Hi, Ah, ok. Well it wouldn't be much effort to implement a reader for this format, I think. For example, I made one for the .cc1 format this week and it didn't take long.
On the other hand, molgen and OMG produce SDF files which can be easily read by CDK (IteratingSDFReader, for example) so that might be handier. You would have to call the structure diagram generator on the results, but since SMOG's layout looked awful to me, that might be an improvement! gilleain On 11/23/12, C Anthony Lewis <[email protected]> wrote: > Hi Gilleain, > > It's a while since I fired it up and I remember there was a bit of a > learning curve to get it to do what I wanted! The data structure I have is > as below. This is for one isomer (actually > 3-tert-butyl-2,2,3,4,4-pentamethylpentane) and the file contains all the > isomers enumerated. The first number is an atom count, and the connection > table is the final (triangular) block of 0s and 1s while the two proceeding > numbers are the x and y co-ordinates. If I could somehow extract the > connection table then I could reconstruct the structure so I can calculate > various indices. > > Isomer 1 (1#1) // _1_ > 1 1 C 4 126 86 > 2 1 C 4 151 71 1 > 3 1 C 4 94 74 10 > 4 1 C 4 147 105 100 > 5 1 C 4 106 98 1000 > 6 1 C 4 174 77 01000 > 7 1 C 4 141 58 010000 > 8 1 C 4 171 58 0100000 > 9 1 C 4 100 60 00100000 > 10 1 C 4 74 83 001000000 > 11 1 C 4 71 64 0010000000 > 12 1 C 4 133 117 00010000000 > 13 1 C 4 171 101 000100000000 > 14 1 C 4 164 119 0001000000000 > 15 1 C 4 90 108 00001000000000 > 0 2 H 000023333333333 > > Thanks for the suggestions, I'll take a look at them and see what I can sort > out. > > Anthony > > -----Original Message----- > From: gilleain torrance [mailto:[email protected]] > Sent: 23 November 2012 16:48 > To: C Anthony Lewis > Cc: [email protected] > Subject: Re: [Cdk-user] Interpreting output frmo SMOG using CDK > > Hi Anthony, > > What output format does SMOG produce? I downloaded it recently, and tried > running it in a DOS emulator, but that didn't work so well... > > The alternative option of re-running with a newer generator is a > possibility. There is of course molgen (very fast), or OMG (which uses the > CDK). It depends on what functionality you need, of course. > > gilleain > > On 11/23/12, C Anthony Lewis <[email protected]> wrote: >> Dear All, >> >> I have a large number of output files from SMOG, an old DOS-based >> program that I downloaded ages ago. I would like to access the >> connection tables saved in the files for all the isomers enumerated >> and I'm wondering whether I can use CDK to do this. Alternatively, >> maybe it's easier to re-run the enumeration process using something a >> little more modern. >> >> Many thanks for any advice, >> >> Anthony Lewis >> >> >> >> C. Anthony Lewis >> Petroleum & Environmental Geochemistry Group & Centre for Chemical >> Sciences, School of Geography, Earth and Environmental Sciences, >> University of Plymouth, Plymouth, Devon PL4 8AA, U.K. >> >> tel: +44 (0)1752 584554 >> email: [email protected]<mailto:[email protected]> >> web: http://www.pegg.org.uk<http://www.pegg.org.uk/> >> http://www.plymouth.ac.uk/chemistry >> >> > ------------------------------------------------------------------------------ Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
