上手く動かない...
本家様 https://kiharalab.org/emsuites/emap2sec.php
「Emap2sec identifies the secondary structures of proteins in cryo-EM maps of intermediate resolution range (~5 to 10 Å) .
Emap2sec uses convolutional deep neural network as its core algorithm and assigns a secondary structure to each of the grid points in an EM map」
とある
DeepL先生訳
「Emap2secは、中程度の分解能（〜5〜10Å）の低温電子顕微鏡マップに含まれるタンパク質の二次構造を同定します。
Emap2secは、畳み込みニューラルネットワークをコアアルゴリズムとして使用し、EMマップの各グリッドポイントに二次構造を割り当てる。」
GoogleさんのアカウントがあればGoogle Colabでお試しできそうです.
ここではgithubで提供されているソースコードを使ってローカルの計算機に入れて使ってみます
インストール †
githubの先はhttps://github.com/kiharalab/Emap2secです
そこを拝見すると必要なのは
とある. eman2が必要って事なので、
[root@rockylinux ~]# conda create -n emap2sec python=3.6 tensorflow=1.15 scikit-learn=0.24 pandas=1.1 numpy=1.16
git clone https://github.com/kiharalab/Emap2sec
cd Emap2sec/map2train_src
make
cd ..
[saber@rockylinux Emap2sec]$ ./data_generate/map2train data/1733.mrc -c 2.75 > data/trimmap
[saber@rockylinux Emap2sec]$ python3 -V
Python 3.6.8
[saber@rockylinux Emap2sec]$
[saber@rockylinux Emap2sec]$ python3 data_generate/dataset.py data/trimmap data/protein_dataset
[saber@rockylinux Emap2sec]$ mkdir models
[saber@rockylinux Emap2sec]$ cd models/
[saber@rockylinux models]$ mkdir emap2sec_models_exp1 emap2sec_models_exp2
[saber@rockylinux models]$ cd emap2sec_models_exp1
[saber@rockylinux emap2sec_models_exp1]$ wget https://kiharalab.org/Emap2sec_models/emap2sec_models_exp1/checkpoint
[saber@rockylinux emap2sec_models_exp1]$ wget https://kiharalab.org/Emap2sec_models/emap2sec_models_exp1/emap2sec_L1_exp.ckpt-108000.data-00000-of-00001
[saber@rockylinux emap2sec_models_exp1]$ wget https://kiharalab.org/Emap2sec_models/emap2sec_models_exp1/emap2sec_L1_exp.ckpt-108000.index
[saber@rockylinux emap2sec_models_exp1]$ wget https://kiharalab.org/Emap2sec_models/emap2sec_models_exp1/emap2sec_L1_exp.ckpt-108000.meta
[saber@rockylinux emap2sec_models_exp1]$ cd ../emap2sec_models_exp2
[saber@rockylinux emap2sec_models_exp2]$ wget https://kiharalab.org/Emap2sec_models/emap2sec_models_exp2/checkpoint
[saber@rockylinux emap2sec_models_exp2]$ wget https://kiharalab.org/Emap2sec_models/emap2sec_models_exp2/emap2sec_L2_exp.ckpt-20000.data-00000-of-00001
[saber@rockylinux emap2sec_models_exp2]$ wget https://kiharalab.org/Emap2sec_models/emap2sec_models_exp2/emap2sec_L2_exp.ckpt-20000.index
[saber@rockylinux emap2sec_models_exp2]$ wget https://kiharalab.org/Emap2sec_models/emap2sec_models_exp2/emap2sec_L2_exp.ckpt-20000.meta
[saber@rockylinux emap2sec_models_exp2]$ cd ~/Emap2sec
[saber@rockylinux Emap2sec]$ echo data/protein_dataset > dataset_location_file
[saber@rockylinux Emap2sec]$ export PATH=/apps/pyenv/versions/anaconda3-2023.03/envs/emap2sec/bin:$PATH
[saber@rockylinux Emap2sec]$ which python
/apps/pyenv/versions/anaconda3-2023.03/envs/emap2sec/bin/python
[saber@rockylinux Emap2sec]$ python -V
Python 3.6.13 :: Anaconda, Inc.
[saber@rockylinux Emap2sec]$
[saber@rockylinux Emap2sec]$ python emap2sec/Emap2sec.py dataset_location_file
INFO : Running Emap2sec Phase1 for dataset data/protein_dataset
OMP: Info #155: KMP_AFFINITY: Initial OS proc set respected: 0-3
OMP: Info #217: KMP_AFFINITY: decoding x2APIC ids.
OMP: Info #157: KMP_AFFINITY: 4 available OS procs
OMP: Info #158: KMP_AFFINITY: Uniform topology
OMP: Info #288: KMP_AFFINITY: topology layer "LL cache" is equivalent to "socket".
OMP: Info #288: KMP_AFFINITY: topology layer "L3 cache" is equivalent to "socket".
OMP: Info #288: KMP_AFFINITY: topology layer "L2 cache" is equivalent to "socket".
