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rna-tools-index.csv
1 | Index | Group Name | Tool Group | Tool | Category | Help |
---|---|---|---|---|---|---|
2 | 1 | Swiss army knife tool | rna_pdb_tools.py | --get-rnapuzzle-ready | original | format PDB file to be compatible with the 'RNA-Puzzle PDB format' |
3 | 2 | Swiss army knife tool | rna_pdb_tools.py | --report | original | get report |
4 | 3 | Swiss army knife tool | rna_pdb_tools.py | --renum-atoms | original | renumber atoms, tested with --get-seq |
5 | 4 | Swiss army knife tool | rna_pdb_tools.py | --renum-residues-dirty | original | renumber residues, dirty way |
6 | 5 | Swiss army knife tool | rna_pdb_tools.py | --renumber-residues | original | by defult is false |
7 | 6 | Swiss army knife tool | rna_pdb_tools.py | --delete-anisou | original | remove files with ANISOU records, works with --inplace |
8 | 7 | Swiss army knife tool | rna_pdb_tools.py | --split-alt-locations | original | split into many structures based on alt locations |
9 | 8 | Swiss army knife tool | rna_pdb_tools.py | --clean | original | get clean structure |
10 | 9 | Swiss army knife tool | rna_pdb_tools.py | --is-pdb | original | check if a file is in the pdb format |
11 | 10 | Swiss army knife tool | rna_pdb_tools.py | --is-nmr | original | check if a file is NMR-style multiple model pdb |
12 | 11 | Swiss army knife tool | rna_pdb_tools.py | --un-nmr | original | split NMR-style multiple model pdb files into individual models [biopython required] |
13 | 12 | Swiss army knife tool | rna_pdb_tools.py | --orgmode | original | get a structure in org-mode format <sick!> |
14 | 13 | Swiss army knife tool | rna_pdb_tools.py | --get-chain GET_CHAIN | original | get a chain |
15 | 14 | Swiss army knife tool | rna_pdb_tools.py | --fetch | original | fetch file from the PDB db |
16 | 15 | Swiss army knife tool | rna_pdb_tools.py | --fetch-ba | original | fetch biological assembly from the PDB db |
17 | 16 | Swiss army knife tool | rna_pdb_tools.py | --get-seq | original | get seq |
18 | 17 | Swiss army knife tool | rna_pdb_tools.py | --compact | original | with --get-seq, get it in compact view |
19 | 18 | Swiss army knife tool | rna_pdb_tools.py | --get-ss | original | get secondary structure |
20 | 19 | Swiss army knife tool | rna_pdb_tools.py | --rosetta2generic | original | convert ROSETTA-like format to a generic pdb |
21 | 20 | Swiss army knife tool | rna_pdb_tools.py | --collapsed-view | original | collapsed view of pdb file. Only lines with C5’ atoms are shown and TER, MODEL, END |
22 | 21 | Swiss army knife tool | rna_pdb_tools.py | --replace-hetatm | original | replace 'HETATM' with 'ATOM' [tested only with --get-rnapuzzle-ready] |
23 | 22 | Swiss army knife tool | rna_pdb_tools.py | --mutate MUTATE | original | mutate residues, uses ModeRNA |
24 | 23 | Swiss army knife tool | rna_pdb_tools.py | --edit EDIT | original | edit 'A:6>B:200', 'A:2-7>B:2-7' |
25 | 24 | Swiss army knife tool | rna_pdb_tools.py | --rename-chain RENAME_CHAIN | original | rename chain |
26 | 25 | Swiss army knife tool | rna_pdb_tools.py | --swap-chains SWAP_CHAINS | original | swap two chains |
27 | 26 | Swiss army knife tool | rna_pdb_tools.py | --replace-chain REPLACE_CHAIN | original | replace a chain |
28 | 27 | Swiss army knife tool | rna_pdb_tools.py | --delete DELETE | original | delete the selected fragment, e.g., A:10-16, or for more than one fragment --delete 'A:1-25+30-57' |
29 | 28 | Swiss army knife tool | rna_pdb_tools.py | --extract EXTRACT | original | extract the selected fragment, e.g., A:10-16, or for more than one fragment --extract 'A:1-25+30-57' |
30 | 29 | Swiss army knife tool | rna_pdb_tools.py | --extract-chain EXTRACT_CHAIN | original | extract chain |
31 | 30 | RNA sequence | RNASequence | predict_ss() | wrapper | ContextFold, also used for Jupyter Notebook |
32 | 31 | RNA sequence | RNASequence | predict_ss() | wrapper | CentroidFold, also used for Jupyter Notebook |
33 | 32 | RNA sequence | RNASequence | eval() | wrapper | RNAeval (ViennaRNA) with constraints, also used for Jupyter Notebook |
34 | 33 | RNA sequence | RNASequence | predict_ss() | wrapper | RNAfold (ViennaRNA) with constraints, also used for Jupyter Notebook |
35 | 34 | RNA sequence | RNASequence | predict_ss() | wrapper | ipknot also used for Jupyter Notebook |
36 | 35 | RNA sequence | RNASequence | predict_ss() | wrapper | MC-Fold also used for Jupyter Notebook |
