| Time |
S |
Nick |
Message |
| 06:34 |
|
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rojasm joined #bioclipse |
| 07:11 |
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malick joined #bioclipse |
| 07:40 |
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jonalv joined #bioclipse |
| 08:43 |
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thomas_ku joined #bioclipse |
| 08:53 |
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masak joined #bioclipse |
| 08:53 |
|
masak |
what's the difference between cdk and cdk10? |
| 08:54 |
|
CIA-44 |
bioclipse: carl_masak * r5530 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.jchempaint/src/net/bioclipse/cdk10/jchempaint/Activator.java: |
| 08:54 |
|
CIA-44 |
bioclipse: [Activator.java] |
| 08:54 |
|
CIA-44 |
bioclipse: * typo |
| 09:01 |
|
|
egonw joined #bioclipse |
| 09:07 |
|
CIA-44 |
bioclipse: jonalv * r5531 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): |
| 09:07 |
|
CIA-44 |
bioclipse: Fixed the last DAO test. All DAO tests and all internal manager tests now |
| 09:07 |
|
CIA-44 |
bioclipse: passes. Problem left is with running multiple local database instances which |
| 09:07 |
|
CIA-44 |
bioclipse: might not be worth it. Also no SDF file parsing done yet. And will also need |
| 09:07 |
|
CIA-44 |
bioclipse: some sort of lazy loading of huge amounts of structures from the database |
| 09:09 |
|
egonw |
"Also no SDF file parsing done yet."? |
| 09:09 |
|
egonw |
jonalv: anything I can do? |
| 09:09 |
|
egonw |
btw, the editor is now looking like an editor... |
| 09:09 |
|
jonalv |
hm for structuredb? |
| 09:10 |
|
egonw |
except that the data model is not updated... |
| 09:10 |
|
egonw |
about SDF parsing |
| 09:10 |
|
masak |
egonw: what's the difference between cdk and cdk10? |
| 09:10 |
|
jonalv |
not unless you are good with hsqldb :) |
| 09:10 |
|
egonw |
masak: version |
| 09:10 |
|
egonw |
cdk10 is CDK 1.0.x |
| 09:10 |
|
egonw |
cdk is trunk/ |
| 09:10 |
|
masak |
ah |
| 09:10 |
|
egonw |
the latter is generally better, but does not have a ported JCP yet |
| 09:10 |
|
jonalv |
I think you did the troublesome part of SDF parsing. I just need to use it somehow :) |
| 09:10 |
|
egonw |
jonalv: ack |
| 09:11 |
|
jonalv |
brb |
| 09:17 |
|
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EskilA joined #bioclipse |
| 09:26 |
|
egonw |
masak: what was channel for the logger again? |
| 09:27 |
|
masak |
egonw: #irclogger |
| 11:12 |
|
CIA-44 |
bioclipse: ospjuth * r5532 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/net/bioclipse/ui/views/ActionHistoryView.java: Remove listener on dispose. |
| 11:12 |
|
|
olas joined #bioclipse |
| 11:13 |
|
olas |
hi all |
| 11:14 |
|
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olas left #bioclipse |
| 12:00 |
|
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olas joined #bioclipse |
| 12:23 |
|
CIA-44 |
bioclipse: ospjuth * r5533 /bioclipse2/trunk/plugins/net.bioclipse.services/src/net/bioclipse/services/business/ (3 files): Services are run with generic Object as input, not List<Object>. Resource extraction pushed to manager instead of in DropAdapter. |
| 12:23 |
|
CIA-44 |
bioclipse: ospjuth * r5534 /bioclipse2/trunk/plugins/net.bioclipse.services/src/net/bioclipse/services/views/ServiceViewDropAdapter.java: Updated the dropAdapter accordingly. |
| 12:31 |
|
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masak joined #bioclipse |
| 13:46 |
|
egonw |
hi all |
| 13:47 |
|
egonw |
who is using subclipse and who subversion? |
| 13:47 |
|
egonw |
