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:
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 $(MAKE)... yes
checking whether make supports nested variables... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking whether make supports the include directive... yes (GNU style)
checking for gcc... icc
checking whether the C compiler works... no
configure: error: in `/Open3DQSAR/open3dqsar':
configure: error: C compiler cannot create executables
See `config.log' for more details
prepare file
wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.6.tar.bz2
install manually
apt update && apt upgrade -y
apt install -y build-essential gcc g++ gfortran cmake make wget tar libatlas-base-dev liblapacke-dev libblas-dev git
apt install -y build-essential gcc g++ gfortran cmake make wget tar libatlas-base-dev liblapacke-dev libblas-dev libedit-dev zlib1g-dev openbabel libeigen3-dev
wget http://open3dqsar.org/downloads/editline-3.0.tar.bz2
apt install -y libedit-dev
apt install -y zlib1g-dev
git
git clone https://github.com/UnixJunkie/Open3DQSAR
cd Open3DQSAR/
ls
cd open3dqsar/
apt install -y build-essential cmake libatlas-base-dev
./bootstrap
apt update
apt install -y build-essential automake autoconf libtool
./bootstrap
./configure --with-atlas
make -j$(nproc)
make install
cd test
./test.sh
Open3DGrid 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
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.