1.7.301 Fix dms-select
1.7.300 Add a default 60s timeout to AssignBondOrderAndFormalCharges
No provenance in etr metadata.
Add scripts for building binary wheel files.
Detect when clone() breaks bonds.
Make protein" selection include ACE and NMA.
1.7.299 Support numpy integers in System.clone()
Don't write zero-length metadata frames.
1.7.298 Fix for MAE export of empty m_depend fields.
1.7.297 New use_index keyword for clone().
1.7.296 Skip mae ct properties with conflicting type.
1.7.295 Add compare_frames tool.
1.7.294 Don't fail on empty stk.
Remove phi0 from dihedral_fourier schema.
1.7.293 Add rudimentary psf export.
Drop support for ddparams.
Maintain atom order when writing pdb files.
1.7.292 Added softened_stretch_harm schema.
Improve speed of reading stk cache files
Isotope support for sdf and to/from oechem.
1.7.291 Fix bug in ct property handling introduced in 1.7.284.
1.7.290 Fix reading of stks with empty framesets.
1.7.289 Drop python2 from build and tests, again.
1.7.288 Restore the python2 build, for now.
1.7.287 Docstring fix for findContactIds.
Fix very old bug in SSSR which may not have affected anyone.
Added dms-hmr.
Add metadata keyword to DtrWriter constructor.
Use bytearray when unicode conversion fails reading dtr keyvals.
1.7.284 Add msys.ConvertFromRdkit.
Better handling of ct properties in dms files.
1.7.283 Bring tests/files back into the main repo.
Fixes and notes for external builds.
Handle empty string in mae vdwtype.
Add testModifiedInteractionConsistency to validate.
Expose metadata keyvals from Python via DtrReader.metadata.
Add benchmark program.
Add dms-restrain-dihedrals script.
1.7.282 Support for compressed positions in dtr frames
New dms-randomized-atoms and dms-diff-ff scripts
Fix for ConvertToRdkit when vsites are present.
1.7.281 canonicalize atoms and bonds before calculating
bond orders and formal charges
bugfix for usage of msys.* in MatchFragments python code
1.7.280 Handle UNREAD as jobstep_id in stk cache.
1.7.279 Ensure ConvertToOEChem gives deterministic order of bonds
Add documentation on extracting force-field parameters
Fixed docs for improper definition (DESRESCode4243)
Drop python2 from build and tests.
Better error message when addProp fails.
1.7.278 Silence some compile warnings.
Fix for ParamTable::compare.
Routine to build amber-style pairs and exclusions.
Make json format use full precision parsing.
Make json format handle aux tables.
Skip writing of blank provenance entries.
Add a close() method to DtrWriter.
Handle mae export when ct fields contain whitespace.
Bump python version.
Don't prereq a desres-python from lib-python.
1.7.277 Make System.hash sort terms by default.
dtr-validate: require constraints only if there are hydrogens.
Run anton2 tests by default.
Drop #include of boost/thread.
Initial implementation of experimental json format.
1.7.276 Store atom name in ConvertToRdkit.
DtrReader.keyvals() automatically unpacks ETR frames
Allow ETRs to be written by DtrWriters
1.7.275 Fix stk cache file writing.
1.7.274 Fix dms-tile.
Fix dms-sequence.
Bump python versions.
1.7.273 Fix dms-neutralize for neutral systems.
Support reading mol2 files with no residues.
1.7.272 Support reading bond order 0 in sdf.
1.7.271 Remove old desmond validation routines.
Python3 fix for dms-select.
1.7.270 Propagate return code in dms-diff.
Added System.save().
Fix structure-only for dms-neutralize.
Documention DMS functional forms.
Load mathjax in docs.
Use python3 as executable in tools.
1.7.266 Turn off water-pad by default in Neutralize.
Fix for within selections when atoms have been deleted.
1.7.265 Support molecular ionic species in Neutralize.
Add support for VMD-style sequence selection.
1.7.264 Conda support.
Replace some test files with synthetic data.
desres-python/3.7.2-08.
1.7.262 Fix dms-neutralize and add --structure-only option.
1.7.261 Added neutralize.Neutralize and dms-neutralize.
Replace spaces with '_' in mol2 names and resnames.
1.7.259 New FindDistinctFragments interface.
1.7.258 Fix broken dms-info caused by remove of msys.vdw.
1.7.257 Remove dms-scale-vdw and dms-override-vdw.
Make dms-find-knot agree with dms-validate.
Added msys.MatchFragments.
1.7.256 Fix for Graph to support viparr-style graph matching.
1.7.255 desres-python/3.7.2-04
Fix for writing dms files with tables containing more than 10 atoms.
1.7.254 desres-python/3.7.2-02.
1.7.253 Bump desres-python/3.7.0 to 3.7.2.
Support the != operator in atomsel.
Fix documentation in molfile.
1.7.252 Fix ParseSDF for python3.
1.7.251 Added vtfplugin.
1.7.250 msys.ConvertFromOEChem now preserves chain and residue information.
1.7.249 Make InChI ignore vsites.
1.7.248 Add consider_stereo flag to FindDistinctFragments.
Fix missing call to updateFragids in ImportSdf.
1.7.247 Include pseudos when validating against nonbonded contacts [DESRESCode#4042]
Fix missing shlib version on msys.so.
1.7.246 Fix msys.Load(jobid) for both return types of yas_job.input_ark
Read CRYSIN records from mol2 files.
Wrap ImportPDBUnitCell.
Added periodic option to System.findBonds.
Add docs on msys.sequence and a few other tools.
Added color option to Graph.
1.7.245 Use bytearray for dtr unsigned char fields.
New "degree" selection keyword for bonds between real atoms.