37 | 36 | RNA sequence | RNASequence | get_foldability() | wrapper | get foldability with ENTRNA |
38 | 37 | RNA sequence: misc | reverse.py | original | reverse sequence #cmd #stdin | |
39 | 38 | RNA sequence: misc | translate.py | original | translate sequence #cmd #stdin | |
40 | 39 | RNA sequence search | BlastPDB.py | search() | wrapper | a simple Blast search designed to be used mostly in Jupyter Notebooks |
41 | 40 | RNA sequence search | RfamSearch.py | cmscan() | wrapper | a simple Rfam search designed to be used mostly in Jupyter Notebooks |
42 | 41 | RNA secondary structure | SecondaryStructure | draw_ss() | wrapper | Draw Secondary Structure using VARNA, also used for Jupyter Notebook |
43 | 42 | RNA secondary structure | SecondaryStructure | parse_vienna_to_pairs() | original | Parse Vienna (dot-bracket notation) to get pairs including pseudoknot (only one layer of psuedoknots implemented at the moment) |
44 | 43 | RNA secondary structure | SecondaryStructure | rna-pk-simrna-to-one-line.py | original | convert simrna multi-line format for secondary structure into one line secondary structure notation |
45 | 44 | RNA Alignment | RNASeq | get_seq() | original | get sequence from an alignment |
46 | 45 | RNA Alignment | RNASeq | get_ss() | original | get secondary structure for a given sequence |
47 | 46 | RNA Alignment | RNAalignment | fetch() | original | fetch an alignment from Rfam |
48 | 47 | RNA Alignment | RNAalignment | cmalign() | wrapper | aligns the RNA sequences in to the covariance model (CM) with Infernal |
49 | 48 | RNA Alignment | RNAalignment | Rchie()* | wrapper | plot arc diagrams of RNA secondary structures |
50 | 47 | RNA Alignment | RNAalignment | find_core() | original | finds core of molecules in alignment |
51 | 48 | RNA 3D structure comparison | rna_calc_rmsd | rna_calc_rmsd.py | original | calculate RMSDs of structures to the target |
52 | 49 | RNA 3D structure comparison | rna_calc_rmsd | --target-selection TARGET_SELECTION & --model-selection MODEL_SELECTION | original | target & model selection |
53 | 50 | RNA 3D structure comparison | rna_calc_rmsd | --method METHOD | original | methods: --align and --fit (both taken from PyMOL) or the default method, all atom RMSD |
54 | 51 | RNA 3D structure comparison | rna_calc_rmsd | rna_calc_rmsd_all_vs_all.py | original | calculate RMSDs all vs all and save it to a matrix |
55 | 52 | RNA 3D structure comparison | rna_calc_rmsd | rna_calc_rmsd_multi_targets.py | original | calculate RMSDs of structures to multiple targets:: |
56 | 53 | RNA 3D structure comparison | rna_calc_rmsd | --target-selection TARGET_SELECTION & --model-selection MODEL_SELECTION | original | target & model selection |
57 | 54 | RNA 3D structure comparison | rna_calc_evo_rmsd | rna_calc_evo_rmsd.py* | original | calculate RMSD between structures based on a given alignment and selected residues as defined in the "x line" used in EvoClustRNA {Magnus:2019gsa} |
58 | 55 | RNA 3D structure comparison | rna_calc_inf | rna_calc_inf.py* | original/wrapper | including multiprocessing based on ClaRNA (in Python 2!) |
59 | 56 | RNA 3D structure comparison | Clustering | rna_clanstix.py* | original | a tool for visualizing RNA 3D structures based on pairwise structural similarity with CLANS |
60 | 57 | RNA 3D structure comparison | rna_prediction_significance.py | wrapper | calculate significance of an RNA tertiary structure prediction, wrapper to | |
61 | 58 | RNA 3D Structure Prediction | Rosetta | rna_rosetta_n.py | wrapper | show me # of structure in a silent file |
62 | 59 | RNA 3D Structure Prediction | Rosetta | rna_rosetta_check_progress.py | wrapper | check progress for many simulations of Rosetta |
63 | 60 | RNA 3D Structure Prediction | Rosetta | rna_rosetta_min.py | wrapper | a script to do minimization |
64 | 61 | RNA 3D Structure Prediction | Rosetta | rna_rosetta_cluster.py | wrapper | cluster silent Rosetta files |
65 | 62 | RNA 3D Structure Prediction | Rosetta | rna_rosetta_extract_lowscore_decoys.py | wrapper | a simple wrapper to extract_lowscore_decoys.py |
66 | 63 | RNA 3D Structure Prediction | Rosetta | rna_rosetta_run.py | wrapper | prepare & run ROSETTA simulations |
67 | 64 | RNA 3D Structure Prediction | Rosetta | rna_rosetta_head.py | wrapper | get a head of a Rosetta silent file. |
