| running a DW macro in batch [message #2039] |
Thu, 30 November 2023 16:36  |
SM2020
Messages: 14
Registered: June 2020
Location: UK
|
Junior Member |
|
|
Hi,
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.
I tried to use a previous post describing looping a macro over multiple dwar files to get started (see below) but I am getting stuck.
https://openmolecules.org/forum/index.php?t=msg&goto=109 3&&srch=loop#msg_1093
My macro attempt is given below.
<macro name="batch-conformers">
<task name>="repeatNextTasks"
dir=C:\PATH #path is specified when run
filetype=datawarrior
all=true
<task>
<task name="openFile">
fileName=$FILENAME
<task>
<task name="generate2DAtomCoordinates">
scaffoldMode=centralRing
structureColumn=Structure
automatic=true
colorizeScaffolds=false
</task>
<task name="generateConformers">
poolConformers=false
neutralize=false
fileName=$FILENAME_conf.dwar
torsionSource=crystallDB
largestFragment=true
stereoIsomerLimit=16
minimize=mmff94+
algorithm=lowEnergyRandom
maxConformers=16
structureColumn=Structure
fileType=dwar
<task>
<task name="closeWindow">
</task>
</macro>
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.
|
|
|
|
|
|
|
|
| Re: running a DW macro in batch [message #2443 is a reply to message #2039] |
Tue, 18 November 2025 15:40  |
SM2020
Messages: 14
Registered: June 2020
Location: UK
|
Junior Member |
|
|
Hi,
This is a follow up to a previous forum support request.
I would like some help with running a DW macro over multiple .sdf files in a folder, please.
I am running DW version [6.05.02] on Windows 11 – the macro (see below) used to work in earlier versions of DW, but which I now can’t reproduce.
Aim: To generate 3D conformers for each molecule represented in a list of individual .sdf files in a specified directory
Intended result: an output of multiple .sdf files of molecule conformers from each original .sdf input file.
The previous working macro is given below.
<macro name="batch-conformers">
<task name="repeatNextTasks">
dir=#ask#
filetype=sd
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=mmff94s+
algorithm=lowEnergyRandom
maxConformers=16
structureColumn=Structure
fileType=sdf3
</task>
<task name="closeWindow">
saveChanges=no
</task>
</macro>
Result when running the macro: When I try to run the macro, it seems to run but displays transient error/dialog messages (which are not left on the screen long enough to read) and the require output files are not created in the output directory.
When I have tried to re-run the macro on an older version of DW (on ubuntu), the macro will run but need to manually 'hit a key' type of operation to move onto the next conformer generation...
If someone can help – and suggest where the syntax in the macro is at fault - it would be very much appreciated.
Thanks.
|
|
|
|
Search
Help
Members
Register
Login
Home
