TM-align_mass

TM-align https://zhanggroup.org/TM-align/ for large dbs.

Main differences with the original TM-align:

• Check alignment state in one more previous step in TMscore8_search(_standard) function.
• Force one of the NWDP_TM function to be inline.
• Added binary file mode.
• Support gzip-ed file.

Anyway, I expect that result is completely the same with that of the original TM-align.

The above modifications reduced processing time just 8% or so, therefore, you can use the original version with this small loss of processing time.

Compile:

clone https://github.com/yamule/TM-align_mass.git
cd TM-align_mass
mkdir bin
g++ -static -O3 -ffast-math -lm -o bin/TMalign_mass.exe TMalign_mass.cpp -lz

An example usage:

mkdir UP000000625_83333_ECOLI
cd UP000000625_83333_ECOLI
wget https://ftp.ebi.ac.uk/pub/databases/alphafold/UP000000625_83333_ECOLI.tar
tar xvf UP000000625_83333_ECOLI.tar
gunzip *.pdb.gz
ls *.pdb > pdblist.dat
cd ..
bin/TMalign_mass.exe UP000000625_83333_ECOLI/AF-P36677-F1-model_v1.pdb -dir2 UP000000625_83333_ECOLI/ UP000000625_83333_ECOLI/pdblist.dat

Perform multi-processing:

(You have to be in the directory of this repo & finished "An example usage" except for the last line.)

find UP000000625_83333_ECOLI | grep -E "\.pdb$" | xargs -I {} bin/TMalign_mass.exe {} -bin_convert {}.bxyz 
ls UP000000625_83333_ECOLI | grep -E "\.pdb.bxyz$"  > UP000000625_83333_ECOLI/pdblist_binary.dat
perl scripts/multi_process.pl --query UP000000625_83333_ECOLI/AF-P36677-F1-model_v1.pdb --dir UP000000625_83333_ECOLI/ --list UP000000625_83333_ECOLI/pdblist_binary.dat --num_threads 6 --tmscore_threshold 0.5 

References to cite:

• TM-align
  Y Zhang, J Skolnick. Nucl Acids Res 33, 2302-9 (2005) https://academic.oup.com/nar/article/33/7/2302/2401364

• This repo
  https://github.com/yamule/TM-align_mass

License:

• TM-align
  Please follow the comment in the head of the source code.
• Scripts under the scripts/ dir
  Apache License, Version 2.0 http://www.apache.org/licenses/LICENSE-2.0.html