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added test2/ for testing updated foldx script

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Tanushree Tunstall 2021-02-10 10:16:28 +00:00
parent c8feba90bc
commit 3280cdb2a1
6 changed files with 240045 additions and 0 deletions
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239965
foldx/test2/rotabase.txt Normal file
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foldx/test2/test2_output/gid_foldx.csv Normal file
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mutationinformation,ddg,contacts,electro_rr,electro_mm,electro_sm,electro_ss,disulfide_rr,disulfide_mm,disulfide_sm,disulfide_ss,hbonds_rr,hbonds_mm,hbonds_sm,hbonds_ss,partcov_rr,partcov_mm,partcov_sm,partcov_ss,vdwclashes_rr,vdwclashes_mm,vdwclashes_sm,vdwclashes_ss,volumetric_rr,volumetric_mm,volumetric_sm,volumetric_ss
S2C,0.30861700000000003,-2.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,2.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,-1.0,-1.0,0.0,0.0
S2F,-0.6481899999999999,-8.0,-4.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,2.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,-1.0,-1.0,0.0,0.0
1 mutationinformation ddg contacts electro_rr electro_mm electro_sm electro_ss disulfide_rr disulfide_mm disulfide_sm disulfide_ss hbonds_rr hbonds_mm hbonds_sm hbonds_ss partcov_rr partcov_mm partcov_sm partcov_ss vdwclashes_rr vdwclashes_mm vdwclashes_sm vdwclashes_ss volumetric_rr volumetric_mm volumetric_sm volumetric_ss
2 S2C 0.30861700000000003 -2.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 2.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 -1.0 -1.0 0.0 0.0
3 S2F -0.6481899999999999 -8.0 -4.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 2.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 -1.0 -1.0 0.0 0.0

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foldx/test2/test2_output/pnca_foldx.csv Normal file
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mutationinformation,ddg,contacts,electro_rr,electro_mm,electro_sm,electro_ss,disulfide_rr,disulfide_mm,disulfide_sm,disulfide_ss,hbonds_rr,hbonds_mm,hbonds_sm,hbonds_ss,partcov_rr,partcov_mm,partcov_sm,partcov_ss,vdwclashes_rr,vdwclashes_mm,vdwclashes_sm,vdwclashes_ss,volumetric_rr,volumetric_mm,volumetric_sm,volumetric_ss
L4S,5.7629,22.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,6.0,0.0,0.0,4.0
L159R,1.66524,-56.0,-26.0,0.0,-2.0,-24.0,0.0,0.0,0.0,0.0,-2.0,0.0,-2.0,0.0,0.0,0.0,0.0,0.0,-1.0,0.0,0.0,-1.0,-4.0,0.0,-4.0,0.0
1 mutationinformation ddg contacts electro_rr electro_mm electro_sm electro_ss disulfide_rr disulfide_mm disulfide_sm disulfide_ss hbonds_rr hbonds_mm hbonds_sm hbonds_ss partcov_rr partcov_mm partcov_sm partcov_ss vdwclashes_rr vdwclashes_mm vdwclashes_sm vdwclashes_ss volumetric_rr volumetric_mm volumetric_sm volumetric_ss
2 L4S 5.7629 22.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 6.0 0.0 0.0 4.0
3 L159R 1.66524 -56.0 -26.0 0.0 -2.0 -24.0 0.0 0.0 0.0 0.0 -2.0 0.0 -2.0 0.0 0.0 0.0 0.0 0.0 -1.0 0.0 0.0 -1.0 -4.0 0.0 -4.0 0.0

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foldx/test2/testing_foldx_cmds Normal file
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./runFoldx_test2.py -g pncA --datadir /home/tanu/git/LSHTM_analysis/foldx/test2 -i /home/tanu/git/LSHTM_analysis/foldx/test2 -o /home/tanu/git/LSHTM_analysis/foldx/test2/test2_output -p /home/tanu/git/LSHTM_analysis/foldx/test2/test2_process -pdb 3pl1.pdb -m pnca_muts_sample.csv -c1 A
============
# Example 1: pnca
# Delete processing output, copy rotabase.txt and individual_list_3pl1.txt in place, run a test
============
#
clear; rm -rf test2_process/*; cp individual_list_3pl1.txt test2_process/ ; cp rotabase.txt test2_process/; ./runFoldx_test2.py -g pncA --datadir /home/tanu/git/LSHTM_analysis/foldx/test2 -i /home/tanu/git/LSHTM_analysis/foldx/test2 -o /home/tanu/git/LSHTM_analysis/foldx/test2/test2_output -p ./test2_process -pdb 3pl1.pdb -m /tmp/pnca_muts_sample.csv -c1 A
============
# Example 2: gidb
============
clear
rm Unrecognized_molecules.txt
rm -rf test2_process/*
cp rotabase.txt test2_process/
./runFoldx.py \
-g gid \
--datadir /home/tanu/git/LSHTM_analysis/foldx/test2 \
-i /home/tanu/git/LSHTM_analysis/foldx/test2 \
-o /home/tanu/git/LSHTM_analysis/foldx/test2/test2_output \
-p ./test2_process \
-pdb gid_test2.pdb \
-m gid_test_snps.csv \
-c1 A