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test.sh
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#!/bin/bash
set -v
export PYTHONPATH=$PYTHONPATH:$(pwd)
cd rna_pdb_tools
python update_readme.py
./rna_pdb_tools_lib.py
./rna_pdb_toolsx.py -h | tee rna_pdb_tools.out
./rna_pdb_toolsx.py -r input/1xjr.pdb
./rna_pdb_toolsx.py --no_hr -c input/1xjr.pdb > output/1xjr_clx.pdb
## --rosetta2generic
./rna_pdb_toolsx.py --no_hr --rosetta2generic input/farna.pdb > output/farna_clx.pdb
## --get_chain
./rna_pdb_toolsx.py --get_chain A input/1xjr.pdb > output/1xjr_A_clx.pdb
## extract
./rna_pdb_toolsx.py --no_hr --extract A:1-2 input/pistol_thrs0.50A_clust99-000001_AA.pdb > output/pistol_thrs0.50A_clust99-000001_AA_A-2.pdb
## --clean
./rna_pdb_toolsx.py --no_hr --clean input/1a9l_NMR_1_2_models.pdb > output/1a9l_NMR_1_2_models_tool.pdb
./rna_pdb_toolsx.py --no_hr --clean input/1xjr_GTP.pdb > output/1xjr_GTP.pdb
./rna_pdb_toolsx.py --no_hr --clean input/1osw.pdb > output/1osw_NMR_1.pdb
## --get_rnapuzzle_ready
./rna_pdb_toolsx.py --no_hr --get_rnapuzzle_ready input/1xjr_onlyGTP.pdb
./rna_pdb_toolsx.py --no_hr --get_rnapuzzle_ready input/1xjr_onlyGTP.pdb > output/1xjr_onlyGTP_rnapuzzle_ready.pdb
./rna_pdb_toolsx.py --no_hr --get_rnapuzzle_ready input/1_das_1_rpr_fixed.pdb > output/1_das_1_rpr_fixed.pdb
./rna_pdb_toolsx.py --no_hr --get_rnapuzzle_ready input/4GXY_3firstNt.pdb
./rna_pdb_toolsx.py --no_hr --get_rnapuzzle_ready input/gtp.pdb > output/gtp.pdb
./rna_pdb_toolsx.py --no_hr --get_rnapuzzle input/377D.pdb # should finish with error
./rna_pdb_toolsx.py --no_hr --get_rnapuzzle_ready input/rp13_Dokholyan_1_URI_CYT_ADE_GUA_hydrogens.pdb > output/rp13_Dokholyan_1_URI_CYT_ADE_GUA_hydrogens_rpr.pdb
./rna_pdb_toolsx.py --no_hr --get_rnapuzzle_ready input/7_Chen_2_rpr.pdb > output/7_Chen_2_rpr.pdb
./rna_pdb_toolsx.py --no_hr --rpr input/7_Chen_7_rpr.pdb > output/7_Chen_7_rpr.pdb
./rna_pdb_toolsx.py --no_hr --get_rnapuzzle input/1I9V_YG_HETATM_ATOM.pdb > output/1I9V_YG_HETATM_ATOM_rpr.pdb
./rna_pdb_toolsx.py --no_hr --get_rnapuzzle --replace_hetatm input/1I9V_A.pdb > output/1I9V_A_rpr.pdb
./rna_pdb_toolsx.py --no_hr --rpr input/A_YG_A.pdb --renumber_residues > output/A_YG_A_renumbered.pdb
./rna_pdb_toolsx.py --no_hr --rpr input/A_YG_A.pdb --renumber_residues > output/A_YG_A_renumbered.pdb
./rna_pdb_toolsx.py --no_hr --rpr input/A_YG_A.pdb > output/A_YG_A_norenumbered.pdb
#./rna_pdb_toolsx.py --no_hr --rpr input/4W90_protein_rna.pdb > output/4W90_protein_rna_onlyRNA.pdb
## --get_rnapuzzle_ready and --dont_rename_chains
rna_pdb_toolsx.py --no_hr --rpr input/1osw_nt1-4_ChainRenamedToBC.pdb > output/1osw_nt1-4_ChainRenamedToBC_toAB.pdb
rna_pdb_toolsx.py --no_hr --rpr --dont_rename_chains input/1osw_nt1-4_ChainRenamedToBC.pdb > output/1osw_nt1-4_ChainRenamedToBC_dontRenameChains.pdb
# --rpr inplace fix
cp input/7_Chen_7_rpr.pdb output/7_Chen_7_rpr_inplacefix.pdb
./rna_pdb_toolsx.py --no_hr --rpr output/7_Chen_7_rpr_inplacefix.pdb --inplace
## --delete
./rna_pdb_toolsx.py --no_hr --delete A:10-60 input/rp17.out.1.pdb > output/rp17_rmA10-60.pdb
