PyMOL をテンプレートにして作成
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開始行:
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...
[[https://github.com/schrodinger/pymol-open-source>+https...
&size(10){有償版PyMOLはopen source版よりも機能が強化され...
&size(10){windowsOS向けopen source版は試してないです..};
ver3.1.0になったので改めて作ってみた.
RHEL系はOSに直に作るのは難しいみたい. 直前の3.1.0a0ならい...
ubuntu22はPyMOLのWorkflowに載っているのですんなり行ける. ...
***Rockylinux10 [#y99f7069]
condaでコンパイル環境を作って実行したが「__cxa_call_termi...
恐らくcondaのコンパイル環境の問題っぽいのでOS上に作ってみた
#code(nonumber){{
dnf install epel-release -y
dnf config-manager --enable crb
dnf install xcb-util-wm xcb-util-image xcb-util-keysyms x...
dnf install https://dl.rockylinux.org/pub/rocky/9/devel/x...
dnf --enablerepo=devel install cmake netcdf-devel glew-de...
wget -nv https://anaconda.org/schrodinger/collada2gltf/2....
bzip2 -cd collada2gltf-2.1.4-h6bb024c_0.tar.bz2 | tar xf ...
rm -rf collada2gltf-2.1.4-h6bb024c_0.tar.bz2
git clone --depth 1 https://github.com/rcsb/mmtf-cpp.git
cp -R mmtf-cpp/include/mmtf* /usr/local/include
rm -rf mmtf-cpp
cd /apps/src/
git clone https://github.com/schrodinger/pymol-open-source
cd pymol-open-source/
python3 setup.py install --prefix=/apps/pymol
}}
修正「/apps/pymol/bin/pymol」
#code(nonumber){{
exec "/usr/bin/python3" "/usr/local/lib/python3.12/site-p...
exec "/usr/bin/python3" "/apps/pymol/lib64/python3.12/sit...
}}
/apps/modulefiles/pymol
#code(nonumber){{
#%Module1.0
set root /apps/pymol
prepend-path PATH $root/bin
prepend-path PYTHONPATH $root/lib64/python3.12/site-pack...
}}
***Rockylinux9 [#h332c459]
既定のpythonは3.9 で gcc は gcc-11.5
#code(nonumber){{
(OSパッケージの追加インストールと関連アプリのインストール)
dnf groupinstall "Development Tools" -y
dnf install epel-release -y
dnf install xcb-util-wm xcb-util-image xcb-util-keysyms x...
dnf --enablerepo=devel install cmake netcdf-devel glew-de...
wget -nv https://anaconda.org/schrodinger/collada2gltf/2....
bzip2 -cd collada2gltf-2.1.4-h6bb024c_0.tar.bz2 | tar xf ...
rm -rf collada2gltf-2.1.4-h6bb024c_0.tar.bz2
git clone --depth 1 https://github.com/rcsb/mmtf-cpp.git
cp -R mmtf-cpp/include/mmtf* /usr/local/include
rm -rf mmtf-cpp/
(pyenv-anacondaの敷設)
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install miniforge3-25.3.1-0
}}
#code(nonumber){{
[root@rockylinux9 ~]# source /apps/pyenv/versions/minifor...
[root@rockylinux9 ~]# conda create -n pymol-open-source p...
[root@rockylinux9 ~]# conda activate pymol-open-source
(pymol-open-source) [root@rockylinux9 ~]# cd /apps/src/
(pymol-open-source) [root@rockylinux9 src]# git clone htt...
(pymol-open-source) [root@rockylinux9 src]# cd pymol-open...
(pymol-open-source) [root@rockylinux9 pymol-open-source]#
}}
ここで vtk-m を有効にするためにちょいとソースコードを修正...
#code(diff,nonumber){{
diff --git a/layer0/ContourSurf.cpp b/layer0/ContourSurf....
index 143ce83a..380fcf04 100644
--- a/layer0/ContourSurf.cpp
+++ b/layer0/ContourSurf.cpp
@@ -82,7 +82,7 @@ using ::copysign;
#include <vtkm/Version.h>
#include <vtkm/cont/DataSetBuilderUniform.h>
-#include <vtkm/filter/Contour/Contour.h>
+#include <vtkm/filter/contour/Contour.h>
#include <cassert>
#include <set>
}}
その上で
#code(nonumber){{
(pymol-open-source) [root@rockylinux9 pymol-open-source]#
(pymol-open-source) [root@rockylinux9 pymol-open-source]#...
pip install --prefix=/apps/pymol --config-settings u...
