Changelog¶

Pestifer follows Semantic Versioning and documents changes below.

[Unreleased]¶

[2.5.2] - 2026-05-28¶

bugfix: a plain pip install pestifer (without the optional ligand-paramgen extra) crashed on every CLI invocation with ModuleNotFoundError: No module named 'dimorphite_dl'; the optional rdkit and dimorphite_dl dependencies were imported at module load time in charmmff.ligand_paramgen.protonation and charmmff.ligand_paramgen.mol2_writer, and since subcommands/__init__.py eagerly imports the make-ligand-mol2 subcommand at startup, those imports ran for every command. The imports are now lazy (deferred into the functions that use them) and raise a clear pip install pestifer[ligand-paramgen] hint when actually needed
bugfix: the dependencies array in pyproject.toml was missing its closing ]

[2.5.1] - 2026-05-28¶

bugfix: PSFContents.remove_ignored_residues crashed with TypeError: 'PSFAtom' object is not subscriptable because it wrongly indexed the result of BaseObjList.get() with [0]; get() returns the matched object directly when there is exactly one match (which is always the case for an atom-by-serial lookup), so the trailing [0] was indexing into the atom itself
bugfix: AsymmetricUnit extended ignored_residues twice with the same more_ignored_residues list (a copy-paste duplicate around the intervening grafts.assign_residues call), causing PSFContents.remove_ignored_residues to be called for the same residues twice and crash on the second pass when self.atoms.get() returned None (atoms already removed) and self.atoms.remove(None) invoked PSFAtom.__eq__ against None.serial
bugfix: continuation+psfgen builds that inserted protein residues at glycosylation sites (e.g. extending the HIV-1 gp41 ectodomain from MPER residue 685 through TM residue 710 on a pre-built glycoprotein) emitted glycan-link patches against the protein segment (patch 14ba A:1222 A:1223) instead of the glycan segment (patch 14ba AG01:1222 AG01:1223), causing psfgen to abort with no residue X of segment A / MOLECULE DESTROYED BY FATAL ERROR; two related issues were fixed: (a) Link._from_psflinkpatch populated chainID1/chainID2 from the psfgen segname but left segname1/segname2 unset, so when chainID1 was later remapped from the segname (AG01) to the biological chainID (A) so the lookup against PDB-derived residues could succeed, the writer at PsfgenScripter.write_link (which prefers L.segname1 over L.residue1.chainID) had nothing but the biological chainID to fall back on; (b) ResidueList.renumber, when renaming a glycan residue whose resid collided with a newly inserted protein residue (glycan A:686 → A:1324 after inserting protein A:686), only propagated the resid update to links keyed by biological chainID and skipped links from PSF REMARKS whose chainID1/chainID2 carried the psfgen segname, so those stale links became orphans and the orphan cleanup at LinkList.assign_residues removed the entire glycan tree from the residue list — leaving segment AG01 with only the renumbered root and stripping the patches’ target residues; renumber now also keys its mapper_by_chain by segname when segname differs from chainID