subversive, I meant |
| 13:47 |
|
masak |
subclipse |
| 13:47 |
|
masak |
I don't think I ever used subversive |
| 13:48 |
|
egonw |
I used to use subclipse too... |
| 13:48 |
|
egonw |
but we installed subversive earlier... |
| 13:48 |
|
egonw |
looked really nice... |
| 13:48 |
|
masak |
this all sounds like a commercial :) |
| 13:48 |
|
egonw |
allowed detection of trunk/branches/tags... |
| 13:48 |
|
egonw |
yeah, sorry about that :) |
| 13:48 |
|
masak |
np |
| 13:51 |
|
* jonalv |
is using commandline subversion and subclipse |
| 13:51 |
|
masak |
I'll have a look at subversive |
| 14:22 |
|
CIA-44 |
bioclipse: ospjuth * r5535 /bioclipse2/trunk/plugins/net.bioclipse.services/src/net/bioclipse/services/business/ (ServiceManager.java ServiceManagerHelper.java): Fixed unwrapping lists and selections + parsing of Files in drag and drop depending on accepted inputs in service. |
| 14:24 |
|
|
de_maas joined #bioclipse |
| 14:27 |
|
egonw |
olas: around? |
| 14:28 |
|
olas |
yes |
| 14:28 |
|
egonw |
I got somewhat further last nite... |
| 14:29 |
|
egonw |
mouse events are now passed to JCP |
| 14:29 |
|
egonw |
and there are JCP icons in the global toolbar |
| 14:29 |
|
egonw |
it even sees the model is dirty, when I do an edit action... |
| 14:29 |
|
egonw |
but that's about it... |
| 14:29 |
|
egonw |
need some clean up, but reasonable progress... |
| 14:29 |
|
olas |
great |
| 14:30 |
|
olas |
good job |
| 14:30 |
|
egonw |
tried to figure out where it failed to update the data model, but without success so far... |
| 14:30 |
|
olas |
right |
| 14:30 |
|
olas |
file a bug? |
| 14:30 |
|
egonw |
yeah, possible... |
| 14:30 |
|
egonw |
I'll try to find some time to summarize on the ML |
| 14:37 |
|
jonalv |
Eclipse crached again :( |
| 14:37 |
|
egonw |
use Java 1.5 |
| 14:37 |
|
jonalv |
is that the trick? |
| 14:37 |
|
egonw |
for me it was |
| 14:37 |
|
egonw |
nasty interaction bug with some lib for java 1.6 upwards... |
| 14:38 |
|
egonw |
but that was on linux |
| 14:38 |
|
jonalv |
hm maybe I should download that then |
| 14:38 |
|
jonalv |
I am on linux |
| 14:38 |
|
jonalv |
ubuntu |
| 14:38 |
|
egonw |
right |
| 14:38 |
|
jonalv |
I get Permspace exceptions all the time |
| 14:39 |
|
egonw |
sudo aptitude install sun-java5-jdk or so |
| 14:39 |
|
jonalv |
that works? |
| 14:39 |
|
jonalv |
apt has sun stuff? |
| 14:40 |
|
egonw |
yes |
| 14:40 |
|
jonalv |
seems so. where does it put it then? |
| 14:40 |
|
|
EskilA joined #bioclipse |
| 14:40 |
|
egonw |
/usr/lib/jvm |
| 14:41 |
|
jonalv |
thanks! |
| 14:41 |
|
egonw |
de_maas: thanx for you comment |
| 14:41 |
|
egonw |
+r |
| 14:41 |
|
egonw |
if you don't edit SDF files, BC2 already works fine with Ola's code |
| 14:41 |
|
de_maas |
Gee your fast |
| 14:42 |
|
egonw |
I get an email warning :) |
| 14:42 |
|
de_maas |
Well the editing is not the most important part but also very usefull to get rit of error entries. |
| 14:42 |
|
egonw |
yes indeed |
| 14:43 |
|
egonw |
this is being worked on... that is, porting the JCP editor... |
| 14:43 |
|
egonw |
compared to my blog item, I made some progress.... |
| 14:43 |
|
olas |
we'll need to sort that out, such as removing entries from an SDFile |
| 14:43 |
|
olas |
that is the SDFileEditors concern |
| 14:43 |
|
olas |
also making JCP accept a part of an SDFile is a concern |
| 14:44 |
|
de_maas |
Is there a limit to the number of entries it can process? |
| 14:44 |
|
olas |
egonw? |
| 14:44 |
|
egonw |
the SDF? |
| 14:44 |
|
de_maas |
Yep |
| 14:45 |
|
CIA-44 |