1.7.244 Make "ion" selection atomic number and bond based.
Change old "ion" selection to "legacy_ion".
Handle ComputeTopologicalIds for systems with crazy pseudos.
Handle nonconsecutive resids in mol2 files.
Avoid crashing in find-contacts for unreasonable coordinates.
Fix for undecodeable bytes in DtrReader.keyvals [DESRESCode#4002].
1.7.243 Python3.7.
1.7.242 Atomselection bug for 'all'.
1.7.241 Fix for dms-dump.
Docs for molfile trajectory writing.
Triclinic support for pfx.
Add dms-validate check for virtuals in multiple virtual tables.
1.7.240 Added ReplaceTableWithSortedTerms.
Implement dms-diff in python instead of shell.
Fix the Graph.atoms method.
Use inchi/1.05.
Make msys.Graph check for duplicates.
Tweaks to the build for external users.
1.7.239 DESRESCode#3974: Fix some broken tool scripts.
1.7.238 Fix broken lib-python3 from 1.7.237.
DESRESCode#3964: fix mol2 reading and writing.
1.7.237 Use new sconsutils; should affect developers only.
1.7.235 Add a 'moe' option to msys.SaveMol2 to output guanidinium
groups MOE can will parse correctly. This option is turned
on by default as it seems _most_ tools handle this variant
fine.
1.7.233 Fix dms-dump (broken since 1.7.230).
Added SpatialHash::findPairlist.
Better verbosity API for validate.
1.7.232 Use python/2.7.15 and 3.6.6 megamodules.
Update boost from 1.63 to 1.67.
Add bindings for System.addProvenance.
1.7.230 Added virtual_lc1 schema
Fix for dms-dump with .sqliterc files
Unused param fix for v2 compatibility
1.7.229 Added dtr_frame_{from,as}_bytes.
1.7.228 Added msys.FormatDMS.
Pickled systems use zlib; 3-20x smaller pickles.
FindDistinctFragment returns full map of equivalent fragments.
1.7.227 Support K+ as an ion residue name.
Include tempered_nonbonded and modified_interaction in dms-dump
Add table schemas for constraint_ahNR
1.7.226 Fix molfile.StkFile for python3
Use new megamodules (-03c7).
Check for atom count consistency in stks.
dtr-validate: add check for constrained hydrogens.
Add LoadMany for concatenated dms files.
1.7.225 Use 1/1024 fs as the time quantum for dtr trajectory processing.
Make msys.SaveDMS(..., unbuffered=True) around 10x faster.
Remove vestigial ExportDMSMany reference.
Make SystemImporter python bindings work.
1.7.224 msys.ConvertFromOEChem will no longer complain about
molecules not having hydrogens that don't actually have
hydrogens, e.g., O=S=O.
msys.ConvertToOEChem will always set the dimension of the
molecule to 3D as msys really only traffics in 3D molecules.
1.7.223 Yet another fix for double precision in timekeys files.
Expose error message from numpy version clashes
1.7.222 msys.ConvertToOEChem can take a list of atoms to convert to convert a subset much faster.
1.7.221 msys.Convert(To/From)OEChem will preserve the molecule title
Fix SaveDMS for unbuffered=True.
Added (..., sanitize=True) option to msys.ConvertToRdkit.
1.7.220 Added msys.ConvertFromOEChem (DESRESCode#3785).
1.7.219 Report strerror(errno) when reading dms files (DESRESInfra#39849)
1.7.218 Write .dms.gz files using gzip. DESRESCode#3771.
Added rigid_explicitN schema.
All dms-tools and msys.Load support jobids as arguments.
Sort atoms and bonds by atom ids.
More precise handling of timekeys in large stks.
1.7.216 Fixing msys.ConvertToRdkit to work with RDKit 2017.09.
Sanity check added to Chem.DetectBondStereoChemistry was
being tripped and needed to be worked around.
Refactored test cases and making sure to run RDKit and
OEChem conversion test cases.
1.7.215 Removed v7 stk cache code and added utility to rename
a dtr in an stk cache file.
1.7.214 Make msys.InChI include stereo by default (SNon=True).
Fix mol2 handling of resids (DESRESCode#3747).
1.7.213 Bump megamodule versions.
Don't filter metals in bond order assigner (DESRESCode#3713).
Ignore excluded knots in dms-validate (DESRESCode#3566).
Added an ignore_excluded option to findContactIds()
Fix altloc writing (DESRESCode#3626).
Fix pdb download.
Expose SystemImporter from python.
1.7.212 Added msys.ConvertToOEChem.
Added --without-pos option to dms-dump.
1.7.211 Optionally compute and store resonant charge and bond order.
1.7.210 python3 support.
1.7.208 Added molfile.list_fields()
Make DtrReader.frame(...) not panic if the FORMAT is empty.
Fixed reading of dms files with table properties.
Use new sphinx-rtd-theme for fixed doc search.
Avoid a deadly exception when writing a dms with missing nbtypes.
Handle variable-sized frames in etr files.
1.7.207 DESRESCode#3590 - changes from schrodinger.
1.7.206 Bring back GuessHydrogenPositions
New dms-solvate for those who can't use viparr.
dms-tile checks for reasonable box size.
DESRESCode#3571 : Added dms-validate case for massless atoms
DESRES_ROOT is deprecated, have the cache query DESRES_LOCATION
Bugfix in bond order assigner
Make old, non-monotonic stks only generate warning.
1.7.205 Added PyCapsule interface for easier pybind11 integration.
Added msys.System.hash() function to replace dms-hash.
1.7.204 Added Cl- to 'ion' atom selection.
Using cent7 garden modules.
1.7.203 Fix for dms-frame broken by DESRESCode#3486 in previous release.
Double precision support for SpatialHash in C++.