[2.5.0] - 2026-05-18¶

new feature: pestifer make-ligand-mol2 subcommand that, given a 4-letter RCSB PDB code or a path to a local .pdb file, generates a CGenFF-ready Tripos mol2 file for every HETATM ligand whose resname is not already defined in the loaded CHARMM topologies; for each unknown ligand it fetches the SMILES from the RCSB Chemical Component Dictionary (preferring the OpenEye canonical-stereo descriptor), builds an RDKit Mol whose heavy atoms are in PDB order and carry the original PDB atom names, protonates at the target pH (default 7.4) via Dimorphite-DL, places explicit Hs in 3D, and writes the mol2 via Open Babel with --title <RESNAME> so the CGenFF binary/web tool registers the resulting RESI under the correct residue name (rather than the leaked tempfile path); per-ligand failures are surfaced in a summary table without aborting the run, and --smiles RESNAME=... overrides the RCSB lookup when a custom tautomer or charge state is needed
new feature: new pestifer.charmmff.ligand_paramgen subpackage exposes the building blocks reused by make-ligand-mol2 as a library: fetch_ligand_smiles(comp_id) (RCSB lookup with LRU caching and HTTP-error → RCSBLookupError mapping), protonate_ligand(residue, smiles, ph) (RDKit + Dimorphite-DL pipeline that preserves PDB heavy-atom order and stamps each heavy atom with the original PDB name on the _pdb_name property), write_mol2(mol, resname, outpath) (PDB-block-via-obabel writer that propagates _pdb_name and assigns sequential H1, H2, … names to hydrogens), and generate_ligand_mol2s(parsed, charmmff_content, outdir, ph, smiles_overrides) (the orchestrator the subcommand calls, which the build workflow will also call for unknown ligands)
new feature: well-known per-user toppar cache at ~/.pestifer/toppar/; when this directory exists, pestifer automatically prepends it to charmmff.user_custom.searchpath so .str files dropped there are picked up by every build without requiring a user_custom block in YAML; any project-local searchpath entry is loaded after the cache and overrides it (last-loaded wins) with a warning naming both files; designed as the default destination for .str files produced by running make-ligand-mol2 output through the CGenFF binary or web tool
enhancement: charmmff.user_custom.searchpath entries now expand ~/ (the user’s home directory) and shell environment-variable references like $HOME/foo or ${SCRATCH}/charmm before the directory check; previously those were taken literally and silently failed
behavior change: CHARMMFFContent.add_custom_directory no longer asserts on duplicate-basename clashes between searchpath entries; instead, the later-loaded file wins and a warning is emitted naming both paths (the assertion previously crashed pestifer when, e.g., the user’s project happened to contain a .str file with the same basename as one in the cache); same-resname clashes across differently-named files in the searchpath also emit a warning and follow last-loaded-wins semantics, so a project-local override of a cached parameterization is surfaced without silently merging
new optional dep: [project.optional-dependencies] table in pyproject.toml declares an ligand-paramgen extra (pip install 'pestifer[ligand-paramgen]') that pulls in rdkit and dimorphite_dl; the obabel binary remains a runtime-PATH dependency, documented alongside the new subcommand
test: tests/unit/test_charmmff/test_charmmffcontent.py::TestCharmmffContent.setUpClass was picking the CHARMMFF version directory by mtime rather than by parsed month-year (the production ResourceManager.charmmff_version_dirs() orders semantically); when the feb26 and jul24 directories were extracted out of release order, mtime selected jul24 and the test’s hard-coded counts (calibrated against feb26) failed by ~1400 residues; setUpClass now delegates to ResourceManager.charmmff_version_dirs() so the test always exercises the same CHARMMFF release that production code uses
test: new tests/unit/test_charmmff/ligand_paramgen/ package covers the ligand-paramgen building blocks (29 tests): protonation invariants on five SMILES across a pH=7.4 charge range, RCSB descriptor-priority selection under unittest.mock of requests.get, mol2 title/atom-name round-trip via the real obabel binary, and orchestrator-level altloc dedup and known-resname filtering using real Hetatm objects; test_charmmffcontent.py gains three TestAddCustomDirectory cases (tilde expansion, duplicate-basename warning + last-wins, duplicate-RESI warning + last-wins) that build a stub CHARMMFFContent via __new__ to avoid paying the full tarball-load cost
doc: new docs/source/subs/make-ligand-mol2.rst covers the subcommand with examples (PDB code, local file, SMILES override, pH override) and outlines the CGenFF round-trip workflow (web tool → ~/.pestifer/toppar/); linked from the subcommand toctree in usage.rst; the charmmff.user_custom schema docstring gains “Per-user toppar cache” and tilde-expansion sections

[2.4.13] - 2026-05-14¶

behavior change: make_membrane_system no longer silently turns on NAMD’s on-the-fly pressureProfile calculation during NPT/NPAT bilayer-relaxation stages on CPU NAMD; pressure profile calculation is now opt-in via a new top-level make_membrane_system.compute_pressure_profile block (enabled: false default, plus slabs / freq knobs that map to pressureProfileSlabs / pressureProfileFreq); previously, any NPT/NPAT stage whose other_parameters did not explicitly mention pressureProfile had it auto-injected as on on CPU builds, surprising GPU users (the processor-type guard correctly skipped injection on GPU but the opt-out default was hostile and unintuitive); the mdplot task’s profiles=['pressure'] list, which was unconditionally requested by equilibrate_bilayer, is now likewise gated on the new flag so no spurious pressure-profile plotting is attempted when the data is not produced
new feature: make_membrane_system now hard-errors with PestiferBuildError if compute_pressure_profile.enabled: true is set under GPU NAMD (processor-type: gpu), or if any explicit other_parameters.pressureProfile setting in a stage is truthy on GPU; CUDA-enabled NAMD does not support pressureProfile, and the previous silent-strip behavior masked user misconfiguration; the error message names the offending stage’s ensemble and points at the two ways to fix the conflict (disable the flag, or use a CPU NAMD build)
doc: ex16 and ex17 example YAMLs (membrane-embedded HIV-1 gp41 MPER-TM trimer builds) now carry a header comment explaining that their post-equilibration NPAT stage and packaged production run use pressureProfile, so they must be run with a CPU NAMD build; the comment names the specific other_parameters blocks to strip if a user wants to run them on GPU