bioclipse: ospjuth * r5536 /bioclipse2/trunk/plugins/net.bioclipse.services/src/net/bioclipse/services/business/ (IServiceManager.java ServiceManager.java): Added scriptable version of services.run(String name, Object input). |
| 14:45 |
|
egonw |
I heard some mentioning of 6MB working fine... |
| 14:45 |
|
egonw |
olas: how large was your largest SD file again? |
| 14:45 |
|
jonalv |
I tested with 6MB |
| 14:45 |
|
de_maas |
Hmmm |
| 14:45 |
|
egonw |
de_maas: but, work is ongoing for SDF import into the structuredb |
| 14:45 |
|
jonalv |
and that didn't work great... |
| 14:45 |
|
egonw |
that will solve that issue once and for all |
| 14:46 |
|
de_maas |
That will even be better. |
| 14:46 |
|
de_maas |
6MB is considered very small over here. |
| 14:47 |
|
de_maas |
What format would the structuredb be? |
| 14:47 |
|
jonalv |
how do you mean what format? |
| 14:48 |
|
de_maas |
The sdf import into the structure db. Is the structure db a new format or is it using an existing database format? |
| 14:48 |
|
jonalv |
the database is just a few tables but yes it's a new database format |
| 14:49 |
|
jonalv |
It's more or less a persisting of CDK molecules |
| 14:50 |
|
de_maas |
So you do not rely on an other package. |
| 14:50 |
|
jonalv |
no just cdk |
| 14:51 |
|
jonalv |
there is some information here: <http://wiki.bioclipse.net/inde[…]itle=Structure_DB> |
| 14:51 |
|
jonalv |
not very updated though I just reaslied... :) |
| 14:52 |
|
de_maas |
Thanks |
| 14:52 |
|
de_maas |
but it did not went very good? |
| 14:52 |
|
jonalv |
I have problems yea. But they are related to hsqldb |
| 14:52 |
|
de_maas |
doesn't ring a bell |
| 14:53 |
|
jonalv |
hsqldb is the databasemanager I am using |
| 14:53 |
|
de_maas |
So you are using an existing database engine? |
| 14:54 |
|
jonalv |
uhm yea I wouldn't write that by myself then we wouldn't have system before ten years from now or something :) |
| 14:56 |
|
de_maas |
Sure , but then we misunderstood each other a few rows ago ;-) |
| 14:56 |
|
jonalv |
okey I see, I thought you where talking about formats like biomart (not sure what that is either) |
| 14:59 |
|
de_maas |
I don't know to much about hsqldb , would someone be able to exchange a hsqldb to somebody else like an acces database? |
| 14:59 |
|
egonw |
no without some conversion |
| 14:59 |
|
jonalv |
we are planning on supporting MySQL later on too |
| 15:00 |
|
de_maas |
It's more widely use I think. |
| 15:00 |
|
CIA-44 |
bioclipse: jonalv * r5537 /bioclipse2/trunk/plugins/ (5 files in 3 dirs): Added test.sdf file to the structuredb tests and more fighting with hsqldb. No sucess yet on tht front though... |
| 15:00 |
|
jonalv |
hsqldb is going to be used for local database instances and MySQL is gonna be used for public databases shared among many but that's a bit in the future... |
| 15:01 |
|
egonw |
jonalv: jerome pansanel has mychem |
| 15:01 |
|
egonw |
but that's really targeted as molecules... |
| 15:01 |
|
egonw |
where the bioclipse2 db stuff aims at a more general framework |
| 15:01 |
|
egonw |
to support any 'bioresource'... |
| 15:01 |
|
* jonalv |
has no idea about what mychem is. |
| 15:01 |
|
olas |
egonw: not really |
| 15:01 |
|
egonw |
http://mychem.sourceforge.net/ |
| 15:01 |
|
jonalv |
the structuredb is VERY much targeted at molecules |
| 15:02 |
|
egonw |
ask jpansanel on #cdk |
| 15:02 |
|
olas |
only I'd say |
| 15:02 |
|
egonw |
sure, structuredb is... |
| 15:02 |
|
egonw |
but the choice for hsqldb is not, I assume? |
| 15:02 |
|
olas |
there is no other |
| 15:02 |
|
egonw |
