CHANGES
=======

v1.8.0
------

* Update pypi\_deploy.yml
* Update pypi\_deploy.yml
* remove legacy test
* Update pypi\_deploy.yml
* Update setup.cfg
* Update polyply/src/meta\_molecule.py
* add tests for errors
* add tests for build file parsing
* fix bug in mass guessing
* rename mapping to be compatible
* fix behaviour
* Update polyply/src/meta\_molecule.py
* :Merge branch 'master' into split\_w\_cgs
* change var name
* Update polyply/src/meta\_molecule.py
* update docstirng
* Apply suggestions from code review
* enable relabling from a build file
* add relable from cgsmiles for all-atom FFs as well
* add relable from cgsmiles as option
* update docstring
* Apply suggestions from code review
* test and API update
* add cgsmiles to test requirements
* merge master
* Fix monomer list in test
* Fix seq\_pars test
* Fix parsing of fasta files for RNA
* Add cellulose to LIBRARY.md (CEL, M3)
* use vermouth defaultcitations
* Rename PEPP,PMAP,PVBP links files to follow naming convention
* Add tests for PVBP,PMAP,PEPP (ligpargen)
* Make PEPP,PMAP,PVBP use the same CH3.ter; remove redundant CH3ter.ff, CH3Oter.ff
* Make opls\_links.ff files naming consistent
* Fix links\_PTMA.ff and update test result
* Resolve LIBRARY.md conflicts
* Fix LIBRARY.md formatting: different versions in different lines
* Fix PTMA|CH3 link in links\_PTMA.ff
* trim citations in martini3-go
* Have unique CH3.ff (opls) for all polymers - test on PTMA
* typo in library listing
* Added lib test for new aminoacids.ff
* corrected lib tests
* missed modifications.ff for go
* files for martini3IDP force field added to martini3 data directory. martini3 go parameters moved to own force field directory
* add notes to logging for modifications, revert template generation iteration out
* move modifications sanitisation to own function and write tests to cover it
* fix filtering of modifications for where residues are targeted both by default and by user
* Add Py13
* Remove leftover print
* update coverage
* update coverage
* ignore tests in pylint
* fix pylint
* fix CI
* fix test\_persistence.py
* Fix wcm function
* fix resspec parsing so that default protein ones are overwritten if others are given
* move resname in gen\_templates so can find it
* correct atomlist selection in apply\_modifications.py
* added integration test for complex histidine modifications: - input -seq HIS:5 - with two modifications, HIS1:HIS-HD HIS1:NH2-ter, so the first residue is modified twice, both in its terminal type, and in its histidine variant
* added integration test for complex histidine modifications: - input -seq HIS:5 - with two modifications, HIS1:HIS-HD HIS1:NH2-ter, so the first residue is modified twice, both in its terminal type, and in its histidine variant
* improved itp test
* added test for file coming from itp
* fixed modifcation parsing - -mods flag now only read once for all modifications - patch all molecule termini as proteins, so any modification in addition to these ones are also applied. - add more modifications from vermouth to martini3 forcefield - change logging level and fix tests as per #385
* fixed modifcation parsing - -mods flag now only read once for all modifications - patch all molecule termini as proteins, so any modification in addition to these ones are also applied. - add more modifications from vermouth to martini3 forcefield - change logging level and fix tests as per #385
* added one letter AA code for HYP for fasta parsing
* check bending before overlap
* only concatanate if length is larger than 10
* add test for when volume but no template is provided
* add additional test
* remove annoying tqdm
* use graph hashes consistently
* fix case where template coordinates are provided
* added extra tests for modification addition
* Updated tests for latest improvements
* Made requested changes - removed -ter flag from polyply - -ter flag is not necessary anymore because apply\_modifications.py will automatically add protein termini to the resspec if no modifications are given - the modifications in the resspec will then only be applied if the target residue is in fact a protein residue
* make sure graph hash is always annotated
* Add PMAP,PEPP,PVBP to LIBRARY.md
* Add 10.1021/jacsau.4c00276 polymers
* implement cgsmiles
* move simple sequence interpreter to appropiate file
* implement cgsmiles
* added test for ApplyModifications class
* modifications missed off somehow
* Update modifications.ff
* cleaned up tests
* addressed comments for apply\_modifications.py and gen\_itp.py
* indent lint
* use hashes consistently and add test when skipping filter
* update doc-string and function name; clean up tests
* fix doc-string
* add test
* add docstrings
* use hashes for fast graph comparions
* remove comment
* added simple modification tests
* fixed test failure
* added -protter as shorthand for protein termini
* Convert apply\_termini.py to apply\_modifications.py to treat modifications more generally
* add cystein bridge back in
* propagate the skip flag
* add integration test for skip
* some refactor
* integration test for handling non-unique residue names
* fixed existing tests - updated m3 command to include -ter - new m3/prot.itp with correct parameters
* added martini3 modifications.ff and updated martini3 aminoacids.ff to remove terminal modifications
* Initial commit - with the -ter flag, add modifications read from the force field to the n and c termini
* update codecov version
* fixed position restraint directives. had too many parameters
* fixed position restraint directives. had too many parameters