Eliminate dms-hash.
1.7.202 DESRESCode#3486 - changes from schrodinger.
Added SpatialHash::findContactsReuseVoxels.
dms-validate skips knot check when system is alchemical.
New libmsys-core and versioned libmsys.
gcc/6.3 portability.
Remove cealign.
1.7.157 DESRESCode#3438 - fix reading sdf files without trailing delim.
DESRESCode#3472 - fix msys.System.guessBonds.
DESRESCode#3450 - pickle support for residues and chains.
DESRESCode#3461 - fix ComputeTopologicalIds bindings.
DESRESCode#3452 - use garden flex and bison for CentOS7 support.
use desres-python/2.7.13-02.
1.7.156 Fix build of docs.
1.7.155 Python/2.7.12-03st.
1.7.154 Python/2.7.12-02st, gcc/5.2.0-33x, boost/1.59-06.
1.7.153 Fixed reading of dms files with table properties.
Experimental new msys to rdkit converter.
Experimental new IndexedFileLoader.
Support for ETR writing.
Added ElectronegativityForElement.
Don't write mae files with bad key names.
Rip out resonant_charge and resonant_order.
Removed msys2mol2 - use dms-select instead.
Don't grow the SpatialHash grid too large.
SpatialHash input checks.
Fixes for smiles charge parsing.
Fix LoadDMS(buffer).
1.7.149 Pass --reorder to dms-dump in dms-diff.
Handle coordinate-only Amber crd files. (DESRESCode#3183).
Fix dms-frame (DESRESCode#3205).
1.7.148 Fixed typo in dtr-validate.
1.7.147 C++: TermTable::atomsFast() and paramFAST().
Pickle support for Systems (DESRESCode#3148).
Include all of msys module in the docs.
Fixes for Mac build/test.
1.7.145 Use just SSE4_1 for findContacts since drdb has only that.
1.7.144 C++: Replace boost::shared_ptr with std::shared_ptr.
Better smiles support (DESRESCode#3109)
SSE4 acceleration of findContacts.
Fix AnnotatedSystem.repr (DESRESCode#3108)
Added optional weights argument to pfx.aligned_rmsd.
Throw exception on empty atom selections.
1.7.143 C++: Spatial hash doesn't compute the square root anymore.
C++: Fix installation of atomsel headers.
Skip over newlines and tabs in atom selections.
1.7.142 NEW: msys-fetch-pdb tool
NEW: SpatialHash.findContacts (supports minimum image checks)
FIXED: parsing of negative integers in atom selections
FIXED: dms-grease periodic wrapping.
IMPROVED: error reporting in atom selections.
Tracking ticket: DESRESCode#3040.
1.7.141 Fix incorrect check for leading zero in json int.
Disable multithreaded molfile.read_frames.
Handle negative integers in atom selections.
Report line number in sdf import errors.
Fix empty atom selections in System.atomsel.
Fix preservation of absolute stereo in sdf I/O.
Move alchemical system generation to sw/libs/atommatch.
1.7.140 Using Python/2.7.11-03st
DESRESCode#2857: Fix msys.Term.system property.
DESRESCode#2779: dms-replicate sets resid, chain or ct as needed.
C++: Move ThreeRoe out of dtrplugin header.
1.7.139 Make molfile use sequential access for dtr.
Fix bug with ETRs if no TSS values followed FORMAT.
1.7.138 mol2 processing fixes: preserve sybyl_type; fix aromatic bond type.
Make dms-frame complain about -t or -n without -i.
Added dtr-validate to tools documentation.
1.7.137 SDF file processing just uses LoadMany now.
ScanSDF is gone; use LoadMany, to read, FormatSDF to write.
1.7.136 Fix bug in System.atomsel when alignment produces reflections.
1.7.135 System.selectIds takes optional pos and box.
The 'fragment' atom selection keyword is now a synonym for 'fragid'.
dtr-validate now takes only a single path.
Molfile handles single-row seqfiles.
Make dms-validate handle systems with virtuals more intelligently.
1.7.134 Double the speed of within searches for small target selections.
1.7.133 Don't put inchi strings in alchemical dms.
1.7.132 rst7 support in dms-frame.
dms-frame no longer wraps by default.
Added MakeAlchemical python bindings.
Build with latest OS X compiler.
1.7.131 Added near-workalike fstime and fsdump.
Added DtrReader.keyvals().
C++: AnnotatedSystem no longer holds a SystemPtr, and is itself not
a shared_ptr.
Made smarts matching around 3x faster.
Better error checking on archive file writing.
Added etr as valid extension type for dtr.
1.7.130 Support for alchemical ffio_morsebonds.
Handle NULL chains, segids, etc. in dms files.
Allow extra blank line after M END in ScanSDF.
C++: make pfx::Graph constructible directly from SystemPtr.
Fix a memory leak affecting all dms file reading (!).
1.7.129 Support for ffio_morsebonds in mae files.
More efficient term table indexing.
Support for .gz files in ScanSDF.
1.7.128 Handle stk files containing empty dtrs (DESRESCode#2406).
1.7.127 Added --energy option to dtr-validate.
1.7.126 Alchemical fix for multiple dihedrals.
1.7.125 Fix reading of stk files whose parent directory changed.
1.7.124 Added AllowBadCharges option to AnnotatedSystem.
Support more valences for heavy atoms.
Fix writing of sdf files with formal charge=4.
Fix pfx for very extended system.
Use pandas.read_csv for eneseq files when available.
Accomodate empty eneseq files.
1.7.123 New stk caching ready to roll out.
Added SmartsPattern.match for Python.
1.7.122 Handle long title lines in ScanSDF.
1.7.121 Fixed charge parsing in ScanSDF.
Added --add-hydrogens and --guess-hydrogen-positions to dms-select.