[2.4.12] - 2026-05-13¶

bugfix: PackmolLogParser failed on logs produced by packmol 21.x because the new release reorganized its header in three breaking ways: the Periodic boundary condition activated: line became multi-line with indented Minimum coordinates: and Maximum coordinates: rows, the PBC Reference box: line was removed entirely (its information now carried by the min/max rows), and the per-type Maximum number of GENCAN loops for type: lines were dropped in favor of the aggregate for all molecule packing: value alone; the parser now auto-detects the PBC format by checking whether numeric tokens trail the activation line and reconstructs both pbc_boxsize (max-min) and pbc_reference_box (concatenated min+max) so downstream consumers see the same metadata schema; logs from packmol 20.15.1 continue to parse correctly via the legacy code path
bugfix: PackmolLogParser initialized each structure’s current_gencan_loops counter only inside the per-type Maximum number of GENCAN loops for type: block, so a KeyError was raised on the first GENCAN report for any structure whose type lacked that header line (always the case in packmol 21.x); the counter is now initialized to 0 at structure-creation time
bugfix: PackmolLogParser.finalize() crashed with 'Axes' object is not subscriptable for single-structure packs because plt.subplots(1, 1) returns a bare Axes rather than a 1-element array; squeeze=False plus ax.flatten() makes the indexing uniform

[2.4.11] - 2026-05-13¶

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

[2.4.10] - 2026-05-11¶

enhancement: GPU mode is now auto-detected by comparing paths.namd3 and paths.namd3gpu; if the two paths differ and namd3gpu is found in PATH, pestifer switches to GPU mode automatically — no namd.processor-type setting required; processor-type is retained in the schema for backward compatibility but is ignored; paths.namd3gpu defaults to namd3 (CPU mode when identical); workstation users with separate CPU and GPU-resident NAMD3 builds simply set paths.namd3gpu to the GPU binary name/path; the --gpu CLI flag now correctly propagates GPU mode to both the config and the live NAMD scripter
bugfix: GPU-resident NAMD3 config parameter renamed from GPUResident to CUDASOAintegrate to match current NAMD3 release notes; outputEnergies: 500 added to the gpu-resident schema section (NAMD recommends 500–1000 for GPU-resident mode); writescript now suppresses any param key that appears in gpu-resident (case-insensitive) so each parameter appears exactly once in the generated config file
enhancement: multi-GPU GPU-resident launches now include +pmepes K to assign fewer PEs to the PME device and reduce load imbalance; K is computed as total PEs minus 8×(N−1) for N GPUs, matching the NAMD3 recommended work distribution examples

[2.4.9] - 2026-05-11¶

enhancement: mdplot timeseries plots now use simulation time on the bottom x-axis instead of raw timestep index; units are auto-selected by magnitude (ps when total duration < 1000 ps, ns otherwise); the integer timestep index is shown on the top spine via a secondary x-axis; NAMDLogParser.finalize() adds a dt_fs constant column to the energy dataframe so that chained runs with different timestep sizes are handled correctly — simulation time is computed in the plot task as cumsum(dt_fs × ΔTS / 1000) across the concatenated dataframe, which correctly accumulates time across run segments regardless of whether the timestep changes between segments
enhancement: mdplot timeseries y-axis unit labels now default to the correct physical units for known NAMD output columns (kcal/mol for energy terms, K for temperature, bar for pressure, Å³ for volume) rather than *; energy quantities whose maximum absolute value exceeds 1000 kcal/mol are automatically scaled by 1/1000 and labeled 1000 kcal/mol to avoid unwieldy tick magnitudes

[2.4.8] - 2026-05-11¶

bugfix: scripts/release.sh did not update CITATION.cff, causing the release workflow to fail when it checked that the citation version matched the release; release.sh now bumps both version and date-released in CITATION.cff alongside pyproject.toml

[2.4.7] - 2026-05-11¶

bugfix: pestifer mdplot --timeseries crashed with KeyError: 'pressureprofile' when --profiles was not supplied; the --profiles argument defaulted to ['pressure'], causing the task to look for a pressure-profile dataframe that was never loaded; fixed by changing the default to []; also added a guard in the task to filter profiles to only those whose dataframe was actually loaded, so the same crash cannot recur even when profiles are explicitly requested but absent from the log files
bugfix: pestifer.core.config imported Yclept via from ycleptic.yclept import Yclept, a path that no longer exists after ycleptic’s 2.0.5 src/ restructure; updated to from ycleptic import Yclept using the new stable public API (requires ycleptic >= 2.0.6)

[2.4.5] - 2026-05-11¶

bugfix: CharmmParamFile.merge() incorrectly deduplicated multi-term dihedral parameters; CHARMM sums all dihedral terms for the same atom-type quartet that have different periodicities n, so deduplication must key on (canonical_quartet, n) rather than the quartet alone; the old code collapsed all terms for a quartet to a single entry, silently discarding all but one periodicity; added five static key methods (_bond_key, _angle_key, _dihedral_key, _improper_key, _nbfix_key) and rewrote merge() to use them; also added 8 unit tests covering bond/dihedral/nonbonded deduplication and multi-term dihedral preservation

