一次性添加

docker/README.md

@@ -0,0 +1,134 @@
+
+```shell
+wget https://registrationcenter-download.intel.com/akdlm/IRC_NAS/dfc4a434-838c-4450-a6fe-2fa903b75aa7/intel-oneapi-base-toolkit-2025.0.1.46_offline.sh
+sh ./intel-oneapi-base-toolkit-2025.0.1.46_offline.sh -a --silent --cli --eula accept
+./configure CC=icc --with-intel-mkl && make && make install
+```
+
+error:
+```shell
+root@efb88430e4ba:/Open3DQSAR/open3dqsar# ./configure CC=icc --with-intel-mkl
+checking for a BSD-compatible install... /usr/bin/install -c
+checking whether build environment is sane... yes
+checking for a race-free mkdir -p... /usr/bin/mkdir -p
+checking for gawk... no
+checking for mawk... mawk
+checking whether make sets $(MAKE)... yes
+checking whether make supports nested variables... yes
+checking build system type... x86_64-pc-linux-gnu
+checking host system type... x86_64-pc-linux-gnu
+checking whether make supports the include directive... yes (GNU style)
+checking for gcc... icc
+checking whether the C compiler works... no
+configure: error: in `/Open3DQSAR/open3dqsar':
+configure: error: C compiler cannot create executables
+See `config.log' for more details
+```
+
+## prepare file
+
+```shell
+wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.6.tar.bz2
+```
+
+## install manually
+
+```shell
+apt update && apt upgrade -y
+apt install -y build-essential gcc g++ gfortran cmake make wget tar                libatlas-base-dev liblapacke-dev libblas-dev git
+apt install -y build-essential gcc g++ gfortran cmake make wget tar                libatlas-base-dev liblapacke-dev libblas-dev libedit-dev zlib1g-dev                openbabel libeigen3-dev
+wget http://open3dqsar.org/downloads/editline-3.0.tar.bz2
+apt install -y libedit-dev
+apt install -y zlib1g-dev
+git
+git clone https://github.com/UnixJunkie/Open3DQSAR
+cd Open3DQSAR/
+ls
+cd open3dqsar/
+apt install -y build-essential cmake libatlas-base-dev
+./bootstrap
+apt update
+apt install -y build-essential automake autoconf libtool
+./bootstrap
+./configure --with-atlas
+make -j$(nproc)
+make install
+cd test
+./test.sh
+```
+
+## [Open3DGrid](https://opensourcemolecularmodeling.github.io) download and install
+
+Open3DGrid and Open3DQSAR are a suite of related tools that build 3D QSAR models. Open3DGrid generates molecular interaction fields (MIFs) in a variety of formats, and Open3DQSAR builds predictive models from the MIFs of aligned molecules. Calculations can be visualized in real time in PyMOL.
+
+Open3DGRID
+----------
+
+An open-source software aimed at high-throughput
+generation of molecular interaction fields (MIFs)
+
+Paolo Tosco (a,*), Thomas Balle (b)
+
+a) Department of Drug Science and Technology,
+   University of Turin, via Pietro Giuria 9, 10125 Torino, Italy;
+   e-mail: paolo.tosco@unito.it
+
+b) Department of Medicinal Chemistry,
+   The Faculty of Pharmaceutical Sciences, University of Copenhagen,
+   2 Universitetsparken, 2100 Copenhagen, Denmark
+
+http://open3dgrid.org
+
+
+
+
+Open3DGRID is an open-source software aimed at high-throughput generation
+of molecular interaction fields (MIFs). Open3DGRID can generate steric
+potential, electron density and MM/QM electrostatic potential fields;
+furthermore, it can import GRIDKONT binary files produced by GRID and
+CoMFA/CoMSIA fields (exported from SYBYL with the aid of a small SPL
+script).
+
+High computational performance is attained through implementation of
+parallelized algorithms for MIF generation.
+
+Most prominent features in Open3DGRID include:
+
+    * Seamless integration with OpenBabel, PyMOL, GAUSSIAN, FIREFLY,
+    GAMESS-US, MOLDEN, Molecular Discovery GRID
+
+    * Multi-threaded computation of MIFs (both MM and QM); support for
+    MMFF94 and GAFF force-fields with automated assignment of atom types
+    to the imported molecular structures
+
+    * Human and machine-readable text output, integrated with 3D maps
+    in several formats to allow visualization of results in PyMOL, MOE,
+    Maestro and SYBYL
+
+    * User-friendly interface to all major QM packages (e.g. GAUSSIAN,
+    FIREFLY, GAMESS-US, MOLDEN), allows calculation of QM electron
+    density and electrostatic potential 3D maps from within Open3DGRID
+
+    * User-friendly interface to Molecular Discovery GRID to compute
+    GRID MIFs from within Open3DGRID
+
+
+Open3DGRID is controlled through a command line interface; commands can
+be either entered interactively from a command prompt or read from a
+batch script. If PyMOL is installed on the system while Open3DGRID is
+being operated interactively, the setup of 3D grid computations can be
+followed in real time on PyMOL's viewport, allowing to tweak grid size and
+training/test set composition very easily.  The main output is arranged
+as human-readable plain ASCII text, while a number of additional files
+are generated to store data and to export the results of computations for
+further analysis and visualization with third party tools. In particular,
+Open3DGRID can export 3D maps for visualization in PyMOL, MOE, Maestro
+and SYBYL.
+
+Open3DGRID is written in C; while pre-built binaries are available for
+mainstream operating systems (Windows 32/64-bit, Linux 32/64-bit, Solaris
+x86 32/64-bit, FreeBSD 32/64-bit, Intel Mac OS X 32/64-bit), source
+code is portable and can be compiled under any platform supporting POSIX
+threads. The modular nature of the code allows for easy implementation
+of new features, so that the core application can be customized to meet
+individual needs.