Re: SV: Re: SV: Re: [Cdk-user] Where is the DBReader class

2005-12-30 Thread Ola Spjuth
On Fri, 2005-12-30 at 15:34, Christoph Steinbeck wrote: > You need some way of in-memory presreening for fast substructure searching. > And > this cannot be done efficiently with SQL functions. > In NMRShiftDB, we do this with fingerprints stored in a special buffered > MySQL > table, which is

Re: SV: Re: SV: Re: [Cdk-user] Where is the DBReader class

2005-12-30 Thread Christoph Steinbeck
Ola Spjuth wrote: I agree with Chris, a Hibernate-based solution would probably be the best. I have never used MySQL "user defined functions" but I assume they are similar to oracle's "stored procedures". In my opinion such a solution has some disadvantages; they tend to be slow and also break th

Re: SV: Re: SV: Re: [Cdk-user] Where is the DBReader class

2005-12-30 Thread Stefan Kuhn
> Yes, but I mean if wedge bonds are not explicitly specified. If wedge bonds are not spedified there is no stereo detection possible - that's the case of weird 3d-drawings. In this case you are lost anyway, no matter if it is a single structure or a bulk load. Stefan > Nina > > > Stefan > > > >

Re: SV: Re: SV: Re: [Cdk-user] Where is the DBReader class

2005-12-30 Thread Stefan Kuhn
> Yes, but I mean if wedge bonds are not explicitly specified. If wedge bonds are not spedified there is no stereo detection possible - that's the case of weird 3d-drawings. In this case you are lost anyway, no matter if it is a single structure or a bulk load. Stefan > > Nina > > > Stefan > > >

Re: SV: Re: SV: Re: [Cdk-user] Where is the DBReader class

2005-12-30 Thread Nina Jeliazkova
Stefan Kuhn <[EMAIL PROTECTED]> wrote: > Am Friday 30 December 2005 11:32 schrieb Nina Jeliazkova: > > Stefan Kuhn <[EMAIL PROTECTED]> wrote: > > > Am Friday 30 December 2005 11:07 schrieb Nina Jeliazkova: > > > > Hi, > > > > > > > > Stefan Kuhn <[EMAIL PROTECTED]> wrote: > > > > > > Ok, that mak

Re: SV: Re: SV: Re: [Cdk-user] Where is the DBReader class

2005-12-30 Thread Stefan Kuhn
Am Friday 30 December 2005 11:32 schrieb Nina Jeliazkova: > Stefan Kuhn <[EMAIL PROTECTED]> wrote: > > Am Friday 30 December 2005 11:07 schrieb Nina Jeliazkova: > > > Hi, > > > > > > Stefan Kuhn <[EMAIL PROTECTED]> wrote: > > > > > Ok, that makes the sql a lot easier than the fingerprints. Is that

Re: SV: Re: SV: Re: [Cdk-user] Where is the DBReader class

2005-12-30 Thread Nina Jeliazkova
Stefan Kuhn <[EMAIL PROTECTED]> wrote: > Am Friday 30 December 2005 11:07 schrieb Nina Jeliazkova: > > Hi, > > > > Stefan Kuhn <[EMAIL PROTECTED]> wrote: > > > > Ok, that makes the sql a lot easier than the fingerprints. Is that > > > > good enough to use smiles for duplicate checking? are you au

Re: SV: Re: SV: Re: [Cdk-user] Where is the DBReader class

2005-12-30 Thread Stefan Kuhn
Am Friday 30 December 2005 11:07 schrieb Nina Jeliazkova: > Hi, > > Stefan Kuhn <[EMAIL PROTECTED]> wrote: > > > Ok, that makes the sql a lot easier than the fingerprints. Is that > > > good enough to use smiles for duplicate checking? are you aure to find > > > them > > all? > > > Given the smile

Re: SV: Re: SV: Re: [Cdk-user] Where is the DBReader class

2005-12-30 Thread Nina Jeliazkova
Hi, Stefan Kuhn <[EMAIL PROTECTED]> wrote: > > Ok, that makes the sql a lot easier than the fingerprints. Is that good > > enough to use smiles for duplicate checking? are you aure to find them all? > Given the smiles implemenatation is not buggy it should work for identity > search (and theref

Re: SV: Re: SV: Re: [Cdk-user] Where is the DBReader class

2005-12-30 Thread Stefan Kuhn
Dear Claus, glad I could help you. Some remarks: I won't force you to use any sort of OR mapper, it just has advantages. I found it mainly convinient with respect to code organisation - you can nicely organize your methods (like the stuff in SubmittingData, which should really go in DBMolecule,