PyMOL の変更点

• 追加された行はこの色です。
• 削除された行はこの色です。
• PyMOL へ行く。
• PyMOL の差分を削除

#author("2024-09-02T05:24:01+00:00","default:sysosa","sysosa")
#author("2024-10-29T13:14:10+00:00","default:sysosa","sysosa")
本家様 [[http://pymol.org/>+http://pymol.org/]]
シュレーディンガー社様から販売されております. 一方でそのオープンソース版が存在していてここではそのオープンソース版を作ってみました.
[[https://github.com/schrodinger/pymol-open-source>+https://github.com/schrodinger/pymol-open-source]]

&size(10){有償版PyMOLはopen source版よりも機能が強化されてます};
&size(10){windowsOS向けopen source版は試してないです..};

ver3.0になったので改めて作ってみた.

***下準備 [#h332c459]
#code(nonumber){{
(RockyLinux9)
dnf groupinstall "Development Tools" -y
dnf install epel-release -y
dnf --enablerepo=devel install python3-numpy cmake netcdf-devel glm-devel python-devel glew-devel libpng-devel libxml2-devel freetype-devel python3-qt5 -y
}} 

***構築 [#lb3a3b5c]
#code(nonumber){{
(RockyLinux9)
mkdir -p /apps/src && cd /apps/src
git clone https://github.com/schrodinger/pymol-open-source
cd pymol-open-source/
pip install --prefix /apps/PyMOL .
}}


***EnvironmentModules [#if7310ad]

/apps/modulefiles/PyMOL
#code(nonumber){{
#%Module1.0
set root /apps/PyMOL
prepend-path PATH        $root/bin
prepend-path PYTHONPATH  $root/lib64/python3.9/site-packages
}}


***メモ [#pb70f2b6]
以上でrockylinux9向けには出来た.

ver3.0から pthon3.9以上が必要となりました.

rockylinux8のpythonは 3.6、python39もありますが、python3-qt5がpython3.6ベースなので無理.  &size(10){「--glut」で逃げれるけど構築が複雑だった..};
なので condaで python3.9 以上の環境を作ってそこでpymolを作ってみました.


***conda環境内で作る(rockylinux8向け) [#b6b7fcfb]
condaで仮想環境を作りpymolをコンパイルします。

#code(nonumber){{
(RockyLinux8の下拵え)
dnf groupinstall "Development Tools" -y
dnf install epel-release -y
dnf install --enablerepo=devel,epel  cmake netcdf-devel glew-devel libpng-devel libxml2-devel freetype-devel -y
dnf install xcb-util-wm xcb-util-image xcb-util-keysyms xcb-util-renderutil -y

dnf install https://dl.rockylinux.org/pub/rocky/9/devel/x86_64/os/Packages/g/glm-devel-0.9.9.8-3.el9.noarch.rpm
}}
pyenv/anacondaを用意します. &size(10){miniforgeでもいいけど};
#code(nonumber){{
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install anaconda3-2024.06-1

source /apps/pyenv/versions/anaconda3-2024.06-1/etc/profile.d/conda.sh
}}
既にpyenv/anaconda環境があるのなら下記のみを実施します
#code(nonumber){{
source /apps/pyenv/versions/anaconda3-2024.06-1/etc/profile.d/conda.sh
}}

次にpymol向けの仮想環境を作ります
#code(nonumber){{
[root@rockylinux ~]# conda create -n pymol-open-source python numpy qt pyqt

[root@rockylinux ~]# conda activate pymol-open-source

(pymol-open-source) [root@rockylinux ~]# cd /apps/src

(pymol-open-source) [root@rockylinux src]# git clone https://github.com/schrodinger/pymol-open-source

(pymol-open-source) [root@rockylinux src]# cd pymol-open-source

(pymol-open-source) [root@rockylinux pymol-open-source]# pip install --prefix=/apps/PyMOL .
 :
Successfully installed pymol-3.1.0a0
 :
(pymol-open-source) [root@rockylinux pymol-open-source]# conda deactivate

[root@rockylinux pymol-open-source]#
}}

EnvironmentModules は下記のようにします
/apps/modulefiles/PyMOL
#code(nonumber){{
#%Module1.0
prepend-path PATH        /apps/PyMOL/bin
prepend-path PYTHONPATH  /apps/PyMOL/lib/python3.12/site-packages
}}
これで「module use /apps/modulefiles」「module load PyMOL」として「pymol」で起動します


起動画面はこんな感じ. versionは「3.1.0a0」

&ref(2024y08m23d_024425128.png,nolink,80%);

