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Add fast grant sentinel cases for retrospective benchmarking #7

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Aug 10, 2020
Merged

Add fast grant sentinel cases for retrospective benchmarking #7

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966e061
Add fastgrant-table1
jchodera Aug 6, 2020
43d57f5
Add fast grant sentinel cases for retrospective benchmarking.
jchodera Aug 7, 2020
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Add fastgrant-table1
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@jchodera
jchodera committed Aug 6, 2020
commit 966e061a9bcf75c3369a7a9152d8d82bc0ae28e7
7 changes: 4 additions & 3 deletions synthetic-enumeration/02-generate-poses.py
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Expand Up @@ -313,7 +313,7 @@ def generate_poses(receptor, refmol, target_molecules_filename, output_filename,
refmol : openeye.oechem.OEGraphMol
Reference molecule which shares some part in common with the proposed molecule
target_molecules_filename : str
Molecules to build
Input file of molecules to build
output_filename : str
Output filename for generated conformers
filter_series : str, optional, default=None
Expand Down Expand Up @@ -391,7 +391,8 @@ def generate_poses(receptor, refmol, target_molecules_filename, output_filename,

# Load all fragments
for prefix in [
'aminopyridine_compounds_for_FEP_benchmarking',
'fastgrant-table1',
#'aminopyridine_compounds_for_FEP_benchmarking',
#'nucleophilic_displacement_enumeration_for_FEP-permuted',
#'activity-data-2020-07-29',
#'primary_amine_enumeration_for_chodera_lab_FEP-permuted',
Expand Down Expand Up @@ -428,6 +429,6 @@ def generate_poses(receptor, refmol, target_molecules_filename, output_filename,
break

# Generate poses for all molecules
target_molecules_filename = prefix + f'-conformers-{fragment}.sdf'
target_molecules_filename = prefix + f'.csv'
output_filename = f'{prefix}-dockscores-{fragment}.sdf'
generate_poses(receptor, refmol, target_molecules_filename, output_filename)
1 change: 1 addition & 0 deletions synthetic-enumeration/README.md
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Expand Up @@ -11,6 +11,7 @@ Modeling of design conformations suggested by this [excellent blog post from Pat
* `nucleophilic_displacement_enumeration_for_FEP.csv` - nucleophilic displacement series (15918)
* `activity-data-2020-07-29.csv` - all compounds with activity data for retrospective benchmarking (888)
* `aminopyridine_compounds_for_FEP_benchmarking.csv` - 3-aminopyridine retrospective benchmarking compounds from Matthew Robinson (70)
* `fastgrant-table1.csv` - sentinel cases from Fast Grant application (Alpha Lee) (11)

### Docked conformers
* `primary_amine_enumeration_for_chodera_lab_FEP-permuted-conformers-x10789.sdf.gz`
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