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Revision: 50
Committed: Fri Sep 19 16:18:22 2008 UTC (10 years, 11 months ago) by wdelano
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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