(pymol-open-source) [root@rockylinux9 pymol-open-source]#
}}
EnvironmentModules は下記になる.
「/apps/modulefiles/pymol」
#code(nonumber){{
#%Module1.0
set root /apps/pymol
prepend-path PATH $root/bin
prepend-path PYTHONPATH $root/lib/python3.10/site-packages
}}
&ref(2025y09m16d_040350139.png,nolink);
***Rockylinux8 [#o04b017b]
condaで仮想環境を作りpymolをコンパイルします。
#code(nonumber){{
(OSパッケージの追加インストールと関連アプリのインストール)
dnf groupinstall "Development Tools" -y
dnf install epel-release -y
dnf install xcb-util-wm xcb-util-image xcb-util-keysyms x...
dnf install --enablerepo=epel,devel cmake netcdf-devel gl...
dnf remove glm-devel -y
dnf install https://dl.rockylinux.org/pub/rocky/9/devel/x...
wget -nv https://anaconda.org/schrodinger/collada2gltf/2....
bzip2 -cd collada2gltf-2.1.4-h6bb024c_0.tar.bz2 | tar xf ...
rm -rf collada2gltf-2.1.4-h6bb024c_0.tar.bz2
git clone --depth 1 https://github.com/rcsb/mmtf-cpp.git
cp -R mmtf-cpp/include/mmtf* /usr/local/include
rm -rf mmtf-cpp/
(pyenv-anacondaの敷設)
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install miniforge3-25.3.1-0
}}
#code(nonumber){{
[root@rockylinux8 ~]# source /apps/pyenv/versions/minifor...
[root@rockylinux9 ~]# conda create -n pymol-open-source p...
[root@rockylinux8 ~]# conda activate pymol-open-source
(pymol-open-source) [root@rockylinux8 ~]# cd /apps/src/
(pymol-open-source) [root@rockylinux8 src]# git clone htt...
(pymol-open-source) [root@rockylinux8 src]# cd pymol-open...
(pymol-open-source) [root@rockylinux8 pymol-open-source]#
}}
vtk-m を有効にしたいのですが、ソースコード側でタイポがあ...
#code(nonumber){{
(pymol-open-source) [root@rockylinux8 pymol-open-source]#...
#include <vtkm/filter/Contour/Contour.h>
↓
#include <vtkm/filter/contour/Contour.h>
}}
その上で
#code(nonumber){{
(pymol-open-source) [root@rockylinux8 pymol-open-source]#...
(pymol-open-source) [root@rockylinux8 pymol-open-source]#...
pip install --prefix=/apps/pymol --config-settings u...
(pymol-open-source) [root@rockylinux8 pymol-open-source]#...
[root@rockylinux8 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/python3.10/site-...
}}
これで「module use /apps/modulefiles」「module load pymol...
&ref(2025y10m29d_152254985.png,nolink);
***ubuntu24.04 [#z3365d01]
Python 3.12.3
gcc 13.3.0
#code(nonumber){{
(準備)
apt-get update
apt-get install catch2 cmake libfreetype6-dev libglew-dev...
python3-biopython python3-dev python3-setuptools python3...
wget -nv https://anaconda.org/schrodinger/collada2gltf/2....
bzip2 -cd collada2gltf-2.1.4-h6bb024c_0.tar.bz2 | tar xf ...
git clone --depth 1 https://github.com/rcsb/mmtf-cpp.git
cp -R mmtf-cpp/include/mmtf* /usr/local/include
}}
っで構築
#code(nonumber){{
root@ubuntu22:~# mkdir -p /apps/src ; cd /apps/src
root@ubuntu22:/apps/src# git clone https://github.com/sch...
root@ubuntu22:/apps/src# cd pymol-open-source/
root@ubuntu22:/apps/src/pymol-open-source# pip install -v...
}}
テスト確認を行ってみたが、「catch2/catch.hpp」が存在しな...
#code(nonumber){{
rm -rf build/
pip install -v --config-settings testing=True --prefix=/a...
