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setting_dscore.yaml
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setting_dscore.yaml
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# Basic setting
c_val: 1.0
# threshold_type: [time, generation_num]
threshold_type: generation_num
#hours: 0.01
generation_num: 300000
output_dir: result/dscore_c10
model_setting:
model_json: model/model.tf25.json
model_weight: model/model.tf25.best.ckpt.h5
token: model/tokens.pkl
reward_setting:
reward_module: reward.dscore_reward
reward_class: Dscore_reward
# Advanced setting
expansion_threshold: 0.995
simulation_num: 3
flush_threshold: -1
policy_setting:
policy_module: policy.ucb1
policy_class: Ucb1
# Restart setting
save_checkpoint: False
restart: False
checkpoint_file: chemtsv2.ckpt.pkl
# Filter setting
use_lipinski_filter: False
lipinski_filter:
module: filter.lipinski_filter
class: LipinskiFilter
type: rule_of_5
use_radical_filter: True
radical_filter:
module: filter.radical_filter
class: RadicalFilter
use_pubchem_filter: False
pubchem_filter:
module: filter.pubchem_filter
class: PubchemFilter
use_sascore_filter: False
sascore_filter:
module: filter.sascore_filter
class: SascoreFilter
threshold: 3.5
use_ring_size_filter: False
ring_size_filter:
module: filter.ring_size_filter
class: RingSizeFilter
threshold: 6
use_pains_filter: False
pains_filter:
module: filter.pains_filter
class: PainsFilter
type: [pains_a]
include_filter_result_in_reward: False
# User settings
# Set the scaling functions and weights for each objective.
# When using min_gauss or max_gauss, set the gaussian parameters alpha, mu, and sigma.
# When using minmax, set the maximum and minimum values.
# When using rectangular, set the minimum and maximum desirable values.
Dscore_parameters:
EGFR: {type: max_gauss, alpha: 1, mu: 9, sigma: 2, weight: 8}
ERBB2: {type: min_gauss, alpha: 1, mu: 2, sigma: 2, weight: 1}
ABL: {type: min_gauss, alpha: 1, mu: 2, sigma: 2, weight: 1}
SRC: {type: min_gauss, alpha: 1, mu: 2, sigma: 2, weight: 1}
LCK: {type: min_gauss, alpha: 1, mu: 2, sigma: 2, weight: 1}
PDGFRbeta: {type: min_gauss, alpha: 1, mu: 2, sigma: 2, weight: 1}
VEGFR2: {type: min_gauss, alpha: 1, mu: 2, sigma: 2, weight: 1}
FGFR1: {type: min_gauss, alpha: 1, mu: 2, sigma: 2, weight: 1}
EPHB4: {type: min_gauss, alpha: 1, mu: 2, sigma: 2, weight: 1}
Solubility: {type: max_gauss, alpha: 1, mu: -2, sigma: 0.6, weight: 1}
Permeability: {type: max_gauss, alpha: 1, mu: 1, sigma: 1, weight: 1}
Metabolic_stability: {type: max_gauss, alpha: 1, mu: 75, sigma: 20, weight: 1}
Toxicity: {type: min_gauss, alpha: 1, mu: 5.5, sigma: 0.5, weight: 1}
# SAscore is made negative when scaling because a smaller value is more desirable.
SAscore: {type: max_gauss, alpha: 1, mu: -3, sigma: 2, weight: 1}
QED: {type: max_gauss, alpha: 1, mu: 0.8, sigma: 0.25, weight: 1}
molecular_weight: {type: rectangular, min: 200, max: 600, weight: 1}
tox_alert: {type: identity, weight: 1}
has_chembl_substruct: {type: identity, weight: 1}