Re: [Open Babel] separate fragments

2011-12-08 Thread Geoffrey Hutchison
> But babel reports "1 molecule", see below > Please advise, This is more of a wording question. "1 molecule converted" really means "I read in one molecular system 'record', where a record may contain more than one fragment." Obviously the latter is a little too long to print easily. :-) Hope

[Open Babel] separate fragments

2011-12-08 Thread Kilin, Dmitri S
Question to experts: How to use key "--separate" for the xyz file. The file evidently contains more than 5 fragments. But babel reports "1 molecule", see below Please advise, Thank you, Dmitri babel --separate -ixyz movie_last.xyz -oxyz last.xyz 1 molecule converted movie_last.xyz Descrip

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