radi0sus / xyz2tab Goto Github PK

Hi, thank you very much for your code! It has been really useful for me and my research!

Just one small question: is there anyway of getting rid of the atomic labels when the visualization option is enabled for showing a molecular plane?

Hi,

Thanks for your code!

After calculating the bond length, if this code could add the function of "color the bond according to different bond lengths"? And the range of the color bar also could be tuned.

Thank you!!!

Best regards,
Lulu

Hello, I'm trying to use your code but i cannot solve this problem, can you check it out ?
tysm

Is there any option to calculate the distance between specific atoms? I have considered changing my .xyz files such that the atoms are consecutive but maybe there is something already implemented and capable of doing so.

python3 xyz2tab.py h2o.com
Traceback (most recent call last):
File "xyz2tab.py", line 19, in
sys.stdout.reconfigure(encoding='utf-8')
AttributeError: '_io.TextIOWrapper' object has no attribute 'reconfigure'

After commenting line 19 I get:

python3 xyz2tab.py h2o.com

Filename : h2o.com
Number of atoms : 3
Sum formula : H₂O
Formula weight : 18.02 g/mol
Excluded atoms : None
Excluded elements : None
Included contacts : None
Covalent radius + : 8.00 %

dist_df['cov_radius2'])+(dist_df['cov_radius1'] +

File "/Users/derwiszck/anaconda3/lib/python3.6/site-packages/pandas/core/ops/init.py", line 1048, in wrapper
result = na_op(lvalues, rvalues)
File "/Users/derwiszck/anaconda3/lib/python3.6/site-packages/pandas/core/ops/init.py", line 965, in na_op
import pandas.core.computation.expressions as expressions
File "/Users/derwiszck/anaconda3/lib/python3.6/site-packages/pandas/core/computation/expressions.py", line 19, in
from pandas.core.computation.check import _NUMEXPR_INSTALLED
File "/Users/derwiszck/anaconda3/lib/python3.6/site-packages/pandas/core/computation/check.py", line 3, in
ne = import_optional_dependency("numexpr", raise_on_missing=False, on_version="warn")
File "/Users/derwiszck/anaconda3/lib/python3.6/site-packages/pandas/compat/_optional.py", line 90, in import_optional_dependency
module = importlib.import_module(name)
File "/Users/derwiszck/anaconda3/lib/python3.6/importlib/init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/Users/derwiszck/anaconda3/lib/python3.6/site-packages/numexpr/init.py", line 48, in
nthreads = _init_num_threads()
File "/Users/derwiszck/anaconda3/lib/python3.6/site-packages/numexpr/utils.py", line 137, in _init_num_threads
requested_threads = int(os.environ['OMP_NUM_THREADS'])
ValueError: invalid literal for int() with base 10: '2,1'

Please let me know if there is a need of any information.
Cheers,

derwiszck