./rna_pdb_toolsx.py --no_hr --delete A:10-60 input/rp17.out.1.pdb > output/rp17_rmA10-60.pdb
## --edit
./rna_pdb_toolsx.py --no_hr --edit 'A:6>B:200' input/tetraloop.pdb > output/tetraloop_a6_b200.pdb
./rna_pdb_toolsx.py --no_hr --edit 'A:1-5>B:200-204' input/tetraloop.pdb > output/tetraloop_a1-b200-204.pdb
./rna_pdb_toolsx.py --no_hr --edit 'A:2672>A:1' input/1msy_A2672.pdb > output/1msy_A1.pdb
## --get_seq
./rna_pdb_toolsx.py --get_seq input/5k7c.pdb > output/get_seq.txt
./rna_pdb_toolsx.py --get_seq input/tetraloop.pdb >> output/get_seq.txt
./rna_pdb_toolsx.py --get_seq input/1xjr.pdb > output/1xjr.seq
./rna_pdb_toolsx.py --get_seq input/2_bujnicki_1_rpr.pdb > output/2_bujnicki_1_rpr.txt
./rna_pdb_toolsx.py --get_seq input/2_bujnicki_1_rpr_BA_chain_swap.pdb > output/2_bujnicki_1_rpr_BA_chain_swap.txt
## --replace_hetatm
./rna_pdb_toolsx.py --no_hr --rpr input/A_YG_A.pdb --replace_hetatm > output/A_YG_A.pdb
## --get_ss
./rna_pdb_toolsx.py --get_ss input/1xjr*.pdb > output/secondary_structures.txt
# off for now
#./rna_pdb_seq.py input/1ykq_clx.pdb > output/1ykq_clx.seq
#./rna_pdb_seq.py input/1xjr.pdb > output/1xjr2.seq
#./rna_pdb_seq.py input/5k7c_clean_onechain_renumber_as_puzzle_srr.pdb > output/5k7c_clean_onechain_renumber_as_puzzle_srr.seq
#./rna_pdb_seq.py input/6_solution_0.pdb > output/6_solution_0.seq
./rna_pdb_toolsx.py --get_seq input/1ykq_clx.pdb > output/1ykq_clx.seq
./rna_pdb_toolsx.py --get_seq input/1xjr.pdb > output/1xjr2.seq
./rna_pdb_toolsx.py --get_seq input/5k7c_clean_onechain_renumber_as_puzzle_srr.pdb > output/5k7c_clean_onechain_renumber_as_puzzle_srr.seq
./rna_pdb_toolsx.py --get_seq input/6_solution_0.pdb > output/6_solution_0.seq
## --orgmode
./rna_pdb_toolsx.py --orgmode input/2_das_1_rpr.pdb > output/2_das_1_rpr.org
## --replace-chain
./rna_pdb_toolsx.py --replace-chain output/205d_rmH2o_mutant_A.pdb input/205d_rmH2o.pdb
## --mutate
./rna_pdb_toolsx.py --mutate 'A:1A+2A+3A+4A' input/205d_rmH2o.pdb > output/205d_rmH2o_mutA1234.pdb
cp input/205d_rmH2o.pdb output/205d_rmH2o_mutA1234-B1_inplace.pdb
./rna_pdb_toolsx.py --mutate 'A:1A+2A+3A+4A,B:13A' --inplace output/205d_rmH2o.pdb
./rna_pdb_toolsx.py --mutate 'A:1A+2A+3A+4A,B:13A' input/205d_rmH2o.pdb > output/205d_rmH2o_mutA1234-B1.pdb
## --is_pdb
./rna_pdb_toolsx.py --is_pdb input/1I9V_A.pdb
./rna_pdb_toolsx.py --is_pdb input/image.png
./rna_pdb_toolsx.py --is_pdb input/image.png.zip
## --renumber_residues
./rna_pdb_toolsx.py --no_hr --renumber_residues input/rp03_solution.pdb > output/rp03_solution_renumber.pdb
./BlastPDB.py
if [ "$1" == "--full" ]; then
./RfamSearch.py
fi
./Seq.py
if [ "$1" == "--full" ]; then
./SecondaryStructure.py
fi
# ClashCalc
cd ./utils/ClashCalc/
./ClashCalc.py
cd ../..
cd ./utils/rna_calc_rmsd/
./test.sh
cd ../..
cd ./utils/rnashape2ascii/
./test.sh
cd ../..
cd ./utils/rna_pdb_edit_occupancy_bfactor
./test.sh
cd ../..
cd ./utils/rna_filter/
./test.sh
cd ../..
cd ./utils/renum_pdb_to_aln/
./test.sh
cd ../..
if [ "$1" == "--full" ]; then
cd ./utils/rna_refinement/
./test.sh
cd ../..
fi
if [ "$1" == "--full" ]; then
cd ..
codecov --token=e78310dd-7a28-4837-98ef-c93533a84c5b
fi