***condaなしでOS提供で作る [#z62bb429]
#code(nonumber){{
dnf install epel-release -y
dnf install xcb-util-wm xcb-util-image xcb-util-keysyms xcb-util-renderutil -y
dnf install --enablerepo=epel,devel glew-devel netcdf-devel freetype-devel libxml2-devel libpng-devel cmake -y
dnf remove glm-devel -y
dnf install https://dl.rockylinux.org/pub/rocky/9/devel/x86_64/os/Packages/g/glm-devel-0.9.9.8-3.el9.noarch.rpm -y
dnf --enablerepo=devel install python39-devel python39-numpy -y
python3.9 -m pip install --upgrade pip
pip3.9 install pyqt5
cd /apps/src
git clone https://github.com/schrodinger/pymol-open-source
cd pymol-open-source/
pip3.9 install --prefix=/apps/PyMOL .
}}
/apps/modulefiles/PyMOL
#code(nonumber){{
#%Module1.0
prepend-path PATH        /apps/PyMOL/bin
prepend-path PYTHONPATH  /apps/PyMOL/lib64/python3.9/site-packages
}}




***centos7では？ [#oeedb894]

基本rockylinux8のようにconda仮想環境でpymolを用意します

#code(nonumber){{
(centos7なら)
yum install centos-release-scl-rh epel-release
yum install devtoolset-11
yum install --enablerepo=epel glew-devel netcdf-devel libpng-devel libxml2-devel freetype-devel cmake
yum install xcb-util-wm xcb-util-image xcb-util-keysyms xcb-util-renderutil
source scl_source enable devtoolset-11
git clone https://github.com/g-truc/glm
cd glm
git checkout 0.9.9.8
cp -r glm /usr/include

alternatives --install /usr/bin/cmake cmake /usr/bin/cmake3 1     <-- 「cmake」が必要なのでcmake3をcmakeにしてみた
}}
OSパッケージ側はこれでokで、次にcondaになります
#code(nonumber){{
[root@centos7 ~]# conda create -n pymol-open-source python numpy qt pyqt

[root@centos7 ~]# conda activate pymol-open-source

(pymol-open-source) [root@rockylinux ~]# cd /apps/src

(pymol-open-source) [root@centos7 src]# git clone https://github.com/schrodinger/pymol-open-source

(pymol-open-source) [root@centos7 src]# cd pymol-open-source

(pymol-open-source) [root@centos7 pymol-open-source]# pip install .
 :
Successfully installed pymol-3.1.0a0
 :
(pymol-open-source) [root@centos7 pymol-open-source]# conda deactivate
[root@centos7 pymol-open-source]#
}}

EnvironmentModules は rockylinux8 と同じ



*** ubuntuでは？ [#ffc94e15]

#code(nonumber){{
(ubuntu24.04)

root@ubuntu24:~# grep PRETTY_NAME /etc/os-release
PRETTY_NAME="Ubuntu 24.04.1 LTS"

root@ubuntu24:~# apt install cmake git libnetcdf-dev libglm-dev libglew-dev libpng-dev libfreetype-dev  python3-numpy python3-pyqt5.qtopengl python3-pip environment-modules
root@ubuntu24:~# cd /apps/src
root@ubuntu24:/apps/src# git clone https://github.com/schrodinger/pymol-open-source
root@ubuntu24:/apps/src# cd pymol-open-source
root@ubuntu24:/apps/src/pymol-open-source# pip install --prefix=/apps/PyMOL .
root@ubuntu24:/apps/src/pymol-open-source# cd 

root@ubuntu24:~# vi /apps/modulefiles/PyMOL
#%Module1.0
prepend-path PATH        /apps/PyMOL/local/bin
prepend-path PYTHONPATH  /apps/PyMOL/local/lib/python3.12/dist-packages

root@ubuntu24:~#
}}
&size(10){なぜか local が中間に入ってしまう...};



&color(red){みかんせい};
#code(nonumber){{
(ubuntu22.04)
root@ubuntu22:~# grep PRETTY_NAME /etc/os-release
PRETTY_NAME="Ubuntu 22.04.3 LTS"

root@ubuntu22:~# apt install cmake git libnetcdf-dev libglm-dev libglew-dev libpng-dev libfreetype-dev  python3-numpy python3-pyqt5.qtopengl python3-pip environment-modules libxml2-dev
root@ubuntu22:~# cd /apps/src
root@ubuntu22:/apps/src# git clone https://github.com/schrodinger/pymol-open-source
root@ubuntu22:/apps/src# cd pymol-open-source
root@ubuntu22:/apps/src/pymol-open-source# pip install --prefix=/apps/PyMOL .
root@ubuntu22:/apps/src/pymol-open-source# cd 

root@ubuntu24:~# vi /apps/modulefiles/PyMOL
#%Module1.0
prepend-path PATH        /apps/PyMOL/local/bin
prepend-path PYTHONPATH  /apps/PyMOL/local/lib/python3.10/dist-packages

root@ubuntu24:~#
}}