OMP: Info #288: KMP_AFFINITY: topology layer "L1 cache" is equivalent to "socket".
OMP: Info #192: KMP_AFFINITY: 4 sockets x 1 core/socket x 1 thread/core (4 total cores)
OMP: Info #219: KMP_AFFINITY: OS proc to physical thread map:
OMP: Info #172: KMP_AFFINITY: OS proc 0 maps to socket 0 core 0 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 1 maps to socket 2 core 0 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 2 maps to socket 4 core 0 thread 0
OMP: Info #172: KMP_AFFINITY: OS proc 3 maps to socket 6 core 0 thread 0
OMP: Info #255: KMP_AFFINITY: pid 8865 tid 8865 thread 0 bound to OS proc set 0
OMP: Info #255: KMP_AFFINITY: pid 8865 tid 8869 thread 1 bound to OS proc set 1
OMP: Info #255: KMP_AFFINITY: pid 8865 tid 8870 thread 2 bound to OS proc set 2
OMP: Info #255: KMP_AFFINITY: pid 8865 tid 8871 thread 3 bound to OS proc set 3
WARNING:tensorflow:From emap2sec/Emap2sec.py:306: The name tf.reset_default_graph is deprecated. Please use tf.compat.v1.reset_default_graph instead.
WARNING:tensorflow:From emap2sec/Emap2sec.py:308: The name tf.placeholder is deprecated. Please use tf.compat.v1.placeholder instead.
WARNING:tensorflow:From emap2sec/Emap2sec.py:312: The name tf.Session is deprecated. Please use tf.compat.v1.Session instead.
2023-05-12 22:40:54.180496: I tensorflow/core/platform/cpu_feature_guard.cc:145] This TensorFlow binary is optimized with Intel(R) MKL-DNN to use the following CPU instructions in performance critical operations: SSE4.1 SSE4.2 AVX AVX2 FMA
To enable them in non-MKL-DNN operations, rebuild TensorFlow with the appropriate compiler flags.
2023-05-12 22:40:54.182872: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 3791995000 Hz
2023-05-12 22:40:54.182949: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x56173d6be1b0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:
2023-05-12 22:40:54.182962: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version
2023-05-12 22:40:54.183024: I tensorflow/core/common_runtime/process_util.cc:115] Creating new thread pool with default inter op setting: 2. Tune using inter_op_parallelism_threads for best performance.
WARNING:tensorflow:From emap2sec/Emap2sec.py:313: The name tf.train.import_meta_graph is deprecated. Please use tf.compat.v1.train.import_meta_graph instead.
2023-05-12 22:40:54.203496: W tensorflow/core/graph/graph_constructor.cc:1491] Importing a graph with a lower producer version 17 into an existing graph with producer version 134. Shape inference will have run different parts of the graph with different producer versions.
2023-05-12 22:40:54.204282: W tensorflow/core/framework/op_def_util.cc:357] Op TFRecordReader is deprecated. It will cease to work in GraphDef version 26. Use TFRecordReaderV2.
WARNING:tensorflow:The saved meta_graph is possibly from an older release:
'local_variables' collection should be of type 'byte_list', but instead is of type 'node_list'.
WARNING:tensorflow:From /apps/pyenv/versions/anaconda3-2023.03/envs/emap2sec/lib/python3.6/site-packages/tensorflow_core/python/training/queue_runner_impl.py:391: QueueRunner.__init__ (from tensorflow.python.training.queue_runner_impl) is deprecated and will be removed in a future version.
Instructions for updating:
To construct input pipelines, use the `tf.data` module.
WARNING:tensorflow:From emap2sec/Emap2sec.py:316: The name tf.get_default_graph is deprecated. Please use tf.compat.v1.get_default_graph instead.
OMP: Info #255: KMP_AFFINITY: pid 8865 tid 8879 thread 4 bound to OS proc set 0
OMP: Info #255: KMP_AFFINITY: pid 8865 tid 8880 thread 5 bound to OS proc set 1
OMP: Info #255: KMP_AFFINITY: pid 8865 tid 9114 thread 6 bound to OS proc set 2
OMP: Info #255: KMP_AFFINITY: pid 8865 tid 9115 thread 7 bound to OS proc set 3
OMP: Info #255: KMP_AFFINITY: pid 8865 tid 9116 thread 8 bound to OS proc set 0
INFO : Wrote the output of Phase1 to outputP1_protein_dataset
INFO : Running Emap2sec Phase2 for dataset data/protein_dataset
WARNING:tensorflow:The saved meta_graph is possibly from an older release:
'local_variables' collection should be of type 'byte_list', but instead is of type 'node_list'.
INFO : Wrote the output of Phase2 to outputP2_protein_dataset
[saber@rockylinux Emap2sec]$
[saber@rockylinux Emap2sec]$ chmod +x Visual/Visual.pl
[saber@rockylinux Emap2sec]$ Visual/Visual.pl data/trimmap outputP2_protein_dataset -p > out_fin.pdb
![[PukiWiki]](image/picc.png "[PukiWiki]")
