pub_soft/D-SCRIPT
3
0
Fork 0
mirror of https://github.com/samsledje/D-SCRIPT.git synced 2026-06-04 15:04:24 +08:00
Code Issues Packages Projects Releases Wiki Activity

Commit Graph

  • 04dedc91ed bug fix; add if/else for predict_interaction_cmap lynntao04 2022-12-01 08:43:44 -05:00
  • 4cc085e63e fixed small bug passing batch_size for cmap data loading lynntao04 2022-11-30 16:30:17 -05:00
  • 8950dc6e38 Update version no Samuel Sledzieski 2022-11-23 10:51:39 -05:00
  • 1775742d62 Remove double setting seed Samuel Sledzieski 2022-11-23 10:50:14 -05:00
  • 1b75c1e38d 2022-11-23 Merge cmaps into foldseek Samuel Sledzieski 2022-11-23 10:38:34 -05:00
  • d5485c082a Merge pull request #43 from samsledje/kapil_foldseek_branch Samuel Sledzieski 2022-11-23 09:13:45 -05:00
  • 952447d34e Merge branch 'ismb22-contacts' into kapil_foldseek_branch Samuel Sledzieski 2022-11-23 09:11:40 -05:00
  • 7e4726b0a9 debugging process for cmap embedding Lynn Tao 2022-11-20 11:57:48 -05:00
  • 25086c64fc fixing processing bugs to integrate contact maps Lynn Tao 2022-11-18 15:08:58 -05:00
  • 16c45acf7c fixing bugs in process.py, preparing integration of cmaps into train.py Lynn Tao 2022-11-18 12:22:00 -05:00
  • d989609126 Update CHANGELOG.md Samuel Sledzieski 2022-11-16 13:43:11 -05:00
  • 6ec9dbb331 Update CHANGELOG.md Samuel Sledzieski 2022-11-16 13:42:01 -05:00
  • 324be05f22 added ability to set random seed for training samsledje 2022-11-16 13:39:29 -05:00
  • 07a1d7386f setting seed for training validation Lynn Tao 2022-11-15 12:33:57 -05:00
  • 919349dace Added foldseek branch Kapil Devkota 2022-11-12 00:50:00 -05:00
  • a3ad39c6b3 debugging train.py, added t/f flag for cmaps, fixing Relu/Sigmoid mismatch Lynn Tao 2022-11-06 18:31:46 -05:00
  • 1ab8ea8d2d Merge branch 'dev-contacts' of https://github.com/samsledje/D-SCRIPT into dev-contacts Lynn Tao 2022-11-06 11:51:41 -05:00
  • fc98d041e3 updated README, made some arg name changes in process.py Lynn Tao 2022-11-06 11:51:25 -05:00
  • 3b8548801a Merge branch 'dev-contacts' of github.com:samsledje/D-SCRIPT into dev-contacts samsledje 2022-11-02 10:43:43 -04:00
  • 9bf409fa2f Merge branch 'main' into dev-contacts samsledje 2022-11-02 10:43:30 -04:00
  • 3364c48e36 updating docstrings, etc. revisions Lynn Tao 2022-11-02 07:39:48 -04:00
  • 7753bf8c72 added new args, debugging fixes Lynn Tao 2022-10-28 16:51:32 -04:00
  • 7dd095b582 debugging, fixing errors detected Lynn Tao 2022-10-27 20:08:14 -04:00
  • 54b3c6a989 final changes, adding new args, more filtering Lynn Tao 2022-10-26 10:57:08 -04:00
  • 224e80289d made several revisions: added argument for # of chains, all possible combinations of chains, altered filtering requirements, updated fasta and tsv writing Lynn Tao 2022-10-16 20:16:03 -04:00
  • 51e430730a made processing a module Lynn Tao 2022-10-11 10:58:50 -04:00
  • 62877bb556 fixing mod res substitutions, checking chain pairs, etc. Lynn Tao 2022-10-08 08:44:42 -04:00
  • 9f6f45b590 fixing stopiterations and all resulting issues. Lynn Tao 2022-10-01 11:25:34 -04:00
  • d54190fcb4 fixing code modifications after testing on dataset Lynn Tao 2022-09-20 11:57:56 -04:00
  • ade8f3bf15 fixing code modifications after testing on dataset Lynn Tao 2022-09-20 11:57:21 -04:00