v1.7.0
------

* fixed minimization
* updated minimizer
* removed space around = in Go citation
* fixed citations
* removed misc tag
* added biorxiv citation
* remove my name
* remove maxbend option
* remove maxbend option
* address comments
* address comments
* address comments
* remove print
* fix spelling
* fix spelling

v1.6.1
------

* add tests for gen\_coords box input usual
* fix box warning
* fix bug in box check
* Update citation for PTMA.martini3.ff
* Small fix to LIBRARY.md that got undone at some point
* retrigger checks
* Rename ibi\_GBNO2 to ibi\_gbcg (PTMA ibi GBNO2 model)
* Remove extra paranthesis from line in LIBRARY.md
* Rename ibi\_CGM3 to ibi\_cgm3 (lower-case)

v1.6.0
------

* Update pypi\_deploy.yml
* fix partial paths in tests
* fix typo in path variable
* fix path to test-data
* fix path usage in simple\_seq parse test
* update path usage
* update path usage
* update path usage in test\_simple\_seq\_parsers
* update path usage in test\_topology
* update path usage in test\_lib\_files
* update path usag in gen\_seq test
* run gen\_param in tmp\_dir
* only write temp files with standard name for testing gen\_params
* update tests meta molecule to use TEST\_DATA as Path
* fix typo
* use pathlib in case importlib fails
* use API of gen\_params instead of argparse
* fix typo
* change deprecated pkg\_resources to importlib
* allow nx3
* minor opt
* minor opt
* have bending as threefold tuple
* test and implementation of bending potential in RW  module
* test and implementation of bending potential
* fix spelling error
* address comments
* cleaner transfer of box
* fix docstring for topology box argument
* allow sequence specific bending
* initial draft
* fix vermouth dependency
* add box tests for gro and pbd
* increase vermouth version
* Add [non-edges] to [warning] of links\_PTMA.ff
* Add test for ibi\_GBNO2/PTMA
* Add PTMA-GBNO2-IBI-ff to LIBRARY.md
* Add ibi\_GBNO2 ff file
* News article for the PTMA paper; version=0.1
* News article for the PTMA paper; version=0
* Add PTMA CGM3 IBI to LIBRARY.md
* Add test for ibi\_CGM3 PTMA
* Rename folder for PTMA CGM3 IBI from ibi/ to ibi\_CGM3/
* Add [info] section with links to https://doi.org/10.5281/zenodo.8287521
* use box from pdb in correct fashion
* Add warning if PTMA is not patched with CH3 groups
* Update citation for PTMA.CGM3.ibi.ff
* trigger GitHub actions
* Re-trigger the test
* Add PTMA AA opls to LIBRARY.md
* Add test for PTMA AA (opls)
* Somehow, PTMA citation was not working; fixed
* Update citation for PTMA.oplsaa.LigParGen.ff
* Use standard OPLS atomtype labels for PTMA
* extend tests for box coord parsing
* fix loglevel for box coord warnings
* fix gen\_coords and topology calling of box dimensions
* increment martinize2 dependency
* add warning when density is overwritten
* Update setup.cfg
* fix logic mistake and add tests
* improve box handling
* add box to topology
* remove nodes also from fragment graphs; check missing edges for all molecules
* fix logging for ig format error & add test
* fix test & iterator
* add warning for ig format missing title line
* fix error message in gen\_dna
* add test for unkown DNA residue error
* add circle link
* add backmap attribute in add\_node function
* fix DNA API in gen\_itp
* make max\_resid a class variable that gets updated automagically; update DNA convention
* implement the proper DNA convention when completing strands from sequence file; also fix cyclic sequences
* add dsDNA test
* use standard convention for DNA
* fix 3,5 link to only apply in one specific case
* add link for 3->5 direction
* carry over edge attributes
* keep edge attributes
* fix test and add circular test-case
* add test for function to generate complementary DNA strand for dsDNA
* add function to generate complementary DNA strand for dsDNA
* fix comments
* add white space
* adjust error message
* filter molecule for templates
* add tests for parsing #error statements
* parse #error statements
* improve volume tests
* add scipy 1.11 patch
* add scipy 1.11 patch
* add test for new IDP parameters
* fix typo and add edges
* fix exclusions
* fix issue 285
* Switch to default OPLS atomtype names (instead of redundant LigParGen-generated ones)
* Update .codecov.yml
* Update python-app.yml
* Update pypi\_deploy.yml
* add token for Coverage
* Update python-app.yml
* Update python-app.yml
* Update pypi\_deploy.yml
* ignore tests with coverage
* add verbose to coverage test
* change CI in deploy file
* Update python-app.yml
* Update python-app.yml
* fix yml syntax error
* Update python-app.yml
* Update python-app.yml
* Update CI
* changed some defaults in main script
* added error message to gen\_seq
* added ide ignore to gitignore
* fix indent in comment
* fix spellig error
* add tests for non finite coords and more tests
* remove print
* remove contaminating test from other PR
* add error for non finite coordinates
* remove contaminating line from other PR
* fix docstring and typoes
* require scipy 1.6.0 to be complient with change in KDTree naming
* provide more detail for error message on too large inital coords
* add test for logic check
* implement warning; replace cKDTree by KDTree as per deprecation
* remove pbc\_complete and max\_dim check from rw module
* move pbc\_complete and max\_dim check to linalg module
* assign proper resid to first residue
* test resid starting with higher number than 1
* assign proper resid to first residue
* This might fix the test
* Trying to figure out why the tests fail
* Fixed test for older python versions
* Add test for unknown file warning
* Improved docstrings and variable names
* Return storage object
* Warning when unkown file in library
* rename file\_ to file\_path
* add optional forcefield argument to load\_ff\_library
* only accept one ff to load templates from
* tests for library loading behaviour
* fix parsing behaviour: selectively ignore files in data library
* assign proper resid to first residue
* test resid starting with higher number than 1
* assign proper resid to first residue

