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phi-grib / PaDEL-descriptor-ws

PaDEL ws descriptors engine
GNU General Public License v3.0
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When I use it to generate 3D descriptors, most of the descriptors are NULL values #4

Open huan-xiao opened 5 years ago

huan-xiao commented 5 years ago

I use PaDEL to generate 3D descriptors. The input file is a .sdf file, however, the output file has many lines consisted with NULL values.

Please refer to the screenshot below, many lines are empty: snip20190102_1

How to solve this problem? Thanks in advance.

OriolLopezMassaguer commented 5 years ago

Hello; First of all, this project is only a web wrapper for the command line version of PaDEL descriptors.

PaDEL decriptors original software

The goal of the project is to have running in memory copy of the descriptor engine to improve performance because of the overhead of the JVM startup time.

This is critical when there is the need compute the descriptors molecule by molecule (see README)

So in principle this version of the software and the original compute the same descriptors in the same way.

So if the "NULL" values are returned is caused by the original padel software and you have to refer to the original software authors.

Have you computed the descriptors through the web interface? Or through the command line? Can you send me the sdf file? or is it private?

Example of the two modes are located in: Examples

huan-xiao commented 5 years ago

Hi Oriol,

Many thanks for your reply.

I think the "NULL" values are caused by the original PaDEL software because I run the "PaDEL-Descriptor.jar" to generate those descriptors.

Yes, I can send you the .sdf file. I would appreciate it if you can have a look at it. example.txt

You may rename it as "example.sdf" after downloading, as I cannot upload a .sdf file here.

Thanks, Huan

OriolLopezMassaguer commented 5 years ago

Thanks I will try as son as possible

huan-xiao commented 5 years ago

Thank you! Is it an easy problem to solve?