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# How to compute CARMSD for many PDB files
# You need a wrapper to your CARMSD computing software.
# If you are using TM-score, you can create a wrapper
# like the following and save it in ~/bin/ca_rmsd
# for example.
--- wrapper file ---
#!/bin/bash
[ "$#" -ne "2" ] && exit 1 || tmscore $1 $2 | awk '/^RMSD/{print $6}'
--- wrapper file ---
# don't forget to enable its use
chmod 755 ~/bin/ca_rmsd
# With such a wrapper, a user can compute many CARMSD by creating a
# file containing all the commands to execute.
# For example, if you are in the same directory than your many PDB files,
# you could issue the following command:
ls | egrep '\.pdb$' | awk '{print ``tmscore ''$1'' 1m6t.pdb''}' > \
compute_RMSDs.sh
# Once this file is created, parallel.py can be called.
# It will use all the cores of your machine and
# kindly refresh a completion percentage while the job is progressing.
parallel.py -v -i compute_RMSDs.sh -o RMSDs.txt