1.7.120 Added --sorted option to dms-select.
Fixed .gro box size unit conversion.
Fixed bond order assignment for systems with bonds to pseudos.
1.7.119 Experimental ETR support and new STK caching - do not use!
1.7.118 Added paramtype atom selection keyword.
1.7.117 More ScanSDF robustness improvements.
1.7.116 Improvements to ScanSDF and FormatSDF.
1.7.115 Add checkpoint option to dtr-validate to turn off delta_t checks.
1.7.114 Make dtr-validate perform some additional checks on timekeys.
1.7.113 dtr-validate backwards compatibility.
Fix sdf import bug handling entries containing doublet radical.
Start using the new stk cache.
1.7.112 Disregard difference in type and memo in identifying alchemical terms.
Accommodate missing tables in both A and B states in alchemical mapping.
1.7.111 Support for gromacs files (gro, g96, trr, trj, xtc).
Build with C++11.
Better error handling in dms export.
1.7.110 Stk cache files are placed alongside original stk.
DtrReader class supports sequential reading for stk.
1.7.109 Revert the 1.7.103 changes to structure_only. structure_only now
excludes pseudos. Also excluded in mae files (previously wasn't).
Added new without_tables option to Load(), which causes term tables
to be ignored during loading but otherwise gives you all particles.
1.7.108 Another shot at build fixes.
1.7.107 Build fixes.
1.7.106 Added --unrotate option to dms-frame.
1.7.105 Smiles functionality factored out into its own garden module.
1.7.104 Experimental SMILES parsing.
Added LoadSDF function.
The mol2 exporter mistakenly assigned C.cat atom type in some cases.
1.7.103 Loading structure-only now includes pseudos.
Fix a bug in import where residues were sometimes erroneously split.
1.7.100 No more versioned libmsys.so.
1.7.99 Create a versioned libmsys.so.
Fix molfile-based reading of dms with pseudos.
More HBond finder improvements.
Added raw dtr I/O support for Python.
1.7.98 Better xyz, dx, and Amber prm/rst7 file support.
HBondFinder allows multiple donor hydrogens.
Eliminate primegen dependency.
1.7.97 Fix mol2 bond type output.
Fix molfile xyz plugin.
Added dx plugin.
1.7.96 Fix mol2 atom type output.
1.7.95 Fix the /lib submodule, which behaved differently under garden.
1.7.94 Bump lp_solve version to get tighter symbol visibility.
Fix race condition in build script.
mol2 exporter now always assigns Sybyl atom types.
1.7.93 Hydrogen bond finder.
1.7.92 Added weights option to Pfx.align.
Fix OSX compilation issues.
Enhance molfile.Timekeys Python interface.
1.7.91 Added ostream operator to SmallString.
1.7.90 Incorporated molfile into msys. Use 'from msys import molfile'.
pbwithin selection now handles rotated unit cell correctly.
[pb]nearest now handles empty subselection.
Slight change to SpatialHash interface.
1.7.88 Added SmartsPattern::match().
1.7.87 Use Python/2.7.9-05st.
Added boost::serialization-based archive format (.msys extension).
1.7.86 Bump to numpy/1.6.2-35A
Fix tools scripts so they use the right version of numpy and molfile.
Make the rms routines more general.
1.7.85 Fixed construction of provenance from Python.
Improvements to mmod_type handling in dms2mae.
Table properties in TermTable. New msys_table_properties in dms.
Incorporate fastjson and pfx into msys.
1.7.84 IMPROVED: Alchemical mapping now merges dummy fragments connected to the same real atom into one fragment, and thus retains more permissible terms.
1.7.83 System.topology now returns a pfx.Graph object.
1.7.82 Fixed reading and writing of large (>2GB) dms files.
1.7.80 Fix memory leak in msys.pfx.aligned_rmsd.
Added Python bindings for CalcDihedralGeometry.
1.7.79 Revert boost version change.
1.7.78 C++ header fixes for spatial_hash.
C++ - Bump boost and zlib versions.
1.7.77 FIXED: dms-alchemical typos.
1.7.76 NEW: SpatialHash Python class for efficient findWithin and findNearest.
NEW: System.selectArr to return atom selections as numpy array of ids.
NEW: C++ within.hxx renamed to spatial_hash.hxx.
1.7.75 FIXED: Allow structure-only saves with partial nonbonded params.
FIXED: Use sse2 rather than sse4 in new FindWithin code.
FIXED: FindWithin crashed on empty subselection.
NEW: keep-none for dms-alchemical.
NEW: Write msys_file_offset in mol2 files.
1.7.74 FIXED: xyz files now written with element name rather than number.
FIXED: better bond guessing for systems with virtuals.
NEW: distance based atom selections got a lot faster.
1.7.72 FIXED: bfactor and occupancy output in pdb files wasn't quite working.
FIXED: System.append() and PDB importer now always preserve atom order.
FIXED: permissions on dms-fix-water-residues.
1.7.71 FIXED: write bfactor and occupancy to pdb files.
NEW: C++ system.hxx no longer includes {term,param}_table.hxx.
1.7.70 FIXED: handling of element names with extraneous characters
FIXED: addTable should be no-op when table already exists.
NEW: dms-set takes any supported file type.
1.7.69 FIXED: Fix error handling in certain Python bindings.
FIXED: dms-validate for check-gruops.
FIXED: validate output formatting
FIXED: read/write PDB space group
NEW: Saving to stdout.sdf writes to stdout.
NEW: API change for msys.groups
1.7.68 NEW: dms-validate --anton checks for contacts shorter than 1A,
including those that cross periodic boundaries.
