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initial fastfold

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* @Author: zhuww
* @email: zhuww@sugon.com
* @Date: 2023-03-31 17:09:07
* @LastEditTime: 2023-04-01 09:53:01
* @FilePath: \FastFold\README.md
-->
# FastFold
## 模型介绍
FastFold基于蛋白质结构预测模型,进行推理的性能优化
## 模型结构
模型基于Transformer架构,主要结构包括Evofomer(48 blocks)和Struture module(8 blocks)两个模块。
## 数据集
推荐使用AlphaFold2中的开源数据集，包括BFD、MGnify、PDB70、Uniclust、Uniref90等,数据集大小约3TB。
我们提供了一个脚本download_all_data.sh用于下载使用的数据集和模型文件：
./scripts/download_all_data.sh 数据集下载目录
## 推理
### 环境配置
提供[光源](https://www.sourcefind.cn/#/service-details)拉取推理的docker镜像：
* 推理镜像：docker pull image.sourcefind.cn:5000/dcu/admin/base/custom:fastfold-0.2.1-centos7.6-dtk-22.10-patch4-py38-latest
激活镜像环境：
`source /opt/dtk-22.10/env.sh`
`source /opt/openmm-dtk-22.10/env.sh`
测试目录：
`/opt/docker/test`
### 推理
我们分别提供了基于Pytorch的单体和多体的推理脚本，版本依赖：
* Pytorch(DCU版本) >= 1.10.0a0
#### 单体
python inference.py T1024.fasta data/pdb_mmcif/mmcif_files/ \
--output_dir ./ \
--gpus 2 \
--use_precomputed_alignments alignments/ \
--param_path /data/params/params_model_1.npz \
--uniref90_database_path data/uniref90/uniref90.fasta \
--mgnify_database_path data/mgnify/mgy_clusters_2018_12.fa \
--pdb70_database_path data/pdb70/pdb70 \
--uniclust30_database_path data/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \
--bfd_database_path data/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
--jackhmmer_binary_path `which jackhmmer` \
--hhblits_binary_path `which hhblits` \
--hhsearch_binary_path `which hhsearch` \
--kalign_binary_path `which kalign` \
--chunk_size 4 \
--inplace
或者使用`./inference.sh`
##### 单体推理参数说明
T1024.fasta为推理的单体序列；data修改为数据集下载目录；
--output_dir为输出目录；--gpus为使用的gpu数量；
--use_precomputed_alignments为搜索对齐目录，可以加载已经搜索对齐的序列，若不添加则进行搜索对齐；
--param_path为加载单体模型路径，需要和--model_name保持一致,默认为model_1；
--chunk_size为分块数量，设置为4，并且使用--inplace来降低显存占用。
Alphafold的数据预处理需要花费大量时间，因此我们通过[ray]加快了数据预处理(https://docs.ray.io/en/latest/workflows/concepts.html)工作流程。
要使用ray工作流运行推理，应将参数--enable_workflow添加到cmdline或`./inference.sh`脚本中。
#### 多体
python inference.py SUGP1.fasta data/pdb_mmcif/mmcif_files/ \
--output_dir ./ \
--gpus 2 \
--use_precomputed_alignments alignments/ \
--model_preset multimer \
--uniref90_database_path data/uniref90/uniref90.fasta \
--mgnify_database_path data/mgnify/mgy_clusters_2018_12.fa \
--pdb70_database_path data/pdb70/pdb70 \
--uniclust30_database_path data/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \
--bfd_database_path data/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
--uniprot_database_path data/uniprot/uniprot_sprot.fasta \
--pdb_seqres_database_path data/pdb_seqres/pdb_seqres.txt \
--param_path data/params/params_model_1_multimer.npz \
--model_name model_1_multimer \
--jackhmmer_binary_path `which jackhmmer` \
--hhblits_binary_path `which hhblits` \
--hhsearch_binary_path `which hhsearch` \
--kalign_binary_path `which kalign` \
--chunk_size 4 \
