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