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Merge pull request #55 from rs-station/refactor-args
Refactor argument parsers to avoid duplication
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,244 @@ | ||
| """ | ||
| Dictionaries for arguments parsed by one or more matchmaps utilities | ||
| """ | ||
|
|
||
| matchmaps_description = ( | ||
| "Compute a real-space difference map. " | ||
| "You will need two MTZ files, which will be referred to throughout as 'on' and 'off', " | ||
| "though they could also be light/dark, bound/apo, mutant/WT, hot/cold, etc. " | ||
| "Each mtz will need to contain structure factor amplitudes and uncertainties; you will not need any phases. " | ||
| "You will, however, need an input model (assumed to correspond with the 'off' state) which will be used to determine phases. " | ||
| "The input file may be in .pdb or .cif format. " | ||
| "Please note that both ccp4 and phenix must be installed and active in your environment for this function to run. " | ||
| "" | ||
| "More information can be found online at https://rs-station.github.io/matchmaps/index.html" | ||
| ) | ||
|
|
||
| matchmaps_mr_description = ( | ||
| "Compute a real-space difference map between inputs in different space groups / crystal packings. " | ||
| "You will need two MTZ files, which will be referred to throughout as 'on' and 'off', " | ||
| "though they could also be light/dark, bound/apo, mutant/WT, hot/cold, etc. " | ||
| "Each mtz will need to contain structure factor amplitudes and uncertainties; you will not need any phases. " | ||
| "You will, however, need an input model (assumed to correspond with the 'off' state) which will be used to determine phases. " | ||
| "The input file may be in .pdb or .cif format. " | ||
| "Please note that phenix must be installed and active in your environment for this function to run. " | ||
| "" | ||
| "If your mtzoff and mtzon are in the same spacegroup and crystal packing, see the basic matchmaps utility. " | ||
| "More information can be found online at https://rs-station.github.io/matchmaps/index.html" | ||
| ) | ||
|
|
||
| matchmaps_ncs_description = ( | ||
| "Compute an 'internal' real-space difference map between NCS-related molecules. " | ||
| "You will need an MTZ file with structure factor amplitudes and optionally containing phases, and a PDB/CIF file." | ||
| "" | ||
| "Please note that phenix must be installed and active in your environment for this function to run. " | ||
| "" | ||
| "More information can be found online at https://rs-station.github.io/matchmaps/index.html" | ||
| ) | ||
|
|
||
| base_and_mr_args = ( | ||
| (("--mtzoff", "-f"), { | ||
| "nargs": 3, | ||
| "metavar": ("mtzfileoff", "Foff", "SigFoff"), | ||
| "required": True, | ||
| "help": ( | ||
| "MTZ or sfCIF containing off/apo/ground/dark state data. " | ||
| "Specified as [filename F SigF]" | ||
| ), | ||
| }), | ||
|
|
||
| (("--mtzon", "-n"), { | ||
| "nargs": 3, | ||
| "metavar": ("mtzfileon", "Fon", "SigFon"), | ||
| "required": True, | ||
| "help": ( | ||
| "MTZ or sfCIF containing on/bound/excited/bright state data. " | ||
| "Specified as [filename F SigF]" | ||
| ), | ||
| }), | ||
|
|
||
| (("--pdboff", "-p"), { | ||
| "required": True, | ||
| "help": ( | ||
| "Reference PDB or mmCIF corresponding to the off/apo/ground/dark state. " | ||
| "Used for rigid-body refinement of both input MTZs to generate phases." | ||
| ), | ||
| }), | ||
| (("--on-as-stationary",), { | ||
| "required": False, | ||
| "action": "store_true", | ||
| "default": False, | ||
| "help": ( | ||
| "Include this flag to align 'off' data onto 'on' data. By default, 'off' data is stationary and 'on' data is moved." | ||
| ), | ||
| }), | ||
|
|
||
| (("--alpha",), { | ||
| "required": False, | ||
| "type": float, | ||
| "default": 0, | ||
| "help": ( | ||
| "Alpha to use for error weighting of F-obs prior to Fourier Transform. " | ||
| "Weights are computed as: 1 / ((1+(alpha*(SigF^2)) / <SigF>^2). " | ||
| "Default value is alpha=0, e.g., no weighting is performed. " | ||
| ) | ||
| }), | ||
|
|
||
| (("--unmasked-radius",), { | ||
| "required": False, | ||
| "type": float, | ||
| "default": 5, | ||
| "help": ( | ||
| "Maximum distance (in Anstroms) away from protein model to include voxels. Only applies to the 'unmasked' difference map output. " | ||
| "Defaults to 5. " | ||
| "Note that the regular difference map (e.g. the 'masked' version) is not affected by this parameter and maintains a solvent mask radius of 2 Angstroms." | ||
| ), | ||
| }), | ||
|
|
||
| (("--rbr-selections", "-r"), { | ||
| "required": False, | ||
| "default": None, | ||
| "nargs": "*", | ||
| "help": ( | ||