--inplace
或者使用`./inference_multimer.sh`
##### 多体推理参数说明
SUGP1.fasta为推理的多体序列；--param_path为加载多体模型路径，需要和--model_name保持一致，其他参数同单体推理参数说明一致。
## 性能和准确率数据
测试数据：[casp14](https://www.predictioncenter.org/casp14/targetlist.cgi)、[uniprot](https://www.uniprot.org/)，使用的加速卡:DCU 1代-16G
性能数据：
| 卡数 | 数据类型 | 序列类型 | 序列标签 | 序列长度 | Speed(s) |
| :------: | :------: | :------: | :------: |:------: |:------: |
| 4 | fp32 | 单体 | T1024 | 408 | 80 |
| 4 | fp32 | 单体 | Q9NYK1 | 1046 | 488 |
| 4 | fp32 | 单体 | Q8CHI8 | 3072 | 8718 |
| 4 | fp32 | 多体 | H1036 | 856 | 324 |
| 4 | fp32 | 多体 | H1060 | 1106 | 449 |
| 4 | fp32 | 多体 | 6h3c | 2030 | 2142 |
准确性数据：
| 卡数 | 数据类型 | 序列类型 | 序列标签 | 序列长度 | GDT-TS | GDT-HA | LDDT | TM score | MaxSub | RMSE |
| :------: | :------: | :------: | :------: |:------: |:------: | :------: | :------: | :------: |:------: |:------: |
| 4 | fp32 | 单体 | T1026 | 172 | 91.4 | 76.5 | 79.6 | 94.1 | 90.7 | 1.3 |
| 4 | fp32 | 单体 | T1053 | 580 | 93.7 | 78.2 | 92.3 | 98.4 | 92.9 | 1.1 |
| 4 | fp32 | 单体 | Q9NYK1 | 1046 | 90.1 | 74.4 | 86.6 | 96.2 | 90.5 | 5.8 |
## 历史版本
* https://developer.hpccube.com/codes/modelzoo/FastFold
## 参考
* [https://github.com/deepmind/alphafold](https://github.com/deepmind/alphafold)
* [https://github.com/hpcaitech/FastFold](https://github.com/hpcaitech/FastFold)
SUGP1.fasta 0 → 100644
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>sp_Q8IWZ8_SUGP1_HUMAN_SURP_and_G-patch_domain-containing_protein_1_OS_Homo_sapiens_OX_9606_GN_SUGP1_PE_1-SV_2_188_242
TRKVIEKLARFVAEGGPELEKVAMEDYKDNPAFAFLHDKNSREFLYYRKKVAEIR
>sp_Q15637_SF01_HUMAN_Splicing_factor_1_OS_Homo_sapiens_OX_9606_GN_SF1_PE_1_SV_4_292_370
CKFQRPGDPQSAQDKARMDKEYLSLMAELGEAPVPASVGSTSGPATTPLASAPRPAAPANNPPPPSLMSTTQSRPPWMN
T1024.fasta 0 → 100644
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>T1024 LmrP, , 408 residues|
MKEFWNLDKNLQLRLGIVFLGAFSYGTVFSSMTIYYNQYLGSAITGILLALSAVATFVAGILAGFFADRNGRKPVMVFGTIIQLLGAALAIASNLPGHVNPWSTFIAFLLISFGYNFVITAGNAMIIDASNAENRKVVFMLDYWAQNLSVILGAALGAWLFRPAFEALLVILLLTVLVSFFLTTFVMTETFKPTVKVDEKAENIFQAYKTVLQDKTYMIFMGANIATTFIIMQFDNFLPVHLSNSFKTITFWGFEIYGQRMLTIYLILACVLVVLLMTTLNRLTKDWSHQKGFIWGSLFMAIGMIFSFLTTTFTPIFIAGIVYTLGEIVYTPSVQTLGADLMNPEKIGSYNGVAAIKMPIASILAGLLVSISPMIKAIGVSLVLALTEVLAIILVLVAVNRHQKTKLN
alignments/T1024 LmrP, , 408 residues_/bfd_uniclust_hits.a3m 0 → 100644
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# STOCKHOLM 1.0
#=GF ID query
#=GF AU hmmsearch (HMMER 3.3.2)
#=GS 2dnx_A/41-41 DE [subseq from] mol:protein length:130 Syntaxin-12
#=GS 2dnx_A/60-107 DE [subseq from] mol:protein length:130 Syntaxin-12
#=GS 2gut_A/47-61 DE [subseq from] mol:protein length:77 ARC/MEDIATOR, Positive cofactor 2 glutamine/Q-rich-associated protein
#=GS 7jil_E/162-177 DE [subseq from] mol:protein length:183 50S ribosomal protein L5
2dnx_A/41-41 -----------------------------G-------------------------------------------------
#=GR 2dnx_A/41-41 PP .............................2.................................................
