rcedgar / reseek Goto Github PK
View Code? Open in Web Editor NEWProtein structure alignment and search algorithm
License: GNU General Public License v3.0
Protein structure alignment and search algorithm
License: GNU General Public License v3.0
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.
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.
Can you specify what license it's released under?
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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