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FreeMOL Design Document |
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FreeMOL Design Document (draft ideas subject to further refinement) |
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Goal: |
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Aggregate a small set open-source software projects together into a |
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maintainable form which can support integration with PyMOL and other |
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interactive applications via platform-specific binary distributions. |
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Aggregate a managable set of open-source molecular software tools |
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together into a maintainable form which can support integration with |
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PyMOL and other interactive applications via quality-controlled |
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platform-specific binary distributions. |
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Structure: |
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"src" top-level directory with a set of subdirectories containing |
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source code for the various FreeMOL packages |
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"src" top-level directory with distinct subdirectories containing |
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configure scripts and source code for the various FreeMOL packages |
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"freemol" top-level directory is a prototype framework for holding |
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executables and other required runtime files in typical "unix-like" |
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subdirectories: (freemol/bin, freemol/lib, freemol/share, |
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freemol/man, and so forth) The FREEMOL environment variable should |
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point at this directory. |
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"freemol" top-level directory is a prototype framework for a freemol |
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binary distribution that would contain executables and other |
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required runtime files in a typical "unix-/usr-like" tree: |
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(freemol/bin, freemol/lib, freemol/share, freemol/man, and so |
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forth). The FREEMOL environment variable should be set to point at |
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this directory. Please note that platform-specific binary |
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executables should not be checked into subversion into this |
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prototype directory tree. |
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Compilation: |
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Assuming the the FREEMOL environment variable has been defined, |
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each package can be compiled and installed into $FREEMOL by cd'ing |
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to its souce directory and issuing the following sequence of commands: |
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./configure |
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make |
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make install |
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Followed by a |
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make clean |
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to get rid of object code, intermediate files, etc. |
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Deployment: |
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A FreeMOL binary distribution would be a tar or zipped archive of |
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the freemol folder with executables compiled for a specific |
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architecture and which can be subsequently be located an relied upon |
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by PyMOL an other packages through the FREEMOL environment variable. |
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the $FREEMOL folder containing executables compiled for a specific |
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architecture. |
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Installation will amount to extraction of the archive and setting |
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of the FREEMOL environment variable to that PyMOL and other packages |
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can subquently locate and rely upon the freemol executables. |
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Pragmatic decisions: |
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Confirmed FreeMOL Packages: |
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mengine |
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mengine |
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mpeg_encode |
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apbs |
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pdb2pqr |
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Proposed FreeMOL Packages |
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apbs |
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mpeg_encode |
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python |
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rdkit |
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openbabel |
