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View Code? Open in Web Editor NEWA Python tool for local chemical space exploration of any structure based on their 3D geometry
License: MIT License
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chemspax's Issues
[BUG] Steric hindrance causes weird .xyz to be formed after xtb geometry optimization
Describe the bug
When doing a functionalization that interferes with a atom that's at the same position, xtb geometry optimization fragments the whole complex resulting in loose atoms.
To Reproduce
Steps to reproduce the behavior:
- bash functionalize_and_optimize.sh
- Visualize the optimized structures that are formed after 4 or 5 functionalizations
Expected behavior
The complex is functionalized --> optimized --> the optimized complex is functionalized etc. Until a functionalized and optimized version of the complex is built.
Screenshots
This is the result of 6 functionalizations and optimizations on a RuPNP-tBut complex.
[BUG] Overlapping hydrogens of previous functionalizations on skeleton
Describe the bug
After 10+ functionalizations the hydrogens of some substituents collapse and get the same xyz coordinates. These are substituents that were placed in a previous iteration and it is possible to see them come closer together.
To Reproduce
Steps to reproduce the behavior:
Add this functionalization_list to the Rutrop2dad skeleton: [[52,51],[54,53],[56,55],[58,57],[1,0],[3,2],[7,6],[17,14],[19,11],[18,15],[16,12],[26,22],[28,25],[29,21],[27,24],[9,8],[46,42],[48,45],[49,41],[47,44],[37,34],[39,31],[38,35],[36,32]]
Use these substituents in functionalize_and_optimize_obabel.sh:
CH3
F F F F CCH3CH3CH3 C2H5NOCH3 C2H5NOH CCH3CH3OCH3 CCH3CH3ONH2 CH2OCH3 CH2CH3 CH2ONH2 CH3 CH4N2OCH3 OH CH2OCH3 CH3 OH NH2 NC2H6 CH2OH CHCH3OH CH3
When using UFF in ff_optimize() in iteration 13 the 2 hydrogens of the CH2OCH3 group will collapse as shown in the picture below
Expected behavior
Previous placed groups should remain correctly oriented and have no overlapping atoms.
Screenshots
[BUG] Elongated C-H bond after GAFF UFF optimization
Describe the bug
After functionalization of a Co-porphyrin an elongated C-H bond appears that stretches between a phenyl ring. GFN2-xTB, GFN-FF, UFF and GAFF are not able to handle this. Convergence issues were observed with ~40 of the 280 functionalizations.
To Reproduce
Steps to reproduce the behavior:
- Take the co_por_C6H6-CH3_meta_1 skeleton
- add functionalization_list = [[40,36],[45,43],[39,34],[42,38],[41,37],[54,50],[58,57],[53,48],[56,52],[55,51],[68,64],[73,71],[67,62],[70,66],[69,65],[82,78],[86,85],[81,76],[84,80],[83,79],[2,6],[5,4],[13,12],[11,10],[27,26],[24,25],[16,17],[19,22]] to the skeleton .xyz file
- in functionalize_and_optimize_obabel.sh change the variables to the following input:
STARTING_C_SUBSTITUENT = 1-octanol
RANDOM_C_SUBSTITUENTS = C2H5NOH CCH3CH3CH3 C2H5NOH 1-octanol 1-octanol C2H5NOH CCH3CH3CH3 C2H5NOH 1-octanol 1-octanol C2H5NOH CCH3CH3CH3 C2H5NOH 1-octanol 1-octanol C2H5NOH CCH3CH3CH3 C2H5NOH 1-octanol NH2 CH3 CH3 NH2 NH2 CH3 CH3 NH2
Expected behavior
A symmetrically functionalized Co-porphyrin with normal bond lengths which GFN2-xTB can optimize further
Screenshots
MDL Molfile of structure shown in screenshot:
[[23, 22], [20, 21], [12, 13], [15, 18]]
OpenBabel11262017193D
419430 0 0 1 0 0 0 0 0999 V2000
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M END
Change relative paths to absolute paths
The path to folders containing various scripts and relevant files (e.g. skeleton, substituents) are all provided as relative.
This should be preferably changed to absolute paths. Not urgent, but should be done for robustness.
This would also make scripting on top of our code easily possible for users.
[BUG] Environment problem
There is a typo in the conda_env.yml file. This typo make chemspax installation impossible. The proper code should look like this:
name: chemspax
channels:
- conda-forge
- anaconda
- defaults
- rdkit
- mordred-descriptor
dependencies:
- python=3.10.5
- ase==3.22.1
- openbabel==3.1.1
- pandas==1.4.3
- numpy==1.23.2
- rdkit==2022.09.1
- morfeus-ml==0.7.1
- mordred==1.2.0
- openpyxl
[FEATURE]Modify only one position
Is your feature request related to a problem? Please describe.
It seems that currently it is not possible to generate a database of structures, where only one position in the initial skeleton is functionalized with a set of substituents. That would be highly beneficial to study the influence of substituents at specific ligand positions in a complex
Describe the solution you'd like
It would be great if only one specific position could be functionalized, with one substituent at a time. E.g. turning a specific C-H bond into a set of C-X groups with different Xs.
Additional context
Add any other context or screenshots about the feature request here.
Organize docs in single folder
[BUG] Recursive printing
I tried to use the code like this:
for index, sub_list in enumerate(self.substituent_list):
main([os.path.join(path_to_skeletons, skeleton_list_[index])], sub_list, self.path_to_database, path_to_substituents,\
os.path.join(path_to_skeletons), chemspax_working_directory, path_to_output)
My intent was to do one skeleton + 1 list of substituents at a time coming from a pandas dataframe. The following output is displayed at some point:
The program works as intended, but the printing seems to also occur recursively.
Write tests for core functionalities
- write simple system test
- unit tests for attach_substituents.py
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