FIXED: The bond guesser (used during loading of pdb files) sometimes
handled hydrogens bonded to multiple atoms incorrectly.
FIXED: System.findContactIds should be stable now.
FIXED: System.topology was too slow.
1.7.67 FIXED: AppendSystem is smarter about merging global cells.
FIXED: PDB readers weren't storing the global cell.
FIXED: pfx.apply() wasn't returning the correct global cell,
and the Python bindings for rsmd() failed for double
precision inputs.
1.7.66 FIXED: msys.pfx.rmsd() was invalid when given double precision
coordinates, and pfx.apply() was not returning the transformed
unit cell when doing an alignment.
MODULE SPLITS: atommatch now lives in the atommatch garden module.
psfgen now lives in the desres-psfgen garden module.
1.7.65 IMPROVED: dms-validate checks that each water molecule has
its own resid and lives in its own residue
NEW: dms-fix-water-residues for putting each water molecule in
its own residue.
FIXED: appending systems now correctly merges nonbonded_info.
1.7.64 FIXED: SDF writer checks for isfinite() before calling floatify.
1.7.63 IMPROVED: SDF reader is more robust and handles multi-line values.
1.7.62 NEW: Bond.other(atom) from Python.
NEW: C++ interface for FindWithin.
1.7.61 IMPROVED: Across-the-board speedups for all atom selections.
IMPROVED: Notable improvements to "nearest" selections.
NEW: "pbnearest" selection.
NEW: lc5-l schemas.
FIXED: Loading webpdb crashed in 1.7.60.
1.7.60 NEW: dms-find-knot has a --untie option to remove knots.
NEW: LoadMany support for PDB files.
IMPROVED: dms-find-knot has a --ignore-excluded-knots that uses
the exclusion table
IMPROVED: "nearest k to subsel" is much faster.
IMPROVED: Delete property in ct block using python del operator.
1.7.59 FIXED: mol2 importer choked on resid 0.
IMPROVED: read and writes TER records between chains in pdb files
NEW: System.getTable() returns None on missing table.
FIXED: (C++) don't link against libmolfile or libpython.
1.7.58 IMPROVED: dms-tile permits multiple input files, and requires -o.
1.7.57 IMPROVED: mol2 export includes original resids.
1.7.55 FIXED: dms-thermalize with --remove-drift doesn't accelerate pseudos.
FIXED: addTableWithSchema accepts user-supplied name.
IMPROVED: dms-frame gets otuput format from path name.
NEW: Use pfx instead of periodicfix in dms-frame and other places.
1.7.54 FIXED: pdb export includes insertion code.
1.7.53 FIXED: dms-tile sets nonbonded_info and cell.
IMPROVED: dms-info shows counts of pseudos and nucleic.
NEW: Load handles PSF files.
NEW: ReadPDBCoordinates() function.
1.7.52 CentOS6 portability.
1.7.49 FIXED: mol2 export was missing residues not in the first chain.
IMPROVED: mol2 export now includes chain name.
1.7.48 FIXED: sdf export writes bond type 4 for resonant bond.
FIXED: clone() and append() preserve bond resonant_order.
1.7.47 IMPROVED: psfgen.Psfgen got setCoordinates.
IMPROVED: update to molfile/1.11.16.
FIXED: psfgen.write() to dms was writing uninitialized global cell.
1.7.43 FIXED: System.name wasn't set when loading a pdb.
FIXED: The segid atom selection keyword was missing.
FIXED: The web pdb access code regex was too restrictive.
FIXED: dms-reorder atoms: reference selection applies to all atoms.
IMPROVED: load mae files with multiple consecutive m2io_version blocks.
IMPROVED: Better error reporting of truncated mae files.
1.7.42 FIXED: Added POPS to the lipid atom selection macro.
FIXED: The structure analyzer recognized waters with pseudos now.
FIXED: Allow writing mae files with multi-line ct properties.
IMPROVED: Added share_params option to clone().
NEW: Can load from the pdb databank by specifying an accession code.
1.7.41 IMPROVED: SaveDMS accepts structure_only flag.
IMPROVED: dms-validate --desmond runs the dms-check-groups test.
FIXED: System.delXXX was confused by empty selections.
1.7.40 FIXED: build of command line tool documentation.
IMPROVED: error recovery in msys.LoadMany (yield None on bad entry)
IMPROVED: dms-validate checks for nonzero volume.
IMPROVED: dms-thermalize has a --remove-drift option, on by default.
1.7.39 treetop/57-Anton2
1.7.38 IMPROVED: dms-select replaced its --append option with support for
multiple input files.
IMPROVED: Compilation improvements.
1.7.37 IMPROVED: PDB reader guesses atomic number form name if element is
missing. END and ENDMDL records split PDB into cts.
IMPROVED: PDB reader and writer handle formal charge in columns 79-80.
IMPROVED: dms-select has -A/--assign option to assign formal charge
and bond order.
NEW: dms-tile and dms-replicate scripts.
1.7.35 FIXED: dms-dump truncated its fields to 10 characters; now output
is separated by '|' rather than being formatted into columns.
1.7.34 IMPROVED: annotated system is now handles radicals
(bond order assigner still does not)
1.7.33 FIXED: SDF counts line specification
1.7.32 FIXED: SDF exporter writes ct key-values.
1.7.31 FIXED: Read MAE files with fields containing hash symbols.
NEW: Atommatch takes optional pair of atoms which must be matched.
1.7.30 FIXED: Another maegz fix.
1.7.29 FIXED: MAE export was confused by bonds to pseudos.
FIXED: Bad image filename for latex2pdf documentation.
1.7.28 FIXED: Handle MAE files with m2io_version block at the end.
1.7.27 FIXED: Documentation of command line tools matches result of -h.
FIXED: SaveMAE supports lists of Systems again.