[2.4.4] - 2026-04-28¶

bugfix: graft alignment VMD selections produced zero atoms for all grafts in structures where native glycan resids were renumbered by the narrow convention; the N-point alignment code introduced in v2.3.0 used post-renumbering resids from G.residues instead of the original shortcode resids (G.target_root / G.target_partners); since $m4 is the raw source PDB which has not yet been renumbered at the time graft alignment runs in the Tcl script, the selections must use the original PDB resids; reverted to the pre-v2.3.0 approach of using G.target_root and G.target_partners directly, generalized to N alignment points
bugfix: terminus-management patches (NTER, CTER, GLYP, PROP, ACE, CNEU, etc.) and their pestifer undo-counterparts (XCTR, XNTR, XGLP, XPRP) recorded in REMARKS patch lines of a continuation PSF were being re-propagated into the next psfgen script as generic patches; CTER/NTER loop-boundary records were emitted as last/first segment directives (applying to the wrong, segment-terminal residues), while XCTR/XNTR records were emitted as standalone patch commands against residues whose C=O / N-HN bonds had never been removed, producing duplicate bonds and a degenerate C O C angle that NAMD cannot parameterize; fixed by filtering all terminus-management and undo patches out of PSFContents.generic_patches

[2.4.3] - 2026-04-28¶

bugfix: generic single-residue patches (NTER, CTER, GLUP, ASPP, NNEU, and custom patches) recorded in REMARKS patch lines of an input PSF were silently dropped when a psfgen task followed a continuation task; PSFContents now extracts these patches into generic_patches and AsymmetricUnit propagates them through the objmanager pipeline so they are re-emitted as first/last/patch commands in the new psfgen script
bugfix: ring_check task now operates correctly without an XSC file (vacuum / non-periodic systems); previously the task assumed a periodic box was always available; in non-periodic mode the bounding box is derived from coordinate extents and minimum-image wrapping is skipped
test: added tests/unit/test_tasks/test_psfgen.py — slow regression test that builds a vacuum BPTI PSF/PDB (6pti, mirroring example 1), then loads it via a continuation task and re-runs psfgen with one non-cysteine mutation, verifying that all three DISU patch REMARK records survive into the stage-2 PSF

[2.4.2] - 2026-04-28¶

bugfix: PSFContents used BaseObjList.get() to filter atoms by segtype when building the topology-active atom list for ring_check; get() returns None for zero matches and a bare object for exactly one match, causing a TypeError on len(); replaced with filter(), which always returns a BaseObjList
new feature: custom exception hierarchy (PestiferError, PestiferBuildError) replaces bare RuntimeError/ValueError/Exception raises throughout the task and molecule layers; the CLI top-level handler catches any PestiferError and logs a clean error message with sys.exit(1) rather than printing a Python traceback; ring_check with delete: none now raises PestiferBuildError instead of silently logging

[2.4.1] - 2026-04-27¶

change: ring_check task now terminates the build with an error when any glycan ring is found to be pierced; because glycan residues are covalently bonded to the protein they cannot be deleted, so pestifer logs each offending segment and residue and raises a PestiferBuildError; the recommended remedy is to rebuild with a different random seed or add more minimization before the ring_check task; non-glycan piercings (e.g. sterol rings) continue to be handled by the delete parameter as before

[2.4.0] - 2026-04-27¶

new feature: setup-vmd subcommand generates ~/.pestifer/vmd_init.tcl with the absolute path to pestifer’s Tcl root and appends a one-line source hook to ~/.vmdrc; re-running after upgrading pestifer or switching conda environments keeps VMD’s Tcl package paths in sync
new feature: align mod accepts a new ref_sourceID field (RCSB PDB ID) as an alternative to ref_pdb; the reference structure is downloaded to the working directory automatically, keeping base_coordinates and base_molecule invariant without requiring a second fetch task; downloaded files are registered as pipeline artifacts and swept into the artifacts tarball on cleanup
new feature: terminate task logs a structured system report at the end of every build: output file sizes, topology feature counts (atoms, bonds, angles, dihedrals, impropers, cross-terms from the PSF), and periodic box vectors and lengths from the XSC file
change: package.basename in the terminate task now controls only the tarball filename and NAMD configuration script name; coordinate state files (PSF, PDB, COOR, XSC, VEL) retain their terminate-task basename inside the tarball and are no longer renamed
bugfix: VMDScripter.writescript() used substring matching to detect an existing exit statement, causing exit 1 in error-branch Tcl code to suppress injection of the final bare exit and leaving VMD hanging after script completion; fixed to require an exact line match
change: progress bar timer widget now uses progressbar.utils.len_color (ANSI-aware) instead of Python’s built-in len so bars correctly fill to the terminal’s right edge regardless of color escape sequences in the timer label

