[Open Babel] problem with aromaticity

2012-04-06 Thread Tom Allison
Hi all: When I use the following file named ("2175908.xyz") 32 C -0.291523 0.3160533892 0.391375 C -0.0001205266 1.6897724142 -0.354856 C -1.1476732403 2.5783557540 -0.2608024912 C -0.7134957259 3.8662394928

Re: [Open Babel] [Chimera-users] UCSF Dock mol2 files

2012-04-06 Thread Conrad Huang
Our approach to file formats in Chimera is to support the "native" form from the developers. The use of ## for Dock mol2 format is obviously easiest for us since it is in use and already works in Chimera, but we're happy to accommodate a more broadly useful format. Conrad On 4/3/12 2:

Re: [Open Babel] UCSF Dock mol2 files

2012-04-06 Thread Scott Brozell
Hi, This is a good suggestion. But before implementation, 1) do the DOCK developers or users have any comments ? 2) do the Chimera developers or users have any comments ? In particular, does Chimera use ## as the lexeme for the DOCK token ? It might be useful to have a consistent lex

Re: [Open Babel] [Chimera-users] UCSF Dock mol2 files

2012-04-06 Thread Scott Brozell
Hi, Sticking with ## appears to be the best approach. Thanks everyone for the comments. scott ps. http://tripos.com/data/support/mol2.pdf @COMMENT Note: This RTI has not been implemented. Instead comments appear in the file immediately above the @ATOM line. On Wed, Apr 04, 2012 at 09: