From 7399d58d0429a0de0873b8f7766875d9bd7cdd58 Mon Sep 17 00:00:00 2001 From: Shoufa Chen Date: Thu, 29 Sep 2022 17:25:15 +0800 Subject: [PATCH] update AlphaFold links Data links in `alphafolddb.py` are outdated. From https://ftp.ebi.ac.uk/pub/databases/alphafold/, latest AlphaFold is **v3**. Some data, e.g., `UP000006548_3702_ARATH_v2.tar` does not exist in v3. Just change the `xxx/latest/xxx` to `xxx/v2/xxx` in the links. Moreover, the md5sum values are not right. I just double-checked and modified the md5sum of `UP000006548_3702_ARATH_v2.tar`. Other md5sum values might also need to be updated. --- torchdrug/datasets/alphafolddb.py | 110 +++++++++++++++--------------- 1 file changed, 55 insertions(+), 55 deletions(-) diff --git a/torchdrug/datasets/alphafolddb.py b/torchdrug/datasets/alphafolddb.py index 919dae2..fd0a43b 100644 --- a/torchdrug/datasets/alphafolddb.py +++ b/torchdrug/datasets/alphafolddb.py @@ -28,63 +28,63 @@ class AlphaFoldDB(data.ProteinDataset): """ urls = [ - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000006548_3702_ARATH_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000001940_6239_CAEEL_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000000559_237561_CANAL_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000000437_7955_DANRE_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000002195_44689_DICDI_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000000803_7227_DROME_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000000625_83333_ECOLI_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000008827_3847_SOYBN_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000005640_9606_HUMAN_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000008153_5671_LEIIN_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000000805_243232_METJA_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000000589_10090_MOUSE_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000001584_83332_MYCTU_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000059680_39947_ORYSJ_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000001450_36329_PLAF7_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000002494_10116_RAT_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000002311_559292_YEAST_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000002485_284812_SCHPO_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000008816_93061_STAA8_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000002296_353153_TRYCC_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000007305_4577_MAIZE_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/swissprot_pdb_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000001631_447093_AJECG_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000006672_6279_BRUMA_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000000799_192222_CAMJE_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000094526_86049_9EURO1_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000274756_318479_DRAME_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000325664_1352_ENTFC_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000053029_1442368_9EURO2_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000000579_71421_HAEIN_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000000429_85962_HELPY_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000007841_1125630_KLEPH_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000008153_5671_LEIIN_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000078237_100816_9PEZI1_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000000806_272631_MYCLE_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000001584_83332_MYCTU_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000020681_1299332_MYCUL_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000000535_242231_NEIG1_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000006304_1133849_9NOCA1_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000024404_6282_ONCVO_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000002059_502779_PARBA_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000001450_36329_PLAF7_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000002438_208964_PSEAE_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000001014_99287_SALTY_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000008854_6183_SCHMA_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000002716_300267_SHIDS_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000018087_1391915_SPOS1_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000008816_93061_STAA8_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000000586_171101_STRR6_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000035681_6248_STRER_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000030665_36087_TRITR_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000008524_185431_TRYB2_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000002296_353153_TRYCC_v2.tar", - "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000270924_6293_WUCBA_v2.tar" + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000006548_3702_ARATH_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000001940_6239_CAEEL_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000000559_237561_CANAL_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000000437_7955_DANRE_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000002195_44689_DICDI_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000000803_7227_DROME_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000000625_83333_ECOLI_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000008827_3847_SOYBN_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000005640_9606_HUMAN_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000008153_5671_LEIIN_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000000805_243232_METJA_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000000589_10090_MOUSE_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000001584_83332_MYCTU_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000059680_39947_ORYSJ_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000001450_36329_PLAF7_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000002494_10116_RAT_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000002311_559292_YEAST_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000002485_284812_SCHPO_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000008816_93061_STAA8_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000002296_353153_TRYCC_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000007305_4577_MAIZE_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/swissprot_pdb_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000001631_447093_AJECG_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000006672_6279_BRUMA_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000000799_192222_CAMJE_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000094526_86049_9EURO1_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000274756_318479_DRAME_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000325664_1352_ENTFC_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000053029_1442368_9EURO2_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000000579_71421_HAEIN_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000000429_85962_HELPY_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000007841_1125630_KLEPH_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000008153_5671_LEIIN_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000078237_100816_9PEZI1_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000000806_272631_MYCLE_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000001584_83332_MYCTU_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000020681_1299332_MYCUL_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000000535_242231_NEIG1_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000006304_1133849_9NOCA1_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000024404_6282_ONCVO_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000002059_502779_PARBA_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000001450_36329_PLAF7_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000002438_208964_PSEAE_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000001014_99287_SALTY_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000008854_6183_SCHMA_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000002716_300267_SHIDS_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000018087_1391915_SPOS1_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000008816_93061_STAA8_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000000586_171101_STRR6_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000035681_6248_STRER_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000030665_36087_TRITR_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000008524_185431_TRYB2_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000002296_353153_TRYCC_v2.tar", + "https://ftp.ebi.ac.uk/pub/databases/alphafold/v2/UP000270924_6293_WUCBA_v2.tar" ] md5s = [ - "82b14d14404e39793cf73c1e0f083865", "9e26602ba2d9f233ef4fcf82703ddb59", + "4cd5f596ebfc3d45d9f6b647dc5684af", "9e26602ba2d9f233ef4fcf82703ddb59", "60a09db1e1c47a98763d09879784f536", "a0ab562b7372f149673c4518f949501f", "6205138b14fb7e7ec09b366e3e4f294b", "31f31359cd7254f82304e3886440bdd3", "a590096e65461ed4eb092b2147b97f0b", "8f1e120f372995644a7101ad58e5b2ae",