oh, no sequencedb anymore? |
| 15:02 |
|
olas |
mysql will also be supported |
| 15:02 |
|
olas |
not yet |
| 15:02 |
|
olas |
but will be |
| 15:02 |
|
olas |
might bi BioSQL though |
| 15:03 |
|
jonalv |
egonw, no sequencdb yet no |
| 15:03 |
|
olas |
not yet, but will be, yes |
| 15:03 |
|
olas |
after structuredb |
| 15:03 |
|
olas |
but no "general" db for IBioObjects, no |
| 15:03 |
|
olas |
(that's impossible) |
| 15:04 |
|
jonalv |
at lest it wouldn't make any sence |
| 15:05 |
|
egonw |
then drop hsqldb? |
| 15:05 |
|
egonw |
and make a custom general interface? |
| 15:05 |
|
jonalv |
egonw, how do you mean? |
| 15:06 |
|
* jonalv |
is looking at mychem but not really understanding. Is it Perl based? |
| 15:06 |
|
egonw |
well, I'd rather see something easy to maintain/develop, than using a off-the-shelf tool which does not really add extra features |
| 15:06 |
|
egonw |
[17:02] <egonw> ask jpansanel on #cdk |
| 15:07 |
|
egonw |
though he seems a sleep... |
| 15:07 |
|
jonalv |
are you saying that you don't think there should be a relational database engine running it? |
| 15:07 |
|
* jonalv |
is lost thne... |
| 15:07 |
|
egonw |
no, there should! |
| 15:08 |
|
egonw |
mychem uses mysql as RDBS |
| 15:08 |
|
jonalv |
egonw, what are you trying to say? |
| 15:08 |
|
egonw |
ummm... |
| 15:08 |
|
egonw |
that I feel sorry for your struggle with hsqldb |
| 15:08 |
|
jonalv |
yea what I can't do with it for the moment is the following. |
| 15:08 |
|
jonalv |
after I ahve started a database server |
| 15:08 |
|
jonalv |
stop it |
| 15:09 |
|
jonalv |
and created another database instance |
| 15:09 |
|
jonalv |
and restart it |
| 15:09 |
|
jonalv |
with two database instances running |
| 15:10 |
|
jonalv |
but most of the structuredb is java code and iBatis mappigns |
| 15:10 |
|
de_maas |
Why do you want multiple instances? Isn't there something like mutiple scheme's? |
| 15:15 |
|
jonalv |
multipple schemes? |
| 15:15 |
|
* jonalv |
has never heard about that |
| 15:16 |
|
de_maas |
Well I'm an oracle user. |
| 15:16 |
|
jonalv |
oh might be something oracle specific perhaps? |
| 15:16 |
|
de_maas |
within oracle running multiple instances is take up a lot of memory. |
| 15:16 |
|
jonalv |
okey |
| 15:16 |
|
de_maas |
But within oracle you create users which can hold a set of tables and sources. |
| 15:17 |
|
jonalv |
MAybee I haven't thougth this through wnough.... |
| 15:17 |
|
de_maas |
Usually you create a user which holds an application. |
| 15:17 |
|
jonalv |
ANyway we wan't to be able to do both sequencedaabases and structuredatabses |
| 15:18 |
|
jonalv |
so anyway I need to be able to have multiple databses running but maybe I could start them all at once? |
| 15:18 |
|
de_maas |
In one go, I guess you will be unique in creating an application focussed on both. |
| 15:18 |
|
jonalv |
well you know Bioclipse is targeting all of it... :) |
| 15:18 |
|
de_maas |
Hear hear! |
| 15:19 |
|
jonalv |
huh? |
| 15:20 |
|
de_maas |
just saying I'm please with your comment, targetting all of it |
| 15:20 |
|
CIA-44 |
bioclipse: ospjuth * r5538 /bioclipse2/trunk/plugins/net.bioclipse.services/src/net/bioclipse/services/business/ (ServiceManager.java ServiceManagerHelper.java): Tried to parse String inputs as IResource if accepted input is IResource. |
| 15:21 |
|
jonalv |
well I spend 50% of my time with a high troughput cell screening LIS for Bioclipse and sits in an office with a guy working on a multiple sequence alignment editor :) |
| 15:25 |
|
de_maas |