  • fff17416de made some changes to input and processing details Lynn Tao 2022-09-16 16:37:30 -04:00
  • 3ee1a437c0 made some changes to input and processing details Lynn Tao 2022-09-16 11:44:05 -04:00
  • bddb63edeb more changes to input, logging, incorporation Lynn Tao 2022-09-16 11:40:55 -04:00
  • 3d7b954908 made some changes to input and processing details Lynn Tao 2022-09-16 09:39:22 -04:00
  • 8954c308ff made some changes to input and processing details discussed in meeting Lynn Tao 2022-09-16 08:59:40 -04:00
  • 0c8c6eaf36 resolving filtering methods and checking for errors Lynn Tao 2022-09-08 10:02:40 -04:00
  • ea9eb6b504 edited processing.py to take in inputs, changed __main__ to include processing Lynn Tao 2022-09-07 15:40:33 -04:00
  • bce623ceb3 updating docstring Lynn Tao 2022-09-06 12:40:21 -04:00
  • a57810424a added helper methods into data processing, wrote more docstrings Lynn Tao 2022-09-06 11:48:38 -04:00
  • 8acd513789 added docstrings to processing file Lynn Tao 2022-09-06 06:53:27 -04:00
  • bde88ced0c made updates to processing.py, incorporating/debugging filtering and sequence alginment code Lynn Tao 2022-09-05 06:45:33 -04:00
  • 091a8936c7 committing data processing changes and resolved merge conflicts Lynn Tao 2022-08-31 10:04:43 -04:00
  • a76d9dd99e Merge pull request #41 from samsledje/fix/update_pretrained Samuel Sledzieski 2022-08-26 15:02:49 -04:00
  • 5b95875b98 change language_model.py to use with h5py context samsledje 2022-08-26 14:56:34 -04:00
  • d858bd6851 rename scripts and update train samsledje 2022-08-22 17:26:11 -04:00
  • 8ceaa8f7c0 Finishing merge samsledje 2022-08-22 16:37:09 -04:00
  • e3428d1613 Resolve merge dev samsledje 2022-08-18 12:27:49 -04:00
  • 988c1b35ff update language model to fix issue #35 samsledje 2022-08-18 12:10:32 -04:00
  • b7834b6caa update version number samsledje 2022-08-18 11:40:29 -04:00
  • 2dcf240101 add topsy turvy pretrained model to api and docs samsledje 2022-08-18 11:32:07 -04:00
  • d90069646a fixing training for cuda Lynn Tao 2022-07-26 22:22:05 -04:00
  • 2a0e656fb5 training fixing cuda errors Lynn Tao 2022-07-26 22:09:36 -04:00
  • 6907a009ec pushing new train and val cmap dataset and edited training code Lynn Tao 2022-07-26 15:57:21 -04:00
  • 178b70ec65 committing b4 debugging Lynn Tao 2022-07-26 11:12:39 -04:00
  • daf9899a2f training cmap edits Lynn Tao 2022-07-26 10:32:38 -04:00
  • d10d725b00 adding data processing files Lynn Tao 2022-07-25 16:15:37 -04:00
  • 27d5d89524 making train.py more readable, more data processing Lynn Tao 2022-07-19 14:31:46 -04:00
  • 0f62ae017f dataset fixing Lynn Tao 2022-07-19 07:37:38 -04:00
  • d9d33f1346 last of pdb files Lynn Tao 2022-07-18 23:23:51 -04:00
  • 6cc7f0dabc last of pdb files Lynn Tao 2022-07-18 23:18:06 -04:00
  • 740bc3dc5f last of pdb files Lynn Tao 2022-07-18 23:14:13 -04:00
  • 429d26e3c5 adding in last pdb files Lynn Tao 2022-07-18 22:07:12 -04:00
  • 48bf2685c7 Delete dscript/data directory lynntao04 2022-07-18 14:09:09 -04:00
  • 2cfc6b203a Delete make_training.py lynntao04 2022-07-18 14:07:03 -04:00
  • 4b315456ec Delete create_cmap.py lynntao04 2022-07-18 14:06:40 -04:00
  • 5ac5bd5876 Delete contact_map.py lynntao04 2022-07-18 14:06:23 -04:00
