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1 < Hello!
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.
8 >
9 > Structure:
10 >
11 >  "src" top-level directory with a set of subdirectories containing
12 >  source code for the various FreeMOL packages
13 >
14 >  "freemol" top-level directory is a prototype framework for holding
15 >  executables and other required runtime files in typical "unix-like"
16 >  subdirectories: (freemol/bin, freemol/lib, freemol/share,
17 >  freemol/man, and so forth) The FREEMOL environment variable should
18 >  point at this directory.
19 >
20 > Compilation:
21 >
22 >  Assuming the the FREEMOL environment variable has been defined,
23 >  each package can be compiled and installed into $FREEMOL by cd'ing
24 >  to its souce directory and issuing the following sequence of commands:
25 >
26 >    ./configure
27 >    make
28 >    make install
29 >    
30 >  Followed by a
31 >
32 >    make clean
33 >
34 >  to get rid of object code, intermediate files, etc.
35 >
36 > Deployment:
37 >
38 >  A FreeMOL binary distribution would be a tar or zipped archive of
39 >  the $FREEMOL folder containing executables compiled for a specific
40 >  architecture.  
41 >
42 >  Installation would amount to extraction of the archive and setting
43 >  of the FREEMOL environment variable to that PyMOL and other packages
44 >  can subquently locate and rely upon the freemol executables.
45 >
46 > Pragmatic decisions:
47 >
48 >  Rely upon unix-like shell-based compilation (MinGW/Cygwin on Win32)
49 >
50 >  Stick with standalone, command-line only packages which have few if
51 >  any dependencies
52 >
53 > Confirmed FreeMOL Packages:
54 >
55 >  mengine (TJ)
56 >  mpeg_encode (Warren)
57 >  
58 > Proposed FreeMOL Packages
59 >
60 >  apbs
61 >  python
62 >  rdkit
63 >  openbabel
64 >
65 >
66 >
67 >
68 >
69 >
70 >
71 >

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