I tried to read structures with R-group from SMILES to depict them with PIKAChU and failed. Hence, I made some changes to enable it:

atomproperties.py:

• Added constructor that adds "R", "X" and "Z" as well as combinations of these variables with indices (0-99) to the atom property dictionaries
• Discussion point: There is a bit of a problem when it comes to how to handle these "atoms" as the R group variables can represent many different things. Right now, they are treated like carbon atoms. This can lead to "Rogue electron" warnings when constructing a molecule from a SMILES string. My first thought was to treat them like the existing placeholder variable "*", but that comes with the problem that the R groups can then only be terminal. Something like "CC[X]CC" is not possible as "*" is treated very similar to hydrogen atoms. Right now, I don't really have an idea for an elegant solution. When the R group variables are treated like carbon atoms, there are warnings, but everything is depicted correctly.

drawing.py:

• Added a function that recognises digits that come behind "R", "X" and "Z" and returns the same string with subscript digits (so that the depiction contains "R₁" instead of "R1").

test_drawing.py:

• Unit test for added function in drawing.py

smiles.py:

• Treat digits that come behind "R", "X" or "Z" as a part of the "element"

Result:

from pikachu.smiles.smiles import read_smiles
from pikachu.general import draw_structure

structure = read_smiles("[R12]C1C([X2])[X]([R])[Z]([Z1])=C([Z2])C1[X1]")
draw_structure(structure)

Hello!

I met a problem while trying to save the structure with smile.general.smiles_to_molfile(). I would be grateful if you could help.

To check if there is an issue with the molecular, I also try to draw it with the NCBI online tool(https://pubchem.ncbi.nlm.nih.gov//edit3/index.html). The SMILE string, structure and error message are following.

CC1=C(/C=C/C(C)=C/C=C/C(C)=C/C=O)C(C)(C)CCC1.NC(=O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)OP(=O)(O)OC[C@H]3O[C@@H](n4cnc5c(N)ncnc54)[C@H](O)[C@@H]3O)[C@@H](O)[C@H]2O)c1.O

Thank you!

Added a convenience function:

• Added the option to instantiate MolFileReader with the String content of a molfile instead of the path of the molfile
• Everything else should behave the same way, the constructor of MolFileReader now simply also accepts and processes the argument molfile_str if the normal "molfile" argument is not given
• Added unit tests for the things I have touched to make sure it behaves the way it is supposed to behave

Hey,

Really nice python package. Excited to see further developments. I tried the draw functionality of the package and found the default Bond thickness to be higher than most of the other toolkits. Probably setting a lower thickness would benefit most of the users. SMILES: CN1C=NC2=C1C(=O)N(C(=O)N2C)C

pikachu

CDK-Depict

Do let me know once you have updated the documentation.

Kind regards, Kohulan

Added a convenience function:

• Added the option to instantiate MolFileReader with the String content of a molfile instead of the path of the molfile
• Everything else should behave the same way, the constructor of MolFileReader now simply also accepts and processes the argument molfile_str if the normal "molfile" argument is not given
• Added unit tests for the things I have touched to make sure it behaves the way it is supposed to behave

Hey there!

We have run into a problem with the depiction functionalities in PIKAChU. When depicting large molecules, Python simply crashes. We don't get an exception that can be caught or something like that. If I execute the code below in my Python shell, the Python shell simply closes.

Minimal example for the reproduction of the problem:

