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update to dtk23.10

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README.md
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...@@ -2,7 +2,7 @@ ...@@ -2,7 +2,7 @@
* @Author: zhuww * @Author: zhuww
* @email: zhuww@sugon.com * @email: zhuww@sugon.com
* @Date: 2023-03-31 17:09:07 * @Date: 2023-03-31 17:09:07
* @LastEditTime: 2023-08-24 09:07:01 * @LastEditTime: 2023-11-2430 10:07:01
--> -->
# FASTFOLD # FASTFOLD
## 论文 ## 论文
...@@ -21,22 +21,19 @@ FastFold通过搜索同源序列和模板进行特征构造，基于蛋白质结 ...@@ -21,22 +21,19 @@ FastFold通过搜索同源序列和模板进行特征构造，基于蛋白质结
## 环境配置 ## 环境配置
提供[光源](https://www.sourcefind.cn/#/service-details)拉取推理的docker镜像： 提供[光源](https://www.sourcefind.cn/#/service-details)拉取推理的docker镜像：
``` ```
docker pull image.sourcefind.cn:5000/dcu/admin/base/custom:fastfold-0.2.1-centos7.6-dtk-22.10-patch4-py38-latest docker pull image.sourcefind.cn:5000/dcu/admin/base/custom:fastfold-0.2.0-dtk23.10-py38-latest
# <Image ID>用上面拉取docker镜像的ID替换 # <Image ID>用上面拉取docker镜像的ID替换
# <Host Path>主机端路径 # <Host Path>主机端路径
# <Container Path>容器映射路径 # <Container Path>容器映射路径
docker run -it --name fastfold --shm-size=32G --device=/dev/kfd --device=/dev/dri/ --cap-add=SYS_PTRACE --security-opt seccomp=unconfined --ulimit memlock=-1:-1 --ipc=host --network host --group-add video -v <Host Path>:<Container Path> <Image ID> /bin/bash docker run -it --name fastfold --privileged --shm-size=32G --device=/dev/kfd --device=/dev/dri/ --cap-add=SYS_PTRACE --security-opt seccomp=unconfined --ulimit memlock=-1:-1 --ipc=host --network host --group-add video -v <Host Path>:<Container Path> <Image ID> /bin/bash
``` ```
镜像版本依赖： 镜像版本依赖：
* DTK驱动：dtk22.10 * DTK驱动：dtk23.10
* Pytorch: 1.10 * Pytorch: 1.13
* fastfold: 0.2.1 * fastfold: 0.2.0
* python: python3.8 * python: python3.8
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： 测试目录：
`/opt/docker/tests` `/opt/docker/tests`
...@@ -96,7 +93,7 @@ $DOWNLOAD_DIR/ ...@@ -96,7 +93,7 @@ $DOWNLOAD_DIR/
python inference.py T1024.fasta data/pdb_mmcif/mmcif_files/ \ python inference.py T1024.fasta data/pdb_mmcif/mmcif_files/ \
--output_dir ./ \ --output_dir ./ \
--gpus 2 \ --gpus 1 \
--use_precomputed_alignments alignments/ \ --use_precomputed_alignments alignments/ \
--param_path /data/params/params_model_1.npz \ --param_path /data/params/params_model_1.npz \
--uniref90_database_path data/uniref90/uniref90.fasta \ --uniref90_database_path data/uniref90/uniref90.fasta \
...@@ -117,7 +114,7 @@ $DOWNLOAD_DIR/ ...@@ -117,7 +114,7 @@ $DOWNLOAD_DIR/
T1024.fasta为推理的单体序列；data修改为数据集下载目录； 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； `--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； `--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；
默认进行relax操作，若不需要，添加`--relaxation`；默认不保存输出的.pkl文件，若需要，添加`--save_outputs`. 默认不进行relax操作，若需要，添加`--relaxation`；默认不保存输出的.pkl文件，若需要，添加`--save_outputs`.
