Skip to content

Files

Latest commit

356b31d · Sep 14, 2022

History

History
101 lines (101 loc) · 11.7 KB

rna-tools-index.csv

File metadata and controls

101 lines (101 loc) · 11.7 KB
1
IndexGroup NameTool GroupToolCategoryHelp
2
1Swiss army knife toolrna_pdb_tools.py --get-rnapuzzle-readyoriginalformat PDB file to be compatible with the 'RNA-Puzzle PDB format'
3
2Swiss army knife toolrna_pdb_tools.py --reportoriginalget report
4
3Swiss army knife toolrna_pdb_tools.py --renum-atomsoriginalrenumber atoms, tested with --get-seq
5
4Swiss army knife toolrna_pdb_tools.py --renum-residues-dirtyoriginalrenumber residues, dirty way
6
5Swiss army knife toolrna_pdb_tools.py --renumber-residuesoriginalby defult is false
7
6Swiss army knife toolrna_pdb_tools.py --delete-anisouoriginalremove files with ANISOU records, works with --inplace
8
7Swiss army knife toolrna_pdb_tools.py --split-alt-locationsoriginalsplit into many structures based on alt locations
9
8Swiss army knife toolrna_pdb_tools.py --cleanoriginalget clean structure
10
9Swiss army knife toolrna_pdb_tools.py --is-pdboriginalcheck if a file is in the pdb format
11
10Swiss army knife toolrna_pdb_tools.py --is-nmroriginalcheck if a file is NMR-style multiple model pdb
12
11Swiss army knife toolrna_pdb_tools.py --un-nmroriginalsplit NMR-style multiple model pdb files into individual models [biopython required]
13
12Swiss army knife toolrna_pdb_tools.py --orgmodeoriginalget a structure in org-mode format <sick!>
14
13Swiss army knife toolrna_pdb_tools.py --get-chain GET_CHAINoriginalget a chain
15
14Swiss army knife toolrna_pdb_tools.py --fetchoriginalfetch file from the PDB db
16
15Swiss army knife toolrna_pdb_tools.py --fetch-baoriginalfetch biological assembly from the PDB db
17
16Swiss army knife toolrna_pdb_tools.py --get-seqoriginalget seq
18
17Swiss army knife toolrna_pdb_tools.py --compactoriginalwith --get-seq, get it in compact view
19
18Swiss army knife toolrna_pdb_tools.py --get-ssoriginalget secondary structure
20
19Swiss army knife toolrna_pdb_tools.py --rosetta2genericoriginalconvert ROSETTA-like format to a generic pdb
21
20Swiss army knife toolrna_pdb_tools.py --collapsed-vieworiginalcollapsed view of pdb file. Only lines with C5’ atoms are shown and TER, MODEL, END
22
21Swiss army knife toolrna_pdb_tools.py --replace-hetatmoriginalreplace 'HETATM' with 'ATOM' [tested only with --get-rnapuzzle-ready]
23
22Swiss army knife toolrna_pdb_tools.py --mutate MUTATEoriginalmutate residues, uses ModeRNA
24
23Swiss army knife toolrna_pdb_tools.py --edit EDIToriginaledit 'A:6>B:200', 'A:2-7>B:2-7'
25
24Swiss army knife toolrna_pdb_tools.py --rename-chain RENAME_CHAINoriginalrename chain
26
25Swiss army knife toolrna_pdb_tools.py --swap-chains SWAP_CHAINSoriginalswap two chains
27
26Swiss army knife toolrna_pdb_tools.py --replace-chain REPLACE_CHAINoriginalreplace a chain
28
27Swiss army knife toolrna_pdb_tools.py --delete DELETEoriginaldelete the selected fragment, e.g., A:10-16, or for more than one fragment --delete 'A:1-25+30-57'
29
28Swiss army knife toolrna_pdb_tools.py --extract EXTRACToriginalextract the selected fragment, e.g., A:10-16, or for more than one fragment --extract 'A:1-25+30-57'
30
29Swiss army knife toolrna_pdb_tools.py --extract-chain EXTRACT_CHAINoriginalextract chain
31
30RNA sequenceRNASequencepredict_ss()wrapperContextFold, also used for Jupyter Notebook
32
31RNA sequenceRNASequencepredict_ss()wrapperCentroidFold, also used for Jupyter Notebook
33
32RNA sequenceRNASequenceeval()wrapperRNAeval (ViennaRNA) with constraints, also used for Jupyter Notebook
34
33RNA sequenceRNASequencepredict_ss()wrapperRNAfold (ViennaRNA) with constraints, also used for Jupyter Notebook
35
34RNA sequenceRNASequencepredict_ss()wrapperipknot also used for Jupyter Notebook
36
35RNA sequenceRNASequencepredict_ss()wrapperMC-Fold also used for Jupyter Notebook
37