Just looked at hsqldb, it uses the same concept as Oracle with user and roles. So why not create an user for every application? |
| 15:26 |
|
olas |
SF is REALLY slow today |
| 15:26 |
|
CIA-44 |
bioclipse: ospjuth * r5539 /bioclipse2/trunk/plugins/net.bioclipse.services/src/net/bioclipse/services/ (2 files in 2 dirs): Deprecated service.run() that did not take service name as input. All for better recording. Also made DropAdapter use new run(String servicename, Object input). |
| 15:26 |
|
jonalv |
de_maas, I have no idea what that means... :( |
| 15:27 |
|
de_maas |
OK , you want me to explain? |
| 15:27 |
|
jonalv |
sure |
| 15:28 |
|
jonalv |
that would be great |
| 15:28 |
|
de_maas |
Let;'s say you want an application which does chemistry and you have one for biology. You can create 2 users: chemy and bioot |
| 15:29 |
|
de_maas |
Any of them can create tables without seeing each others tables. |
| 15:29 |
|
de_maas |
Of course you should be able to grant rights too each other. |
| 15:29 |
|
jonalv |
running on the same database instance... |
| 15:29 |
|
de_maas |
YES! |
| 15:30 |
|
jonalv |
what's the benefit (except that I don't neeed to restart the server) |
| 15:30 |
|
de_maas |
So when you connect using jdbc you will provide the database name , username and password you will see one application or the other . |
| 15:30 |
|
de_maas |
Advantage is in adminstration. 1 database to maintain. |
| 15:30 |
|
de_maas |
and memory on you computer. |
| 15:31 |
|
jonalv |
hm interesting, maybe I should go with that aprroach |
| 15:31 |
|
de_maas |
But also, you can use each others tables and source |
| 15:31 |
|
jonalv |
No I don't want that Ietink |
| 15:31 |
|
jonalv |
but say that I want multiple instances of the structure database? |
| 15:32 |
|
de_maas |
OK , you can you do not have to. |
| 15:32 |
|
de_maas |
Be creative and give them several names. |
| 15:32 |
|
jonalv |
yea |
| 15:32 |
|
de_maas |
You can copy the tables , load different structures but use the same code! |
| 15:33 |
|
jonalv |
yea I use java and iBatis and stuff for all that |
| 15:33 |
|
jonalv |
I am not that great with databases though. I wanna do as little as possible with them :) |
| 15:33 |
|
de_maas |
For instance, we are hosting our one database on www.specs.net but the same database is also used for hosting the journal of heterocyclic chemistry. |
| 15:33 |
|
de_maas |
on www.jhetchem.com |
| 15:34 |
|
jonalv |
okey |
| 15:34 |
|
jonalv |
I didn't know hasldb supported thios |
| 15:34 |
|
de_maas |
OK, but some basics is never bad right? |
| 15:35 |
|
jonalv |
but how do you create new users? |
| 15:35 |
|
jonalv |
you need some sort of admin user to the databse able to do such things? |
| 15:36 |
|
de_maas |
usually you do but as I said, I do not know hsqldb. |
| 15:36 |
|
jonalv |
hm I know MySQL works like this but I have never done it yet |
| 15:36 |
|
de_maas |
http://hsqldb.org/doc/guide/ch[…]eate_user-section |
| 15:37 |
|
jonalv |
The thing about hsqldb is that it's 100% java and can just come with Bioclipse and run without alot of configuration |
| 15:37 |
|
jonalv |
I have only used it for testing my java persisting and retrieving yet though. (that works great btw) :) |
| 15:38 |
|
de_maas |
Well there you go. |
| 15:38 |
|
de_maas |
Keep i mind that jdbc is not know for best performance. |
| 15:38 |
|
de_maas |
But I guess you're not targetting to get the biggest database out. |
| 15:39 |
|
olas |
hsqldb is mainly for smaller local databases |
| 15:39 |
|
jonalv |
I am using java so I sort of don't get best perforamcne by default :) |
| 15:39 |
|
olas |
