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DCoupry / autografs

Python library for generation of MOFs, COFs, Zeolites...
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sql topology doesnt rotate the linker #3

Open mersadkhan opened 4 years ago

mersadkhan commented 4 years ago

If you use a random liker with several atoms in 3D(not like the example of benzene just in 2D), it doesn't connect the linker and the center properly correctly. It is supposed to the linker two X atoms make a line, and this line aligns with the line that comes from center two X atom and then they align. But AuToGraFs just connect them randomly without attention to the junction point. attached is a linker and the python AuToGraFs code which shows this problem. test.tar.gz

mersadkhan commented 4 years ago

it seems this issue arises whenever the liker is expanded in 3D. I test the PCU topology and the problem remained.

DCoupry commented 4 years ago

I'll try and take a look. If you manage to track down the cause yourself, feel free to submit a pull request! (I'm working full time in industry now, with few moments for maintenance.)

mersadkhan commented 4 years ago

It seems the problem is somewhere that the dummies should join. I tried to align the linker to solve the problem but I failed. practically most people use the old version 02042016. they dont use this version because of this critical bug. but if you solve this problem I can use this version in a workfelow. solving this bugs should not be something hard. some where you add a constance to the dummies. but if I try to find it it may takes lots of time to understand undocumented code.

DCoupry commented 4 years ago

Hi Mersad, "solving this bugs should not be something hard" -> It kinda is: I have not used this software in a while (since my PhD) and again, I am otherwise employed and have little time to give to keep this up to date. "it may takes lots of time to understand undocumented code" -> Sorry that you find it undocumented. I made sure to add lots of comments and docstring when I wrote that. But on a side note, isn't it always recommended to have some understanding of the code you use?

Finally, can you please post here a reproducible bit of code for the problem?

mersadkhan commented 1 year ago

I sent a sample code and linker for you. In the first comment. The problem is still for both pcu and SQL topology and I had an other problem to for example having a specific linker as pillar linker and other linker as layer linker in PCU. there is no way to control this . in the version of https://github.com/maddicoat/AuToGraFS I have none of these problems.