36RNA sequenceRNASequenceget_foldability()wrapperget foldability with ENTRNA
38
37RNA sequence: miscreverse.pyoriginalreverse sequence #cmd #stdin
39
38RNA sequence: misctranslate.pyoriginaltranslate sequence #cmd #stdin
40
39RNA sequence searchBlastPDB.pysearch()wrappera simple Blast search designed to be used mostly in Jupyter Notebooks
41
40RNA sequence searchRfamSearch.pycmscan()wrappera simple Rfam search designed to be used mostly in Jupyter Notebooks
42
41RNA secondary structureSecondaryStructuredraw_ss()wrapperDraw Secondary Structure using VARNA, also used for Jupyter Notebook
43
42RNA secondary structureSecondaryStructureparse_vienna_to_pairs()originalParse Vienna (dot-bracket notation) to get pairs including pseudoknot (only one layer of psuedoknots implemented at the moment)
44
43RNA secondary structureSecondaryStructurerna-pk-simrna-to-one-line.pyoriginalconvert simrna multi-line format for secondary structure into one line secondary structure notation
45
44RNA AlignmentRNASeqget_seq()originalget sequence from an alignment
46
45RNA AlignmentRNASeqget_ss()originalget secondary structure for a given sequence
47
46RNA AlignmentRNAalignmentfetch()originalfetch an alignment from Rfam
48
47RNA AlignmentRNAalignmentcmalign()wrapperaligns the RNA sequences in to the covariance model (CM) with Infernal
49
48RNA AlignmentRNAalignmentRchie()*wrapperplot arc diagrams of RNA secondary structures
50
47RNA AlignmentRNAalignmentfind_core()originalfinds core of molecules in alignment
51
48RNA 3D structure comparisonrna_calc_rmsdrna_calc_rmsd.pyoriginalcalculate RMSDs of structures to the target
52
49RNA 3D structure comparisonrna_calc_rmsd --target-selection TARGET_SELECTION & --model-selection MODEL_SELECTIONoriginaltarget & model selection
53
50RNA 3D structure comparisonrna_calc_rmsd --method METHODoriginalmethods: --align and --fit (both taken from PyMOL) or the default method, all atom RMSD
54
51RNA 3D structure comparisonrna_calc_rmsdrna_calc_rmsd_all_vs_all.pyoriginalcalculate RMSDs all vs all and save it to a matrix
55
52RNA 3D structure comparisonrna_calc_rmsdrna_calc_rmsd_multi_targets.pyoriginalcalculate RMSDs of structures to multiple targets::
56
53RNA 3D structure comparisonrna_calc_rmsd --target-selection TARGET_SELECTION & --model-selection MODEL_SELECTIONoriginaltarget & model selection
57
54RNA 3D structure comparisonrna_calc_evo_rmsdrna_calc_evo_rmsd.py*originalcalculate RMSD between structures based on a given alignment and selected residues as defined in the "x line" used in EvoClustRNA {Magnus:2019gsa}
58
55RNA 3D structure comparisonrna_calc_infrna_calc_inf.py*original/wrapperincluding multiprocessing based on ClaRNA (in Python 2!)
59
56RNA 3D structure comparisonClusteringrna_clanstix.py*originala tool for visualizing RNA 3D structures based on pairwise structural similarity with CLANS
60
57RNA 3D structure comparisonrna_prediction_significance.pywrappercalculate significance of an RNA tertiary structure prediction, wrapper to
61
58RNA 3D Structure PredictionRosettarna_rosetta_n.pywrappershow me # of structure in a silent file
62
59RNA 3D Structure PredictionRosettarna_rosetta_check_progress.pywrappercheck progress for many simulations of Rosetta
63
60RNA 3D Structure PredictionRosettarna_rosetta_min.pywrappera script to do minimization
64
61RNA 3D Structure PredictionRosettarna_rosetta_cluster.pywrappercluster silent Rosetta files
65
62RNA 3D Structure PredictionRosettarna_rosetta_extract_lowscore_decoys.pywrappera simple wrapper to extract_lowscore_decoys.py
66
63RNA 3D Structure PredictionRosettarna_rosetta_run.pywrapperprepare & run ROSETTA simulations
67
64RNA 3D Structure PredictionRosettarna_rosetta_head.pywrapperget a head of a Rosetta silent file.
68
65RNA 3D Structure PredictionSimRNArna_simrna_cluster.pywrappercluster SimRNA trajectories
69
66RNA 3D Structure PredictionSimRNArna_simrna_extract.pywrapperextract full atom structures from a SimRNA trajectory file