if working on something larger, mySQL is probably a better solution |
| 15:39 |
|
olas |
(or similar) |
| 15:40 |
|
jonalv |
we would still be using jdbc... |
| 15:40 |
|
jonalv |
but that's the only way as far as I see |
| 15:40 |
|
egonw |
you'll always use jdbc |
| 15:40 |
|
egonw |
what ever database, whatever wrapper lib |
| 15:40 |
|
de_maas |
Check, OK. |
| 15:42 |
|
de_maas |
Egonw: about the sd-file editor. Will it catch to disk or will it try to read every thing to memory? |
| 15:42 |
|
egonw |
olas? memory, not? |
| 15:42 |
|
egonw |
or does RCP some caching by default? |
| 15:43 |
|
jonalv |
so I shouldn't have multiple databaseinstances but multiple users of one databseinstance... Hm I wonder how to make this work but it should be possible :) |
| 15:43 |
|
olas |
Would that create different files? |
| 15:44 |
|
jonalv |
we where talking about using that iterator I think and load to memory as you scroll. right? |
| 15:44 |
|
de_maas |
For instance, I read some big sd-files (> 40.000) into Knime and it keeps working with a reasonable performance. |
| 15:44 |
|
egonw |
yeah, KNIME has db caching... |
| 15:44 |
|
egonw |
that's what this structuredb will basically do too for SD files |
| 15:44 |
|
olas |
hsqldb? |
| 15:44 |
|
egonw |
olas: the current SDF editor does not cache anything, does it? |
| 15:44 |
|
olas |
in KNIME? |
| 15:44 |
|
egonw |
in bioclipse |
| 15:45 |
|
olas |
does KNIME use hsqldb? |
| 15:45 |
|
egonw |
olas: not sure hwat db KNIME is using... |
| 15:45 |
|
olas |
current SDFEditor reads all SDFile |
| 15:45 |
|
olas |
does not use iterator |
| 15:45 |
|
olas |
egonw: would it be OK to omit the TextEditor tab from the SDFileEditor? |
| 15:46 |
|
jonalv |
but it instantiates the guio stuff lazily at least right? |
| 15:46 |
|
egonw |
olas: yes |
| 15:46 |
|
de_maas |
knime is using file system on disk. Every node you create makes a directory containing meta data and real data. |
| 15:46 |
|
egonw |
olas: was thinking of doing the same for MDLMolfileEditor... |
| 15:46 |
|
olas |
yes |
| 15:46 |
|
olas |
but for SDFiles it really does not make sense to show texteditor |
| 15:47 |
|
egonw |
yes |
| 15:47 |
|
egonw |
and for MDLMofiles, it would just make my life easier |
| 15:47 |
|
egonw |
which I find important too :) |
| 15:48 |
|
olas |
ok |
| 15:50 |
|
olas |
egonw: how should we handle SDFiles where mols have 3D coordinates? |
| 15:51 |
|
egonw |
good point |
| 15:51 |
|
egonw |
well... isn't there a Jmol SWT widget? |
| 15:51 |
|
olas |
no |
| 15:51 |
|
olas |
and that would not be feasible |
| 15:51 |
|
egonw |
how so? |
| 15:51 |
|
olas |
for large SDFiles |
| 15:51 |
|
egonw |
why not? |
| 15:51 |
|
olas |
why so? |
| 15:52 |
|
olas |
why would you want interactivity in a list? |
| 15:52 |
|
egonw |
well, Jmol is more performant than JCP, I think |
| 15:52 |
|
olas |
if you double-click on individual mols, yes you can get it in Jmol |
| 15:52 |
|
egonw |
no, but one would like 3D, not? |
| 15:52 |
|
olas |
JCP just generates an image |
| 15:52 |
|
olas |
which is cached |
| 15:52 |
|
egonw |
you could use the CDK SDG... |
| 15:52 |
|
olas |
hence quite performant |
| 15:52 |
|
egonw |
ah, nice |
| 15:52 |
|
olas |
is that OK? |
| 15:53 |
|
olas |
is there no 3D renderer in CDK? |
| 15:53 |
|
olas |
which is fast? |
| 15:53 |
|
olas |
I think rendering images with Jmol would be slow |
| 15:53 |
|
olas |
but hey, I don't know |
| 15:53 |
|
olas |
what do you think, egonw? |
| 15:54 |
|
olas |
SDG doesn't feel right |
| 15:54 |
|
olas |
what do other software do in this case? |