(途中でコンパイルエラー)
export PATH=/apps/PyMOL/local/bin:$PATH
export PYTHONPATH=/apps/PyMOL/local/lib/python3.12/dist-p...
pymol -ckqy testing/testing.py --run all
}}
environment-modules
「/apps/modulefiles/PyMOL」
#code(nonumber){{
#%Module1.0
prepend-path PATH /apps/PyMOL/local/bin
prepend-path PYTHONPATH /apps/PyMOL/local/lib/python3.12...
}}
&ref(2025y02m01d_195740885.png,nolink);
もし「&color(red){ERROR: Cannot uninstall numpy 1.26.4, R...
&size(10){ただ、OS提供のパッケージなので影響があるかもし...
***ubuntu22.04 [#ae15f725]
Python 3.10.12
gcc 11.4.0
#code(nonumber){{
apt-get update
apt-get --no-install-recommends install catch2 cmake libf...
python3-biopython python3-dev python3-setuptools python3...
wget -nv https://anaconda.org/schrodinger/collada2gltf/2....
bzip2 -cd collada2gltf-2.1.4-h6bb024c_0.tar.bz2 | tar xf ...
git clone --depth 1 https://github.com/rcsb/mmtf-cpp.git
cp -R mmtf-cpp/include/mmtf* /usr/local/include
pip install --upgrade pip
root@ubuntu22:~# mkdir -p /apps/src ; cd /apps/src
root@ubuntu22:/apps/src# git clone https://github.com/sch...
root@ubuntu22:/apps/src# cd pymol-open-source/
root@ubuntu22:/apps/src/pymol-open-source# pip install -v...
(テスト確認)
rm -rf build/
pip install -v --config-settings testing=True --prefix=/a...
export PATH=/apps/PyMOL/local/bin:$PATH
export PYTHONPATH=/apps/PyMOL/local/lib/python3.10/dist-p...
pymol -ckqy testing/testing.py --run all
}}
environment-modules
「/apps/modulefiles/PyMOL」
#code(nonumber){{
#%Module1.0
prepend-path PATH /apps/PyMOL/local/bin
prepend-path PYTHONPATH /apps/PyMOL/local/lib/python3.10...
}}
&ref(2025y02m01d_053045320.png,nolink);
終了行:
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...
[[https://github.com/schrodinger/pymol-open-source>+https...
&size(10){有償版PyMOLはopen source版よりも機能が強化され...
&size(10){windowsOS向けopen source版は試してないです..};
ver3.1.0になったので改めて作ってみた.
RHEL系はOSに直に作るのは難しいみたい. 直前の3.1.0a0ならい...
ubuntu22はPyMOLのWorkflowに載っているのですんなり行ける. ...
***Rockylinux10 [#y99f7069]
condaでコンパイル環境を作って実行したが「__cxa_call_termi...
恐らくcondaのコンパイル環境の問題っぽいのでOS上に作ってみた
#code(nonumber){{
dnf install epel-release -y
dnf config-manager --enable crb
dnf install xcb-util-wm xcb-util-image xcb-util-keysyms x...
dnf install https://dl.rockylinux.org/pub/rocky/9/devel/x...
dnf --enablerepo=devel install cmake netcdf-devel glew-de...
wget -nv https://anaconda.org/schrodinger/collada2gltf/2....
bzip2 -cd collada2gltf-2.1.4-h6bb024c_0.tar.bz2 | tar xf ...
rm -rf collada2gltf-2.1.4-h6bb024c_0.tar.bz2
git clone --depth 1 https://github.com/rcsb/mmtf-cpp.git
cp -R mmtf-cpp/include/mmtf* /usr/local/include
rm -rf mmtf-cpp
cd /apps/src/
git clone https://github.com/schrodinger/pymol-open-source
cd pymol-open-source/
python3 setup.py install --prefix=/apps/pymol
}}
修正「/apps/pymol/bin/pymol」
#code(nonumber){{
exec "/usr/bin/python3" "/usr/local/lib/python3.12/site-p...
exec "/usr/bin/python3" "/apps/pymol/lib64/python3.12/sit...
}}
/apps/modulefiles/pymol
#code(nonumber){{
#%Module1.0
set root /apps/pymol
prepend-path PATH $root/bin
prepend-path PYTHONPATH $root/lib64/python3.12/site-pack...