[2.3.1] - 2026-04-24¶

bugfix: GraftList.assign_residues() now removes base-structure residues downstream of the outermost receiver (and their links) before applying graft external links; previously, if the base structure carried any sugars beyond the outermost receiver resid, psfgen would apply both the existing glycosidic patch and the new graft external link to the same acceptor oxygen, producing a doubly-bonded OC301 and a CC3162 OC301 CC3162 CC3161 dihedral that NAMD cannot parameterize

[2.3.0] - 2026-04-24¶

bugfix: six pdbalias atom entries for sialic acid (ANE5AC) in labels.py incorrectly used ANE5 as the residue prefix; psfgen applies atom aliases using the post-residue-alias CHARMM name (ANE5AC), so these aliases were silently ignored and coordinate assignment for SIA atoms failed; all six entries corrected to ANE5AC
new feature: glycan grafts now support N-point alignment with dihedral pre-conditioning; the graft shortcode target now accepts any number of alignment residues separated by # (e.g., G_572#573#574), and the source accepts the same number of index resids (e.g., 4b7i,C_1#2#3-8); before computing the measure fit transformation, pestifer matches each glycosidic dihedral (phi, psi, and omega for 1→6/2→6 linkages) in the source stem to the corresponding angle in the target stub by rotating the outer branch around the appropriate bond axis; this substantially improves donor atom placement when the target already carries a multi-sugar stub

[2.2.11] - 2026-04-24¶

bugfix: toppar_all36_carb_imlab.str added to the default CHARMM stream file list; this file contains supplementary carbohydrate parameters (e.g., CC3162 OC301 CC3162 angle) needed for certain glycan-glycan ether linkages in N-glycan trees; its absence caused NAMD to abort with “UNABLE TO FIND ANGLE PARAMETERS” on glycosylated systems built from multi-donor glycan grafts
new feature: ring_check task now includes glycan segments in its default segtypes (previously only lipid); glycan pyranose rings are now detected and checked for lipid-chain piercing by default; note that for glycan rings pierced by lipid chains, delete: piercer is more appropriate than the default delete: piercee
new feature: mdplot task now saves PNG output to a subdirectory (default mdplots/) specified by the new output_dir spec; plots are marked keep=True so they survive the artifacts tarball sweep and are immediately visible after the run
change: mdplot default colormap changed from viridis to tab10 for better perceptual separation of discrete traces on multi-trace plots
change: mdplot single-trace plots no longer show a legend even when legend: True is set

[2.2.10] - 2026-04-20¶

bugfix: graft source molecules (e.g., a standalone glycan PDB fetched for grafting) are no longer subjected to glycan chainID/segname/resid reassignment; the original chainIDs and resids are preserved so that activate() can correctly locate the source segment by its original chainID
bugfix: graft donor residues now go into a dedicated psfgen segment (e.g., NG01) instead of being mixed into the protein segment; the segname is computed from the target chain and existing glycan count, consistent with the base molecule glycan naming convention
bugfix: graft bond patch segnames now correctly reference the base molecule’s psfgen segnames; receiver-side residues are looked up via res_segname_map, donor-side residues use the graft’s dedicated segname (graft_segname), eliminating stale source-PDB chainID references in patch commands
test: added test_graft_segname_and_link_segnames to tests/unit/test_objs/test_graft.py covering the full segname/resid pipeline for a glycan graft
test: added tests/unit/test_molecule/test_graft_molecule.py — integration tests using real PDB structures (4b7i chain C glycan grafted onto 1gc1 chain G protein) verifying activation counts, graft_segname assignment, and link segname correctness end-to-end through the AsymmetricUnit pipeline

[2.2.9] - 2026-04-20¶

new feature: two glycan resid numbering conventions are now available via sequence.glycans.numbering
- narrow (default): glycan blocks start above the maximum protein resid of the parent chain; block size controlled by sequence.glycans.max_glycan_size (default 30)
- wide: the root glycan monomer (directly bonded to the protein) gets the protein attachment resid plus sequence.glycans.wide_shift (default 3000); subsequent monomers increment by 1 in BFS order from the root (e.g. NAG on ASN 123 → resid 3123, next monomer → 3124)
bugfix: --ncpus CLI option and namd.ncpus config key now correctly override NAMD PE count; the processor-info banner reflects the effective count at startup
bugfix: under SLURM, NAMD (CPU/multicore mode) is now launched as numactl --localalloc namd3 +p N script.namd; both charmrun +p N and bare +p N bypass SLURM’s CPU affinity mask, scattering Charm++ worker threads across all NUMA nodes and causing severe startup slowdown due to cross-NUMA memory access during bond-table construction; numactl --localalloc preserves Charm++’s thread placement while ensuring each thread’s memory allocations land on its local NUMA node
bugfix: glycan resid block allocation in the narrow convention now correctly starts above the parent chain’s maximum protein resid rather than from 1, eliminating clashes between glycan and protein resids within the same chainID

