mirror of
https://github.com/HannesStark/boltzgen.git
synced 2026-06-04 11:54:23 +08:00
100 lines
2.3 KiB
YAML
100 lines
2.3 KiB
YAML
_target_: boltzgen.task.predict.predict.Predict
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data:
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_target_: boltzgen.task.predict.data_from_yaml.FromYamlDataModule
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cfg:
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_target_: boltzgen.task.predict.data_from_yaml.DataConfig
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tokenizer:
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_target_: boltzgen.data.tokenize.tokenizer.Tokenizer
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atomize_modified_residues: false
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featurizer:
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_target_: boltzgen.data.feature.featurizer.Featurizer
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moldir: null
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yaml_path: null
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output_dir: ${output}
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diffusion_samples: ${diffusion_samples}
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# Design
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backbone_only: false
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atom14: true
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atom37: false
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disulfide_prob: 1.0
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disulfide_on: true
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batch_size: 1
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num_workers: 4
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pin_memory: true
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writer:
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_target_: boltzgen.task.predict.writer.DesignWriter
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output_dir: ${output}
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res_atoms_only: false
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atom14: ${data.cfg.atom14}
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atom37: ${data.cfg.atom37}
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backbone_only: ${data.cfg.backbone_only}
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write_native: false
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trainer:
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accelerator: gpu
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devices: 1
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precision: bf16-mixed
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name: null
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output: null
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checkpoint: null
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matmul_precision: high
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recycling_steps: 3
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sampling_steps: 500
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diffusion_samples: 1
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compile_pairformer: false
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compile_structure: false
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override:
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masker_args:
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mask: true
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mask_backbone: false
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validators: null
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step_scale_schedule:
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- step_scale: 1.8
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period: 0.25
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- step_scale: 2.0
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period: 0.25
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- step_scale: 1.8
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period: 0.25
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- step_scale: 2.0
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period: 0.25
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noise_scale_schedule:
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- noise_scale: 0.95
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period: 0.25
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- noise_scale: 0.88
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period: 0.25
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- noise_scale: 0.95
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period: 0.25
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- noise_scale: 0.88
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period: 0.25
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diffusion_process_args:
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sigma_min: 0.0004 # min noise level
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sigma_max: 160.0 # max noise level
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sigma_data: 16.0 # standard deviation of data distribution
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rho: 7 # controls the sampling schedule
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P_mean: -1.2 # mean of log-normal distribution from which noise is drawn for training
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P_std: 1.5 # standard deviation of log-normal distribution from which noise is drawn for training
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gamma_0: 0.8
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gamma_min: 1.0
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noise_scale: null
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step_scale: null
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mse_rotational_alignment: true
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coordinate_augmentation: true
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alignment_reverse_diff: true
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synchronize_sigmas: false
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sampling_schedule: "dilated"
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time_dilation: 2.667
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time_dilation_start: 0.6
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time_dilation_end: 0.8
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