Package coan
[hide private]

Package coan

source code

This is the base module of the CoAn package that acts as a general framework for subpackages.


Version: 1.0.beta1

Submodules [hide private]
  • coan.__selftests__: Test suite hooks, these aren't imported in normal coan use
  • coan.__tests__: Test suite hooks, these aren't imported in normal coan use
  • coan.coma: Coordinate Manipulation toolbox (CoMa)
    • coan.coma.contacts: This module defines a Contacts class for evaluating contacts between two molecular structure objects of the coordinate manipulation toolbox (CoMa)
    • coan.coma.general: This module defines general functions that operate on molecular structure objects for the coordinate manipulation toolbox (CoMa)
    • coan.coma.io: This module populates and defines the high-level and molecular structure objects for the coordinate manipulation toolbox (CoMa)
  • coan.deman: Density Manipulation toolbox (DeMan)
    • coan.deman.__tests__: Unit testing, this module will not be imported in normal coan use
    • coan.deman._io
    • coan.deman.curves: This module defines a class for 1D data, Curve.
    • coan.deman.filters: This module defines filter functions that operate on density objects for the density manipulation toolbox (DeMan)
    • coan.deman.general: This module defines general functions that operate on density objects for the density manipulation toolbox (DeMan)
    • coan.deman.io: This module defines the volume and image classes and their methods for the Density Manipulation toolbox (DeMan)
    • coan.deman.masking: This module contains routines for masking
    • coan.deman.phantoms: Module to make various types of phantoms
    • coan.deman.stacks: This defines stack-like list classes and their methods for the Density Manipulation toolbox (DeMan)
    • coan.deman.stats: This module defines an object and functions for handling statistically connected densities such as an average and the corresponding variance or a difference and the corresponding confidence map.
  • coan.fortran: fortran library module of the various CoAn packages
  • coan.utils: This is the utility module of the CoAn packages.
  • coan.viewers: This is the viewers module of the CoAn packages.

Imports: cylinder, convolveFilt, Stats, itk, Img, minFilt, combmax, maxMask, histoequiFilt, boxFilt, sphere, CTF, getMask, fftpack, filters, findMin, itkOK, backgaussFilt, LImg, phases, difference, ellipsoid, findMax, apply_b_factor, numarrayOK, unsharpenFilt, synthetic_data, makeMask, sogFilt, filterFor, medianFilt, IMPORTERS, modeFilt, apply_laplacian, apply_ctf, homoFilt, rectangle, memtester, combmin, cube, applyMask, apply_noise, elevate_image, apply_curve, Curve, adaptFilt, imedFilt, beltramiFilt, denCC, plane, gaussFilt, IO, spherical_avg, line, distance_transform, maxFilt, psmFilt, butterworth, rankFilt, sigmoidFilt, autoMask, average, denMSE, dogFilt, match_amplitudes, curvatureFlowFilt, calc_fsc, openingFilt, closingFilt, LMap, mapFor, nadFilt, Residue, make_refmac_def, istandard, lsqkab, ismedium, lsq, isaliphatic, homologize, islarge, minidist, acepairwise, ishydrophobic, acevalue, Contacts, Ensemble, MolStruc, isaromatic, residuePP, Atom, isbasic, partialcharge, Coord, isacidic, GenStruc, residue_mass, REFMAC_DEF, bfac_match, issmall, rmsd, Chain, StringIO, biopythonSeq, morph, closedist, ispolar, RESET, OneToThree, runLoc, principal, degrees, getCCstats, EMData_to_Img, coan_history, euclDist, load_obj, ThreeToOne, Magic, fileCheck, scipy, split_list, rotate, signal, radians, Numeric, coanObj, only_standard_chars, cosh, Version, angle_stats, stats, asarray, LObj, BLINK, ndimage, log2, getRPP, interpolate, EMData_to_Map, simplex, miniInput, sinc, cos, mtzPar, argvInt, arccos, std_of_variance, backup, Img_to_EMData, argvFloat, save_obj, Transform, arctan2, notify, Map_to_EMData, RED, plot, findangles, log, std_of_std, NOBLINK, optimize, findDot, translate, arcsin, rlen, ACEtab, except_light, copy, crossprod, info, pi, tanh, log10, get_time, chkERR, checkFile, scan, transformFor, ACEid, deepcopy, tan, revstr, imod, angle_diff, sqrt, arctan, sin, RfromEul, warnings, glob, sys, sinh, calc_pix_size, pymol, coan_last, exp, humantime, Map, socket, tempfile, os, Image, subprocess, Queue, threading, Chimera, Structure, CoAnSocketClient, time, chimera, InvalidSendObjectError, numpy, math, CoAnSocketServer, coma, contacts, curves, deman, fortran, general, interactive, io, listobject, masking, misc, phantoms, stacks, transform, utils, viewers