[2.2.7] - 2026-04-19¶

new feature: all glycan trees (both polymeric and monomeric) now share the chainID of their attached protein chain, each receives a unique segname ({chainID}G{k:02d}), and resids are block-allocated per chain in attachment-resid order so each glycan owns a non-overlapping resid range allowing future monomer additions; controlled by new sequence.glycans.max_glycan_size parameter (default 30)
new feature: link resid1/resid2 fields are synchronized from residue objects after segment building to keep topology consistent through prune_topology

[2.2.6] - 2026-04-19¶

bugfix: stale pstr() call on StateInterval in loop-declashing debug log replaced with valid attribute access
bugfix: assign_obj_to_attr in BaseObj now correctly handles multi-match lists — previously used type(x) != objList (always True) instead of type(x) != type(objList), causing a ResidueList to be assigned where a single residue was expected, leading to downstream AttributeError
bugfix: prune_topology in SegmentList now uses identity (is) rather than equality (==) when locating and removing residues — after all glycan chainIDs are remapped to their parent protein chain, glycan residues from different source chains (e.g., chain A NAG1 and chain D NAG1) become value-equal but are distinct objects; using __eq__ caused the wrong segment’s residues to be deleted, breaking the glycan patch application
bugfix: unregister_chain is no longer called for pruned glycan segments (e.g., GG03) whose segname is not a registered chainID — previously raised KeyError when a glycan segment was fully pruned by prune_topology
bugfix: asymmetric-unit builder now detects C-terminal insertions and ensures they are built even when include_C_termini: False is set

[2.2.5] - 2026-04-18¶

bugfix: merge task now writes injected PSF REMARKS with a leading space, consistent with psfgen’s own output format

[2.2.4] - 2026-04-18¶

Exclusion logic expressions now tolerate atom-only attributes (e.g., altloc) on objects that lack them, returning False rather than raising an error — so altloc == 'B' can be used safely in a psfgen source exclude list

[2.2.3] - 2026-04-17¶

Now generates a custom “minimal” CHARMM parameter file customized for every system
New merge task for merging independent PSF/PDBs into a single system (no coordinate transformations!)

[2.2.0] - 2026-03-04¶

Now uses Feb 26 CHARMMFF release (Jul 24 is still available as an option)

[2.1.9] - 2026-03-03¶

bugfix: placeholder residues (insertions) now inherit correct segnames
bugfix: psfgen task can now follow a continuation task and add atoms and residues successfully

[2.1.8] - 2026-02-18¶

bugfix: desolvate no longer assumes solvent and non-solvent atoms must have different segnames (but they should)

[2.1.7] - 2025-11-19¶

bugfix: insertion resid incrementation bug fixed

[2.1.6] - 2025-10-22¶

bugfix: glycan declashing

[2.1.5] - 2025-10-22¶

testing GLYCAN_PENDANT crotation

[2.1.4] - 2025-10-12¶

multiple bugfixes in desolvate and make-namd-restart subcommands

[2.1.3] - 2025-10-10¶

multiple bugfixes in make-pdbrepository
dynamic patch for toppar_all36_lipid_cardiolipin.str to correct bad IC’s
deleted unnecessary double-counting check for glycosylation-type validation
added cardiolipin substream to built-in pdbrepository

[2.1.2] - 2025-09-30¶

bugfix for orienting transmembrane proteins before calculating membrane x,y dimensions
bugfix for grafts onto targets that have H’s from sources that do not

[2.1.1] - 2025-09-23¶

bugfixes in mdplot (pressure profiles) and make_membrane_system (dum_pdb)
updated input configs for examples 16 and 17

[2.1.0] - 2025-09-19¶

bugfixes in cif-to-pdb resid mapping output, production NAMD script writer, and mispelling of rcsb
new feature: test_standards optional subtask added to terminate task to enable generation of gold standard results and comparisons to them

[2.0.3] - 2025-09-15¶

mdplot now correctly treats cpu_time and wall_time as running sums over chained MD runs
bugfixes in new-system subcommand and terminate task
bugfix in bilayer_embed.tcl for z-translation
updated pidibble dependency to allow for downloading structures from OPM

[2.0.1] - 2025-09-04¶

on-the-fly patching toppar_all36_prot_modify_res.str so that PRES ZNHD and PRES ZNHE are correct
validate task introduced to allow for validation of psfgen-produced PSF and PDB files
include and exclude now allow full logical expressions for better control of inclusion and exclusion of atoms and residues from source structures
fetch task now separately responsible for downloading necessary pdb files
continuation task now separately responsible for starting from a given state (PSF/PDB/COOR/XSC)
mdplot now correctly treats cpu_time and wall_time as running sums over chained MD runs
complete refactoring to use pydantic’s BaseModel