2dnx_A/60-107 --------------TNQLAKETNELLKELGSLPLPLSTSEQRQQRLQKERLMNDFSAALNNF-----------------
#=GR 2dnx_A/60-107 PP ..............56778899999*************999888777666665555554443.................
2gut_A/47-61 --------------KAKTRDEYLSLVARL--------------------------------------------------
#=GR 2gut_A/47-61 PP ..............9***********976..................................................
7jil_E/162-177 --------------TAKTDKEAKSLLAELG-------------------------------------------------
#=GR 7jil_E/162-177 PP ..............599************9.................................................
#=GC PP_cons ..............689999*******997********999888777666665555554443.................
#=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
//
alignments/sp_Q15637_SF01_HUMAN_Splicing_factor_1_OS_Homo_sapiens_OX_9606_GN_SF1_PE_1_SV_4_292_370/mgnify_hits.sto 0 → 100644
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# STOCKHOLM 1.0
#=GF ID chain_sp_Q15637_SF01_HUMAN_Splicing_factor_1_OS_Homo_sapiens_OX_9606_GN_SF1_PE_1_SV_4_292_370-i1
#=GF AU jackhmmer (HMMER 3.3.2)
#=GS MGYP000669028722/41-104 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
#=GS MGYP000831674948/138-183 DE [subseq from] PL=11 UP=0 BIOMES=0000000011000
chain_sp_Q15637_SF01_HUMAN_Splicing_factor_1_OS_Homo_sapiens_OX_9606_GN_SF1_PE_1_SV_4_292_370 CKFQRPGDPQSAQDKARMDKEYLSLMAELGEAPVPASVGSTSGPATTPLASAPRPAAPANNPPPPSLMSTTQSRPPWMN
MGYP000669028722/41-104 ----RPGDPQSAQDKARMDKEYLSLMAELGEAPVPASVGSTSGPATTPLASAPRPAAPANNPPPPVSL-----------
#=GR MGYP000669028722/41-104 PP ....9***********************************************************9654...........
MGYP000831674948/138-183 CKFQRPGDPQSAQDKARMDKEYLSLMAELGEAPVPASVGSTSGPAT---------------------------------
#=GR MGYP000831674948/138-183 PP 9*******************************************98.................................
#=GC PP_cons 9***9***************************************99******************9654...........
#=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
//
alignments/sp_Q15637_SF01_HUMAN_Splicing_factor_1_OS_Homo_sapiens_OX_9606_GN_SF1_PE_1_SV_4_292_370/uniprot_hits.sto 0 → 100644
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# STOCKHOLM 1.0
#=GF ID chain_sp_Q15637_SF01_HUMAN_Splicing_factor_1_OS_Homo_sapiens_OX_9606_GN_SF1_PE_1_SV_4_292_370-i1
#=GF AU jackhmmer (HMMER 3.3.2)
#=GS sp|Q15637|SF01_HUMAN/292-370 DE [subseq from] Splicing factor 1 OS=Homo sapiens OX=9606 GN=SF1 PE=1 SV=4
#=GS sp|Q64213|SF01_MOUSE/292-370 DE [subseq from] Splicing factor 1 OS=Mus musculus OX=10090 GN=Sf1 PE=1 SV=6
chain_sp_Q15637_SF01_HUMAN_Splicing_factor_1_OS_Homo_sapiens_OX_9606_GN_SF1_PE_1_SV_4_292_370 CKFQRPGDPQSAQDKARMDKEYLSLMAELGEAPVPASVGSTSGPATTPLASAPRPAAPANNPPPPSLMSTTQSRPPWMN
sp|Q15637|SF01_HUMAN/292-370 CKFQRPGDPQSAQDKARMDKEYLSLMAELGEAPVPASVGSTSGPATTPLASAPRPAAPANNPPPPSLMSTTQSRPPWMN
#=GR sp|Q15637|SF01_HUMAN/292-370 PP 9*****************************************************************************8
sp|Q64213|SF01_MOUSE/292-370 CKFQRPGDPQSAQDKARMDKEYLSLMAELGEAPVPASVGSTSGPATTPLASAPRPAAPASNPPPPSLMSTTQSRPPWMN
