make_lineage_figures.py

[Emma]

Hello,
I am getting this error everytime I try run make_lineage_figures:

Traceback (most recent call last):
File "../autogrow4/accessory_scripts/make_lineage_figures.py", line 967, in <module>
run_everything(VARS)
File "../autogrow4/accessory_scripts/make_lineage_figures.py", line 864, in run_everything
lineage_dict = get_all_ancestors(mol_name, master_shortname_mol_dict)
File "../autogrow4/accessory_scripts/make_lineage_figures.py", line 392, in get_all_ancestors
parents_to_check = get_parents_full_names(mol_name, master_shortname_mol_dict)
File "../autogrow4/accessory_scripts/make_lineage_figures.py", line 328, in get_parents_full_names
+ " a ligand. missing parrent is: {}".format(parent_1_short))
Exception: a parent is not in master_shortname_mol_dict this means that the dictionary is missing information on a ligand. missing parrent is: NSC170273

To run make_lineage_figures.py :
python ../autogrow4/accessory_scripts/make_lineage_figures.py -o output/lineage1 -i output/Run_0/ –source_compound_file NCI_Top_300_Scores.smi –mol_name Gen_1_C
ross_968450

NCI_Top_300_Scores.smi is my original file with the database of molecules that I used to run AutoGrow on.
output/Run_0/ has the output from the AutoGrow run
Gen_1_Cross_968450 is the name of the molecule I want to trace the lineage from

Please let me know how to fix this error. Thank you!

[Jacob Durrant]

Hi Emma. Much thanks for your interest in AutoGrow4, and thanks for identifying this bug. My student just updated the code. The fixed version can be found at https://git.durrantlab.pitt.edu/jdurrant/autogrow4/-/archive/master/autogrow4-master.zip

Would you mind letting me know if it works for you? If so, I’ll go ahead and push these changes to a new version.

After downloading the fixed version, you’ll need to clear the script’s cache. Here’s how:

python ../autogrow4/accessory_scripts/make_lineage_figures.py -o output/lineage1 -i output/Run_0/ \
--source_compound_file NCI_Top_300_Scores.smi --mol_name Gen_1_Cross_968450 \
--use_docked_source_compounds False --purge_previous_pickled_files True 

You should then be able to rerun the script without errors, like this:

python ../autogrow4/accessory_scripts/make_lineage_figures.py -o output/lineage1 -i output/Run_0/ \
--source_compound_file NCI_Top_300_Scores.smi --mol_name Gen_1_Cross_968450 \
--use_docked_source_compounds False --purge_previous_pickled_files False 

Take care.

[Author]

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