🔧rna-pdb-tools

(under heavy development)

Magnus, Marcin. (2016). rna-pdb-tools. Zenodo. 10.5281/zenodo.60933

If you find the tools helpful, you can cite the repo using the DOI above :-)

A library and a program to run various Python functions related to work with PDB files of RNA structures.

The software is used by me in my servers NPDock (RNA/DNA-protein docking method, http://genesilico.pl/NPDock/) and SimRNAweb (RNA 3D structure prediction method, http://iimcb.genesilico.pl/SimRNAweb/) and mqapRNA (RNA 3D quality control, http://iimcb.genesilico.pl/mqapRNA/, in progress)

What is fun here?

you see input & output -- this is what you want to get?
it's tested via Travis! -- it (should) always works as you just want!
you lack a converter you would like to have one? Just Do It Yourself - compose your converter/parser from LEGO brick-like functions, see for example --rosetta2generic)

.. or you might want to use the lib in the program.

Take a tour http://mmagnus.github.io/rna-pdb-tools/#/ and/or read the doc rna-pdb-tools.rtfd.io/en/latest/.

Tour

Take a tour http://mmagnus.github.io/rna-pdb-tools/#/

Docs

Read the documentations at rna-pdb-tools.rtfd.io/en/latest/.

RNA Puzzle Submission

Prepare your structures in the folder and run to get them RNApuzzle ready (_rpr):

$ for i in `ls *.pdb`; do rna-pdb-tools.py --get_rnapuzzle_ready $i > ${i/.pdb/_rpr.pdb}; done

.. merge them as one file in the order as you like (or use *):

$ rna-pdb-merge-into-one.py 02_19pz_v1_SimRNA3.22_thrs6.60A_clust02-000001_AA_out_rpr.pdb 09_19pz_v2_SimRNA3.22_thrs6.60A_clust03-000001_AA_out_rpr.pdb d311d821-a075-4df0-bd7d-1dcf7669dad9_ALL_thrs6.20A_clust01-000001_AA_out_rpr.pdb d311d821-a075-4df0-bd7d-1dcf7669dad9_ALL_thrs6.20A_clust03-000001_AA_out_rpr.pdb 05_19pz_v1_SimRNA4.xx_thrs6.60A_clust02-000001_AA_out_rpr.pdb  > rp19_bujnicki.pdb

and verify your file with the template provided by the organizers:

$ diffpdb --method diff Reference_19.pdb rp19_bujnicki.pdb
#<empty = no difference but xyz columns, OK!>

diffpdb is a part of the rna-pdb-tools package.

$ head -n 5 Reference_19.pdb rp19_bujnicki.pdb
==> Reference_19.pdb <==
MODEL        1
ATOM      1  P     G A   1       0.000   0.000   0.000  1.00  0.00           P
ATOM      2  OP1   G A   1       0.000   0.000   0.000  1.00  0.00           O
ATOM      3  OP2   G A   1       0.000   0.000   0.000  1.00  0.00           O
ATOM      4  O5'   G A   1       0.000   0.000   0.000  1.00  0.00           O
==> rp19_bujnicki.pdb <==
MODEL        1
ATOM      1  P     G A   1      31.463  14.180  -0.676  1.00  0.00           P
ATOM      2  OP1   G A   1      31.412  12.806  -1.223  1.00  0.00           O
ATOM      3  OP2   G A   1      30.646  15.083  -1.517  1.00  0.00           O
ATOM      4  O5'   G A   1      30.955  14.212   0.842  1.00  0.00           O

$ tail -n 5 Reference_19.pdb rp19_bujnicki.pdb
==> Reference_19.pdb <==
ATOM   1325  C5    C B  22       0.000   0.000   0.000  1.00  0.00           C
ATOM   1326  C6    C B  22       0.000   0.000   0.000  1.00  0.00           C
TER    1327        C B  22
ENDMDL
END
==> rp19_bujnicki.pdb <==
ATOM   1325  C5    C B  22      29.927  21.506  -6.542  1.00  0.00           C
ATOM   1326  C6    C B  22      29.822  22.338  -5.500  1.00  0.00           C
TER    1327        C B  22
ENDMDL
END

Tricks

$ for i in *; do echo $i; rna-pdb-tools.py --delete A:48-52 $i > noloop/${i/.pdb/_noloop.pdb}; done
10_rp17c.out.14.pdb
10_rp17c.out.14_out.pdb
[..]

