import os import importlib import pkgutil import sys import unittest import numpy as np from config import model_config from openfold.model.model import AlphaFold from openfold.utils.import_weights import import_jax_weights_ from tests.config import consts # Give JAX some GPU memory discipline # (by default it hogs 90% of GPU memory. This disables that behavior and also # forces it to proactively free memory that it allocates) os.environ["XLA_PYTHON_CLIENT_ALLOCATOR"] = "platform" os.environ["JAX_PLATFORM_NAME"] = "gpu" def alphafold_is_installed(): return importlib.util.find_spec("alphafold") is not None def skip_unless_alphafold_installed(): return unittest.skipUnless(alphafold_is_installed(), "Requires AlphaFold") def import_alphafold(): """ If AlphaFold is installed using the provided setuptools script, this is necessary to expose all of AlphaFold's precious insides """ if("alphafold" in sys.modules): return sys.modules["alphafold"] module = importlib.import_module("alphafold") # Forcefully import alphafold's submodules submodules = pkgutil.walk_packages( module.__path__, prefix=("alphafold.") ) for submodule_info in submodules: importlib.import_module(submodule_info.name) sys.modules["alphafold"] = module globals()["alphafold"] = module return module def get_alphafold_config(): config = alphafold.model.config.model_config("model_1_ptm") config.model.global_config.deterministic = True return config _param_path = "openfold/resources/params/params_model_1_ptm.npz" _model = None def get_global_pretrained_openfold(): global _model if(_model is None): _model = AlphaFold(model_config("model_1_ptm").model) _model = _model.eval() if(not os.path.exists(_param_path)): raise FileNotFoundError( """Cannot load pretrained parameters. Make sure to run the installation script before running tests.""" ) import_jax_weights_(_model, _param_path) _model = _model.cuda() return _model _orig_weights = None def _get_orig_weights(): global _orig_weights if(_orig_weights is None): _orig_weights = np.load(_param_path) return _orig_weights def _remove_key_prefix(d, prefix): for k, v in list(d.items()): if(k.startswith(prefix)): d.pop(k) d[k[len(prefix):]] = v def fetch_alphafold_module_weights(weight_path): orig_weights = _get_orig_weights() params = { k:v for k,v in orig_weights.items() if weight_path in k } if('/' in weight_path): spl = weight_path.split('/') spl = spl if len(spl[-1]) != 0 else spl[:-1] module_name = spl[-1] prefix = '/'.join(spl[:-1]) + '/' _remove_key_prefix(params, prefix) params = alphafold.model.utils.flat_params_to_haiku(params) return params