}}
***Rockylinux9 [#h332c459]
既定のpythonは3.9 で gcc は gcc-11.5
#code(nonumber){{
(OSパッケージの追加インストールと関連アプリのインストール)
dnf groupinstall "Development Tools" -y
dnf install epel-release -y
dnf install xcb-util-wm xcb-util-image xcb-util-keysyms x...
dnf --enablerepo=devel install cmake netcdf-devel glew-de...
wget -nv https://anaconda.org/schrodinger/collada2gltf/2....
bzip2 -cd collada2gltf-2.1.4-h6bb024c_0.tar.bz2 | tar xf ...
rm -rf collada2gltf-2.1.4-h6bb024c_0.tar.bz2
git clone --depth 1 https://github.com/rcsb/mmtf-cpp.git
cp -R mmtf-cpp/include/mmtf* /usr/local/include
rm -rf mmtf-cpp/
(pyenv-anacondaの敷設)
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install miniforge3-25.3.1-0
}}
#code(nonumber){{
[root@rockylinux9 ~]# source /apps/pyenv/versions/minifor...
[root@rockylinux9 ~]# conda create -n pymol-open-source p...
[root@rockylinux9 ~]# conda activate pymol-open-source
(pymol-open-source) [root@rockylinux9 ~]# cd /apps/src/
(pymol-open-source) [root@rockylinux9 src]# git clone htt...
(pymol-open-source) [root@rockylinux9 src]# cd pymol-open...
(pymol-open-source) [root@rockylinux9 pymol-open-source]#
}}
ここで vtk-m を有効にするためにちょいとソースコードを修正...
#code(diff,nonumber){{
diff --git a/layer0/ContourSurf.cpp b/layer0/ContourSurf....
index 143ce83a..380fcf04 100644
--- a/layer0/ContourSurf.cpp
+++ b/layer0/ContourSurf.cpp
@@ -82,7 +82,7 @@ using ::copysign;
#include <vtkm/Version.h>
#include <vtkm/cont/DataSetBuilderUniform.h>
-#include <vtkm/filter/Contour/Contour.h>
+#include <vtkm/filter/contour/Contour.h>
#include <cassert>
#include <set>
}}
その上で
#code(nonumber){{
(pymol-open-source) [root@rockylinux9 pymol-open-source]#
(pymol-open-source) [root@rockylinux9 pymol-open-source]#...
pip install --prefix=/apps/pymol --config-settings u...
(pymol-open-source) [root@rockylinux9 pymol-open-source]#
}}
EnvironmentModules は下記になる.
「/apps/modulefiles/pymol」
#code(nonumber){{
#%Module1.0
set root /apps/pymol
prepend-path PATH $root/bin
prepend-path PYTHONPATH $root/lib/python3.10/site-packages
}}
&ref(2025y09m16d_040350139.png,nolink);
***Rockylinux8 [#o04b017b]
condaで仮想環境を作りpymolをコンパイルします。
#code(nonumber){{
(OSパッケージの追加インストールと関連アプリのインストール)
dnf groupinstall "Development Tools" -y
dnf install epel-release -y
dnf install xcb-util-wm xcb-util-image xcb-util-keysyms x...
dnf install --enablerepo=epel,devel cmake netcdf-devel gl...
dnf remove glm-devel -y
dnf install https://dl.rockylinux.org/pub/rocky/9/devel/x...
wget -nv https://anaconda.org/schrodinger/collada2gltf/2....
bzip2 -cd collada2gltf-2.1.4-h6bb024c_0.tar.bz2 | tar xf ...
rm -rf collada2gltf-2.1.4-h6bb024c_0.tar.bz2
git clone --depth 1 https://github.com/rcsb/mmtf-cpp.git
cp -R mmtf-cpp/include/mmtf* /usr/local/include
rm -rf mmtf-cpp/
(pyenv-anacondaの敷設)
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install miniforge3-25.3.1-0
}}
#code(nonumber){{
[root@rockylinux8 ~]# source /apps/pyenv/versions/minifor...
[root@rockylinux9 ~]# conda create -n pymol-open-source p...
[root@rockylinux8 ~]# conda activate pymol-open-source
(pymol-open-source) [root@rockylinux8 ~]# cd /apps/src/
(pymol-open-source) [root@rockylinux8 src]# git clone htt...
(pymol-open-source) [root@rockylinux8 src]# cd pymol-open...