$ for i in `ls *.pdb`; do rna-pdb-tools.py --c $i > ${i/.pdb/_clx.pdb}; done

$ for i in `ls *.pdb`; do rna-pdb-tools.py --get_rnapuzzle_ready $i > ${i/.pdb/_rpr.pdb}; done

.. keep original structures in original and use rpr:

➜  bujnicki_server_ss for i in `ls original/*.pdb`; do rna-pdb-tools.py --get_rnapuzzle_ready $i > ${i/.pdb/_rpr.pdb}; done
➜  bujnicki_server_ss ls
17pz_withSS_all_thrs6.00A_clust01-000001_AA_rpr.pdb 17pz_withSS_all_thrs6.00A_clust06-000001_AA_rpr.pdb
17pz_withSS_all_thrs6.00A_clust02-000001_AA_rpr.pdb 17pz_withSS_all_thrs6.00A_clust07-000001_AA_rpr.pdb
17pz_withSS_all_thrs6.00A_clust03-000001_AA_rpr.pdb 17pz_withSS_all_thrs6.00A_clust08-000001_AA_rpr.pdb
17pz_withSS_all_thrs6.00A_clust04-000001_AA_rpr.pdb 17pz_withSS_all_thrs6.00A_clust09-000001_AA_rpr.pdb
17pz_withSS_all_thrs6.00A_clust05-000001_AA_rpr.pdb original

.. or to get SimRNAready structures:

$ for i in `ls *pdb`; do rna-pdb-tools.py --get_simrna_ready $i >  ${i/.pdb/_srr.pdb}; done

Main program

rna-pdb-tools.py -h
usage: rna-pdb-tools.py ver: 37c5b4e-dirty [-h] [-r] [-c]
                                           [--get_chain GET_CHAIN] [--get_seq]
                                           [--rosetta2generic]
                                           [--get_rnapuzzle_ready] [--no_hr]
                                           [--renumber_residues]
                                           [--get_simrna_ready] [--edit EDIT]
                                           [--delete DELETE]
                                           file

positional arguments:
  file                  file

optional arguments:
  -h, --help            show this help message and exit
  -r, --report          get report
  -c, --clean           get clean structure
  --get_chain GET_CHAIN
                        get chain, .e.g A
  --get_seq             get seq
  --rosetta2generic     convert ROSETTA-like format to a generic pdb
  --get_rnapuzzle_ready
                        get RNApuzzle ready (keep only standard atoms,
                        renumber residues)
  --no_hr               do not insert the header into files
  --renumber_residues
  --get_simrna_ready
  --edit EDIT           edit 'A:6>B:200', 'A:2-7>B:2-7'
  --delete DELETE       delete the selected fragment, e.g. A:10-16

Utils

See Utils for simple but useful rna pdb tools.

diffpdb

diffpdb - a simple tool to compare text-content of PDB files

rmsd_calc

rna_calc_rmsd - various ways how to calc rmsd.

rna_convert_pseudoknot_formats

misc

rnashape2ascii ▅▄▆▄▂▁▁▁▁▁▁▁▁▁▁▂▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▂▅▇▅▄▃▂▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▂▂▁▁▁▁▁▁▁▁▁▁

Inspiration (and alternatives):

Features

get RNA seq
get chain
get only first model
remove RNA modifications (from seq and output file) (at least, GTP)

find missing atoms and report them (--get_rnapuzzle) if atoms are missing you get the info

  ➜  rna-pdb-tools git:(master) ✗ ./rna-pdb-tools.py --get_rnapuzzle_ready input/1xjr_missing_atom.pdb
  HEADER Generated with rna-pdb-tools
  HEADER ver c54c2ca-dirty
  HEADER https://github.com/mmagnus/rna-pdb-tools
  HEADER Mon Aug 22 18:37:00 2016
  REMARK 000 Missing atoms:
  REMARK 000  + C8 A <Residue G het=  resseq=2 icode= > residue # 2
  ATOM      1  P     G A   1      72.825  38.053  40.710  1.00 93.61           P
  ATOM      2  OP1   G A   1      74.267  37.687  40.422  1.00 92.76           O
  ATOM      3  OP2   G A   1      72.042  36.929  41.364  1.00 93.84           O

remove H3T atom:

  Wrong middle line:  ATOM    279  H3T  RG A  13      31.479  26.388  41.463  1.00  0.00 H3T
      Wrong middle line:  ATOM    514  H3T RC3 B  24       7.142  23.044  10.287  1.00  0.00 H3T
      [          ]   1 0.04 % 2746 decoy3308.pdb                                           -0.1      -1.0     29.17    -67.13 104916.67     12.74     10.28      -0.0     28.28

add version of the tool (based on https://github.com/mmagnus/curr_version )
add a header to pdb file with version of the program (and add --no_hr option if you don't like the header :-)

