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Utils

RNA Sequence

.. automodule:: rna_pdb_tools.Seq
   :members:
   :undoc-members:

RNA Secondary Structure

.. automodule:: rna_pdb_tools.SecondaryStructure
   :members:
   :undoc-members:

Blast PDB

A super-simple wrapper around Blast on the PDB db (online).

.. automodule:: rna_pdb_tools.BlastPDB
   :members:
   :undoc-members:

Blastn - select sequences from teh database matched by BLASTn

A super-simple wrapper to parse by headers a BLASTn output (outfmt - 6) sequences in fasta from the database of sequences.

.. argparse::
   :ref: rna_pdb_tools.utils.rna_seq_search_BLASTn_outfmt-6.get_parser
   :prog: select_seq_fromBLAStn_6outfm.py

.. automodule:: rna_pdb_tools.utils.rna_seq_search_BLASTn_outfmt-6
   :members:
   :undoc-members:


Rfam Search

A super-simple wrapper around cmscan (Infernal) on local RFAM.

.. automodule:: rna_pdb_tools.RfamSearch
   :members:
   :undoc-members:

PDB Edit Bfactor/Occupancy

.. argparse::
   :ref: rna_pdb_tools.utils.rna_pdb_edit_occupancy_bfactor.rna_pdb_edit_occupancy_bfactor.get_parser
   :prog: rna_pdb_edit_occupancy_bfactor.py

.. autofunction:: rna_pdb_tools.utils.rna_pdb_edit_occupancy_bfactor.rna_pdb_edit_occupancy_bfactor.edit_occupancy_of_pdb

RNA Alignment

.. automodule:: rna_pdb_tools.utils.rna_alignment.rna_alignment

RNASeq

.. autoclass:: rna_pdb_tools.utils.rna_alignment.rna_alignment.RNASeq
   :members:
   :undoc-members:

RNAalignment

.. autoclass:: rna_pdb_tools.utils.rna_alignment.rna_alignment.RNAalignment
   :members:
   :undoc-members:

Random assignment of nucleotides

.. argparse::
   :ref: rna_pdb_tools.utils.rna_alignment.random_assignment_of_nucleotides.get_parser
   :prog: random_assignment_of_nucleotides

.. automodule:: rna_pdb_tools.utils.rna_alignment.random_assignment_of_nucleotides
   :members:
   :undoc-members:


CMAlign

.. autoclass:: rna_pdb_tools.utils.rna_alignment.rna_alignment.CMAlign
   :members:
   :undoc-members:


RChie

.. autoclass:: rna_pdb_tools.utils.rna_alignment.rna_alignment.RChie
   :members:
   :undoc-members:

Renumber a pdb file according to alignment

.. argparse::
   :ref: rna_pdb_tools.utils.renum_pdb_to_aln.renum_pdb_to_aln.get_parser
   :prog: renum_pdb_to_aln

.. automodule:: rna_pdb_tools.utils.renum_pdb_to_aln.renum_pdb_to_aln
   :members:
   :undoc-members:

RNA clustering with CLANS (clanstix)

.. automodule:: rna_pdb_tools.utils.clanstix.rna_clanstix
   :members:
   :undoc-members:

Calculate Root Mean Square Deviation (RMSD)

rna_calc_rmsd

.. argparse::
   :ref: rna_pdb_tools.utils.rna_calc_rmsd.rna_calc_rmsd.get_parser
   :prog: rna_calc_rmsd

.. automodule:: rna_pdb_tools.utils.rna_calc_rmsd.rna_calc_rmsd
   :members:
   :undoc-members:

rna_calc_evo_rmsd

.. automodule:: rna_pdb_tools.utils.rna_calc_evo_rmsd.rna_calc_evo_rmsd
   :undoc-members:

.. argparse::
   :ref: rna_pdb_tools.utils.rna_calc_evo_rmsd.rna_calc_evo_rmsd.get_parser
   :prog: rna_calc_evo_rmsd

rna_calc_rmsd_trafl

.. argparse::
   :ref: rna_pdb_tools.utils.rna_calc_rmsd_trafl.rna_calc_rmsd_trafl.get_parser
   :prog: rna_calc_evo_rmsd

.. argparse::
   :ref: rna_pdb_tools.utils.rna_calc_rmsd_trafl.rna_cal_rmsd_trafl_plot.get_parser
   :prog: rna_cal_rmsd_trafl_plot


rna_calc_rmsd_all_vs_all

.. argparse::
   :ref: rna_pdb_tools.utils.rna_calc_rmsd.rna_calc_rmsd_all_vs_all.get_parser
   :prog: rna_calc_rmsd_all_vs_all

.. automodule:: rna_pdb_tools.utils.rna_calc_rmsd.rna_calc_rmsd_all_vs_all
   :members:
   :undoc-members:

