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Revision: 50
Committed: Fri Sep 19 16:18:22 2008 UTC (11 years ago) by wdelano
File size: 2011 byte(s)
Log Message:
update README
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1 wdelano 49 FreeMOL Design Document (draft ideas subject to further refinement)
2 wdelano 21
3     Goal:
4    
5 wdelano 49 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 wdelano 21
10     Structure:
11    
12 wdelano 49 "src" top-level directory with distinct subdirectories containing
13     configure scripts and source code for the various FreeMOL packages
14 wdelano 21
15 wdelano 49 "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 wdelano 21
24 wdelano 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 wdelano 21 Deployment:
41    
42     A FreeMOL binary distribution would be a tar or zipped archive of
43 wdelano 24 the $FREEMOL folder containing executables compiled for a specific
44     architecture.
45 wdelano 21
46 wdelano 49 Installation will amount to extraction of the archive and setting
47 wdelano 24 of the FREEMOL environment variable to that PyMOL and other packages
48 wdelano 49 can subquently locate and rely upon the freemol executables.
49 wdelano 24
50 wdelano 21 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 wdelano 49 mengine
60     mpeg_encode
61     apbs
62     pdb2pqr
63 wdelano 21
64     Proposed FreeMOL Packages
65    
66     python
67     rdkit
68     openbabel