.. get report on missing atoms and fixes:

➜  rna-pdb-tools git:(master) ✗ ./rna-pdb-tools.py --no_hr --get_simrna_ready input/1xjr_no_op3.pdb
ATOM      1  P     G A   1      71.654  38.099  39.901  1.00 11.89           P
ATOM      2  OP1   G A   1      70.650  37.330  40.676  1.00 14.35           O
ATOM      3  OP2   G A   1      71.684  38.022  38.432  1.00 12.68           O
ATOM      4  O5'   G A   1      71.581  39.644  40.259  1.00 10.34           O
ATOM      5  C5'   G A   1      71.461  40.065  41.599  1.00 84.73           C
ATOM      6  C4'   G A   1      71.633  41.579  41.677  1.00 79.18           C
ATOM      7  O4'   G A   1      72.883  42.002  41.159  1.00 77.89           O
ATOM      8  C3'   G A   1      70.593  42.265  40.817  1.00 76.34           C
ATOM      9  O3'   G A   1      69.396  42.552  41.496  1.00 73.29           O
ATOM     10  C2'   G A   1      71.299  43.523  40.389  1.00 75.44           C
ATOM     11  O2'   G A   1      71.216  44.501  41.398  1.00 74.42           O
ATOM     12  C1'   G A   1      72.736  43.064  40.223  1.00 74.81           C
ATOM     13  N9    G A   1      72.976  42.656  38.801  1.00 74.23           N
ATOM     14  C8    G A   1      73.267  41.400  38.317  1.00 73.69           C
ATOM     15  N7    G A   1      73.414  41.450  36.965  1.00 72.93           N
ATOM     16  C5    G A   1      73.208  42.724  36.560  1.00 73.22           C
ATOM     17  C6    G A   1      73.225  43.337  35.306  1.00 73.35           C
ATOM     18  O6    G A   1      73.467  42.698  34.278  1.00 73.29           O
ATOM     19  N1    G A   1      72.963  44.689  35.217  1.00 73.64           N
ATOM     20  C2    G A   1      72.694  45.430  36.351  1.00 73.30           C
ATOM     21  N2    G A   1      72.443  46.732  36.271  1.00 73.22           N
ATOM     22  N3    G A   1      72.686  44.816  37.581  1.00 73.20           N
ATOM     23  C4    G A   1      72.935  43.487  37.697  1.00 73.60           C
TER
ATOM     24  P     A B   1      68.016  29.973  42.762  1.00 11.89           P
ATOM     25  OP1   A B   1      69.285  29.495  43.362  1.00 14.35           O
ATOM     26  OP2   A B   1      67.894  31.357  42.277  1.00 12.68           O
ATOM     27  O5'   A B   1      67.577  29.043  41.552  1.00 10.34           O
ATOM     28  C5'   A B   1      67.571  27.600  41.741  1.00 78.31           C
ATOM     29  C4'   A B   1      66.989  26.984  40.472  1.00 77.28           C
ATOM     30  O4'   A B   1      65.603  27.391  40.333  1.00 75.64           O
ATOM     31  C3'   A B   1      67.638  27.460  39.170  1.00 77.12           C
ATOM     32  O3'   A B   1      68.855  26.813  38.845  1.00 75.76           O
ATOM     33  C2'   A B   1      66.539  27.221  38.136  1.00 77.78           C
ATOM     34  O2'   A B   1      66.460  25.908  37.605  1.00 79.71           O
ATOM     35  C1'   A B   1      65.296  27.546  38.956  1.00 75.44           C
ATOM     36  N9    A B   1      64.827  28.889  38.626  1.00 74.84           N
ATOM     37  C8    A B   1      64.960  30.064  39.315  1.00 74.59           C
ATOM     38  N7    A B   1      64.406  31.108  38.719  1.00 74.09           N
ATOM     39  C5    A B   1      63.880  30.580  37.549  1.00 74.21           C
ATOM     40  C6    A B   1      63.167  31.140  36.461  1.00 74.02           C
ATOM     41  N6    A B   1      62.831  32.427  36.365  1.00 73.72           N
ATOM     42  N1    A B   1      62.804  30.314  35.448  1.00 74.64           N
ATOM     43  C2    A B   1      63.120  29.008  35.513  1.00 75.10           C
ATOM     44  N3    A B   1      63.782  28.360  36.477  1.00 75.34           N
ATOM     45  C4    A B   1      64.140  29.212  37.472  1.00 75.58           C
TER
END

