41 Commits

Author	SHA1	Message	Date
Lynn Tao	285dea5e6d	adding processing files	2023-02-09 19:47:44 -05:00
Lynn Tao	67b9efd424	revised processing interaction filter limit	2022-12-09 12:24:21 -05:00
Lynn Tao	5dc966adf2	revised processing interaction filter limit	2022-12-09 12:22:53 -05:00
Lynn Tao	7e4726b0a9	debugging process for cmap embedding	2022-11-20 11:57:48 -05:00
Lynn Tao	25086c64fc	fixing processing bugs to integrate contact maps	2022-11-18 15:08:58 -05:00
Lynn Tao	16c45acf7c	fixing bugs in process.py, preparing integration of cmaps into train.py	2022-11-18 12:22:00 -05:00
Lynn Tao	fc98d041e3	updated README, made some arg name changes in process.py	2022-11-06 11:51:25 -05:00
Lynn Tao	3364c48e36	updating docstrings, etc. revisions	2022-11-02 07:39:48 -04:00
Lynn Tao	7753bf8c72	added new args, debugging fixes	2022-10-28 16:51:32 -04:00
Lynn Tao	7dd095b582	debugging, fixing errors detected	2022-10-27 20:08:14 -04:00
Lynn Tao	54b3c6a989	final changes, adding new args, more filtering	2022-10-26 10:57:08 -04:00
Lynn Tao	224e80289d	made several revisions: added argument for # of chains, all possible combinations of chains, altered filtering requirements, updated fasta and tsv writing	2022-10-16 20:16:03 -04:00
Lynn Tao	51e430730a	made processing a module	2022-10-11 10:58:50 -04:00
Lynn Tao	62877bb556	fixing mod res substitutions, checking chain pairs, etc.	2022-10-08 08:44:42 -04:00
Lynn Tao	9f6f45b590	fixing stopiterations and all resulting issues.	2022-10-01 11:25:34 -04:00
Lynn Tao	ade8f3bf15	fixing code modifications after testing on dataset	2022-09-20 11:57:21 -04:00
Lynn Tao	fff17416de	made some changes to input and processing details	2022-09-16 16:37:30 -04:00
Lynn Tao	3ee1a437c0	made some changes to input and processing details	2022-09-16 11:44:05 -04:00
Lynn Tao	bddb63edeb	more changes to input, logging, incorporation	2022-09-16 11:40:55 -04:00
Lynn Tao	3d7b954908	made some changes to input and processing details	2022-09-16 09:39:22 -04:00
Lynn Tao	8954c308ff	made some changes to input and processing details discussed in meeting	2022-09-16 08:59:40 -04:00
Lynn Tao	0c8c6eaf36	resolving filtering methods and checking for errors	2022-09-08 10:02:40 -04:00
Lynn Tao	ea9eb6b504	edited processing.py to take in inputs, changed __main__ to include processing	2022-09-07 15:40:33 -04:00
Lynn Tao	bce623ceb3	updating docstring	2022-09-06 12:40:21 -04:00
Lynn Tao	a57810424a	added helper methods into data processing, wrote more docstrings	2022-09-06 11:48:38 -04:00
Lynn Tao	8acd513789	added docstrings to processing file	2022-09-06 06:53:27 -04:00
Lynn Tao	bde88ced0c	made updates to processing.py, incorporating/debugging filtering and sequence alginment code	2022-09-05 06:45:33 -04:00
Lynn Tao	091a8936c7	committing data processing changes and resolved merge conflicts	2022-08-31 10:04:43 -04:00
Lynn Tao	6907a009ec	pushing new train and val cmap dataset and edited training code	2022-07-26 15:57:21 -04:00
Lynn Tao	178b70ec65	committing b4 debugging	2022-07-26 11:12:39 -04:00
Lynn Tao	d10d725b00	adding data processing files	2022-07-25 16:15:37 -04:00
Lynn Tao	27d5d89524	making train.py more readable, more data processing	2022-07-19 14:31:46 -04:00
Lynn Tao	0f62ae017f	dataset fixing	2022-07-19 07:37:38 -04:00
Lynn Tao	d9d33f1346	last of pdb files	2022-07-18 23:23:51 -04:00
Lynn Tao	6cc7f0dabc	last of pdb files	2022-07-18 23:18:06 -04:00
Lynn Tao	740bc3dc5f	last of pdb files	2022-07-18 23:14:13 -04:00
Lynn Tao	03a3318575	more data processing addressing hidden files	2022-07-18 13:31:50 -04:00
Lynn Tao	4adc8e374e	removing fasta usage for server	2022-07-18 13:28:36 -04:00
Lynn Tao	0fc47dee5b	adding pdb ids for batch download	2022-07-18 13:21:46 -04:00
Lynn Tao	50985f00cd	file of pdb id for machine download	2022-07-18 12:17:58 -04:00
Lynn Tao	1b60e18687	trying to fix too large files	2022-07-18 11:18:43 -04:00