rna_calc_rmsd_pymol.py: test.sh, explore this

Author: mmagnus

rna_tools/tools/rna_calc_rmsd/rna_calc_rmsd_pymol.py

@@ -1,8 +1,5 @@
-#!/Applications/PyMOL3.app/Contents/bin/python3
 #-*- coding: utf-8 -*-
-
 """rna_calc_rmsd_pymol.py - calculate RMSDs of structures with PyMOL
-
 """
 from __future__ import print_function
 

rna_tools/tools/rna_calc_rmsd/test.sh

@@ -1,32 +1,10 @@
-set -x
-
-./rna_calc_rmsd_biopython.py -t test_data/2nd_triplex_FB_1AUA3_rpr.pdb test_data/triples/*.pdb --ignore-files CGA --way backbone+sugar > test_output/2nd_triplex_FB_CBA_ignore_files_CGA.csv
-
-./rna_calc_rmsd_biopython.py -t test_data/2nd_triplex_FB_1AUA3_rpr.pdb test_data/triples/*.pdb --way=backbone+sugar \
-			     > test_output/2nd_triplex_FB_CBA_ignore_files_CGA.csv
-
-./rna_calc_rmsd_biopython.py -t test_data/2nd_triplex_FB_1AUA3_rpr.pdb test_data/triples/*.pdb --save --way=backbone+sugar \
-			     > test_output/2nd_triplex_FB_CBA_ignore_files_CGA.csv
-
-./rna_calc_rmsd_biopython.py -t test_data/2nd_triplex_FB_1AUA3_rpr.pdb  test_data/triples/*.pdb --save --suffix 'alignedXXX' --way=backbone+sugar \
-			     > test_output/2nd_triplex_FB_CBA_ignore_files_CGA.csv
-
-# ./rna_calc_rmsd_biopython.py -t test_data/triples/2nd_triplex_FB_1AUA3_rpr.pdb test_data/triples/Triple_cWW_tSH_GCA_exemplar_rpr_ren.pdb  --way backbone+sugar --save --column-name 'AAAA' --triple-mode > test_output/2nd_triplex_FB_1AUA3_rpr_Triple_cWW_tSH_GCA_exemplar_rpr_ren_way_backbone+sugar_save_column-name_AAAA_triple-mode.txt
-
-# ./rna_calc_rmsd.py --model-selection='A:52+53+59+60+61+80+B:21+22+23' --target-selection='A:52+53+59+60+61+80+B:21+22+23' -t test_data/ways/yC_5LJ3_U2U6_core_mdrFx_onlyTriplex_rpr.pdb test_data/ways/*fixChains.pdb -pr --way c1p -o test_data/ways/rmsd_c1p.csv
-
-# ./rna_calc_rmsd.py --model-selection='A:52+53+59+60+61+80+B:21+22+23' --target-selection='A:52+53+59+60+61+80+B:21+22+23' -t test_data/ways/yC_5LJ3_U2U6_core_mdrFx_onlyTriplex_rpr.pdb test_data/ways/*fixChains.pdb -pr --way bases -o test_data/ways/rmsd_bases.csv
-
-# ./rna_calc_rmsd.py --model-selection='A:52+53+59+60+61+80+B:21+22+23' --target-selection='A:52+53+59+60+61+80+B:21+22+23' -t test_data/ways/yC_5LJ3_U2U6_core_mdrFx_onlyTriplex_rpr.pdb test_data/ways/*fixChains.pdb -pr --way all -o test_data/ways/rmsd_all.csv
-
-# ./rna_calc_rmsd.py --model-selection='A:52+53+59+60+61+80+B:21+22+23' --target-selection='A:52+53+59+60+61+80+B:21+22+23' -t test_data/ways/yC_5LJ3_U2U6_core_mdrFx_onlyTriplex_rpr.pdb test_data/ways/*fixChains.pdb -pr -sr -o test_data/ways/rmsd_all.csv
-
-# ./rna_calc_rmsd.py --model-selection='A:52+53+59+60+61+80+B:21+22+23' --target-selection='A:52+53+59+60+61+80+B:21+22+23' -t test_data/ways/yC_5LJ3_U2U6_core_mdrFx_onlyTriplex_rpr.pdb test_data/ways/*fixChains.pdb -pr --way backbone+sugar -o test_data/ways/backbone+sugar.csv
-
-./rna_calc_rmsd.py -t test_data/pistol/5k7c_clean_onechain_renumber_as_puzzle_srr.pdb --target-selection A:1-47+52-62 --model-selection A:1-47+52-62 --model-ignore-selection A/57/O2\'+A/58/O2\' test_data/pistol/clusters/*.pdb test_data/pistol/clusters/pistol_thrs0.50A_clust01-000001_AA.pdb --target-column-name -o test_output/pistol_rmsd.csv
-
-./rna_calc_rmsd.py -t test_data/pistol/5k7c_clean_onechain_renumber_as_puzzle_srr.pdb --target-selection A:1-47+52-62 --model-selection A:1-47+52-62 --model-ignore-selection A/57/O2\'+A/58/O2\' test_data/pistol/clusters/*.pdb test_data/pistol/clusters/pistol_thrs0.50A_clust01-000001_AA.pdb --name-rmsd-column RMSDtoPistol -o test_output/pistol_rmsd_name-rmsd-column.csv
-
-# error ;-) fixed with the next line
-##./rna_calc_rmsd_multi_targets.py --models test_data/multi-targets/rp21/*.pdb --targets test_data/multi-targets/rp21/solutions/*.pdb
-#./rna_calc_rmsd_multi_targets.py --models test_data/multi-targets/rp21/*.pdb --targets test_data/multi-targets/rp21/solutions/*.pdb --target-selection A:1-27+29-41 --model-selection A:1-27+29-41
+#pymol -cq rna_calc_rmsd.py -- args /Users/magnus/Desktop/rmsd-all-vs-all/6qn3_A.cif  /Users/magnus/Desktop/rmsd-all-vs-all/5mqf_Z.cif
+
+#./rna_calc_rmsd.py -m align -t /Users/magnus/Desktop/rmsd-all-vs-all/6qn3_A.cif  /Users/magnus/Desktop/rmsd-all-vs-all/5mqf_Z.cif
+/Applications/PyMOL3.app/Contents/bin/python3 rna_calc_rmsd_pymol.py -m align -t /Users/magnus/Desktop/rmsd-all-vs-all/6qn3_A.cif  /Users/magnus/Desktop/rmsd-all-vs-all/5mqf_Z.cif
+cat rmsds.csv
+#
+#set -x
+#
+#p=../../input/comparison
+#./rna_calc_rmsd.py -t $p/4GXY_min.pdb $p/4GXY_min_reconstruction.pdb