FIXED: dms-find-knot finds knots crossing periodic boundaries.
IMPROVED: dms-find-knot is much faster.
NEW: SerializeMAE instead of SaveMAE(path=None) for MAE contents.
NEW: XYZ file export.
NEW: dms-posre takes --max-energy and --max-distance options.
FIXED: dms-grease puts lipids in their own ct, leaving chains unchanged.
1.7.24 IMPROVED: Documentation
REMOVED: ExportMAE() no longer takes a list argument; use append=True.
NEW: ExportMAE() takes path=None to return MAE file contents.
FIXED: Type checks for delAtom, etc.
FIXED: Don't consider saturated elements for hydrogen addition.
1.7.23 FIXED: bond order assignments for disulfides and hypervalent halogens
1.7.22 FIXED: Handle maegz files containing multiple zlib streams.
1.7.21 NEW: Add dms-atommatch program and msys.atommatch Python library
FIXED: dms-alchemical keeps more bonded terms involving dummy atoms
1.7.19 FIXED: dms-alchemical handles constraint tables with extra
informative parameter columns.
1.7.18 FIXED: dms-alchemical handles more complex topologies.
FIXED: dms-alchemical keeps dihedral terms, not just bonds and angles.
1.7.17 NEW: Python bindings for ComputeTopologicalIds.
NEW: dms-check-groups to check for valid initial conformation.
NEW: AddHydrogens routine.
NEW: Can append to a specific ct, rather than always create new cts.
IMPROVED: GuessHydrogenPositions works much better now.
IMPROVED: dms-fix-mass checks for consistency of atomic number and mass.
FIXED: MAE writer now handles negative atomic numbers.
1.7.16 NEW: faster InChI c interface added
IMPROVED: bond order assignment speed (dimension of ILP reduced)
OTHER: resonance bond order/formal charge generation disabled
1.7.15 FIXED: Make dms-select use desres-cleanenv.
1.7.14 NEW: msys.Save() function understands filename extensions.
FIXED: Better hybridization detection.
FIXED: SaveMAE preserves atom order (broken since 1.7.0).
C++: load.hxx was renamed to io.hxx.
1.7.13 NEW: Python bindings for {Period,Group}ForElement.
NEW: Python bindings for Calc{Distance,Angle,Dihedral,Planarity}.
1.7.12 NEW: The GlobalCell class is gone; System.cell is now represented
a 3x3 NumPy array. getCell() still returns a copy of the cell
as before. Small API change but no change in behavior of the
existing interfaces.
NEW: The Vec3 class was removed from the Python interface; it was there
only to support the GlobalCell class.
1.7.11 NEW: AbbreviationForElement in Python interface.
FIXED: ct properties were being improperly shared.
FIXED: mol2 and sdf import/export better supports multiple entries.
FIXED: dms-dump looks for more than six cmap tables.
1.7.10 FIXED: Atom selections with names beginning with digits were broken
since 1.7.7.
1.7.9 FIXED: Amber prm files with nontrivial dihedral phases could be misread.
1.7.8 FIXED: Amber prm file should still add bonds when structure_only=True.
FIXED: Amber prm file was sometimes incorrectly rejected.
FIXED: GuessAtomicNumber for python.
1.7.7 NEW: New atom selection parser based on flex/yacc.
NEW: smarts atom selection keyword.
NEW: ParamTable.addParam() takes keyword arguments.
FIXED: msys.AssignBondOrderAndFormalCharges(mol) is now much faster.
FIXED: dms-validate has more useful options.
FIXED: dms-alchemical does a sanity check.
1.7.6 FIXED: msys.knots was broken, which broke dms-validate.
FIXED: dms-validate didn't properly handle systems with pseudos.
FIXED: Read occupancy and bfactor from PDB files.
FIXED: Bring back msys.GetSSSR.
1.7.5 FIXED: SaveMAE puts quotes around strings containing braces.
FIXED: Catch misuse of System.chain(<string>), etc.
1.7.3 FIXED: maedms didn't apply LJ scale to pair terms with vdw overrides.
1.7.2 NEW: System.clone() accepts a list of atom ids.
NEW: Recipes section in the documentation.
FIXED: Better bond order assigner.
FIXED: Read proper_harm in MAE files.
1.7.1 NEW: dms-select learned --coalesce.
NEW: inchi.InChI function.
FIXED: SDF reader handles formal charge and some keyvals
FIXED: bond order assigner gives up instead of hanging
FIXED: Improved aromaticity and hybridization detection.
1.7.0 NEW: Ct class for multiple components and system attributes.
NEW: ctnumber atom selection keyword (matches VMD's).
NEW: dms_version in the DMS file.
FIXED: Load[Many] failed on some compressed MAE files.
DEPRECATED: all glue functionality (modern periodicfix doesn't need it).
1.6.35 NEW: Class AnnotatedSystem to cache rings and aromaticity
FIXED: Aromaticity detection now operates on entire ring systems
REMOVED: SSSR/ring aromaticity global functions in Python interface
REMOVED: SSSR cache and AllRelevantSSSR function in System
1.6.33 NEW: NBFix support in ExportMAE.
NEW: ExportMAEMany. msys.SaveMAE accepts list of Systems.
NEW: msys_provenance and msys_forcefield blocks in exported MAE systems.
NEW: msys.LoadMany works with all filetypes.
NEW: msys.Graph.matchAll can do substructure searches.
1.6.32 NEW: msys.LoadMany and C++ LoadIterator interface for working with
multi-structure files.
NEW: msys.Atomsel class with RMSD calculation and superposition.
FIXED: dms-set was broken.
1.6.31 FIXED: Read m_grow_name in ImportMAE.
1.6.30 FIXED: dms-frame was broken.
FIXED: protein backbone must have minimally correct bond topology.