| 15:54 |
|
olas |
anyone? |
| 15:54 |
|
olas |
I can ask on bioclipse-devel if you have no good suggestion |
| 15:55 |
|
egonw |
don't know a better solution... |
| 15:55 |
|
olas |
than? |
| 15:55 |
|
olas |
what is your best shot? |
| 15:55 |
|
de_maas |
Well I can tell you what isis does. |
| 15:55 |
|
olas |
please |
| 15:56 |
|
de_maas |
It shows you a flattend (so not so nice) 2d structure. If you want to play with it you can take it too rasmol! |
| 15:57 |
|
de_maas |
Or too isis draw, but that's not really a good 3d viewer. |
| 15:57 |
|
olas |
ok |
| 15:57 |
|
olas |
so they generate 2D |
| 15:57 |
|
olas |
thx |
| 15:57 |
|
de_maas |
Chemaxon , makes up it's mind during rendering |
| 15:58 |
|
olas |
so sometimes 2D and sometimes 3D? |
| 15:58 |
|
de_maas |
So if there are 3D coordinates they give you a 3D editor otherwise a 2D editor. |
| 15:58 |
|
olas |
Maybe let users decide? |
| 15:58 |
|
olas |
hmm |
| 15:58 |
|
olas |
yes, but for the list |
| 15:58 |
|
de_maas |
Hmmm the biggest problem is always between the keyboard and the chair. |
| 15:58 |
|
olas |
if you hav 40.000 mols in a list, do thsy open up a 3D-representation for all or just a static image in2D or 3D? |
| 15:58 |
|
* egonw |
got to catch a train |
| 15:59 |
|
olas |
gye egonw! |
| 15:59 |
|
olas |
bye! |
| 15:59 |
|
egonw |
gye to you too :) |
| 15:59 |
|
de_maas |
Later |
| 15:59 |
|
de_maas |
Hmm there is my problem. |
| 16:00 |
|
de_maas |
MDL does not have an sd file viewer. You alway have to convert to a database (local or host) |
| 16:00 |
|
de_maas |
Maybe take a look at accelrys ds viewer. |
| 16:01 |
|
de_maas |
They show first an spreadsheet. they give you 2d structures but you can add a 3D window |
| 16:02 |
|
olas |
but there is never 3D in a large list of mols? |
| 16:02 |
|
olas |
that you can rotate individually? |
| 16:03 |
|
de_maas |
No never seen it like that. |
| 16:03 |
|
olas |
ok |
| 16:03 |
|
olas |
so only 2D in list |
| 16:03 |
|
de_maas |
Maybe not that usefull. |
| 16:03 |
|
olas |
true |
| 16:03 |
|
olas |
ok, I'll go for generating 2D |
| 16:03 |
|
de_maas |
2D like the diagrammer or just a projection? |
| 16:03 |
|
olas |
thanks |
| 16:03 |
|
olas |
? |
| 16:04 |
|
olas |
hmm |
| 16:04 |
|
olas |
fastest would be just to omit Z-values |
| 16:04 |
|
olas |
but using a SDG would be better visualization |
| 16:04 |
|
de_maas |
You could project the initial 3D to the flat screen with out doing calculation of the SDG I think |
| 16:04 |
|
olas |
yes |
| 16:04 |
|
olas |
but that would not look too good |
| 16:05 |
|
olas |
on the other hand |
| 16:05 |
|
olas |
maybe enough |
| 16:05 |
|
de_maas |
SDG would be way to slow I guess. |
| 16:05 |
|
olas |
right |
| 16:05 |
|
olas |
probably true |
| 16:05 |
|
olas |
ok |
| 16:05 |
|
olas |
will just omit Z-values |
| 16:05 |
|
olas |
thanks for the help! |
| 16:05 |
|
de_maas |
You welcome |
| 16:06 |
|
de_maas |
Looking forward to version 2.0 |
| 16:09 |
|
de_maas |
Just check DS Visualizer with a list. The do a full 2D rencering on 3d coordinates (and yes, it's slow). |
| 16:10 |
|
de_maas |
Initially it seems they have some catch for them because you can run through them faster later on. |
| 16:10 |
|
de_maas |
It's free so you might give it a quick shot. |
| 16:12 |
|
olas |
right |
| 16:15 |
|
de_maas |
OK, I'm off . Have a nice evening. |
| 16:15 |
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| 18:10 |
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| 19:18 |
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