| "Specification of multiple rigid-body groups for refinement. By default, everything is refined as one rigid-body group. " | ||
| ), | ||
| }), | ||
| ) | ||
|
|
||
| ncs_args = ( | ||
| (("--mtz", "-m"), { | ||
| "nargs": "*", | ||
| "required": True, | ||
| "help": ( | ||
| "MTZ or sfCIF file containing structure factor amplitudes. " | ||
| "Specified as [filename F SigF] or [filename F]. " | ||
| "SigF is not necessary if phases are also provided" | ||
| ), | ||
| }), | ||
|
|
||
| (("--phases",), { | ||
| "required": False, | ||
| "default": None, | ||
| "help": ( | ||
| "Optional. Column in MTZ/sfCIF file containing phases. " | ||
| "If phases are not provided, phases will be computed via rigid-body refinement of " | ||
| "the provided model and structure factor amplitudes." | ||
| ), | ||
| }), | ||
|
|
||
| (("--pdb", "-p"), { | ||
| "required": True, | ||
| "help": ( | ||
| "Reference PDB or mmCIF. " | ||
| "If phases are not provided, used for rigid-body refinement of input MTZ/sfCIF to generate phases." | ||
| ), | ||
| }), | ||
|
|
||
| (("--ncs-chains", "-n"), { | ||
| "required": True, | ||
| "metavar": ("fixed_chain", "moving_chain"), | ||
| "default": None, | ||
| "nargs": 2, | ||
| "help": ( | ||
| "NCS chains to overlay and subtract, specified as [fixed_chain, moving_chain]." | ||
| "E.g. to overlay chain C onto chain B, specify: --ncs-chains B C" | ||
| ), | ||
| }), | ||
|
|
||
| (("--mapname",), { | ||
| "required": False, | ||
| "default": "matchmaps_ncs", | ||
| "help": "Base filename for the output map files. " | ||
| }) | ||
| ) | ||
|
|
||
| common_args = ( | ||
| # args used by all three utilities | ||
| (("--ligands", "-l"), { | ||
| "help": "Any .cif restraint files needed for refinement", | ||
| "required": False, | ||
| "default": None, | ||
| "nargs": "*", | ||
| }), | ||
|
|
||
| (("--input-dir", "-i"), { | ||
| "help": "Path to input files. Optional, defaults to './' (current directory)", | ||
| "required": False, | ||
| "default": "./", | ||
| }), | ||
|
|
||
| (("--output-dir", "-o"), { | ||
| "help": "Path to which output files should be written. Optional, defaults to './' (current directory)", | ||
| "required": False, | ||
| "default": "./", | ||
| }), | ||
|
|
||
| (("--spacing", "-s"), { | ||
| "help": ( | ||
| "Approximate voxel size in Angstroms for real-space maps. Defaults to 0.5 A. " | ||
| "Value is approximate because there must be an integer number of voxels along each unit cell dimension" | ||
| ), | ||
| "required": False, | ||
| "default": 0.5, | ||
| "type": float, | ||
| }), | ||
|
|
||
| (("--dmin",), { | ||
| "help": ( | ||
| "Highest-resolution (in Angstroms) reflections to include in Fourier transform for FloatGrid creation. " | ||
| "By default, cutoff is the resolution limit of the lower-resolution input MTZ. " | ||
| ), | ||
| "required": False, | ||
| "type": float, | ||
| "default": None, | ||
| }), | ||
|
|
||
| (("--no-bss",), { | ||
| "help": ( | ||
| "Include this flag to skip bulk solvent scaling in phenix.refine. By default, BSS is included." | ||
| ), | ||
| "required": False, | ||
| "action": "store_true", | ||
| "default": False, | ||
| }), | ||
|
|
||
| (("--verbose", "-v"), { | ||
| "help": "Include this flag to print out scaleit and phenix.refine outputs to the terminal. Useful for troubleshooting, but annoying; defaults to False.", | ||
| "required": False, | ||
| "action": "store_true", | ||
| "default": False, | ||
| }), | ||
|
|
||
| (("--eff",), { | ||
| "help": "Custom .eff template for running phenix.refine. ", | ||
| "required": False, | ||
| "default": None, | ||
| }), | ||
|
|
||
| (("--keep-temp-files", "-k"), { | ||
| "required": False, | ||
| "default": None, | ||
| "help": ( | ||
| "Do not delete intermediate matchmaps files, but rather place them in the supplied directory. " | ||
| "This directory is created as a subdirectory of the supplied output-dir." | ||
| )}), | ||
|
|
||
| (("--script",), { | ||
| "required": False, | ||
| "default": "run_matchmaps", | ||
| "help": ( | ||
| "Name for a file {script}.sh which can be run to repeat this command. " | ||
| "By default, this file is called `run_matchmaps.sh`. " | ||
| "Note that this file is written out in the current working directory, NOT the input or output directories" | ||
| ) | ||
| }), | ||
|
|
||
| (("--phenix-version",), { | ||
| "required": False, | ||
| "help": ( | ||
| "Specify phenix version as a string, e.g. '1.20'. " | ||
| "If omitted, matchmaps will attempt to automatically detect the version in use " | ||
| "by analyzing the output of phenix.version" | ||
| ) | ||
| }), | ||
| ) |
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