ó s™xTc@ sdZddlmZddlmZmZddlmZddlZddl Z ddl Z d„Z e dkr‰e e j dƒndS( sü scitbx_rigid_body_essence ========================= - A subset of ``scitbx/rigid_body/essence`` that can be used in isolation. - Plain Python code for rigid body dynamics and gradient-driven minimization. - Main reference:: Rigid Body Dynamics Algorithms. Roy Featherstone, Springer, New York, 2007. ISBN-10: 0387743146 - `Open Source License `_ Context ------- ``scitbx/rigid_body/essence`` grew out of the development of the dynamics engine for the ``phenix.refine`` **torsion angle dynamics** module, which is used as a complementary method to gradient-driven minimization, as a way to escape from local minima. See also: - Rice & Brunger (1994). Proteins: Structure, Function, and Genetics 19, 277-290. - http://phenix-online.org/ Nomenclature ------------ The variable names in the ``scitbx/rigid_body/essence`` source code follow the nomenclature used in Featherstone's *Rigid Body Dynamics Algorithms* as much as possible. Numerous ``RBDA`` comments point to equations, tables, and figures in the book. **When using the source code, it will be essential to have the book available as an introduction and reference.** Details ------- Files:: featherstone.py: dynamics algorithms, based on Roy Featherstone's Matlab library spatial_lib.py: spatial algebra, also based on Roy Featherstone's library joint_lib.py: some joint models body_lib.py: corresponding body objects scitbx_matrix.py: general matrix algorithm (copy of scitbx/matrix/__init__.py) tst_basic.py: unit tests compatible with Python 2.2 or higher Download all files at once: - http://cctbx.sourceforge.net/scitbx_rigid_body_essence.tgz - http://cctbx.sourceforge.net/scitbx_rigid_body_essence.zip To run the unit tests:: cd scitbx_rigid_body_essence python tst_basic.py The full scitbx/rigid_body functionality requires compiled modules, written in C++. Download the entire scitbx from here: - http://cci.lbl.gov/scitbx_bundles/current/ or the entire cctbx (of which scitbx is a subset) from here: - http://cci.lbl.gov/cctbx_build/ Follow the instructions on the latter page to install the cctbx or scitbx bundles (e.g. ``perl scitbx_bundle.selfx``). The cctbx source tree is hosted at SourceForge. The latest versions of the files in scitbx_rigid_body_essence can be found here: - http://cctbx.svn.sourceforge.net/viewvc/cctbx/trunk/scitbx/rigid_body/essence/ A version of featherstone.py that's closer to Roy Featherstone's original Matlab code can be found here: - http://cctbx.svn.sourceforge.net/viewvc/cctbx/trunk/scitbx/rigid_body/proto/ The file ``wx_tardy.py`` is a simple 3D graphical viewer displaying trajectories. It requires ``wxPython`` and the ``gltbx`` module of the cctbx project. An easy way to get everything in one file and install with a single command, is to download the phenix package from: - http://phenix-online.org/ Send questions to: cctbx@cci.lbl.gov or cctbxbb@phenix-online.org iÿÿÿÿ(tdivision(t copy_filet remove_files(teasy_runNc s¶t|ƒdkst‚d}tjj|ƒs@tj|ƒntj|ƒtjj ddƒ‰d‡fd†}|ddƒ|d ƒ|d ƒ|d ƒ|d ƒ|d ƒt ddƒj t ƒtjdƒtj dksûtjjddƒ rÿdStdƒtdƒtjddƒjƒtjjdƒsAt‚tjddƒjƒtjjdƒsot‚tjdƒtjddƒjƒtdƒt ddƒj dƒJdS(Nitscitbx_rigid_body_essencet module_nametscitbxt.c s ttjjˆ|ƒ|ƒdS(N(Rtostpathtjoin(t file_namettarget(t scitbx_dist(sT/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/scitbx/rigid_body/essence/make_bundles.pytcpkssmatrix/__init__.pysscitbx_matrix.pys"rigid_body/essence/featherstone.pys!rigid_body/essence/spatial_lib.pysrigid_body/essence/joint_lib.pysrigid_body/essence/body_lib.pysrigid_body/essence/tst_basic.pys README.txttws..tnttnametdocutilssscitbx_rigid_body_essence.tgzsscitbx_rigid_body_essence.ziptcommands?tar zcf scitbx_rigid_body_essence.tgz scitbx_rigid_body_essences>zip -r scitbx_rigid_body_essence.zip scitbx_rigid_body_essences*docutils.rst2html README.txt > README.htmls .htaccesssOptions Indexes (tlentAssertionErrorRR tisdirtmkdirtchdirtlibtbxtenvt dist_pathtopentwritet__doc__Rt has_moduleRRtfully_bufferedtraise_if_errors_or_outputtisfiletraise_if_errors(targsttmpdirR((R sT/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/scitbx/rigid_body/essence/make_bundles.pytrunds@                  t__main__i(Rt __future__Rt libtbx.utilsRRRRtlibtbx.load_envtsysRR&t__name__targv(((sT/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/scitbx/rigid_body/essence/make_bundles.pyt\s  '