--- trunk/README.TXT	2008/07/07 23:29:55	24
+++ trunk/README.TXT	2008/09/19 16:18:08	49
@@ -1,21 +1,25 @@
-FreeMOL Design Document (DRAFT ideas subject to further refinement)
+FreeMOL Design Document (draft ideas subject to further refinement)
 
 Goal: 
 
-  Aggregate a small set open-source software projects together into a
-  maintainable form which can support integration with PyMOL and other
-  interactive applications via platform-specific binary distributions.
+  Aggregate a managable set of open-source molecular software tools
+  together into a maintainable form which can support integration with
+  PyMOL and other interactive applications via quality-controlled
+  platform-specific binary distributions.
 
 Structure:
 
-  "src" top-level directory with a set of subdirectories containing
-  source code for the various FreeMOL packages
+  "src" top-level directory with distinct subdirectories containing
+  configure scripts and source code for the various FreeMOL packages
 
-  "freemol" top-level directory is a prototype framework for holding
-  executables and other required runtime files in typical "unix-like"
-  subdirectories: (freemol/bin, freemol/lib, freemol/share,
-  freemol/man, and so forth) The FREEMOL environment variable should
-  point at this directory.
+  "freemol" top-level directory is a prototype framework for a freemol
+  binary distribution that would contain executables and other
+  required runtime files in a typical "unix-/usr-like" tree:
+  (freemol/bin, freemol/lib, freemol/share, freemol/man, and so
+  forth).  The FREEMOL environment variable should be set to point at
+  this directory.  Please note that platform-specific binary
+  executables should not be checked into subversion into this
+  prototype directory tree.
 
 Compilation:
 
@@ -39,9 +43,9 @@
   the $FREEMOL folder containing executables compiled for a specific
   architecture.  
 
-  Installation would amount to extraction of the archive and setting
+  Installation will amount to extraction of the archive and setting
   of the FREEMOL environment variable to that PyMOL and other packages
-  can subquently locate and rely upon the freemol executables.
+  can subquently locate and rely upon the freemol executables. 
 
 Pragmatic decisions:
 
@@ -52,12 +56,13 @@
 
 Confirmed FreeMOL Packages:
 
-  mengine (TJ)
-  mpeg_encode (Warren)
+  mengine 
+  mpeg_encode 
+  apbs 
+  pdb2pqr
   
 Proposed FreeMOL Packages
 
-  apbs
   python
   rdkit
   openbabel