Transform fully-fledged silent file(s) into portable minisilent
by storing only the content that can be processed by the rstoolbox.
It is very convenient to store mid-step data in git repositories.
usage: minisilent.py [-h] [-in:file IFILE] [-in:files IFILES [IFILES ...]]
[-out:file OFILE] [-overwrite]
| -in:file | Input silent file (single entry). |
| -in:files | Prefix of input silent files (multiple files).Incompatible with -in:file. |
| -out:file | Output name for minisilent (can be gzipped). |
| -overwrite | Allows overwriting existing file. |
Renames decoys with a new prefix identifier and the same numbering schema that Rosetta uses.
usage: rename_decoys.py [-h] [-in:file IFILE] [-prefix PREFIX]
[-out:file OFILE] [-overwrite]
| -in:file | Input silent file. |
| -prefix | Prefix for the new naming schema. |
| -out:file | Output silent file. |
| -overwrite | Allow overwrite if output file exists. |
Plot any two variables from the Rosetta Silent/Score file.
usage: regplot_rosetta.py [-h] [-in:file IFILE] [-in:files IFILES] [-in:y Y]
[-in:x X] [-plot:title TITLE] [-plot:color COLOR]
[-plot:ylab YLAB] [-plot:xlab XLAB]
[-plot:ylim YLIM YLIM] [-plot:xlim XLIM XLIM]
[-plot:fsize FSIZE FSIZE] [-out:silent]
[-out:file OFILE]
| -in:file | Input silent file (single file) |
| -in:files | Prefix of input silent files (multiple files). Incompatible with -in:file. |
| -in:y | Name of the score for Y axis. |
| -in:x | Name of the score for X axis. |
| -plot:title | Title of the plot. |
| -plot:color | Color of the plot. If number, it refers to the seaborn color palette. Default: 0 |
| -plot:ylab | Label for Y axis. |
| -plot:xlab | Label for X axis. |
| -plot:ylim | Range for Y axis. Default: [None, None] |
| -plot:xlim | Range for X axis. Default: [None, None] |
| -plot:fsize | Size of the figure. Default: [None, None] |
| -out:silent | If True, do not plot on screen. |
| -out:file | Output image file. If None, no file is created. |
Generate a plot for fragment RMSD evaluation. Requires the output from the
r_fraq_qual application in Rosetta.
Note
Depends on rosetta.path and rosetta.compilation, if the quality file is not provided.
See also
usage: plot_fragments_rmsd.py [-h] [-in:frag:small FSMALL]
[-in:qual:small QSMALL] [-in:frag:large FLARGE]
[-in:qual:large QLARGE] [-in:pdb PDB]
[-out:silent] [-out:format FORMAT]
[-out:file OFILE]
| -in:frag:small | Name of the small fragments file. |
| -in:qual:small | Name of the small fragments quality file. |
| -in:frag:large | Name of the large fragments file. |
| -in:qual:large | Name of the large fragments quality file. |
| -in:pdb | PDB file. If quality files are not provided, this input is needed so that r_fraq_qual can be executed. |
| -out:silent | If True, do not plot on screen. |
| -out:format | Make plot vertical (v) or horizontal (h). Default: “h” |
| -out:file | Output image file (.png/.svg). If None, no image is created. |
Check the sequences in the silent files. Creates logo plot and multiple sequence alignment both in text and image format.
usage: check_mutants.py [-h] [-in:file IFILE] [-in:files IFILES]
[-in:fasta IFASTA] [-in:wtfasta FFILE]
[-in:seqID SEQID] [-out:prefix OFILE]
[-out:format {png,svg}] [-out:font IFONT]
| -in:file | Input silent file (single file). |
| -in:files | Prefix of input silent files (multiple files).Incompatible with -in:file. |
| -in:fasta | Input designs in fasta format.Incompatible with -in:file or -in:files. |
| -in:wtfasta | Rerefence sequence (single FASTA). |
| -in:seqID | Sequence chain identifier. Default: “A” |
| -out:prefix | Prefix for the outputs. |
| -out:format | Possible choices: png, svg Ouptut images format (png/svg). Default: “png” |
| -out:font | Font size for logo plot (might need manual adjustment). Default: 35 |