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Cctbx

< MuSR.MuChirp | Index | cctbx initial trial >

Directory

 antlr3          ccp4io_adaptbx   crys3d         iotbx       PyCifRW  spotfinder
 boost           cctbx            fable          lapack_fem  rstbx    TAG
 boost_adaptbx   chiltbx          fftw3tbx       libtbx      scitbx   tbxx
 cbflib_adaptbx  clipper          gltbx          mmtbx       scons    tntbx
 ccp4io          clipper_adaptbx  gui_resources  omptbx      smtbx

non-crystallography related

 antlr3 (parser), boost... (c++ python interface), cbflib (detectors),
 ccp4io... (c++ io), chiltbx (c string handling?)
 fable (parser), fftw3tbx (own fft), gltbx (viewer related), gui_resources (images),
 iotbx (ditto), lapack_fem (ditto) libtbx (contains python tests, not clear),
 omptbx (stubs), spotfinder (works at beamlines, finds spot?) tbxx (c errors)
 tntbx (wrapper for TNT, numerical c++ library)

crystallography related:

• cctbx main project
• clipper_adaptbx python interface to c++ crystallographic library
• crys3d viewers (I don't get a catch)
• mmtbx contains refinements run_tests solvent twinning utils etc
• PyCifRW to read and write cif files, see previous page
• rstbx A reciprocal space toolbox to autoindex small molecule Bragg diffraction, given the reciprocal space vectors.

See README

• scitbx a series of mathematical libraries, examples work outside ipython (find how to run them within)
• smtbx random structures

Howto run_tests? examples? Works e.g from the cctbx_source/scitbx/example/ directory running

 scitbx.python chebyshev_lsq_example.py # or
 libtbx.python chebyshev_lsq_example.py

Have a look at cctbx_source/scitbx/example/rigid_body_refinement_core.txt

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cctbx main library

(from the reference) three main modules:

• eltbx, element toolbox, scattering factors, atomic weights, ionic radii etc.
• uctbx, unit-cell toolbox, UnitCell class, metric tensor...
• sgtbx, space-group toolbox, symmetry operations and transformation matrices INTERNALLY represented as integer matrices and base factors, e.g. default base factor for translation part of symmetry operation is 12, and translation part (x, y, z) internally represented as three integer numbers (12x, 12y, 12z)

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uctbx

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sgtbx ps = sgtbx.parse_string(hall_symbol) # e.g. hall_symbol="P 1" sg=sgtbx.space_group(ps) sgtbx.rot_mx_info(s.r()) sgtbx.translation_part_info(s) ???

Wickoff positions see /homerdr/ipython/ wyk.py

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crystal

b=crystal.symmetry(

    unit_cell=(5.55105, 5.57884, 8.47014, 90, 90, 90),
    space_group_symbol="Cmma")

b.show_summary() # risponde

 # Unit cell: (5.55105, 5.57884, 8.47014, 90, 90, 90)
 # Space group: C m m a (No. 67)

c=b.space_group() c.crystal_system() # risponde 'Orthorhombic' c.gridding() # risponde (2, 2, 1) ???? (c.is_centric(), c.is_chiral(), c.is_origin_centric(), c.is_tidy()) # risponde (True, False, True, True)
(c.laue_group_type(), c.point_group_type()) # ('mmm', 'mmm')
(c.r_den(), c.n_ltr(), c.n_smx(), c.order_p(), c.t_den(), c.order_z())# (1, 2, 4, 8, 12, 16) ????
# number of , lattice translations, representative symmetry operations, , ,total symmetry operations

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others

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References Ralf W. Grosse-Kunstleve et al. J. Appl. Cryst. 35 (2002) 126-136

< MuSR.MuChirp | Index | cctbx initial trial >