generate_spatial.yml

ligand_path: data/example_data/substruct_mod/4w9f_ligand.sdf  # .sdf file for posterior ligand molecule
target_path: data/example_data/4w9f/4w9f_pocket.pdb  # .pdb file for target structure

# input either `substruct_modify_path` or `substruct_modify_pattern`, not both.
substruct_modify_path: data/example_data/substruct_mod/substruct_modify.sdf  # .sdf file for ligand substructure to modify
# substruct_modify_pattern: "[CH2]C1:C:C:C(C2:S:C:N:C:2C):C:C:1" # SMILES or SMARTS string for ligand substructure to modify

pdb_id: 4w9f  # PDB ID for target
output: output/substruct_modify_example  # output directory

n_samples: 10 # number of molecules to generate
random_rotate: true
random_translate: false

zbetas: [0.3, 0.3, 0.3, 0.3]  # list defining prior-posterior interpolation factor for each latent resolution. Or single value for all resolutions.
temps: 1.  # list defining temperature factor for each latent resolution. Or single value for all resolution.


## filter generated molecules
ring_sizes: [5,6]  # only allow rings of this size
ring_system_max: 3 # only allow ring systems up to this size
ring_loops_max: 0  # only allow this many ring loops
dbl_bond_pairs: false  # allow consecutive double bonds
n_atoms_min: 0  # minimum number of atoms allowed in each molecule


## model
checkpoint: model_checkpoints/drughive_model_ch9.ckpt  # model checkpoint
model_id: c9_pdbzinc  # id for model
ffopt_mols: True  # run force field optimization on generated molecules