Release bugfix version: 3.2.1 #158
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This is the crux of this PR: there's too many negatives floating around here. We fold the 'store_false' action and --no- flags together: they cancel each other out. We get a positively worded flag, and make sure to set the default to True. Finally, we assign the ToggleActionFlag type so that both options appear together in the help. Note, we lose some short flags as a result (I don't think this is a loss for clarity). What was -bb, --no-backbone Do not sample backbone using inverse kinematics. (default: True) is now: --[no-]backbone Sample backbone using inverse kinematics. (default: True) This applies to: * -ns, --no-scale → --[no-]scale * -nosub, --no-subtract → --[no-]subtract * -bb, --no-backbone → --[no-]backbone * -sa, --no-sample-angle → --[no-]sample-angle * -T, --no-threshold-selection → --[no-]threshold-selection * -Ts, --no-segment-threshold-selection → --[no-]segment-threshold-selection
… Consistency! --write_intermediate_conformers → --write-intermediate-conformers --resolution_min → --resolution-min --clash_scaling_factor → --clash-scaling-factor --external_clash → --external-clash --bulk_solvent_level → --bulk-solvent-level --rmsd_cutoff → --rmsd-cutoff Dest variables will still maintain underscores.
The logic has to change here, since the variable was a negative.
Flags that changed: * --no-waters → --no-waters-clash Loss of short flags (now-required long form): * -ns (--no-scale) * -nosub (--no-subtract) * -nw (--no-waters-clash) * -bb (--no-backbone) * -sa (--no-sample-angle) * -T (--no-threshold-selection) Now-hyphenated flags: * --resolution_min → --resolution-min * --clash_scaling_factor → --clash-scaling-factor * --external_clash → --external-clash * --bulk_solvent_level → --bulk-solvent-level * --rmsd_cutoff → --rmsd-cutoff New flags: * --write-intermediate-conformers Also: * Remove unused import 'from os import path'
Flags that changed (maintained short form): * --build-stepsize → --dofs-per-iteration (-b) * --stepsize → --dihedral-stepsize (-s) * --no-waters → --no-waters-clash Loss of short flags (now-required long form): * -ns (--no-scale) * -nosub (--no-subtract) * -nw (--no-waters-clash) * -nb (--no-build) * -nl (--no-local) * -T (--no-threshold-selection) Now-hyphenated flags: * --resolution_min → --resolution-min * --clash_scaling_factor → --clash-scaling-factor * --external_clash → --external-clash * --bulk_solvent_level → --bulk-solvent-level * --write_intermediate_conformers → --write-intermediate-conformers
…-in-options Improve flags (& --help) of qfit programs
Described in the paper... functionality had disappeared...
Mechanism was there, needed to add the option into the ArgParser.
QFitSegment pushes its options.random_seed into the relabeller options.
Add --random-seed to provide option for reproducible runs
PDB: 7A4M; ApoFerritin Chain A
0.01=> self.options.rmsd_cutoff (imported via qFit Base options).
Add --rmsd-cutoff option to qFit-ligand
--write-intermediate-conformers => --write_intermediate_conformers
Update setup-miniconda GitHub Action (repairs failing CI)
adding CA option in the B-factor script & changing to remove b-factors from H atoms.
removing ::set-env flag and adding in environmental.yml to propagate to all tests.
adding file to create qfit conda environment
Add new analysis scripts, refactor get_metrics
…ction Correcting README example for post qFit refine cryoEM
1. Previous indentation meant we only looped through residues of the last chain. We now loop through residues for all matching chains. 2. Previously, only the last-calculated chain of rmsd data was stored. We now store RMSD for all matching chains. 3. Use an f-string filename for readability.
Fixup indentation in alpha_rmsd
Preserve SCALE/CRYST1 records through qfit_protein runs
Merge branch 'feature/vscode-development' into dev
…a-forge Switch to conda-forge: - Updated numpy requirements, and on Windows _only_, solving environment.yml was impossible. This is the main reason for the switch. - cvxopt hasn't been updated in a while in anaconda repo. Use the appropriate way to choose blas compiled against mkl, see https://conda-forge.org/docs/maintainer/knowledge_base.html#blas
Previously, this caused > FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. Also: this returns a copy, not a view, but we will still copy just to be sure.
Move to python 3.7, 3.8
The LICENSE file exists for a reason, it is redundant to write the licence on top of every file.
Remove licences, update citation
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Release Notes
Users:
qfit_final_refine_xray.shorqfit_final_refine_cryoem.sh--[no-]sample-angle)--write_intermediate_conformersbetween qfit_ligand and qfit_proteinDevelopment: