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lipelopesoliveira / pyCOFBuilder

A package for Covalent Organic Frameworks structure assembly based on specific building block, topology and functional groups based on the reticular approach
https://lipelopesoliveira.github.io/pyCOFBuilder/
MIT License
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2D square, kagome and Rhombic topology COFs generation #68

Open Rider99 opened 4 months ago

Rider99 commented 4 months ago

Motivation

My goal is to use their tool to generate COF structures with diverse topologies. However, I have encountered several issues:

  1. For square topologies, the tool only allows the connection of building blocks with four connection points each. In practice, it is possible to generate 2D COFs with square topology using building blocks with four connection points and those with two connection points (https://doi.org/10.1038/ncomms8786, https://doi.org/10.1038/s43586-022-00181-z).
  2. Only the L, T, S, and H categories of building blocks have structural images available, while others do not.
  3. The tool currently does not support generating the Kagome and Rhombic category in 2D topologies.

What should be done?

  1. Update the tool to allow the generation of square topology COF structures using a combination of building blocks with four and two connection points.
  2. Add structural images for all categories of building blocks.
  3. Implement support for generating COF structures with the Kagome and Rhombic category in 2D topologies.

Steps for the realization of the task:

  1. Square Topology Update:

Review the current implementation of the tool to understand the limitations regarding building block connections for square topologies. Update the code to support the connection of building blocks with four and two connection points for square topologies. Test the updated tool to ensure it correctly generates 2D COFs with square topology using the specified building blocks. Verify the output against known structures to ensure accuracy and correctness.

  1. Add Structural Images:

Identify the missing structural images for building block categories. Create or obtain structural images for these categories. Integrate the images into the tool and ensure they are correctly displayed.

  1. Implement Kagome and Rhombic Topology

Is there any deadline?

ASAP Thank you so much!!!

lipelopesoliveira commented 4 months ago

Thanks @Rider99 for your interest on pyCOFBuilder and for summarizing some of the main bugs on the current version.

For square topologies, the tool only allows the connection of building blocks with four connection points each. In practice, it is possible to generate 2D COFs with square topology using building blocks with four connection points and those with two connection points.

Please take a look on the SQL-A net. It allows the creation of structures with building blocks S4 + L2.

Only the L, T, S, and H categories of building blocks have structural images available, while others do not.

Thanks for spotting this error. I'll fix it.

The tool currently does not support generating the Kagome and Rhombic category in 2D topologies.

The Rhombic net is indeed missing. I'll try to add it ASAP. Regarding the Kagome net, can you provide an example of a COF that you would call Kagome. I'm only asking it because the HCB net could be seen as a Kagome net. It wold also be possible to create a Kagome net only connecting R4 building blocks, similar to the FXT net. I'll add this option too after I finish the #62 update.

Rider99 commented 3 months ago

Thanks @lipelopesoliveira for your detialed reply. Here is a example for the Kagome 2D-COF:https://pubs.acs.org/doi/abs/10.1021/acsmaterialslett.3c01141.