1.6.28 NEW: dms-sequence tool and msys.sequence.Sequences() function.
NEW: dms-reorder-atoms
FIXED: dms-scale-vdw now requires --scale options.
FIXED: Bond guesser keeps only the shortest bond to hydrogens.
FIXED: Make PDB output more conformant.
FIXED: ExportMAE no longer writes 0-length chain names.
1.6.25 REMOVED: msys.glue module and dms-glue program.
FIXED: No more MSYS_CLEANENV.
1.6.24 REMOVED: mview is now in its own mview module.
1.6.23 NEW: inchi.Strings python interface.
FIXED: mae and dms read and write insertion code.
1.6.21 NEW: Print count of override pairs in dms-info.
NEW: mview tool for viewing dms file contents.
NEW: Added es_funct field to nonbonded_info.
1.6.20 NEW: Enable support for hybridization matching in SMARTS matcher.
FIXED: Deleted printf chatter.
1.6.19 NEW: Load() has a structure_only option.
1.6.18 FIXED: SmartsMatcher for systems with pseudos.
FIXED: TermTable find methods don't return duplicate terms when
the terms contain duplicate atoms.
1.6.17 NEW: class SmartsPattern.
NEW: MassForElement() function.
FIXED: dms-dump handles systems with missing expected tables.
1.6.15 NEW: Added 'insertion' as a residue property.
NEW: PDB reader reads 'altloc' as extra atom property.
NEW: Added System.atomsGroupedBy(prop) convenience method.
NEW: dms-posre learned --reference-structure and --reference-selection
C++: aromatic.hxx is visible.
1.6.14 NEW: Using gcc/4.7.2, Python/2.7.3, and numpy/1.6.2.
1.6.13 FIXED: dms-alchemical handles hoh constraints in the atom map.
1.6.12 FIXED: TermTable.findOnly() makes its input sorted and unique.
NEW: Param.keys() and Term.keys()
1.6.11 NEW: SDF export.
NEW: RadiusForElement() function.
NEW: FindDistinctFragments() function.
NEW: dms-inchi tool.
FIXED: LoadMAE handles forcefield provenance better.
1.6.10 FIXED: CreateSystem() is thread-safe again.
1.6.9 FIXED: System.atoms is now (amortized) constant time.
NEW: dms-select now reads any msys-supported file type, not just dms.
NEW: mae2dms supports fbhw terms.
1.6.8 FIXED: Bug in sidechain detection for residues with non-unique names.
1.6.7 FIXED: FindKnot uses within selections instead of boxing.
FIXED: Restored the max-cycle option to FindKnot.
1.6.6 NEW: 'sidechain' atom selection.
FIXED: bad int and float literals in atom selections are caught.
FIXED: FindKnot uses accurate ring finder from GetSSSR.
REMOVED: stretch_quartic schema.
1.6.5 NEW: stretch_quartic schema.
1.6.4 FIXED: dms-alchemical checks for valid atom maps.
FIXED: dms-alchemical avoid writing unnecessary alchemical terms.
NEW: TermTable.findWithOnly.
1.6.3 FIXED: SavePDB writes element determined from atomic number.
1.6.2 NEW: Heuristic for guessing bonds. From Python: System.guessBonds()
NEW: xyz importer.
NEW: xyz and pdb importers guess bonds.
NEW: pdb importer reads and writes unit cell.
1.6.1 NEW: mol2 import/export support.
NEW: AssignBondOrderAndFormalCharge function (was in Viparr)
NEW: GetSSSR (smallest set of smallest rings) (was in Viparr)
1.6.0 NEW: The Python atom selection handles large selections much more
efficiently.
NEW: Added System.selectIds(), which is more efficient than
System.select() if all you need are the ids.
NEW: C++ interface for working with override tables.
NEW: Experimental support for multiple nonbonded tables. When present,
a new metatable in the DMS file will be created.
1.5.14 NEW: protein, backbone, and water analysis is done on load instead of
being repeated for each selection. This is faster and allows
these selections to work on cloned subsets of the original system.
FIXED: dms-uncharge works again now.
FIXED: examples/alchemical_pair.py (for Schrodinger).
FIXED: Python findWithAny, findWithAll, findExact for empty input.
FIXED: __eq__ and __ne__ methods of System and ParamTable.
FIXED: dms-dump raises an exception on sqlite errors.
1.5.13 NEW: Psfgen.read() and Psfgen.write() handle unit cell.
FIXED: findWith{Any,All} on empty tables.
1.5.12 NEW: Psfgen.applyResidue does point mutations.
NEW: C++ interface for filtered bonds.
NEW: TermTable::resetParams(); in Python TermTable.params is settable.
FIXED: deleting terms is faster now.
FIXED: Psfgen.read() works now.
FIXED: TermTable::hasTerm().
FIXED: Destroyed TermTables appear empty.
FIXED: Document dms-posre better.
1.5.11 NEW: Slightly optimized within selections.
FIXED: dms-alchemical for noncontiguous alchemical ranges.
1.5.8 NEW: dms-fix-mass for fixing inconsitent masses.
NEW: dms-find-knot for finding bonds passing through rings.
NEW: dms-validate runs the knot check.
FIXED: dms-alchemical handles alchemical_improper_harm .
1.5.7 FIXED: dms-alchemical was confused by extra properties in the B state.
1.5.6 FIXED: Memory leak in setPositions and setVelocities.
1.5.5 NEW: {get,set}Positions is ~100x faster due to NumPy integration.
NEW: {get,set}Velocities is ~500x faster due to NumPy integration.
NEW: System.center and Residue.center use NumPy.
