updating #65
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updating #65
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sokrypton
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Sep 9, 2022
* updating (#65) * adding plotting function to color by pLDDT * moving functions to af2rank class * adding option to specify custom params * typo * remove recycle-dimension, in prep for multimer support * missed a few edits to remove recycle dims * adding multimer files * cleaning up the multimer code * initial experiment towards adding multimer support * adding missing geometry files * typos * bugfixes * dropout_scale support for multimer * all_atom_masks -> all_atom_mask (to be consistent with multimer) * debugging template injection for multimers * fixing multimer nan bug see: google-deepmind/alphafold#513 * adding multimers support for binder-hallucination * moving multimer feature creation to prep.py * fixing config * bugfix; adding multimer support for other protocols * cleanup * cleaning up the prep options * fixing crop typo thanks @hunarbatra * v1.0.6-alpha * typo * main updates (#68) * adding plotting function to color by pLDDT * moving functions to af2rank class * fixed crop_feats error * fixing colab link * adding "seq" to inputs (for custom loss) Co-authored-by: Hunar Batra <i@hunarbatra.com> * cleanup, add iptm * typos * standardizing the template-specific options * cleaning template update code * minor edit * adding fape support for multimers * multimer fape loss bugfix * splitting fape/i_fape * change order of verbose print * rewriting fape function to accept number of homo-oligomeric copies * cleaning up the code * adding weights to fape loss * adding option to control fape_cutoff (aka clamp) * adding seq_ent loss * stabilize entropy calculation * removing seq-ent for now * disabling stats correction by default * Update .gitignore * cleaning up the pair loss * adding experimental copies support to partial protocol (for Possu) * bugfixes involving partial+copies * adding homo-oligomeric support to rewire * undo last commit * bugfix * cleanup * adding seq_ent loss * correcting entropy compute based fix_seq * rescaling entropy loss based on number of fixed positions * cleanup * Update loss.py * cleaning up the code * adding alphafold-multimer support to AF2Rank * typo * adding support for repeat/homooligomers for partial hallucination * bugfixes for partial homo-oligomeric support * minor edits (for future) * refactoring prep_pdb, adding option to offset and extend length * updating binder contact loss to include binder2target and target2binder contacts * adding i_con back (as (tb_con+bt_con)/2) * typos * removing i_con * cleanup * design.py - pull _apply_gradient() out of step() * updating defaults - fixbb confidence loss set to zero and is over all positions - binder only positions in PDB are loaded, missing density ignored - adding num_tot option to control number of total contacts to optimize for * rename num_tot to num_pos * bugfix * fix_seq option replaced with fix_pos to allow control which positions are fixed * refactoring * adding experimentally resolved loss on CA * setting default exp_res weight * adding mlm * rename * bugfix * adding option to disable mlm * remove target_feat * temp, broken, updating use_crop * Update design.py * bugfix, crop_feat, remove add_batch * fixing crop options * adding helper functions * fixing typos * adding i_pae for binder design * bugfix, removing 2stage_binder_hallucination for now * cleanup * revert * updating default mlm_dropout default * cleanup * fixing backprop option for multimer model * update - adding "first" recycle mode, thanks @whitead - adding "hard" annealing step to 3 stage design - adding "ramp_recycles" option to 3 stage design * partial revert * revert latest experiments * typos * refactoring recycle code to reduce compile time * typos; changing recycle_mode default to last * improving num_recycles control * adding small plddt loss to binder hallucination default * updating readme * cleanup * Update design.ipynb * cleaning up recycle code, moving experimental crop functions to crop.py * crop.py import fix * cleaning up predict() * bugfix in partial hallucination protocol -[pos]itions not defined if copies not defined * debugging... * bugfix: fix_pos in partial * bugfix for partial fix_pos option * adding fix_pos option to trRosetta * Update joint_model.py * revert Co-authored-by: Hunar Batra <i@hunarbatra.com>
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