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1 < Hello!
1 > FreeMOL Design Document (draft ideas subject to further refinement)
2 >
3 > Goal:
4 >
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 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 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 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 >
52 >  Rely upon unix-like shell-based compilation (MinGW/Cygwin on Win32)
53 >
54 >  Stick with standalone, command-line only packages which have few if
55 >  any dependencies
56 >
57 > Confirmed FreeMOL Packages:
58 >
59 >  mengine
60 >  mpeg_encode
61 >  apbs
62 >  pdb2pqr
63 >  
64 > Proposed FreeMOL Packages
65 >
66 >  python
67 >  rdkit
68 >  openbabel
69 >
70 >
71 >
72 >
73 >
74 >
75 >
76 >

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