(pymol-open-source) [root@rockylinux8 pymol-open-source]#
}}
vtk-m を有効にしたいのですが、ソースコード側でタイポがあ...
#code(nonumber){{
(pymol-open-source) [root@rockylinux8 pymol-open-source]#...
#include <vtkm/filter/Contour/Contour.h>
↓
#include <vtkm/filter/contour/Contour.h>
}}
その上で
#code(nonumber){{
(pymol-open-source) [root@rockylinux8 pymol-open-source]#...
(pymol-open-source) [root@rockylinux8 pymol-open-source]#...
pip install --prefix=/apps/pymol --config-settings u...
(pymol-open-source) [root@rockylinux8 pymol-open-source]#...
[root@rockylinux8 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/python3.10/site-...
}}
これで「module use /apps/modulefiles」「module load pymol...
&ref(2025y10m29d_152254985.png,nolink);
***ubuntu24.04 [#z3365d01]
Python 3.12.3
gcc 13.3.0
#code(nonumber){{
(準備)
apt-get update
apt-get install catch2 cmake libfreetype6-dev libglew-dev...
python3-biopython python3-dev python3-setuptools python3...
wget -nv https://anaconda.org/schrodinger/collada2gltf/2....
bzip2 -cd collada2gltf-2.1.4-h6bb024c_0.tar.bz2 | tar xf ...
git clone --depth 1 https://github.com/rcsb/mmtf-cpp.git
cp -R mmtf-cpp/include/mmtf* /usr/local/include
}}
っで構築
#code(nonumber){{
root@ubuntu22:~# mkdir -p /apps/src ; cd /apps/src
root@ubuntu22:/apps/src# git clone https://github.com/sch...
root@ubuntu22:/apps/src# cd pymol-open-source/
root@ubuntu22:/apps/src/pymol-open-source# pip install -v...
}}
テスト確認を行ってみたが、「catch2/catch.hpp」が存在しな...
#code(nonumber){{
rm -rf build/
pip install -v --config-settings testing=True --prefix=/a...
(途中でコンパイルエラー)
export PATH=/apps/PyMOL/local/bin:$PATH
export PYTHONPATH=/apps/PyMOL/local/lib/python3.12/dist-p...
pymol -ckqy testing/testing.py --run all
}}
environment-modules
「/apps/modulefiles/PyMOL」
#code(nonumber){{
#%Module1.0
prepend-path PATH /apps/PyMOL/local/bin
prepend-path PYTHONPATH /apps/PyMOL/local/lib/python3.12...
}}
&ref(2025y02m01d_195740885.png,nolink);
もし「&color(red){ERROR: Cannot uninstall numpy 1.26.4, R...
&size(10){ただ、OS提供のパッケージなので影響があるかもし...
***ubuntu22.04 [#ae15f725]
Python 3.10.12
gcc 11.4.0
#code(nonumber){{
apt-get update
apt-get --no-install-recommends install catch2 cmake libf...
python3-biopython python3-dev python3-setuptools python3...
wget -nv https://anaconda.org/schrodinger/collada2gltf/2....
bzip2 -cd collada2gltf-2.1.4-h6bb024c_0.tar.bz2 | tar xf ...
git clone --depth 1 https://github.com/rcsb/mmtf-cpp.git
cp -R mmtf-cpp/include/mmtf* /usr/local/include
pip install --upgrade pip
root@ubuntu22:~# mkdir -p /apps/src ; cd /apps/src
root@ubuntu22:/apps/src# git clone https://github.com/sch...
root@ubuntu22:/apps/src# cd pymol-open-source/
root@ubuntu22:/apps/src/pymol-open-source# pip install -v...
(テスト確認)
rm -rf build/
pip install -v --config-settings testing=True --prefix=/a...
export PATH=/apps/PyMOL/local/bin:$PATH
export PYTHONPATH=/apps/PyMOL/local/lib/python3.10/dist-p...
pymol -ckqy testing/testing.py --run all
}}
environment-modules
「/apps/modulefiles/PyMOL」
#code(nonumber){{
#%Module1.0
prepend-path PATH /apps/PyMOL/local/bin
prepend-path PYTHONPATH /apps/PyMOL/local/lib/python3.10...
}}
&ref(2025y02m01d_053045320.png,nolink);
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