FXT_A net bug

[JONATHANMAGNO]

Dear Felipe,
first of all thanks for adding TABQ bb, it will be helpful for me, I obtained materials, but they do not match with the experimental XRD using SQL-A net, then I am trying with FXT_A net, there were bugs you said. There is something we can do to get over this issue?

Our last referring issue was this:
"Dear @JONATHANMAGNO,

The PR #82 adds the new molecule you requested.

Please install version 0.0.9.1 to use the new BB.

The BB in the image you uploaded can be obtained with the name S4_BENZ_NH2_O.

Please be aware that the creation of FXT and FXT_A nets with this building block presents some bugs, so only SQL and SQL_A should work currently. I'm investigating this bug and will fixed asap.

In case you have any problems please let me know.

Please let me know if you could use this BB so I can close this issue.

Best,
Felipe"

That is what happen if I am trying to get the COF structure I want:

import pycofbuilder as pcb

cof = pcb.Framework('S4_BENZ_NH2_O-L2_BENZ_CHO-FXT_A-AA')
Traceback (most recent call last):
File "", line 1, in
File "C:\Users\Jonathan\anaconda3\envs\pycofbuilder-env\lib\site-packages\pycofbuilder\framework.py", line 186, in init
self.from_name(self.name)
File "C:\Users\Jonathan\anaconda3\envs\pycofbuilder-env\lib\site-packages\pycofbuilder\framework.py", line 330, in from_name
self.from_building_blocks(bb1, bb2, Net, Stacking, **kwargs)
File "C:\Users\Jonathan\anaconda3\envs\pycofbuilder-env\lib\site-packages\pycofbuilder\framework.py", line 384, in from_building_blocks
result = net_build_dict[net](bb1, bb2, stacking, **kwargs)
File "C:\Users\Jonathan\anaconda3\envs\pycofbuilder-env\lib\site-packages\pycofbuilder\framework.py", line 3815, in create_fxt_a_structure
raise BondLenghError(i, j, dist_matrix[i][j], self.dist_threshold)
pycofbuilder.exceptions.BondLenghError: WARNING: Atoms 6 and 119 are closer than 0.6845938469289887 A, 0.8
cof.save(fmt='cif', supercell = [1, 1, 2], save_dir = '.')
Traceback (most recent call last):
File "", line 1, in
NameError: name 'cof' is not defined

Thanks
Regards
Jonathan

[lipelopesoliveira]

Hi Jonathan,

Thanks for reaching out.

I have been very busy over the past weeks, so I was unable to complete the fix for this bug.

I will put some effort this weekend and try to finish it.

Best,
Felipe

[JONATHANMAGNO]

Thanks a lot for your time, I think this is going to really help me.
Jonathan