Alphafold的数据预处理需要花费大量时间，因此我们通过[ray](https://docs.ray.io/en/latest/workflows/concepts.html)加快了数据预处理工作流程。 Alphafold的数据预处理需要花费大量时间，因此我们通过[ray](https://docs.ray.io/en/latest/workflows/concepts.html)加快了数据预处理工作流程。
...@@ -126,7 +123,7 @@ Alphafold的数据预处理需要花费大量时间，因此我们通过[ray](ht ...@@ -126,7 +123,7 @@ Alphafold的数据预处理需要花费大量时间，因此我们通过[ray](ht
### 多体 ### 多体
python inference.py SUGP1.fasta data/pdb_mmcif/mmcif_files/ \ python inference.py SUGP1.fasta data/pdb_mmcif/mmcif_files/ \
--output_dir ./ \ --output_dir ./ \
--gpus 2 \ --gpus 1 \
--use_precomputed_alignments alignments/ \ --use_precomputed_alignments alignments/ \
--model_preset multimer \ --model_preset multimer \
--uniref90_database_path data/uniref90/uniref90.fasta \ --uniref90_database_path data/uniref90/uniref90.fasta \
...@@ -164,13 +161,18 @@ alignments/ ...@@ -164,13 +161,18 @@ alignments/
{target_name}_{model_name}_relaxed.pdb {target_name}_{model_name}_relaxed.pdb
``` ```
查看蛋白质3D结构：[https://www.pdbus.org/3d-view](https://www.pdbus.org/3d-view) [查看蛋白质3D结构](https://www.pdbus.org/3d-view)
![img](./docs/result_pdb.png) <div style="display: flex; justify-content: center; align-items: center;">
<img src="./docs/result_pdb.png" alt="Image">
<div style="position: absolute; top: 50%; left: 50%; transform: translate(-50%, -50%); background: rgba(0, 0, 0, 0.5); color: #fff; padding: 10px;">
红色为真实结构，蓝色为预测结构
</div>
</div>
## 精度 ## 精度
测试数据：[casp14](https://www.predictioncenter.org/casp14/targetlist.cgi)、[uniprot](https://www.uniprot.org/)，使用的加速卡:4张 DCU 1代-16G 测试数据：[casp14](https://www.predictioncenter.org/casp14/targetlist.cgi)、[uniprot](https://www.uniprot.org/)，使用的加速卡:1张 Z100L-32G
1、计算lddt的值 1、计算plddts的值
python3 pkl2plddt.py python3 pkl2plddt.py
其中，data_path为推理生成的pkl文件路径。 其中，data_path为推理生成的pkl文件路径。
...@@ -179,9 +181,9 @@ alignments/ ...@@ -179,9 +181,9 @@ alignments/
2、其它精度值计算：[https://zhanggroup.org/TM-score/](https://zhanggroup.org/TM-score/) 2、其它精度值计算：[https://zhanggroup.org/TM-score/](https://zhanggroup.org/TM-score/)
准确性数据： 准确性数据：
| 数据类型 | 序列类型 | 序列标签 | 序列长度 | GDT-TS | GDT-HA | LDDT | TM score | MaxSub | RMSD | | 数据类型 | 序列类型 | 序列标签 | 序列长度 | GDT-TS | GDT-HA | PLDDTS | TM score | MaxSub | RMSD |
| :------: | :------: | :------: | :------: |:------: |:------: | :------: | :------: | :------: |:------: | | :------: | :------: | :------: | :------: |:------: |:------: | :------: | :------: | :------: |:------: |
| fp32 | 单体 | T1026 | 172 | 0.914 | 0.765 | 79.634 | 0.941 | 0.907 | 1.289 | | fp32 | 单体 | T1024 | 408 | 0.595 | 0.441 | 90.828 | 0.663 | 0.489 | 5.779 |
| fp32 | 单体 | T1053 | 580 | 0.937 | 0.782 | 92.284 | 0.984 | 0.929 | 1.105 | | fp32 | 单体 | T1053 | 580 | 0.937 | 0.782 | 92.284 | 0.984 | 0.929 | 1.105 |
| fp32 | 单体 | Q9NYK1 | 1046 | 0.907 | 0.744 | 86.642 | 0.962 | 0.905 | 5.757 | | fp32 | 单体 | Q9NYK1 | 1046 | 0.907 | 0.744 | 86.642 | 0.962 | 0.905 | 5.757 |
......
alignments/T1024 LmrP, , 408 residues_/mgnify_hits.a3m deleted 100644 → 0
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alignments/T1024 LmrP, , 408 residues_/pdb70_hits.hhr deleted 100644 → 0
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alignments/sp_Q15637_SF01_HUMAN_Splicing_factor_1_OS_Homo_sapiens_OX_9606_GN_SF1_PE_1_SV_4_292_370/hmm_output.sto deleted 100644 → 0
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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 deleted 100644 → 0
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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 deleted 100644 → 0
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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 deleted 100644 → 0
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# 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 deleted 100644 → 0
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# 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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inference.py
View file @ cc1d6094
...@@ -526,7 +526,8 @@ if __name__ == "__main__": ...@@ -526,7 +526,8 @@ if __name__ == "__main__":
automatically according to the model name from automatically according to the model name from
./data/params""") ./data/params""")
parser.add_argument( parser.add_argument(
"--relaxation", action="store_false", default=False, "--relaxation", action="store_true", default=False,
help="Whether to relax."
) )
parser.add_argument( parser.add_argument(
"--save_outputs", action="store_true", default=False, "--save_outputs", action="store_true", default=False,
......
inference.sh
View file @ cc1d6094
...@@ -4,8 +4,7 @@ ...@@ -4,8 +4,7 @@
python3 inference.py T1024.fasta /data/pdb_mmcif/mmcif_files \ python3 inference.py T1024.fasta /data/pdb_mmcif/mmcif_files \
--output_dir ./ \ --output_dir ./ \
--gpus 4 \ --gpus 1 \
--use_precomputed_alignments alignments/ \
--param_path /data/params/params_model_1.npz \ --param_path /data/params/params_model_1.npz \
--uniref90_database_path /data/uniref90/uniref90.fasta \ --uniref90_database_path /data/uniref90/uniref90.fasta \
--mgnify_database_path /data/mgnify/mgy_clusters_2018_12.fa \ --mgnify_database_path /data/mgnify/mgy_clusters_2018_12.fa \
......
inference_multimer.sh
View file @ cc1d6094
...@@ -4,7 +4,7 @@ ...@@ -4,7 +4,7 @@
python3 inference.py SUGP1.fasta /data/pdb_mmcif/mmcif_files \ python3 inference.py SUGP1.fasta /data/pdb_mmcif/mmcif_files \
--output_dir ./ \ --output_dir ./ \
--gpus 4 \ --gpus 1 \
--use_precomputed_alignments alignments/ \ --use_precomputed_alignments alignments/ \
--model_preset multimer \ --model_preset multimer \
--uniref90_database_path /data/uniref90/uniref90.fasta \ --uniref90_database_path /data/uniref90/uniref90.fasta \
......
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