rcedgar / reseek Goto Github PK
View Code? Open in Web Editor NEWProtein structure alignment and search algorithm
License: GNU General Public License v3.0
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reseek's Issues
problems/warnings with compilation under MacOS
After some modifications, reseek can be successfully compiled for macOS
major issue: original makefile is not working on MacOs.
clang report flag -fopenmp is not supported.
useful information on:
https://mac.r-project.org/openmp/
during compilation many annoying warnings about using unsafe sprintf , can be easily removed if replace to snprintf.
reseek … redock
just curious: what do you think about idea, using the same mega-alphabet implement fast searching procedure which allow identify best candidates for docking. 3di clearly not suitable for this task.
in a huge pile of locks(alphafold,esmatlas), find those to which the key(query structure) potentially can fit.
Looking on combined distance matrix for two docked proteins I have suspicions it can be done.
As I understand your structural descriptors intrinsically provide structure some flexibility.
algorithm can be trained on existing complexes.
License file
Can you specify what license it's released under?
fatal error: gitver.txt: No such file or directory
Hi, trying to install reseek on Ubuntu 20.04. Ran
cd src/
make
Got the error:
ccache g++ -DNDEBUG -pthread -O3 -fopenmp -ffast-math -msse -mfpmath=sse -c -o o/fileseqsource.o fileseqsource.cpp
ccache g++ -DNDEBUG -pthread -O3 -fopenmp -ffast-math -msse -mfpmath=sse -c -o o/getss.o getss.cpp
ccache g++ -DNDEBUG -pthread -O3 -fopenmp -ffast-math -msse -mfpmath=sse -c -o o/sscluster.o sscluster.cpp
ccache g++ -DNDEBUG -pthread -O3 -fopenmp -ffast-math -msse -mfpmath=sse -c -o o/trainer.o trainer.cpp
ccache g++ -DNDEBUG -pthread -O3 -fopenmp -ffast-math -msse -mfpmath=sse -c -o o/usage.o usage.cpp
ccache g++ -DNDEBUG -pthread -O3 -fopenmp -ffast-math -msse -mfpmath=sse -c -o o/linereader.o linereader.cpp
ccache g++ -DNDEBUG -pthread -O3 -fopenmp -ffast-math -msse -mfpmath=sse -c -o o/lockobj.o lockobj.cpp
ccache g++ -DNDEBUG -pthread -O3 -fopenmp -ffast-math -msse -mfpmath=sse -c -o o/mx.o mx.cpp
ccache g++ -DNDEBUG -pthread -O3 -fopenmp -ffast-math -msse -mfpmath=sse -c -o o/myutils.o myutils.cpp
myutils.cpp:1957:10: fatal error: gitver.txt: No such file or directory
1957 | #include "gitver.txt"
| ^~~~~~~~~~~~
compilation terminated.
make: *** [Makefile:177: o/myutils.o] Error 1
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