  • d68d8f6ebd Delete data_collection.py lynntao04 2022-07-18 14:06:10 -04:00
  • 78c2684751 Delete 1a0n.tsv lynntao04 2022-07-18 14:05:45 -04:00
  • 03a3318575 more data processing addressing hidden files Lynn Tao 2022-07-18 13:31:50 -04:00
  • 4adc8e374e removing fasta usage for server Lynn Tao 2022-07-18 13:28:36 -04:00
  • 0fc47dee5b adding pdb ids for batch download Lynn Tao 2022-07-18 13:21:46 -04:00
  • 223e0c5738 adding batch download script Lynn Tao 2022-07-18 13:10:38 -04:00
  • 50985f00cd file of pdb id for machine download Lynn Tao 2022-07-18 12:17:58 -04:00
  • 3d4d4fc9bb large dataset building Lynn Tao 2022-07-18 11:27:31 -04:00
  • 6deccd290f Merge branch 'dev-contacts' of https://github.com/samsledje/D-SCRIPT into dev-contacts Lynn Tao 2022-07-18 11:18:46 -04:00
  • 1b60e18687 trying to fix too large files Lynn Tao 2022-07-18 11:18:43 -04:00
  • 33b57e514b adding cmap argument to train Lynn Tao 2022-07-15 11:21:57 -04:00
  • d21d44c625 more training and evaluating code for two modes Lynn Tao 2022-07-14 16:17:09 -04:00
  • 7d8fd0dff6 train.py modes and fixing argument passing Lynn Tao 2022-07-14 13:23:22 -04:00
  • 7eea5bf6b4 added new mode arguments to train.py, classification and regression Lynn Tao 2022-07-14 12:10:59 -04:00
  • 9c67c494dc fixing training loss function, etc Lynn Tao 2022-07-14 10:18:50 -04:00
  • 65c257ddba updated train to run, debugging Lynn Tao 2022-07-12 11:51:44 -04:00
  • aa9d7ba474 more train.py edits, getting loss function working Lynn Tao 2022-07-11 17:11:53 -04:00
  • 3145cf2831 updating train.py for loss function Lynn Tao 2022-07-11 14:43:29 -04:00
  • dbcf7e2a15 filtered through data for matching cmaps and fasta files -- 23 pdb files Lynn Tao 2022-07-11 13:55:43 -04:00
  • b49097143c commiting all recent changes in train.py and data collection files for Sam Lynn Tao 2022-07-11 12:23:06 -04:00
  • f7f10ab031 debugging train, fixing data processing files Lynn Tao 2022-07-08 15:55:51 -04:00
  • 558a710d03 further modified training, set up more data processing files Lynn Tao 2022-07-08 10:47:52 -04:00
  • 1495c5a5a4 moved data preparation files into single repository for clarity Lynn Tao 2022-07-07 16:22:47 -04:00
  • aa05b6018e started training (just framework), created tsv training files, edited contact map parsing Lynn Tao 2022-07-07 15:56:30 -04:00
  • 58a678b41b updated contact maps to 2-chain proteins Lynn Tao 2022-07-06 12:58:03 -04:00
  • cb2d5e6520 parsing PDB files into contact maps code Lynn Tao 2022-07-06 10:06:13 -04:00
  • eca37c374f Merge pull request #38 from samsledje/automatic-pytesting Samuel Sledzieski 2022-07-06 09:57:01 -04:00
  • 3bbad37b5e Merge pull request #37 from samsledje/fix/corrupt-pretrained-model-retry Samuel Sledzieski 2022-06-30 12:06:00 -04:00
  • 11997309de Create pypi_publish.yml Samuel Sledzieski 2022-06-30 12:05:15 -04:00
  • 23731a6e91 Update embedding.py Samuel Sledzieski 2022-06-30 11:55:09 -04:00
  • 37759877f5 Delete dscript/legacy directory Samuel Sledzieski 2022-06-30 11:53:37 -04:00
  • 487b5e3f4f Update requirements.txt Samuel Sledzieski 2022-06-30 11:51:11 -04:00
  • 540f9f7977 Update requirements.txt Samuel Sledzieski 2022-06-30 11:47:23 -04:00
  • 9be9dadae1 Update autorun-tests.yml Samuel Sledzieski 2022-06-30 11:46:34 -04:00