from pikachu.general import read_smiles
from pikachu.drawing import drawing

smiles = 'CC(=O)N[C@H]1[C@H]([C@H](O)[C@H](O)CO)O[C@@](O[C@H](CO)[C@@H](O)[C@@H]2O[C@@](O[C@H](CO)[C@@H](O)[C@@H]3O[C@@](O[C@H](CO)[C@@H](O)[C@@H]4O[C@@](O[C@H](CO)[C@@H](O)[C@@H]5O[C@@](O[C@H](CO)[C@@H](O)[C@@H]6O[C@@](O[C@H](CO)[C@@H](O)[C@@H]7O[C@@](O[C@H](CO)[C@@H](O)[C@@H]8O[C@@](O[C@H](CO)[C@@H](O)[C@@H]9O[C@@](O[C@H](CO)[C@@H](O)[C@@H]%10O[C@@](O[C@H](CO)[C@@H](O)[C@@H]%11O[C@@](O[C@H](CO)[C@@H](O)[C@@H]%12O[C@@](O[C@H](CO)[C@@H](O)[C@@H]%13O[C@@](O[C@H](CO)[C@@H](O)[C@@H]%14O[C@@](O)(C(=O)O)C[C@H](O)[C@H]%14NC(C)=O)(C(=O)O)C[C@H](O)[C@H]%13NC(C)=O)(C(=O)O)C[C@H](O)[C@H]%12NC(C)=O)(C(=O)O)C[C@H](O)[C@H]%11NC(C)=O)(C(=O)O)C[C@H](O)[C@H]%10NC(C)=O)(C(=O)O)C[C@H](O)[C@H]9NC(C)=O)(C(=O)O)C[C@H](O)[C@H]8NC(C)=O)(C(=O)O)C[C@H](O)[C@H]7NC(C)=O)(C(=O)O)C[C@H](O)[C@H]6NC(C)=O)(C(=O)O)C[C@H](O)[C@H]5NC(C)=O)(C(=O)O)C[C@H](O)[C@H]4NC(C)=O)(C(=O)O)C[C@H](O)[C@H]3NC(C)=O)(C(=O)O)C[C@H](O)[C@H]2NC(C)=O)(C(=O)O)C[C@@H]1O'

mol = read_smiles(smiles)
drawer = drawing.Drawer(mol)

Expected behaviour:

• Instantiation of a Drawer object.

Observed behaviour:

• Python crashes.

We will build a workaround and simply not use PIKAChU for large structures in our application, but I think it may make sense to look into this.

Have a nice day! Otto

Hey there!

When reading SMILES strings using PIKAChU, @Mar-Gol ran into the following problem:

Minimal example for reproduction:

>>> smiles = 'CCOC1=CC2=C(C=C1)S(=O)C(=C2C3=CC=CC=C3)C(=O)C4=CC=CC=C4'
>>> from pikachu.general import read_smiles
>>> mol = read_smiles(smiles)

Expected behavior:

• The structure is converted into PIKAChU's molecular representation.

Observed behavior:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\Otto Brinkhaus\anaconda3\envs\RanDepict\lib\site-packages\pikachu\general.py", line 45, in read_smiles
    structure = smiles.smiles_to_structure()
  File "C:\Users\Otto Brinkhaus\anaconda3\envs\RanDepict\lib\site-packages\pikachu\smiles\smiles.py", line 496, in smiles_to_structure
    structure.refine_structure()
  File "C:\Users\Otto Brinkhaus\anaconda3\envs\RanDepict\lib\site-packages\pikachu\chem\structure.py", line 916, in refine_structure
    self.aromatic_cycles = self.find_aromatic_cycles()
  File "C:\Users\Otto Brinkhaus\anaconda3\envs\RanDepict\lib\site-packages\pikachu\chem\structure.py", line 781, in find_aromatic_cycles
    self.promote_lone_pairs_in_aromatic_cycles(aromatic_cycles)
  File "C:\Users\Otto Brinkhaus\anaconda3\envs\RanDepict\lib\site-packages\pikachu\chem\structure.py", line 731, in promote_lone_pairs_in_aromatic_cycles
    atom.promote_lone_pair_to_p_orbital()
  File "C:\Users\Otto Brinkhaus\anaconda3\envs\RanDepict\lib\site-packages\pikachu\chem\atom.py", line 512, in promote_lone_pair_to_p_orbital
    p_orbital = p_orbitals[-1]
IndexError: list index out of range

• We used the latest version on pipy which we installed via pip install pikachu-chem.

I will build a work-around for our application for now, but I would appreciate your help a lot! Thank you in advance! Otto

Hi developers, I am very happy that you have developed a new molecular image generation tool, which has been very useful to me. I hope it will support more drawing standards, such as ACS-1996 Document Settings, instead of the commercial software ChemDraw.

If there is a solution, please let me know, thank you.

After playing around with the attributes of drawing.Options(), I have noticed that some of them don't do anything:

• ‘font_size_large’
• ‘font_size_small’
• ‘height’
• ‘width’
• All ‘kk_*’ attributes (although I am not sure what they are responsible for)
• ‘background_color’
• I am not sure what ‘draw_hydrogens’ does, but it does not draw hydrogen atoms
• SMILES: [R12]C1RXZ=C([Z2])C1NC@(F)C(=O)O
  • ‘Draw_hydrogens’ = False:
  • ‘Draw_hydrogens’ = True: