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1 < FreeMOL Design Document
1 > FreeMOL Design Document (draft ideas subject to further refinement)
2  
3   Goal:
4  
5 <  Aggregate a small set open-source software projects together into a
6 <  maintainable form which can support integration with PyMOL and other
7 <  interactive applications via platform-specific binary distributions.
5 >  Aggregate a managable set of open-source molecular software tools
6 >  together into a maintainable form which can support integration with
7 >  PyMOL and other interactive applications via quality-controlled
8 >  platform-specific binary distributions.
9  
10   Structure:
11  
12 <  "src" top-level directory with a set of subdirectories containing
13 <  source code for the various FreeMOL packages
12 >  "src" top-level directory with distinct subdirectories containing
13 >  configure scripts and source code for the various FreeMOL packages
14  
15 <  "freemol" top-level directory is a prototype framework for holding
16 <  executables and other required runtime files in typical "unix-like"
17 <  subdirectories: (freemol/bin, freemol/lib, freemol/share,
18 <  freemol/man, and so forth) The FREEMOL environment variable should
19 <  point at this directory.
15 >  "freemol" top-level directory is a prototype framework for a freemol
16 >  binary distribution that would contain executables and other
17 >  required runtime files in a typical "unix-/usr-like" tree:
18 >  (freemol/bin, freemol/lib, freemol/share, freemol/man, and so
19 >  forth).  The FREEMOL environment variable should be set to point at
20 >  this directory.  Please note that platform-specific binary
21 >  executables should not be checked into subversion into this
22 >  prototype directory tree.
23 >
24 > Compilation:
25 >
26 >  Assuming the the FREEMOL environment variable has been defined,
27 >  each package can be compiled and installed into $FREEMOL by cd'ing
28 >  to its souce directory and issuing the following sequence of commands:
29 >
30 >    ./configure
31 >    make
32 >    make install
33 >    
34 >  Followed by a
35 >
36 >    make clean
37 >
38 >  to get rid of object code, intermediate files, etc.
39  
40   Deployment:
41  
42    A FreeMOL binary distribution would be a tar or zipped archive of
43 <  the freemol folder with executables compiled for a specific
44 <  architecture and which can be subsequently be located an relied upon
45 <  by PyMOL an other packages through the FREEMOL environment variable.
43 >  the $FREEMOL folder containing executables compiled for a specific
44 >  architecture.  
45 >
46 >  Installation will amount to extraction of the archive and setting
47 >  of the FREEMOL environment variable to that PyMOL and other packages
48 >  can subquently locate and rely upon the freemol executables.
49  
50   Pragmatic decisions:
51  
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56  
57   Confirmed FreeMOL Packages:
58  
59 <  mengine
59 >  mengine
60 >  mpeg_encode
61 >  apbs
62 >  pdb2pqr
63    
64   Proposed FreeMOL Packages
65  
40  apbs
41  mpeg_encode
66    python
67    rdkit
68    openbabel

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