test

./pdb_parser_lib.py

./rna-pdb-tools.py -h | tee rna-pdb-tools.out

./rna-pdb-tools.py -r input/1xjr.pdb 

./rna-pdb-tools.py --no_hr -c input/1xjr.pdb > output/1xjr_clx.pdb

##  --rosetta2generic
./rna-pdb-tools.py --no_hr --rosetta2generic input/farna.pdb > output/farna_clx.pdb

## --get_chain
./rna-pdb-tools.py --get_chain A input/1xjr.pdb > output/1xjr_A_clx.pdb

## --clean
./rna-pdb-tools.py --no_hr --clean input/1a9l_NMR_1_2_models.pdb > output/1a9l_NMR_1_2_models_tool.pdb
./rna-pdb-tools.py --no_hr --clean input/1xjr_GTP.pdb > output/1xjr_GTP.pdb
./rna-pdb-tools.py --no_hr --clean input/1osw.pdb > output/1osw_NMR_1.pdb

## --get_rnapuzzle_ready
./rna-pdb-tools.py --no_hr --get_rnapuzzle_ready input/1xjr_onlyGTP.pdb
./rna-pdb-tools.py --no_hr --get_rnapuzzle_ready input/1xjr_onlyGTP.pdb > output/1xjr_onlyGTP_rnapuzzle_ready.pdb
./rna-pdb-tools.py --no_hr --get_rnapuzzle_ready input/4GXY_3firstNt.pdb
./rna-pdb-tools.py --no_hr --get_rnapuzzle_ready input/gtp.pdb  > output/gtp.pdb
./rna-pdb-tools.py --no_hr --get_rnapuzzle input/377D.pdb # should finish with error

## --get_simrna_ready
./rna-pdb-tools.py --no_hr --get_simrna_ready input/1xjr_no_op3.pdb > output/1xjr_no_op3_simrna_ready.pdb

## --delete
./rna-pdb-tools.py --no_hr --delete A:10-60 input/rp17.out.1.pdb > output/rp17_rmA10-60.pdb
./rna-pdb-tools.py --no_hr --delete A:10-60 input/rp17.out.1.pdb > output/rp17_rmA10-60.pdb

## --edit
./rna-pdb-tools.py --no_hr --edit 'A:6>B:200' input/tetraloop.pdb > output/tetraloop_a6_b200.pdb
./rna-pdb-tools.py --no_hr --edit 'A:1-5>B:200-204' input/tetraloop.pdb > output/tetraloop_a1-b200-204.pdb

## --get_seq
./rna-pdb-tools.py --no_hr --get_seq input/5k7c.pdb > output/get_seq.txt
./rna-pdb-tools.py --no_hr --get_seq input/tetraloop.pdb >> output/get_seq.txt
./rna-pdb-tools.py --get_seq input/1xjr.pdb > output/1xjr.seq

# ClashCalc
cd ./utils/ClashCalc/
./ClashCalc.py
cd ../..

cd ./utils/rmsd_calc/
./test.sh

Install

Install requirements and do these three steps:

add the path to the package to your PYTHONPATH (in ~/.bashrc), e.g. PYTHONPATH=$PYTHONPATH:/home/magnus/src/rna-pdb-tools/
add the path to the bin folder of the package to your PATH (in ~/.bashrc), e.g. PATH=$PATH:/home/magnus/src/rna-pdb-tools/bin/

and run the install script:

 ➜  rna-pdb-tools git:(master) ✗ ./install_links_bin.sh
 Installed in ./bin
 rmsd_calc_to_target.py

should be OK now :-)

Requirement

Some functions e.g. .get_rnapuzzle_ready() needs Biopython, rmsd calculations need numpy, .is_mol2() needs OpenBabel. Basically you should be asked to install anything extra only if you need a given function.

Used libraries

This packages uses other pieces of software, it would be impossible without them to develop rna-pdb-tools, thanks!

biopython (https://github.com/biopython/biopython)
rmsd (https://github.com/charnley/rmsd)
forgi (http://www.tbi.univie.ac.at/%7Ethiel/forgi/graph_tutorial.html)

Quick notes

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Name		Name	Last commit message	Last commit date
Latest commit History 359 Commits
docs		docs
rna_pdb_tools		rna_pdb_tools
.codecov.yml		.codecov.yml
.gitignore		.gitignore
.gitmodules		.gitmodules
.travis.yml		.travis.yml
LICENSE		LICENSE
README.md		README.md
__init__.py		__init__.py
install_links_bin.sh		install_links_bin.sh
rna-pdb-tools.ipynb		rna-pdb-tools.ipynb
test.sh		test.sh

License

leemac/rna-pdb-tools

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