectory
from .transform import center, rotate, scale, transform, translate
from .nmr import (
    calc_ired_vector_and_matrix,
    calc_nh_order_parameters,
    ired_vector_and_matrix,
    jcoupling,
    nh_order_parameters,
)
from .pca import pca, projection
from .modes import analyze_modes
from .vector import vector, vector_mask
from .rotation import rotation_matrix
from .geometry import angle, dihedral
from .neighbors import search_neighbors
from .symmrmsd import symmrmsd
from .set_velocity import set_velocity
from .autoimage import autoimage
from .native_contacts import native_contacts
from .atom_map import atom_map
from .check_structure import check_structure
from .check_chirality import check_chirality
from .closest import closest, closest_atom
from .voxel import count_in_voxel
from .density import density
from .volmap import volmap
from .dihedral_rms import dihedral_rms
from .watershell import watershell
from .pairdist import pairdist
from .diffusion import diffusion, tordiff, toroidal_diffusion
from .multidihedral import multidihedral
from .permute_dihedrals import permute_dihedrals
from .ti import ti
from .lowestcurve import lowestcurve
from .randomize_ions import randomize_ions
from .dihedral_tools import rotate_dihedral, set_dihedral
from .atomiccorr import atomiccorr
from .fiximagedbonds import fiximagedbonds
from .surf import surf, molsurf
from .docking import docking, docking_ligplot_svg
from .pucker import pucker
from .rotdif import rotdif
from .multipucker import multipucker
from .xtalsymm import xtalsymm
from .trajectory import ArrayTrajectory

__all__ = [
    "align",
    "align_principal_axis",
    "superpose",
    "ArrayTrajectory",
    "crank",
    "acorr",
    "xcorr",
    "timecorr",
    "velocity_autocorrelation",
    "dssp",
    "dssp_allatoms",
    "dssp_allresidues",
    "energy_analysis",
    "esander",
    "lie",
    "ene_decomp",
    "gist",
    "GistConfig",
    "GistResult",
    "infraredspec",
    "lipidscd",
    "rmsf",
    "atomicfluct",
    "bfactors",
    "covar",
    "mwcovar",
    "dist",
    "correl",
    "mean_structure",
    "make_structure",
    "get_average_frame",
    "strip",
    "radgyr_tensor",
    "get_velocity",
    "wavelet",
    "distance_rmsd",
    "pairwise_rmsd",
    "cluster_trajectory",
    "center",
    "translate",
    "transform",
    "rotate",
    "scale",
    "ired_vector_and_matrix",
    "jcoupling",
    "nh_order_parameters",
    "calc_ired_vector_and_matrix",
    "calc_nh_order_parameters",
    "pca",
    "projection",
    "analyze_modes",
    "vector",
    "vector_mask",
    "rotation_matrix",
    "angle",
    "dihedral",
    "search_neighbors",
    "symmrmsd",
    "set_velocity",
    "autoimage",
    "native_contacts",
    "atom_map",
    "check_structure",
    "check_chirality",
    "closest",
    "closest_atom",
    "count_in_voxel",
    "density",
    "volmap",
    "dihedral_rms",
    "watershell",
    "pairdist",
    "diffusion",
    "tordiff",
    "toroidal_diffusion",
    "multidihedral",
    "permute_dihedrals",
    "ti",
    "lowestcurve",
    "randomize_ions",
    "rotate_dihedral",
    "set_dihedral",
    "atomiccorr",
    "fiximagedbonds",
    "surf",
    "molsurf",
    "docking",
    "docking_ligplot_svg",
    "pucker",
    "rotdif",
    "multipucker",
    "xtalsymm",
]