NEW: Low-level SystemPtr positions and velocities accessors take
optional ids argument to get/set values for specified atoms.
NEW: C++ interface for TermTable provides iterator for efficiency.
1.5.4 FIXED: SaveMAE reports error on failure.
NEW: SaveMAE and SaveDMS print errno information on failure.
1.5.3 FIXED: Support SC{EE,NB}_SCALE_FACTOR in Amber PrmTop importer.
1.5.2 FIXED: System.setCell() converts its input to the correct type.
1.5.1 FIXED: dms-frame reads in double precision if possible.
FIXED: Better error messages when accessing nonexistent Term properties.
NEW: Added getPositions(), getVelocities(), and getCell() to System.
1.5.0 REMOVED: dms-neutralize, dms-solvate
REMOVED: Undocumented "builder" module.
FIXED: Documentation for dms-override-vdw, dms-scale-vdw
NEW: dms-frame tool for extracting coordinates and doing periodic fix.
NEW: C++ interface for guessing file type.
1.4.8 NEW dms-frame script for frame extraction with centering and wrapping.
1.4.7 NEW: ParamTable::find and TermTable::find{WithAny,WithAll,Exact}.
NEW: msys.SavePDB.
NEW: better logging in dms-override-vdw and dms-scale-vdw.
FIXED: reading of alchemical dms files.
FIXED: LoadPDB now uses correct chain/segid logic.
FIXED: dms-dump prints nonbonded_combined information.
1.4.6 Portability (build without C++0x, and on OS X).
1.4.5 Renamed dms-scale-vdw --scale option to --scale-sigma and added
--scale-epsilon.
1.4.4 Add minimal build configuration options.
DMS import no longer panics on empty particle table.
1.4.3 Added dms-scale-vdw.
1.4.2 Make ImportDMS thread-safe.
1.4.1 Another way to handle nonbonded_combined_param tables. We now
store the 2d table directly, so that we don't choke on systems
whose entire vdw table has overrides. API changes at the Python
and C++ level; dms-override-vdw is unchanged.
1.4.0 The nonbonded_combined_param is now loaded into a TermTable
called nonbonded_combined which has a new category called override.
No change to the dms representation, but code that uses msys must
use the new API in override.hxx to handle vdw overrides.
The clone() method now copies provenance.
Reimplemented dms-combine-vdw correctly and renamed it to
dms-override-vdw.
1.3.7 Hide functions that can conflict with other shared libraries.
1.3.6 Added executable path to provenance.
1.3.5 Internal changes to facilitate inclusion in larger builds.
1.3.4 DEPRECATED: dms-neutralize, dms-solvate.
Fixed typo in dms-neutralize.
Fixed equality checks between msys handles of different type.
Fixed hashing of Term and Param handles.
Fixed dms-dump nonbonded output for nonbonded param.
mae2dms and dms2mae now try to preserve ffio_vdwtype names.
1.3.3 Added dms-combine-vdw.
1.3.2 Using 73-Desmond modules.
1.3.1 Fix ImportMAE handling of virtuals (broken in 1.3.0).
Turn off type checking of particle and bond tables.
Fix GuessAtomicNumber (affects ReadParmTop only).
1.3.0 Alchemical terms now appear in their own TermTable, and the paramB
interfaces have been removed.
Alchemical particles are now listed in an "alchemical_nonbonded" table;
the chargeB, moiety, and alchemical properties have been removed.
Alchemical particles can have arbitrary term properties, including
"chargeC".
Msys can now detect sharing of parameters by TermTables that share
a ParamTable, not just within a single TermTable.
1.2.5 Export/import formal_charge to/from dms.
1.2.4 Avoid exporting std::vector of primitive types to python.
Prmtop import bugfix for when torsions contain negative force constants
1.2.3 Export version info to python.
1.2.2 Module file now adds the -lmsys to DESRES_MODULE_LDLIBS
1.2.1 Much improved support for glue, including in clone() and append()
operations. The glue table has been renamed to msys_glue, though
msys will still read from both tables and merge the two.
dms-thermalize: the random seed is now 1 by default so that results
are reproducible.
1.2.0 segid is now a property of Chain.
New tools: dms-set and dms-macro
1.1.1 dms-neutralize: fix for positive solute charge (DESRESCode#1352)
dms-neutralize: remove ions if needed to achieve specified concentration
Fix bug in atom selections on systems with deleted atoms
1.1.0 Added user-defined atom selection macros.
New atom selection documentation.
Bumped the minor version since selection macros are visible in the
dms file.
1.0.13 Disambiguate residues by segid (DESRESCode#1345,1346)
1.0.12 dms-builder fixes
1.0.11 Fixed a memory corruption bug in the dms reading code.
1.0.10 neutralize: set the residue name of ions equal to the atom name.
builder: preliminary support for charmm36.
builder: guess atom type based on name if not provided in top file.
1.0.9 msys.Load() supports .maeff and .maeff.gz now.
Documentation for DMS files converted from Desmond documentation.
dms-validate --desmond to check for bonds between nonbonded atoms.
1.0.8 gzipped dms files are detected and handled automatically.
Added msys.Load() for guessing file type from filename.
dms-info works now on dms, mae, and prmtop files.
Documentation for dms-validate.
1.0.7 Support for importing Amber prmtop and crd files.
Update fastjson dependency.
Documentation fixes.
1.0.6 Anton version: aligning dependencies with treetop/43-Anton.
Blame scarpazz.
1.0.5 System.positions property.
1.0.4 Typo in dms-validate.
1.0.3 Bugfix: clone() and append() did not copy auxiliary tables (e.g. cmap).
1.0.2 Internal: fix symbol conflicts with other packages.
1.0.1 Documentation updates.
Added dms-posre.
1.0.0 First stable release.