[1.21.2] - 2025-07-17¶

first official Zenodo release
fixed bug in user-modifiable segtype handling

[1.21.1] - 2025-07-15¶

Parameterized BMS-806 (resname 83G) from PDB ID 8fad now included

[1.20.3] - 2025-07-14¶

more examples
upgraded example support

[1.19.1] - 2025-07-11¶

fixed namd restart bugs
fixed improper sorting of segment indices in bilayer_embed.tcl
support for adding, renaming, inserting, assigning authorship to, and deleting examples

[1.18.1] - 2025-07-08¶

switched from patches to mutations for protonated histines predicted by pdb2pqr
developer support for adding examples

[1.17.0] - 2025-07-05¶

support for simple nucleic acids added

[1.16.3] - 2025-07-03¶

fixed None-return bug in terminate task
fixed bug in insulin example to correctly assign NE2-Zn bonds
fixed bug causing piericing of PRO807 in model-building missing residues in insulin receptor example
new pdb2pqr task to assign protonation states based on propka3

[1.15.1] - 2025-06-22¶

fixed the dropped filename extensions in mdplot
updated salt concentration implementation in membrane system builder
removed spurious dependence on parmed
added pressure profile calculation capabilities to mdplot task

[1.14.1] - 2025-06-18¶

Implemented standard CHARMM36 patches as mods
Added HIV-1 protease 1f7a as a new example (now there are 16!)

[1.13.3] - 2025-06-17¶

Allow config to contain names of otherwise unnamed lipids in CHARMMFF

[1.13.2] - 2025-06-16¶

Example 15 added with ring-check
changed make-resi-database to make-pdb-collection
updated PDB repository to work with a gzipped folder (all lipids)
converted charmmff contents back into an as-downloaded tarball

[1.12.1] - 2025-06-04¶

added half_mid_zgap parameter to ease membrane packing
added C6DH and C7DH lipid residue aliases for C6DHPC and C7DHCP, respectively
enable inadvertantly unimplemented user selection of number of lipids per leaflet in a patch
misspelled “paramfiles” in ycleptic basefile (one time)

[1.12.0] - 2025-06-03¶

documentation upgrades
better progress bar integration with packmol
fixed residue misnumbering for large membranes
fixed large membrane embedding errors

[1.11.2] - 2025-05-27¶

fixed parsing error converting specstrings to composition dicts
tests passed after minor updates
New bilayer build protocol
New NAMD and packmol on-the-fly log parsing, including in standalone mode with the follow-namd-log subcommand

[1.10.0] - 2025-03-27¶

Updated the pestifer_init TcL script definition to allow the command pestifer_init to replace the clunkier source [pestifer_init]
cleanup subcommand added for cleaning up after an aborted run

[1.9.0] - 2025-03-27¶

transrot mod enabled for global translations and rotations
desolvate subcommand now can output a single pdb file

[1.8.3] - 2025-03-19¶

fixed bug for growing alpha helices in the N-terminal direction in crot.tcl

[1.8.2] - 2025-03-11¶

fixed failure to avoid deprecated namd parameters if using namd2
fixed hard-coded C-direction brot call to detect whether brot is N- or C-terminal
added --gpu option for the run and run-example subcommands

[1.8.1] - 2025-03-10¶

removal of tcllib from resources (I never used it anyway)
bugfix in slow build tests

[1.8.0] - 2025-03-07¶

new source code structure
mmCIF convention updated
mdplot subcommand added

[1.7.4] - 2025-02-23¶

bugfix: xst trace for mdplot fails if empty

[1.7.2] - 2025-02-12¶

bugfix: correct the detection of whether or not a file is a NAMD log file based on the first two Info: records
bugfix: correct the problem with restarts interfering with mdplot

[1.7.1] - 2025-02-10¶

make-namd-restart enhanced with automatic SLURM script updating
bugfix: GPU-resident NAMD3 cannot do mulitple-gpu runs with constraints
all lipids in the charmmff topology file top_all36_lipid.rtf now have PDBs ready for packmol
show-resources subcommand enabled
make-namd-restart subcommand enabled
ycleptic dependency updated to 1.1.0

[1.6.1] - 2025-06-29¶

now able to use namd2 or namd3
can optionally use GPU-resident namd3

[1.5.9] - 2025-01-22¶

bugfix: log write suppressed inadvertently if progress bars not used

[1.5.6] - 2025-01-03¶

desolvate subcommand implemented
wildcard allowed in pdbalias commands for atom renaming
temporary fix for dbRes HIS in any mutations to be named HSD

