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Release v2.4.11

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@github-actions github-actions released this 13 May 20:31
· 31 commits to main since this release
  • new feature: integrated the VMD ssrestraints plugin into the md task as a peer of constraints and colvar_specs; when a top-level ssrestraints sub-dict appears under an md task, pestifer invokes the plugin against the current state's PSF/PDB to emit a NAMD extraBonds file and wires extraBonds=on / extraBondsFile=<basename>.extrabonds into the generated NAMD config; the schema entry exposes all 13 plugin options (selection text, force constants for protein/NA, na mode, ideal, H-bond restraint sub-options) with defaults that mirror the plugin's own; the generated extraBonds file participates in the artifact pipeline via a new NAMDExtraBondsFileArtifact
  • enhancement: packmol is now version-validated at config-load time; pestifer probes the resolved binary by sending it an empty stdin and parses the version banner, refusing any version below 20.15.1 (the first release with the pbc keyword); when the resolved binary lives inside a conda environment, the error message hints at the AmberTools/packmol-memgen shadow problem and recommends installing a standalone packmol outside the conda env; paths.packmol may be set to an absolute path in user YAMLs to bypass PATH resolution entirely; ex16 and ex17 example YAMLs now demonstrate this pattern
  • enhancement: the PackmolScripter post-run log scan now flags lines containing ERROR, Could not open file, or Could not find and forces a non-zero return code so callers raise; older packmol could exit 0 while still failing internally, and this surfaces those failures
  • bugfix: [package vcompare [vmdinfo version] X.Y] returns unreliable results on VMD builds whose version banner has trailing tags or non-numeric components; replaced the comparison in both pestifer/resources/tcl/macros.tcl and the macro generator in pestifer/core/labels.py with [lindex [split [vmdinfo version] .] 0] < MAJOR, an integer-major-version gate that is robust across builds
  • doc: explain that the mdplot subcommand and task emit per-quantity CSV files alongside plots; explain that density is a pestifer-computed timeseries column derived from the cell volume, not a NAMD output; updated the mdplot 2.4.x enhancement docs (time-on-x-axis, automatic unit selection)
  • test: corrected _ARCHIVE_PREFIX in test_desolvate.py to match the schema default ('artifacts') so the test reflects what terminate actually produces by default; relaxed the per-binary path assertions in test_config_help_examples from strict equality to endswith() so legitimate per-example paths.packmol overrides (such as the absolute paths added to ex16/ex17) do not break the smoke test