Cleanup actions: split all_actions.py into modules in actions/ folder

pytraj/__init__.py

@@ -109,89 +109,6 @@
 from .analysis import topology_analysis
 
 from . import all_actions
-from .all_actions import analyze_modes
-from .all_actions import acorr
-from .all_actions import align
-from .all_actions import align_principal_axis
-from .all_actions import atomicfluct
-from .all_actions import atom_map
-from .all_actions import autoimage
-from .all_actions import angle
-from .all_actions import atomiccorr
-from .all_actions import atomicfluct
-from .all_actions import bfactors
-from .all_actions import center_of_geometry
-from .all_actions import center_of_mass
-from .all_actions import diffusion
-from .all_actions import dihedral
-from .all_actions import distance
-from .all_actions import closest_atom
-from .all_actions import count_in_voxel
-from .all_actions import distance_to_point
-from .all_actions import distance_to_reference
-from .all_actions import mindist
-from .all_actions import molsurf
-from .all_actions import multidihedral
-from .all_actions import pairdist
-from .all_actions import pairwise_distance
-from .all_actions import pairwise_rmsd
-from .all_actions import radgyr
-from .all_actions import radgyr_tensor
-from .all_actions import rdf
-from .all_actions import rotdif
-from .all_actions import rmsd_nofit
-from .all_actions import rotation_matrix
-from .all_actions import surf
-from .all_actions import volmap
-from .all_actions import volume
-from .all_actions import watershell
-from .all_actions import center
-from .all_actions import check_structure
-from .all_actions import check_chirality
-from .all_actions import fiximagedbonds
-from .all_actions import closest
-from .all_actions import crank
-from .all_actions import density
-from .all_actions import _dihedral_res
-from .all_actions import distance_rmsd
-from .all_actions import get_average_frame
-from .all_actions import get_velocity
-from .all_actions import set_velocity
-from .all_actions import gist
-from .all_actions import grid
-from .all_actions import _grid
-from .all_actions import image
-# from .all_actions import lifetime
-from .all_actions import lowestcurve
-from .all_actions import make_structure
-from .all_actions import native_contacts
-from .all_actions import pca
-from .all_actions import principal_axes
-from .all_actions import projection
-from .all_actions import pucker
-from .all_actions import randomize_ions
-from .all_actions import replicate_cell
-from .all_actions import rmsd
-from .all_actions import rmsd_perres
-from .all_actions import rotate
-from .all_actions import rotate_dihedral
-from .all_actions import scale
-from .all_actions import search_neighbors
-from .all_actions import set_dihedral
-from .all_actions import strip
-from .all_actions import superpose
-from .all_actions import symmrmsd
-from .all_actions import timecorr
-from .all_actions import transform
-from .all_actions import translate
-from .all_actions import velocityautocorr
-from .all_actions import wavelet
-from .all_actions import xcorr
-from .all_actions import ti
-from .all_actions import lipidscd
-from .all_actions import xtalsymm
-from .all_actions import hausdorff
-from .all_actions import permute_dihedrals
 from .all_actions import *
 
 from .analysis.matrix import dist as distance_matrix

pytraj/actions/__init__.py

@@ -0,0 +1,12 @@
+# Import all actions for backward compatibility
+from .base import *
+from .geometry import *
+from .structure import *
+from .diffusion import *
+from .energy import *
+from .spectroscopy import *
+from .topology_manipulation import *
+from .visualization import *
+from .correlation import *
+from .pca import *
+from .utilities import *