[1.5.4] - 2024-11-05¶

bugfix: incorrect deletion of image seqmods

[1.5.3] - 2024-09-30¶

bugfix: custom_pdb_path bug in bilayer fixed

[1.5.2] - 2024-09-24¶

glycan graph mistake fixed
python dependency updated to >=3.12
ycleptic dependency updated to 1.0.7

[1.4.8] - 2024-09-24¶

updated CHARMM lipid PDB files
updated ycleptic to 1.0.6 to enable interactive help and automatic config documentation

[1.4.7] - 2024-09-18¶

ambertools dependency removed
packmol-memgen integration removed; now use native bilayer task
make-resi-database command added
CHARMM force field files updated to July 2024
salt_con, anion, and cation specs for solvate now available
pidibble dependency updated to 1.1.9
pierced ring detection and remediation via the ring_check task
restart task added
automatic detection of SLURM environment for multi-node MD runs
--config-updates option for fetch-example and run-example subcommands implemented
progress bars enabled for NAMD, psfgen, and packmol
--kick-ass-banner option implemented – check it out!
pidibble dependency updated to 1.1.8
expanded integration of packmol-memgen
added fetch-example subcommand that just copies the respective example YAML file to the CWD
bugfixes:
since packmol-memgen sometimes translates the insert, cannot use packmol’s input coordinates to psfgen the resulting embedded system

[1.4.4] - 2024-07-10¶

now includes Tcllib 2.0
bugfixes:
fixed incorrect charges on the C-terminal CA and HB in the HEAL patch

[1.4.3] - 2024-07-02¶

update ambertools version requirement to 23.6; no more packmol-memgen/pdbremix error
bugfixes:
change packmol-memgen’s weird ion names to be CHARMM-compatible
allow for N-atom position calculation for residues added to a C-terminus (atom name OT1 vs O)

[1.4.2] - 2024-06-27¶

explicit chain mapping in config file

[1.4.1] - 2024-05-16¶

support for empty TER records

[1.4.0] - 2024-04-01¶

initial packmol-memgen integration

[1.3.9] - 2024-03-04¶

added include_C_termini boolean to declash directives; set to False to prevent C-terminal insertions from undergoing automatic declashing

[1.3.8] - 2024-02-29¶

bugfix: spurious code in pestifer-vmd.tcl

[1.3.7] - 2024-02-29¶

bugfix: fixed a spurious hard-coded path in macros.tcl
bugfix: runscript sources TcL proc files with dependencies in proc files that aren’t yet sourced; fixed that
alphafold source directive added to permit download of models from the AlphaFold database by accession code

[1.3.5] - 2024-02-26¶

bugfix: renumbering of author resids in non-protein segments if user adds protein residues by insertion that may conflict
transferance of atomselect macros from YAML input to any VMD script
inittcl subcommand makes this transfer; needs only to be run one time post-installation

[1.3.4] - 2024-02-06¶

new TcL procs for asymmetric unit generation from non-symmetric assemblies
pestifer_init TcL proc provided in docs for user VMD startup script
script subcommand removed
syntax of wheretcl subcommand expanded

[1.3.3] - 2024-01-31¶

NAMDLog class introduced for parsing NAMD2-generated log files
mdplot task for generating plots of various energy-like quantities vs timestep

[1.3.2] - 2024-01-24¶

allow for user-defined links in the config file
all example builds now have tests in the test suite

[1.3.1] - 2024-01-12¶

bug fixes for cleaving

[1.3.0] - 2024-01-11¶

Support for reading from already-built PSF/PDB systems

[1.2.9] - 2023-12-19¶

improved declashing and domain-swapping

[1.2.8] - 2023-12-05¶

grafts for adding glycans
cleave task and CleavageMod
ModManager replaces ModContainer

[1.2.5] - 2023-11-28¶

insertion mod; corrected bug in brot tcl procedure

[1.2.3] - 2023-11-20¶

script subcommand handles local scripts
added wheretcl subcommand
added script subcommand (since removed)

[1.2.0] - 2023-11-16¶

split all namd subtasks out; now they are level-1 tasks
added manipulate task

[1.1.2] - 2023-11-09¶

more control over production NAMD2 config generated by the package directive
position restraints control in minimization and relaxation
other_parameters for any NAMD2 relaxation task

[1.0.9] - 2023-11-07¶

alternate coordinate files and Cfusions
chain-specific control over building in zero-occupancy residues at N and C termini
alpha crotation for folding a span of residues into an alpha helix

[1.0.6] - 2023-10-31¶

cif_residue_map_file generated to report mapping between CIF-residue numbering and author residue numbering
enhancements to packaging task
support for topogromacs added

[1.0.1] - 2023-09-20¶

Initial release