- 10 May, 2022 1 commit
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Vedran Miletić authored
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- 26 Apr, 2022 2 commits
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Vedran Miletić authored
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Patrik Nikolić authored
Partial credit goes to Vedran Miletić <vedran@miletic.net> for cleaning up and fixing the parts of the text.
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- 07 Dec, 2021 1 commit
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Vedran Miletić authored
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- 05 Dec, 2021 1 commit
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Vedran Miletić authored
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- 09 Jun, 2021 1 commit
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Vedran Miletić authored
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- 08 Jun, 2021 1 commit
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Vedran Miletić authored
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- 04 Jun, 2021 1 commit
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Vedran Miletić authored
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- 31 Mar, 2021 1 commit
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Vedran Miletić authored
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- 09 Dec, 2020 1 commit
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Vedran Miletić authored
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- 26 Oct, 2020 2 commits
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Sebastian Jennen authored
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Sebastian Jennen authored
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- 24 Oct, 2020 1 commit
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Sebastian Jennen authored
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- 18 Oct, 2020 2 commits
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Vedran Miletić authored
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Sebastian Jennen authored
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- 15 Sep, 2020 1 commit
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Jon Turney authored
This solves the download issues which started when Eigen finalized the move from Bitbucket to GitLab and removed the old repo on Bitbucket. Eigen 3.3.8 is already out, but it suffers from the compilation issues and can't be used: libeigen/eigen#2011
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- 19 Aug, 2020 1 commit
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Vedran Miletić authored
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- 15 Aug, 2020 1 commit
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Vedran Miletić authored
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- 14 Aug, 2020 1 commit
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Vedran Miletić authored
Added Tabularize command for easy conversion to CSV using CLI. Added Transform command that replaces a number of Perl scripts used for sorting, naming, and filtering with the goal to eventually replace all presently bundled Perl and Python scripts. The public API should be considered work in progress at this point. At the time of the stable release, the public API will support a number of operations and will remain stable over time as the internal program structure continues to change.
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- 12 Aug, 2020 2 commits
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Vedran Miletić authored
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Vedran Miletić authored
Also removed unused headers from Rbt.h and related Config.h.
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- 06 Aug, 2020 5 commits
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Vedran Miletić authored
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Vedran Miletić authored
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Vedran Miletić authored
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Vedran Miletić authored
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Vedran Miletić authored
Headers are now in include/rxdock/, implementations in lib/, executables in tools/, and tests are in tests/ with data in tests/data/.
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- 03 Aug, 2020 1 commit
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Vedran Miletić authored
Removed BaseObject::{Get,Set}Trace functions and TRACE configuration directives from parameter files. Also added wraps for Loguru and {fmt}. Partial credit goes to Luka Vretenar <luka.vretenar@gmail.com> for helping with the grunt work of the conversion.
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- 30 Jul, 2020 1 commit
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Vedran Miletić authored
Also removed obsolete building and installation instructions.
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- 28 Jul, 2020 1 commit
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Vedran Miletić authored
Used nlohmann_json for JSON input and output.
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- 26 Jul, 2020 1 commit
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Vedran Miletić authored
Specifically, chrom, program, ri, and tethered_atoms are now lowercase fields prefixed with rxdock. (e.g. rxdock.ri, rxdock.chrom.0).
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- 25 Jul, 2020 1 commit
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Vedran Miletić authored
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- 24 Jul, 2020 1 commit
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Vedran Miletić authored
Updated data files accordingly and renamed functions and methods as necessary where conflicts occured.
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- 23 Jul, 2020 1 commit
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Vedran Miletić authored
Renamed functions where conflicts occured and added out of class declarations for some operators that were previously declared only as friends in classes to silence GCC warnings and fix MSVC errors. In particular, renamed rxdock::GetVersion() to rxdock::GetProgramVersion() to avoid conflicts with Win32 API function from <sysinfoapi.h> header.
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- 14 Jul, 2020 1 commit
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Vedran Miletić authored
Index variable 'i' in OpenMP 'for' statement in RbtDockingSite must have signed integral type.
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- 13 Jul, 2020 1 commit
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Vedran Miletić authored
In particular, replaced std::unary_function, std::binary_function, and std::ptr_fun with std::function, std::bind2nd with std::bind, and std::mem_fun_ref with std::mem_fn.
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- 02 Jun, 2020 1 commit
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Vedran Miletić authored
That occurence of rDock was wrongly generalized to |Dock| (so it can be rDock or RxDock depending on the value of the replacement text). Thanks to Sergio Ruiz Carmona <Sergio.RuizCarmona@baker.edu.au> for spotting this mistake and reporting it. Also changed one wrong occurence of rDock in the User guide to |Dock|, where we link to download links for RxDock.
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- 01 Jun, 2020 1 commit
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Vedran Miletić authored
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- 24 May, 2020 3 commits
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Sebastian Jennen authored
This yields more performance; in multiple tests I measured about 10-12% speedup using rbcavity.
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Sebastian Jennen authored
The matrices used are self adjoint so the SelfAdjointEigenSolver performs better than the generalized one. In the test performed by the command: rbdock -r 1YET_test.prm -i 1YET_c.sd -p dock.prm -n 2 -s 48151623 -o 1YET_test_out the SelfAdjointEigenSolver saved about 8% of total execution time (measured with the function profiler).
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Sebastian Jennen authored
- default constructors - std::string references - std::move in constructors - auto& and range-based for loops
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