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Re: running a DW macro in batch
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=2059&th=695#msg_2059
]]>SM20202023-12-28T12:27:44-00:00Re: Change default structure copy option
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=2055&th=701#msg_2055
please have a look if the answer in your other thread
Norwid]]>nbehrnd2023-12-19T22:23:38-00:00 Change default structure copy option
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=2053&th=701#msg_2053
I have created a plugin that retrieves data including structures from our internal database.
The structures are rendered in DW successfully.
However, when I try to copy all the data from the datatable including structures, the structures are copied as ID, that chemaxon for excel cannot parse.
When i copy 1 structure at a time, I get option to select MolfileV2 or smile or ID.
But when coping the full table that has data as well as structure, by default ID is selected.
Is it possible to change it MolfileV2 or V3 or smiles or Give an option while coping from the datatable?
Thanks]]>helloWorld222023-12-19T15:37:52-00:00Re: datawarrior descriptor literature refs
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=2051&th=699#msg_2051
I suggest to start the literature search from two points of departure: the seminal paper about DataWarrior (2015JChemInfModel460, https://doi.org/10.1021/ci500588j) as well as the review-like «Limits of Prediction for Machine Learning in Drug Discovery» by Modest von Korff and Thomas (2022FrontPharmacol, https://doi.org/10.3389/fphar.2022.832120, open access).
Norwid]]>nbehrnd2023-12-18T15:02:02-00:00datawarrior descriptor literature refs
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=2050&th=699#msg_2050
Can anyone point me at literature references that discuss the Datawarrior descriptors (FragFp, SkelSpheres etc) and perhaps even discusses comparison with other popular descriptors?
Thanks]]>Maxwell2023-12-18T13:44:09-00:00Re: running a DW macro in batch
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=2044&th=695#msg_2044
It seems that your macro has some syntax errors, e.g. '<task>' are task end tags and should always look be '</task>'. The second line should end with '>'.
A working macro should be the following:
<macro name="batch-conformers">
<task name="repeatNextTasks">
dir=#ask#
filetype=datawarrior
all=true
</task>
<task name="openFile">
fileName=$FILENAME
</task>
<task name="generateConformers">
neutralize=false
fileName=$FILENAME_conf.sdf
torsionSource=crystallDB
largestFragment=true
stereoIsomerLimit=16
minimize=mmff94+
algorithm=lowEnergyRandom
maxConformers=16
structureColumn=Structure
fileType=sdf2
</task>
<task name="closeWindow">
saveChanges=no
</task>
</macro>
]]>thomas2023-12-06T16:31:30-00:00running a DW macro in batch
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=2039&th=695#msg_2039
I would like some help with running a DW macro over multiple .dwar files in a folder, please.
I am running DW version 5.5.0.
Aim: To generate 3D conformers for each molecule represented in a list of individual .dwar files in a specified directory
Intended result: an output of multiple .sdf files of molecule conformers from each original .dwar input file.
When I try to run the macro, I get the following error-
“macro ‘batch conformers’ does not have any tasks”
If someone can help, it would be very much appreciated.
Thanks.
]]>SM20202023-11-30T15:36:56-00:00peediction missing values- descriptors
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=2035&th=693#msg_2035
I would like to predict missing values in database using KNN regression. I calculated all descriptors but FragFP is only available for prediction. Is it some bug or some limitation concerning database content?
Thanks.
Regards,
Jirzy
]]>Jirzy2023-11-23T10:52:06-00:00Re: Free Wilson Analysis
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=1877&th=654#msg_1877
Thanks for the response. Yes that would be perfect, maybe an option to define your own core, similar to the core based SAR analysis and the outputs you suggest would be great.
Many thanks for considering.
Angus
]]>amorrison2023-03-20T07:41:39-00:00Re: Free Wilson Analysis
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=1876&th=654#msg_1876
this cannot be done currently, but it is not the first time to here the request. I may consider...
A way would be (similar to automatic SAR) determining core fragents, e.g. Murcko, and then for all molecules with matching core fragments analyse changing substituents. Then create a result table with these columns:
1 - core fragment with R1,r2,... for every chaging substituent position
2 - substituent position (R1 or R2 or ...)
3 - Structure of substituent at this position
4 - mean contribution of this substituent at this position to activity
5 - count of this substituent found at this position
6 - StdDev of constribution value (this substituent at this position)