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ProPrep 1.19.1

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@Mag14011 Mag14011 released this 16 Sep 06:57
· 4 commits to main since this release
v1.19.1
5a6e097

Added

  • A sander.MPI engine in the MD Manager. AmberTools ships sander and
    sander.MPI but not pmemd, so on the installers the only multi-core
    choice, pmemd.MPI, and the default, pmemd, did not exist. The engine
    menus now list sander, sander.MPI, pmemd, pmemd.MPI, pmemd.cuda in that
    order, mark any engine that is not installed, default to the best engine
    that is, and the automatic recommendation uses sander.MPI when pmemd.MPI
    is absent. Selecting sander.MPI asks for the number of MPI tasks.
  • A "Workshop Protocol (CPU, under an hour)" workflow with its own
    templates: 1000-cycle minimization, 20 ps heating, 100 ps NPT, 300 ps
    production. Measured end to end on a 3923-atom peptide box: 41 minutes
    with sander.MPI on 4 laptop cores.

Changed

  • Session replay matches a recorded menu answer by the option's label, not
    only its number. A recording stores both; when a menu has been reordered
    since (the engine menu above), replay picks the key that now carries the
    recorded label and says so.

Fixed

  • MD Manager: on entering execution with a simulation still running from an
    earlier session, restoring it printed "Warning: Could not restore process
    ...: 'MolecularDynamicsManager' object has no attribute
    '_restore_workflow_pending_steps'" and forgot the running process. The
    call was to a method that never existed; the workflow's pending steps are
    restored by the existing file-wide restore that follows.
  • Protonation State Analyzer failed with "'int' object has no attribute
    'items'" on any multi-model structure (NMR ensembles such as 1UAO) when
    one model was selected in PDB Filter. The chosen model index was stored
    inside filter_selections next to the per-chain selections, so the
    analyzer, the structure viewer's annotation summary and the disulfide
    detector's chain mapping could all trip over it. The index now has its
    own workspace key, selected_model_idx, and the consumers ignore any
    non-chain entry left by an older run.

Installers (SHA-256)

Self-contained installers with AmberTools, MODELLER and every dependency; no conda needed. See INSTALL.md.

a24c55ef2b99b51bf64d8fbeede695a6a48d9f9d1e9b42e5fddad48d5584b45d  ProPrep-1.19.1-Linux-x86_64.sh
017cd5396db673509230978ca544d204142d039bc484c74f5f3dbaeb9b2209b7  ProPrep-1.19.1-MacOSX-arm64.sh
bff5014c7c5ac7c0e33cecbe76ca5a41d9314da58972f41b9ab7c31cbfac9457  ProPrep-1.19.1-MacOSX-x86_64.sh
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