70
67RNA 3D Structure PredictionSimRNArna_simrna_get_datawrapperalias to get data folder for SimRNA
71
68RNA 3D Structure PredictionSimRNArna_simrna_lowest.pywrapperget lowest energy frames out of a SimRNA trajectory file
72
69RNA 3D Structure PredictionSimRNArna_simrna_energy_plot.pywrapperget an energy plot of SimRNA trajectory
73
70RNA 3D Structure PredictionSimRNArna_pk_simrna_to_one_line.pyoriginalconvert multi-line SimRNA secondary structure format to one line bracket format
74
71RNA 3D Structure PredictionSimRNArna_ss_pk_to_simrna.pyoriginaldo opposite as previous one, convert one line bracket format with pseudoknots into multi-line SimRNA secondary structure format
75
72RNA 3D Structure PredictionSimRNAwebrna_simrnaweb_download_job.pyoriginaldownload model files, trajectory for a given SimRNAweb job
76
73RNA 3D Trajectory AnalysisSimRNATrajectoryload_from_string(), load_from_file(), load_from_list()originalClass for processing simulations of SimRNA in Python: classes of Frames, Residues, Atoms
77
74RNA 3D Trajectory AnalysisSimRNATrajectoryplot_energy()originalPlots the SimRNA energy of the trajetory.
78
75RNA 3D Trajectory AnalysisSimRNATrajectoryget_coord() of atoms or residuesoriginalGet coordinates for atoms and residues (middle point) and do mathematics on them
79
76RNA 3D Trajectory AnalysisSimRNATrajectorytrajectory.frames[0:10]originalslice frames and save it into new trajectories
80
77Otherrnakb_utilsoriginalRNAkb-related {Bernauer:2011hf} tools
81
78Otherrnapuzzle_sender*originala script to process files to be send to the RNA-Puzzles organizers
82
79Otherrnashape2ascii originalconvert RNA shape data into ascii characters ;-) ▅▄▆▄▂▁▁▁▁▁▁▁▁▁▁▂▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▂▅▇▅▄▃▂▁
83
80Othercluster_loadoriginalscripts to view cluster load, based on processing qstat
84
81PyMOL4RNAHacky UndooriginalUndo ("Quick Save & Load") for PyMOL, CTRL-S & CTRL-Z
85
82PyMOL4RNAPyMOL4Spliceosome* originalNow own repository https://github.com/mmagnus/PyMOL4Spliceosome
86
83PyMOL4RNAclarna()*wrappercontact classification with ClaRNA directly in PyMOL for selected residues
87
84PyMOL4RNAx3dna()*wrappercontact classification with 3DNA directly in PyMOL for selected residues
88
85PyMOL4RNAss()*original/wrapperget secondary structures of selected objects based on 3DNA
89
86PyMOL4RNAqrnas()wrapperdo minimalization of RNA with QRNAS
90
87PyMOL4RNAsav()originalsave on Desktop a session and a PNG file illustrating the session,
91
88PyMOL4RNArp17() and moreoriginalcolor structure domains according to pre-defined styles, e.g., rp17 (RNA-Puzzles 17)
92
89PyMOLpymol_color_by_conserv.py*originala pipeline to process alignments into coloring scheme for protein conservation <https://github.com/mmagnus/rna-tools/tree/master/rna_tools/tools/pymol_color_by_conserv>
93
90RNA 3D structure processingrna_refinement.pywrappera wrapper for QRNAS (Quick Refinement of Nucleic Acids) {Stasiewicz:2019ea}
94
91RNA 3D structure analysisclarna_app.pywrappera wrapper to ClaRNA, See also PyMOL4RNA, only Python 2 since ClaRNA {Walen:2014jv} is in Python 2
95
92RNA 3D structure analysisrna_x3dna.pywrappera wrapper to 3dna, See also PyMOL4RNA
96
93RNA 3D structure analysisClashCalc.pyoriginala simple clash score calculator, used in NPDock, requires BioPython,
97
94RNA 3D structure formatsdiffpdb*originala simple tool to compare text-content of PDB files
98
95RNA 3D structure formatsrna_pdb_merge_into_one.pyoriginalmerge single files into an NMR-style multiple model file PDB file
99
96RNA 3D structure formatsrna_pdb_edit_occupancy_bfactor.pyoriginaledit occupancy or bfactor in PDB file, used for SimRNAweb
100
97LibrarySelectionengine to parse selection in PyMOL format into Python objects, used for example by rmsd_calc.py
101
#see the newest version at https://github.com/mmagnus/rna-tools/blob/master/rna-tools-index.csv