#=GR sp|Q64213|SF01_MOUSE/292-370 PP 9*****************************************************************************8
#=GC PP_cons 9*****************************************************************************8
#=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
//
alignments/sp_Q8IWZ8_SUGP1_HUMAN_SURP_and_G-patch_domain-containing_protein_1_OS_Homo_sapiens_OX_9606_GN_SUGP1_PE_1-SV_2_188_242/mgnify_hits.sto 0 → 100644
View file @ a83cce97
# STOCKHOLM 1.0
#=GF ID chain_sp_Q8IWZ8_SUGP1_HUMAN_SURP_and_G-patch_domain-containing_protein_1_OS_Homo_sapiens_OX_9606_GN_SUGP1_PE_1-SV_2_188_242-i1
#=GF AU jackhmmer (HMMER 3.3.2)
#=GS MGYP000082224325/20-68 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
#=GS MGYP000082224325/91-127 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
#=GS MGYP000277099866/2-44 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
#=GS MGYP000277099866/68-112 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
#=GS MGYP000491155519/1-26 DE [subseq from] PL=01 UP=0 BIOMES=0000000010100
#=GS MGYP000491155519/50-94 DE [subseq from] PL=01 UP=0 BIOMES=0000000010100
#=GS MGYP000324022611/34-67 DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
#=GS MGYP001127532122/81-114 DE [subseq from] PL=01 UP=0 BIOMES=0000000011000
#=GS MGYP000641555956/33-84 DE [subseq from] PL=11 UP=0 BIOMES=0110000000000
#=GS MGYP000641555956/156-192 DE [subseq from] PL=11 UP=0 BIOMES=0110000000000
#=GS MGYP000511767851/15-64 DE [subseq from] PL=01 UP=0 BIOMES=1000000000000
#=GS MGYP000511767851/114-155 DE [subseq from] PL=01 UP=0 BIOMES=1000000000000
#=GS MGYP000125367204/57-106 DE [subseq from] PL=00 UP=0 BIOMES=0110000000000
#=GS MGYP000170712716/57-106 DE [subseq from] PL=00 UP=0 BIOMES=0110000000000
#=GS MGYP001151811203/323-343 DE [subseq from] PL=11 UP=0 BIOMES=1000000000000
#=GS MGYP001151811203/394-448 DE [subseq from] PL=11 UP=0 BIOMES=1000000000000
#=GS MGYP000251977013/12-60 DE [subseq from] PL=00 UP=0 BIOMES=0110000000000
chain_sp_Q8IWZ8_SUGP1_HUMAN_SURP_and_G-patch_domain-containing_protein_1_OS_Homo_sapiens_OX_9606_GN_SUGP1_PE_1-SV_2_188_242 TRKVIEKLARFVAEGGPE-LEKVAMEDYKDNPAFAFLHDKNSREFLYYRKKVAEIR
MGYP000082224325/20-68 ------EIGPFVAEAGPE-LEKVITEDYKDNLAFPFLHGKNSRQFLYHRKEVAEIR
#=GR MGYP000082224325/20-68 PP ......5678********.***********************************98
MGYP000082224325/91-127 --NLAEKLAEFIARGDPE-METIALQKNRENQAFSFLYEP----------------
#=GR MGYP000082224325/91-127 PP ..678*************.******************986................
MGYP000277099866/2-44 ------------AEAGPE-LEKVITEDYKDNLAFPFLHGKNSRQFLSPRKEGAELR
#=GR MGYP000277099866/2-44 PP ............89****.**********************************997
MGYP000277099866/68-112 ---LAGKLARFVVDWHPE-VETIALQNNCENQAFSFLYETNSQGYKYYR-------
#=GR MGYP000277099866/68-112 PP ...5679***********.*****************************8.......
MGYP000491155519/1-26 ------------------------------NPAFAFLQDKNSREFLYYRKKVAEIR
#=GR MGYP000491155519/1-26 PP ..............................8***********************98
MGYP000491155519/50-94 ---LAGKLARFVVDWHPE-VETIALQNNCENQAFSFLYETNSQGYKYYR-------
#=GR MGYP000491155519/50-94 PP ...5679***********.*****************************8.......
MGYP000324022611/34-67 TRKVIEKLARFVAEGGPE-LEKVAMEDYKDNPAFA---------------------
#=GR MGYP000324022611/34-67 PP 8*****************.***************7.....................
MGYP001127532122/81-114 TRKVIEKLARFVAEGGPE-LEKVAMEDYKDNPAFA---------------------
#=GR MGYP001127532122/81-114 PP 8*****************.***************7.....................
MGYP000641555956/33-84 -RAIVDKTAQFVAKNGPE-FENRILSSEKNNQKFSFLMEKDPY-HAYYRGKIESI-
#=GR MGYP000641555956/33-84 PP .789**************.*********************976.689**999876.
MGYP000641555956/156-192 ---VIKLSAQFVARNGAKFLSGLASREYQ-NPEFAFLKPAH---------------
#=GR MGYP000641555956/156-192 PP ...788889****9887637889999996.9*****97654...............
MGYP000511767851/15-64 --NLIDKTAKSVAQKGPE-LEELVKKNFADNPKFSFLDF-GDPYRPYYDQKVEE--
#=GR MGYP000511767851/15-64 PP ..689*************.*****************954.55556788888877..
MGYP000511767851/114-155 ---VMQHTAQFVAKNGQR-FLVGLTEREKHNPLFDFLKPTHSL-FPY---------
#=GR MGYP000511767851/114-155 PP ...77889*********9.998889999*********887663.545.........
MGYP000125367204/57-106 -RAIVDKTAQFVAKNGPE-FESRILSSEKNNQKFSFLRE-NSPFYSYYRGKIE---
#=GR MGYP000125367204/57-106 PP .789**************.******************86.8999*****9985...
MGYP000170712716/57-106 -RAIVDKTAQFVAKNGPE-FETRILSSEKNNQKFSFLRE-NSPFYSYYRGKIE---
#=GR MGYP000170712716/57-106 PP .789**************.******************86.8999*****9985...
MGYP001151811203/323-343 -----------------------------------YLFDETSQEFKYYQHKLAELR
#=GR MGYP001151811203/323-343 PP ...................................899****************97
MGYP001151811203/394-448 TRETAENLARFMIQLGSD-IEDFNMDSLTNNPDFWFLTKKDSPAHKFYQMKLVEVR
#=GR MGYP001151811203/394-448 PP 79999*************.**********************************997
MGYP000251977013/12-60 -KNIIDKLAQFVARNGPE-FEHMTKQKQKDNPKFSFLFG--GEYFNYYQYKVT---
#=GR MGYP000251977013/12-60 PP .579**************.******************86..567889988875...
#=GC PP_cons 88889999**********.******************9898989999*99998987
#=GC RF xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
//
alignments/sp_Q8IWZ8_SUGP1_HUMAN_SURP_and_G-patch_domain-containing_protein_1_OS_Homo_sapiens_OX_9606_GN_SUGP1_PE_1-SV_2_188_242/uniprot_hits.sto 0 → 100644
View file @ a83cce97
# STOCKHOLM 1.0
#=GF ID chain_sp_Q8IWZ8_SUGP1_HUMAN_SURP_and_G-patch_domain-containing_protein_1_OS_Homo_sapiens_OX_9606_GN_SUGP1_PE_1-SV_2_188_242-i1
#=GF AU jackhmmer (HMMER 3.3.2)
#=GS sp|Q8IWZ8|SUGP1_HUMAN/188-242 DE [subseq from] SURP and G-patch domain-containing protein 1 OS=Homo sapiens OX=9606 GN=SUGP1 PE=1 SV=2
#=GS sp|Q8IWZ8|SUGP1_HUMAN/265-317 DE [subseq from] SURP and G-patch domain-containing protein 1 OS=Homo sapiens OX=9606 GN=SUGP1 PE=1 SV=2
#=GS sp|Q8CH02|SUGP1_MOUSE/184-238 DE [subseq from] SURP and G-patch domain-containing protein 1 OS=Mus musculus OX=10090 GN=Sugp1 PE=1 SV=1
#=GS sp|Q8CH02|SUGP1_MOUSE/261-313 DE [subseq from] SURP and G-patch domain-containing protein 1 OS=Mus musculus OX=10090 GN=Sugp1 PE=1 SV=1