Calculate Interaction Network Fidelity (INF) and not only

rna_calc_inf

.. argparse::
   :ref: rna_pdb_tools.utils.rna_calc_inf.rna_calc_inf.get_parser
   :prog: rna_calc_inf

.. automodule:: rna_pdb_tools.utils.rna_calc_inf.rna_calc_inf
   :members:
   :undoc-members:

rna_calc_dinf

.. argparse::
   :ref: rna_pdb_tools.utils.rna_calc_inf.rna_calc_dinf.get_parser
   :prog: rna_calc_inf

.. automodule:: rna_pdb_tools.utils.rna_calc_dinf.rna_calc_dinf
   :members:
   :undoc-members:


Measure distance between atoms

.. argparse::
   :ref: rna_pdb_tools.utils.pdbs_measure_atom_dists.pdbs_measure_atom_dists.get_parser
   :prog: pdbs_measure_atom_dists

.. automodule:: rna_pdb_tools.utils.pdbs_measure_atom_dists.pdbs_measure_atom_dists
   :members:
   :undoc-members:

diffpdb

.. automodule:: rna_pdb_tools.utils.diffpdb.diffpdb
   :undoc-members:

.. argparse::
   :ref: rna_pdb_tools.utils.diffpdb.diffpdb.get_parser
   :prog: rna_helix_vis

RNA filter

rna_filter.py - calculate distances based on given restrants on PDB files or SimRNA trajectories

.. argparse::
   :ref: rna_pdb_tools.utils.rna_filter.rna_filter.get_parser
   :prog: rna_filter.py

rna_dca_mapping.py

.. argparse::
   :ref: rna_pdb_tools.utils.rna_filter.rna_dca_mapping.get_parser
   :prog: rna_dca_mapping.py


show_dists - show distances in PyMOL

.. automodule:: rna_pdb_tools.utils.rna_filter.pymol_dists
   :undoc-members:

rna_ex2x.py - analyze an evolutionary coupling file.

.. argparse::
   :ref: rna_pdb_tools.utils.rna_filter.rna_ec2x.get_parser
   :prog: rna_ec2x.py

rna_pairs2SimRNArestrs.py - convert pairs to SimRNA restraints

.. argparse::
   :ref: rna_pdb_tools.utils.rna_filter.rna_pairs2SimRNArestrs.get_parser
   :prog: rna_pairs2SimRNArestrs.py

rna_ss_get_bps.py - get a list of base pairs for a given "fasta ss" file.

.. argparse::
   :ref: rna_pdb_tools.utils.rna_filter.rna_ss_get_bps.get_parser
   :prog: rna_ss_get_bps

rna_pairs_diff.py - get a diff of pairs

.. argparse::
   :ref: rna_pdb_tools.utils.rna_filter.rna_pairs_diff.get_parser
   :prog: rna_pairs_diff.py

Secondary structure format conversion

rna_convert_pseudoknot_formats

Run this as:

python rna-pk-simrna-to-one-line.py test_data/simrna.ss

Convert:

> a
....((.(..(((....)))..((((.(.........).)))....).)).......((((......))))
..............................((((...................))))..............

to:

> a
....((.(..(((....)))..((((.(..[[[[...).)))....).))...]]]]((((......))))

and:

>2 chains
(((((......)))))........(.((....(.......)..(((. .)))...)).)
.....((((((......................))))))........ ...........

to:

>2 chains
((((([[[[[[)))))........(.((....(]]]]]].)..(((. .)))...)).)

and:

> b
..(.......(((....)))..((((.(.........).))))).............((((......))))
....((.(......................................).)).....................
..............................((((...................))))..............

to:

> b
..(.[[.[..(((....)))..((((.(..{{{{...).)))))..].]]...}}}}((((......))))

and it works with VARNA:

../../rna_pdb_tools/utils/rna_convert_pseudoknot_formats/doc/varna_2pk.png

.. automodule:: rna_pdb_tools.utils.rna_convert_pseudoknot_formats.rna_ss_pk_to_simrna
   :members:
   :undoc-members:

x3DNA (contacts classification & secondary structure detection)

.. automodule:: rna_pdb_tools.utils.rna_x3dna.rna_x3dna
   :members:
   :undoc-members:

ClaRNA (contacts classification)

If you want to calculate "Interaction Network Fidelity (INF) and not only" see rna_calc_inf in the Utils.

.. automodule:: rna_pdb_tools.utils.clarna_app.clarna_app
   :members:
   :undoc-members:

SimRNA

Select low energy frames

.. argparse::
   :ref: rna_pdb_tools.utils.simrna_trajectory.rna_simrna_lowest.get_parser
   :prog: rna_simrna_lowest.py

Extract

.. argparse::
   :ref: rna_pdb_tools.utils.simrna_trajectory.rna_simrna_extract.get_parser
   :prog: rna_simrna_extract.py

SimRNAweb

Download files of a SimRNAweb run

.. argparse::
   :ref: rna_pdb_tools.rna_simrnaweb_download_job.rna_simrnaweb_download_job.get_parser
   :prog: rna_simrnaweb_download_job.py

SimRNATrajectory

.. automodule:: rna_pdb_tools.utils.simrna_trajectory.simrna_trajectory
   :members:
   :undoc-members:

RNAkb

.. automodule:: rna_pdb_tools.utils.rnakb_utils.rnakb_utils
   :members:
   :undoc-members:

RNA Refinement (QRNAS)

.. argparse::
   :ref: rna_pdb_tools.utils.rna_refinement.rna_refinement.get_parser
   :prog: rna_refinement.py


ROSETTA

A set of wrappers around Rosetta (https://www.rosettacommons.org/), mostly based on C. Y. Cheng, F. C. Chou, and R. Das, Modeling complex RNA tertiary folds with Rosetta, 1st ed., vol. 553. Elsevier Inc., 2015. http://www.sciencedirect.com/science/article/pii/S0076687914000524

Run (modeling)

.. argparse::
   :ref: rna_pdb_tools.utils.rna_rosetta.rna_rosetta_run.get_parser
   :prog: rna_rosetta_run.py

.. automodule:: rna_pdb_tools.utils.rna_rosetta.rna_rosetta_run.py
   :members:
   :undoc-members:

Get a number of structures

.. argparse::
   :ref: rna_pdb_tools.utils.rna_rosetta.rna_rosetta_n.get_parser
   :prog: rna_rosetta_n.py

.. automodule:: rna_pdb_tools.utils.rna_rosetta.rna_rosetta_n.py
   :members:
   :undoc-members:

Get a head of a Rosetta silent file

.. argparse::
   :ref: rna_pdb_tools.utils.rna_rosetta.rna_rosetta_head.get_parser
   :prog: rna_rosetta_n.py

.. automodule:: rna_pdb_tools.utils.rna_rosetta.rna_rosetta_head.py
   :members:
   :undoc-members:

Cluster

.. argparse::
   :nodescription:
   :nosubcommands:
   :ref: rna_pdb_tools.utils.rna_rosetta.rna_rosetta_cluster.get_parser
   :prog: rna_rosetta_cluster.py

.. automodule:: rna_pdb_tools.utils.rna_rosetta.rna_rosetta_cluster
   :members:
   :undoc-members:


Minimize

.. argparse::
   :ref: rna_pdb_tools.utils.rna_rosetta.rna_rosetta_min.get_parser
   :prog: rna_rosetta_min.py

.. automodule:: rna_pdb_tools.utils.rna_rosetta.rna_rosetta_min.py
   :members:
   :undoc-members:

Check progress

.. argparse::
   :ref: rna_pdb_tools.utils.rna_rosetta.rna_rosetta_check_progress.get_parser
   :prog: rna_rosetta_cluster.py

.. automodule:: rna_pdb_tools.utils.rna_rosetta.rna_rosetta_check_progress.py
   :members:
   :undoc-members:

Plotting

.. argparse::
   :ref: rna_pdb_tools.utils.plotting.rna_plot_hist.get_parser
   :prog: rna_plot_hist

.. argparse::
   :ref: rna_pdb_tools.utils.plotting.rna_plot_density.get_parser
   :prog: rna_plot_density

Misc

rna_sali2dotbracket

.. argparse::
   :ref: rna_pdb_tools.utils.rna_sali2dotbracket.rna_sali2dotbracket.get_parser
   :prog: rna_sali2dotbracket

.. automodule:: rna_pdb_tools.utils.rna_sali2dotbracket.rna_sali2dotbracket
   :members:
   :undoc-members:

rna_add_chain

.. automodule:: rna_pdb_tools.utils.misc.rna_add_chain
   :members:
   :undoc-members:

.. argparse::
   :ref: rna_pdb_tools.utils.misc.rna_add_chain.get_parser
   :prog: rna_add_chain

Cluster load

A very simple tool to see your cluster load per user:

MAX_JOBS: 1000
#jobs cluster 917 load:  0.917  to use: 83
#jobs you     749 load:  0.749  to use: 251
{'deepak': 160, 'azyla': 8, 'magnus': 749}
1 azyla        r 8
20 magnus       r 10
16 deepak       r 10
329 magnus       r 1
22 magnus       qw 10
.. automodule:: rna_pdb_tools.utils.cluster_load.cluster_load
   :members:
   :undoc-members: