Re: [Open Babel] Babel Multiple Input Files

2011-12-12 Thread Chris Morley
You haven't included the whole molecule - the bonds are missing. Try again. It would be better to attach files rather than pasting ttext into emails to avoid corruption. Chris On 12/12/2011 10:01, Jochen Schreiber wrote: > Hello, > > sry i havnt seen the posts. > > Here is the head output from

Re: [Open Babel] Babel Multiple Input Files

2011-12-12 Thread Jochen Schreiber
Hello, sry i havnt seen the posts. Here is the head output from the join.txt: 1 OpenBabel1208222D 31 30 0 0 0 0 0 0 0 0999 V2000 2.86600.75000. O 0 0 0 0 0 2.8660 -2.25000. O 0 0 0 0 0 2. -0.75000. O 0 0 0 0 0 3

Re: [Open Babel] Babel Multiple Input Files

2011-12-08 Thread Chris Morley
On 08/12/2011 10:30, Jochen Schreiber wrote: > Hello, > > i have joined all sdf in one (join.sdf). > > Now i want to search: babel join.sdf resultadawd.sdf > -s"B(C1=CC(=CC=C1)N2C(=O)C3CC=C4C(C3C2=O)CC5=C(C4C6=C(C(=CC=C6)F)O)C(=O)C=C(C5=O)Br)(O)O" > > But i became the following output: > > ===

Re: [Open Babel] Babel Multiple Input Files

2011-12-08 Thread Jochen Schreiber
Hello, i have joined all sdf in one (join.sdf). Now i want to search: babel join.sdf resultadawd.sdf -s"B(C1=CC(=CC=C1)N2C(=O)C3CC=C4C(C3C2=O)CC5=C(C4C6=C(C(=CC=C6)F)O)C(=O)C=C(C5=O)Br)(O)O" But i became the following output: == *** Open Babel Warning in ReadMolec

Re: [Open Babel] Babel Multiple Input Files

2011-12-05 Thread Chris Morley
On 05/12/2011 14:30, Noel O'Boyle wrote: > I don't know if Open Babel supports joining fs files, so joining the > sdf may be your only choice. Chris? > > On 5 December 2011 15:20, Jochen Schreiber wrote: >> One question: Sholud i join the fs Files or the sdf Files and create the fs >> File on the

Re: [Open Babel] Babel Multiple Input Files

2011-12-05 Thread Noel O'Boyle
I don't know if Open Babel supports joining fs files, so joining the sdf may be your only choice. Chris? On 5 December 2011 15:20, Jochen Schreiber wrote: > One question: Sholud i join the fs Files or the sdf Files and create the fs > File on the joined sdf Files? > > What is better? > > Am 05.1

Re: [Open Babel] Babel Multiple Input Files

2011-12-05 Thread Jochen Schreiber
One question: Sholud i join the fs Files or the sdf Files and create the fs File on the joined sdf Files? What is better? Am 05.12.2011 um 14:50 schrieb Noel O'Boyle: > If I would you, I would join the sdf files, and then convert that to a > single fs file. > > To join: > cat *.sdf tmp.txt > m

Re: [Open Babel] Babel Multiple Input Files

2011-12-05 Thread Jochen Schreiber
Ok, the joing of the files is an one-time operation. But the file would be very great. I will test it. Thx Am 05.12.2011 um 14:50 schrieb Noel O'Boyle: > If I would you, I would join the sdf files, and then convert that to a > single fs file. > > To join: > cat *.sdf tmp.txt > mv tmp.txt join

Re: [Open Babel] Babel Multiple Input Files

2011-12-05 Thread Noel O'Boyle
If I would you, I would join the sdf files, and then convert that to a single fs file. To join: cat *.sdf tmp.txt mv tmp.txt joined.sdf - Noel On 3 December 2011 11:53, Jochen Schreiber wrote: > Hello to everybody, > > first i want to say hello. My first post in this mailinglist. > > I have a

[Open Babel] Babel Multiple Input Files

2011-12-03 Thread Jochen Schreiber
Hello to everybody, first i want to say hello. My first post in this mailinglist. I have a question. I have downloaded the full pubchem compound database and convert all the sdf files to fs Files. Now i have 2138 fs-Files and i have a query.mol and i want to search the top 5 similarity molecul