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jvermaas / LigninBuilder

VMD Plugin and associated scripts to build lignin structures from topological specifications
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Problem with smilesdemo #2

Closed k0ryphae closed 3 years ago

k0ryphae commented 3 years ago

When activating writepsfgen.py with Python, inside conda rdkit environment, a following error message is given:

[13:26:28] WARNING: no name column found on line 1 Mol: 0 Traceback (most recent call last): File "/home/koryphae/LigninBuilder/smilesdemo/writepsfgen.py", line 243, in c1atom = mol.GetAtomWithIdx(match[c1index]) TypeError: tuple indices must be integers or slices, not float

Any help?

jvermaas commented 3 years ago

Oooh, I'm betting that this is something related to python 3 making everything floats unless told otherwise. Could you list the steps you took to arrive here? I'm especially keen to know what your python/rdkit versions are.

jvermaas commented 3 years ago

Ok, I've just pushed a commit that fixes what was broken when I ran this in python 3.

k0ryphae commented 3 years ago

Of course.

So initially I was testing the Lignin-KMC (possibly one of your projects or your group's projects aswell) which generates SMILES code when given parameters. I wanted to try out the SMILES insert to generate something a close to our lignin structure and then further simulate this in GROMACS. So what I precisely did is:

1) installed everything required for Lignin-KMC in the tutorial. Conda version 4.9.2 numpy 1.19.2 rdkit - i cant find the version number

k0ryphae commented 3 years ago

Ok, I've just pushed a commit that fixes what was broken when I ran this in python 3.

Thanks. Now for whatever reason I'm getting another error [16:28:04] WARNING: no name column found on line 1 [16:28:04] WARNING: no name column found on line 2 [16:28:04] WARNING: no name column found on line 3 Mol: 0 /home/koryphae/LigninBuilder/smilesdemo/writepsfgen.py:143: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information. Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations for i, monoletter in enumerate(resnamelist[np.argsort(np.array(residuelist, dtype=np.int))][::6]): Mol: 1 Mol: 2

when in a conda environment I (accessed via conda activate) I type 'conda list' and there rdkit version is 2021.03.1, numpy: 1.20.2

k0ryphae commented 3 years ago

Ok, I've just pushed a commit that fixes what was broken when I ran this in python 3.

Thanks. Now for whatever reason I'm getting another error [16:28:04] WARNING: no name column found on line 1 [16:28:04] WARNING: no name column found on line 2 [16:28:04] WARNING: no name column found on line 3 Mol: 0 /home/koryphae/LigninBuilder/smilesdemo/writepsfgen.py:143: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information. Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations for i, monoletter in enumerate(resnamelist[np.argsort(np.array(residuelist, dtype=np.int))][::6]): Mol: 1 Mol: 2

when in a conda environment I (accessed via conda activate) I type 'conda list' and there rdkit version is 2021.03.1, numpy: 1.20.2

And python inside conda environment shows version 3.9.2

k0ryphae commented 3 years ago

Ok, I've just pushed a commit that fixes what was broken when I ran this in python 3.