ProteinMPNN_dataset #9810
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ProteinMPNN_dataset #9810
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xnuohz
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Nov 28, 2024
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| Args: | ||
| root (str): Root directory where the dataset should be saved. | ||
| params (dict): Dictionary of parameters for dataset creation: | ||
| LIST: Path to the table with metadata. | ||
| VAL: Path to list of cluster IDs for model validation. | ||
| DIR: Path to dataset. | ||
| DATCUT: Date (YYY-MM-DD) threshold of sequence deposition. | ||
| RESCUT: Resolution cutoff for PDBs. | ||
| HOMO: Minimal sequence identity to detect homodimeric chains. | ||
| set_type (str): Type of expected data, train ("train") or validation ("val") |
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Args are not aligned with __init__ parameters
| force_reload=False | ||
| #name='sample', | ||
| ) -> None: | ||
| assert set_type in {'train', 'val'} |
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missing test?
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| assert set_type in {'train', 'val'} | |
| assert set_type in {'train', 'val', 'test'} |
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| self, | ||
| root, | ||
| set_type, # 'train', 'val', or 'test' | ||
| params, | ||
| transform=None, | ||
| pre_transform=None, | ||
| pre_filter=None, | ||
| log=True, | ||
| force_reload=False | ||
| #name='sample', |
| osp.join(self.root) | ||
| fs.rm(self.raw_dir) | ||
|
|
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| def build_training_clusters(self, params, debug): |
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debug mode should be removed.
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| item_graph = Data( | ||
| seq=seq, | ||
| xyz=torch.cat(xyz, dim=0), | ||
| idx=torch.cat(idx, dim=0), | ||
| masked=torch.Tensor(masked).int(), | ||
| #label = self.item[0] | ||
| ) |
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I didn't see x and edge_index in the dataset, ProteinMPNN's input only includes sequence data, right?
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A new Dataset for ProteinMPNN model was added.
The Dataset was evaluated using the next piece of code: