Closed bill-tatsis closed 1 month ago
Here is a the code snippet used to do the runs:
for folder in dud_folders:
print("{}ligands starting...".format(folder))
get_similarity_scores(
ref_file="query.sdf",
dataset_files_pattern="ligands.smi",
ignore_hs=True,
n_confs=60,
keep_mol=True,
random_seed=109838974,
opt_confs=True,
calc_energy=True,
energy_iters=300,
energy_cutoff=30,
align_confs=True,
rms_cutoff=0.1,
num_threads=46,
method="ETKDGv3",
volume_type="analytic",
n=2,
epsilon=0.5,
use_carbon_radii=True,
color=True,
max_conformers=1,
sort_by="ComboTanimoto",
write_to_file=True,
gpu_id=0,
working_dir="{}/ligands".format(folder),
#smiles_kwargs={"delimiter": "\t"},
)
A few notes:
Thanks!I'll give it a spin 🐡
A quick follow-up question, is query.sdf
a compound from the ligands.smi
file?
Good point - for each target, it is the xtal-lig.pdb file (converted into an .sdf file) found in the DOCKING_GRIDS_AND_POSES folder of dudez.docking.org
Hi, would it be possible to share input files and details used in the benchmark runs? Thanks :)