AlphaFold安装——非docker镜像（2）

AlphaFold安装——非docker镜像（2）

接上一篇，和师兄说完没多久就帮我弄好了，开了一个一个多小时的头脑风暴，然后出去吃完饭，回来继续！

8、应用OpenMM 补丁

其实对于patch 这个package我也是第一次看到，以前没有接触过，自己查了查知道是一个打补丁的package，大家想了解可以自行查询。

cd /share2/pub/yangjy/yangjy/conda3/envs/alphafold/lib/python3.8/site-packages/ && patch -p0 < /share2/pub/yangjy/yangjy/softs/alphafold/docker/openmm.patch

我自己的理解，上面的代码就是根据.patch文件中的difference去更新conda中alphafold环境中的package，我觉得是为了避免后面的工作不匹配！（我自己的理解，大家如果更明白，可以滴滴我~）

9、运行alphafold的脚本

此处有具体的bash脚本，源码地址给大家，不再贴在这里了，因为有点长~
源码地址，直接下载，放在alphafold的目录下就OK
附：参数说明
在这里又想叨叨两句，切身体会，谷歌翻译有的时候真的不准确，翻译过来的文字非常生硬，很难理解，读英文原文真的容易理解，而且不会理解错，往往翻译过来的意思都变味了，容易误导人！还有一个学习的好方法就是，无论是R package 还是python的package或者function，不明白的直接看源代码，里面写的很详细，无论是参数说明还是example。

Usage: ./run_alphafold_v21.sh <OPTIONS>
Required Parameters:
-d <data_dir>         Path to directory of supporting data
-o <output_dir>       Path to a directory that will store the results.
-f <fasta_path>       Path to a FASTA file containing sequence. If a FASTA file contains multiple sequences, then it will be folded as a multimer
-t <max_template_date> Maximum template release date to consider (ISO-8601 format - i.e. YYYY-MM-DD). Important if folding historical test sets
Optional Parameters:
-g <use_gpu>          Enable NVIDIA runtime to run with GPUs (default: true)
-n <openmm_threads>   OpenMM threads (default: all available cores)
-a <gpu_devices>      Comma separated list of devices to pass to 'CUDA_VISIBLE_DEVICES' (default: 0)
-m <model_preset>     Choose preset model configuration - the monomer model, the monomer model with extra ensembling, monomer model with pTM head, or multimer model (default: 'monomer')
-c <db_preset>        Choose preset MSA database configuration - smaller genetic database config (reduced_dbs) or full genetic database config (full_dbs) (default: 'full_dbs')
-p <use_precomputed_msas> Whether to read MSAs that have been written to disk. WARNING: This will not check if the sequence, database or configuration have changed (default: 'false')
-l <is_prokaryote>    Optional for multimer system, not used by the single chain system. A boolean specifying true where the target complex is from a prokaryote, and false where it is not, or where the origin is unknown. This value determine the pairing method for the MSA (default: 'None')
-b <benchmark>        Run multiple JAX model evaluations to obtain a timing that excludes the compilation time, which should be more indicative of the time required for inferencing many proteins (default: 'false')

敲黑板！！划重点！！这个脚本的位置，是直接放在alphafold的文件夹下，不是alphafold的子文件夹alphafold！上个图：

10、准备好的database

（附一张下载好的database的picture，这是师兄之前下载好的，我不想再下载了，去年的是这样子的，今年不知道有没有变了）

11、running

# Example run (Uses the GPU with index id 0 as default)
bash run_alphafold.sh -d /share/pub/zhaohq/project/pumch/alphafold/version1/source/databases/ -o /share2/pub/yangjy/yangjy/softs/alphafold/result/query -f /share2/pub/yangjy/yangjy/softs/alphafold/example/query.fasta -t 2020-05-14

# or for CPU only run
bash run_alphafold.sh -d /share/pub/zhaohq/project/pumch/alphafold/version1/source/databases/ -o /share2/pub/yangjy/yangjy/softs/alphafold/result/query -f /share2/pub/yangjy/yangjy/softs/alphafold/example/query.fasta -t  2020-05-14 -g False

先这样，有报错，是GPU 的问题，我继续查错，解决了继续！