#=GS sp|Q68FU8|SUGP1_RAT/185-239 DE [subseq from] SURP and G-patch domain-containing protein 1 OS=Rattus norvegicus OX=10116 GN=Sugp1 PE=1 SV=1
#=GS sp|Q68FU8|SUGP1_RAT/262-314 DE [subseq from] SURP and G-patch domain-containing protein 1 OS=Rattus norvegicus OX=10116 GN=Sugp1 PE=1 SV=1
#=GS sp|Q8IX01|SUGP2_HUMAN/590-637 DE [subseq from] SURP and G-patch domain-containing protein 2 OS=Homo sapiens OX=9606 GN=SUGP2 PE=1 SV=2
#=GS sp|Q8IX01|SUGP2_HUMAN/786-837 DE [subseq from] SURP and G-patch domain-containing protein 2 OS=Homo sapiens OX=9606 GN=SUGP2 PE=1 SV=2
#=GS sp|Q8CH09|SUGP2_MOUSE/595-619 DE [subseq from] SURP and G-patch domain-containing protein 2 OS=Mus musculus OX=10090 GN=Sugp2 PE=1 SV=2
#=GS sp|Q8CH09|SUGP2_MOUSE/769-820 DE [subseq from] SURP and G-patch domain-containing protein 2 OS=Mus musculus OX=10090 GN=Sugp2 PE=1 SV=2
#=GS sp|Q8CGZ0|CHERP_MOUSE/13-61 DE [subseq from] Calcium homeostasis endoplasmic reticulum protein OS=Mus musculus OX=10090 GN=Cherp PE=1 SV=1
#=GS sp|Q8IWX8|CHERP_HUMAN/13-61 DE [subseq from] Calcium homeostasis endoplasmic reticulum protein OS=Homo sapiens OX=9606 GN=CHERP PE=1 SV=3
#=GS sp|A2VDN6|SF3A1_BOVIN/50-101 DE [subseq from] Splicing factor 3A subunit 1 OS=Bos taurus OX=9913 GN=SF3A1 PE=2 SV=1
#=GS sp|Q8K4Z5|SF3A1_MOUSE/50-101 DE [subseq from] Splicing factor 3A subunit 1 OS=Mus musculus OX=10090 GN=Sf3a1 PE=1 SV=1
#=GS sp|Q15459|SF3A1_HUMAN/50-101 DE [subseq from] Splicing factor 3A subunit 1 OS=Homo sapiens OX=9606 GN=SF3A1 PE=1 SV=1
chain_sp_Q8IWZ8_SUGP1_HUMAN_SURP_and_G-patch_domain-containing_protein_1_OS_Homo_sapiens_OX_9606_GN_SUGP1_PE_1-SV_2_188_242 TRKVIEKLARFVAEGGPELEKVAMEDYKDNPAFAFLHDKNSREFLYYRKKVAEIR
sp|Q8IWZ8|SUGP1_HUMAN/188-242 TRKVIEKLARFVAEGGPELEKVAMEDYKDNPAFAFLHDKNSREFLYYRKKVAEIR
#=GR sp|Q8IWZ8|SUGP1_HUMAN/188-242 PP 8****************************************************98
sp|Q8IWZ8|SUGP1_HUMAN/265-317 --NLAEKLARFIADGGPEVETIALQNNRENQAFSFLYEPNSQGYKYYRQKLEEFR
#=GR sp|Q8IWZ8|SUGP1_HUMAN/265-317 PP ..678*********************************************99976
sp|Q8CH02|SUGP1_MOUSE/184-238 TRRVIEKLARFVAEGGPELEKVAMEDYKDNPAFTFLHDKNSREFLYYRRKVAEIR
#=GR sp|Q8CH02|SUGP1_MOUSE/184-238 PP 89***************************************************98
sp|Q8CH02|SUGP1_MOUSE/261-313 --NLAEKLARFIADGGPEVETIALQNNRENQAFSFLYDPNSQGYRYYRQKLDEFR
#=GR sp|Q8CH02|SUGP1_MOUSE/261-313 PP ..678*********************************************99876
sp|Q68FU8|SUGP1_RAT/185-239 TRRVIEKLARFVAEGGPELEKVAMEDYKDNPAFTFLHDKNSREFLYYRKKVAEIR
#=GR sp|Q68FU8|SUGP1_RAT/185-239 PP 89***************************************************98
sp|Q68FU8|SUGP1_RAT/262-314 --NLAEKLARFIADGGPEVETIALQNNRENQAFSFLYDPNSQGYRYYKQKLEEFR
#=GR sp|Q68FU8|SUGP1_RAT/262-314 PP ..678*********************************************99976
sp|Q8IX01|SUGP2_HUMAN/590-637 ----IDQLVKRVIEGSLSPKE--RTLLKEDPAYWFLSDENSLEYKYYKLKLAEM-
#=GR sp|Q8IX01|SUGP2_HUMAN/590-637 PP ....67777778887644333..334699***********************97.
