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openfold
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Reduce redundancy in seq embedding config presets

This commit is contained in:
Sachin Kadyan 2023-10-02 17:49:19 -05:00
parent 55fd315569
commit f8d517bd00
1 changed files with 8 additions and 18 deletions
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26
openfold/config.py
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@ -154,38 +154,20 @@ def model_config(
c.loss.tm.weight = 0.1
# SINGLE SEQUENCE EMBEDDING PRESETS
elif name == "seqemb_initial_training":
# Tell the data pipeline that we will use sequence embeddings instead of MSAs.
c.data.seqemb_mode.enabled = True
c.globals.seqemb_mode_enabled = True
# In seqemb mode, we turn off the ExtraMSAStack and Evoformer's column attention.
c.model.extra_msa.enabled = False
c.model.evoformer_stack.no_column_attention = True
c.data.train.max_msa_clusters = 1
c.data.eval.max_msa_clusters = 1
elif name == "seqemb_finetuning":
c.data.seqemb_mode.enabled = True
c.globals.seqemb_mode_enabled = True
c.model.extra_msa.enabled = False
c.model.evoformer_stack.no_column_attention = True
c.data.train.max_msa_clusters = 1
c.data.eval.max_msa_clusters = 1
c.data.train.crop_size = 384
c.loss.violation.weight = 1.
c.loss.experimentally_resolved.weight = 0.01
elif name == "seq_model_esm1b":
c.data.seqemb_mode.enabled = True
c.globals.seqemb_mode_enabled = True
c.model.extra_msa.enabled = False
c.model.evoformer_stack.no_column_attention = True
c.data.common.use_templates = True
c.data.common.use_template_torsion_angles = True
c.model.template.enabled = True
c.data.predict.max_msa_clusters = 1
elif name == "seq_model_esm1b_ptm":
c.data.seqemb_mode.enabled = True
c.globals.seqemb_mode_enabled = True
c.model.extra_msa.enabled = False
c.model.evoformer_stack.no_column_attention = True
c.data.common.use_templates = True
c.data.common.use_template_torsion_angles = True
c.model.template.enabled = True
@ -195,6 +177,14 @@ def model_config(
else:
raise ValueError("Invalid model name")
if name.startswith("seq"):
# Tell the data pipeline that we will use sequence embeddings instead of MSAs.
c.data.seqemb_mode.enabled = True
c.globals.seqemb_mode_enabled = True
# In seqemb mode, we turn off the ExtraMSAStack and Evoformer's column attention.
c.model.extra_msa.enabled = False
c.model.evoformer_stack.no_column_attention = True
if long_sequence_inference:
assert(not train)
c.globals.offload_inference = True