68 | 65 | RNA 3D Structure Prediction | SimRNA | rna_simrna_cluster.py | wrapper | cluster SimRNA trajectories |
69 | 66 | RNA 3D Structure Prediction | SimRNA | rna_simrna_extract.py | wrapper | extract full atom structures from a SimRNA trajectory file |
70 | 67 | RNA 3D Structure Prediction | SimRNA | rna_simrna_get_data | wrapper | alias to get data folder for SimRNA |
71 | 68 | RNA 3D Structure Prediction | SimRNA | rna_simrna_lowest.py | wrapper | get lowest energy frames out of a SimRNA trajectory file |
72 | 69 | RNA 3D Structure Prediction | SimRNA | rna_simrna_energy_plot.py | wrapper | get an energy plot of SimRNA trajectory |
73 | 70 | RNA 3D Structure Prediction | SimRNA | rna_pk_simrna_to_one_line.py | original | convert multi-line SimRNA secondary structure format to one line bracket format |
74 | 71 | RNA 3D Structure Prediction | SimRNA | rna_ss_pk_to_simrna.py | original | do opposite as previous one, convert one line bracket format with pseudoknots into multi-line SimRNA secondary structure format |
75 | 72 | RNA 3D Structure Prediction | SimRNAweb | rna_simrnaweb_download_job.py | original | download model files, trajectory for a given SimRNAweb job |
76 | 73 | RNA 3D Trajectory Analysis | SimRNATrajectory | load_from_string(), load_from_file(), load_from_list() | original | Class for processing simulations of SimRNA in Python: classes of Frames, Residues, Atoms |
77 | 74 | RNA 3D Trajectory Analysis | SimRNATrajectory | plot_energy() | original | Plots the SimRNA energy of the trajetory. |
78 | 75 | RNA 3D Trajectory Analysis | SimRNATrajectory | get_coord() of atoms or residues | original | Get coordinates for atoms and residues (middle point) and do mathematics on them |
79 | 76 | RNA 3D Trajectory Analysis | SimRNATrajectory | trajectory.frames[0:10] | original | slice frames and save it into new trajectories |
80 | 77 | Other | rnakb_utils | original | RNAkb-related {Bernauer:2011hf} tools | |
81 | 78 | Other | rnapuzzle_sender* | original | a script to process files to be send to the RNA-Puzzles organizers | |
82 | 79 | Other | rnashape2ascii | original | convert RNA shape data into ascii characters ;-) ▅▄▆▄▂▁▁▁▁▁▁▁▁▁▁▂▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▂▅▇▅▄▃▂▁ | |
83 | 80 | Other | cluster_load | original | scripts to view cluster load, based on processing qstat | |
84 | 81 | PyMOL4RNA | Hacky Undo | original | Undo ("Quick Save & Load") for PyMOL, CTRL-S & CTRL-Z | |
85 | 82 | PyMOL4RNA | PyMOL4Spliceosome* | original | Now own repository https://github.com/mmagnus/PyMOL4Spliceosome | |
86 | 83 | PyMOL4RNA | clarna()* | wrapper | contact classification with ClaRNA directly in PyMOL for selected residues | |
87 | 84 | PyMOL4RNA | x3dna()* | wrapper | contact classification with 3DNA directly in PyMOL for selected residues | |
88 | 85 | PyMOL4RNA | ss()* | original/wrapper | get secondary structures of selected objects based on 3DNA | |
89 | 86 | PyMOL4RNA | qrnas() | wrapper | do minimalization of RNA with QRNAS | |
90 | 87 | PyMOL4RNA | sav() | original | save on Desktop a session and a PNG file illustrating the session, | |
91 | 88 | PyMOL4RNA | rp17() and more | original | color structure domains according to pre-defined styles, e.g., rp17 (RNA-Puzzles 17) | |
92 | 89 | PyMOL | pymol_color_by_conserv.py* | original | a 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 | 90 | RNA 3D structure processing | rna_refinement.py | wrapper | a wrapper for QRNAS (Quick Refinement of Nucleic Acids) {Stasiewicz:2019ea} | |
94 | 91 | RNA 3D structure analysis | clarna_app.py | wrapper | a wrapper to ClaRNA, See also PyMOL4RNA, only Python 2 since ClaRNA {Walen:2014jv} is in Python 2 | |
95 | 92 | RNA 3D structure analysis | rna_x3dna.py | wrapper | a wrapper to 3dna, See also PyMOL4RNA | |
96 | 93 | RNA 3D structure analysis | ClashCalc.py | original | a simple clash score calculator, used in NPDock, requires BioPython, | |
97 | 94 | RNA 3D structure formats | diffpdb* | original | a simple tool to compare text-content of PDB files | |
98 | 95 | RNA 3D structure formats | rna_pdb_merge_into_one.py | original | merge single files into an NMR-style multiple model file PDB file | |
99 | 96 | RNA 3D structure formats | rna_pdb_edit_occupancy_bfactor.py | original | edit occupancy or bfactor in PDB file, used for SimRNAweb | |
100 | 97 | Library | Selection | engine 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 |