sp|Q8IX01|SUGP2_HUMAN/786-837 --ETAEKLARFVAQVGPEIEQFSIENSTDNPDLWFLHDQNSSAFKFYRKKVFEL-
#=GR sp|Q8IX01|SUGP2_HUMAN/786-837 PP ..678**********************************************986.
sp|Q8CH09|SUGP2_MOUSE/595-619 ----------------------------QDPAYWFLSDESSLEYKYYKLKLAE--
#=GR sp|Q8CH09|SUGP2_MOUSE/595-619 PP ............................57*********************98..
sp|Q8CH09|SUGP2_MOUSE/769-820 --ETAEKLARFVAQVGPEIEQFSIENSTDNPDLWFLHDQSSSAFKFYREKVLEL-
#=GR sp|Q8CH09|SUGP2_MOUSE/769-820 PP ..678**********************************************986.
sp|Q8CGZ0|CHERP_MOUSE/13-61 -RNVIDKLAQFVARNGPEFEKMTMEKQKDNPKFSFLFG--GEFYSYYKCKLA---
#=GR sp|Q8CGZ0|CHERP_MOUSE/13-61 PP .88*********************************85..445678877765...
sp|Q8IWX8|CHERP_HUMAN/13-61 -RNVIDKLAQFVARNGPEFEKMTMEKQKDNPKFSFLFG--GEFYSYYKCKLA---
#=GR sp|Q8IWX8|CHERP_HUMAN/13-61 PP .88*********************************85..445678877765...
sp|A2VDN6|SF3A1_BOVIN/50-101 -RNIVDKTASFVARNGPEFEARIRQNEINNPKFNFLNP-NDPYHAYYRHKVSEF-
#=GR sp|A2VDN6|SF3A1_BOVIN/50-101 PP .889****************9999999*********86.677889******996.
sp|Q8K4Z5|SF3A1_MOUSE/50-101 -RNIVDKTASFVARNGPEFEARIRQNEINNPKFNFLNP-NDPYHAYYRHKVSEF-
#=GR sp|Q8K4Z5|SF3A1_MOUSE/50-101 PP .889****************9999999*********86.677889******996.
sp|Q15459|SF3A1_HUMAN/50-101 -RNIVDKTASFVARNGPEFEARIRQNEINNPKFNFLNP-NDPYHAYYRHKVSEF-
#=GR sp|Q15459|SF3A1_HUMAN/50-101 PP .889****************9999999*********86.677889******996.
#=GC PP_cons 89899*************999**9999*********99*999999*****99977
#=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
//
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# add `--gpus [N]` to use N gpus for inference
# add `--enable_workflow` to use parallel workflow for data processing
# add `--use_precomputed_alignments [path_to_alignments]` to use precomputed msa
python3 inference.py T1024.fasta /data/pdb_mmcif/mmcif_files \
--output_dir ./ \
--gpus 4 \
--use_precomputed_alignments alignments/ \
--param_path /data/params/params_model_1.npz \
--uniref90_database_path /data/uniref90/uniref90.fasta \
--mgnify_database_path /data/mgnify/mgy_clusters_2018_12.fa \
--pdb70_database_path /data/pdb70/pdb70 \
--uniclust30_database_path /data/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \
--bfd_database_path /data/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
--jackhmmer_binary_path `which jackhmmer` \
--hhblits_binary_path `which hhblits` \
--hhsearch_binary_path `which hhsearch` \
--kalign_binary_path `which kalign` \
--chunk_size 4 \
--inplace
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