v1.5.0
------

* missed a comma in the list
* corrected test result for protein fasta
* removed unnecessary test header
* made requested changes to test
* added test parametric and removed protein.ig test
* added test for sequence parsing and required files
* corrected typo
* made changes to parser and tests as requested
* missed the change in behaviour of parse\_ig
* added AA parsing to fasta file reading
* bug fix + incorporate comments
* Update polyply/data/martini3/PDMS.martini3.ff
* Update polyply/data/martini3/PDMS.martini3.ff
* Update polyply/data/martini3/PDMS.martini3.ff
* Add full Polydimethylsiloxane name to LIBRARY.md
* add info and force-field parameter link to PDMS
* reduce complexity parsing wrappers
* Update README.md
* Update README.md
* Add Whole Cell to polyply
* add test for logging blocks
* Update polyply/tests/test\_gen\_params.py
* move setting of loglevel inside test function
* add logging test
* update config file
* Update README.md
* change dependency to latest vermouth version
* add warnings to molecules
* move warnings to bottom; add empty line to seperate in screen print
* add log message to PPE
* adjust python versions
* adjust python versions
* add lib test and fix bug in naming of M3 PDMS
* add PDMS parameters
* change name END to PDMSTer in PDMS M3 definition
* add PDMS to library.md
* add PDMS to library
* clean up PPE.ff
* adjust logleves
* add logging messages to gen\_itp
* add logging messages to link

v1.4.1
------

* add comment and change if/else order when expanding multiple interactions
* removed superfluous loop
* fix issue in cellulose bond; bond was made between A +B instead of B +A
* add test for CEL
* add test for CEL
* add preprint parameters for CEL and DEX
* add preprint parameters for CEL and DEX
* remove coverage file
* make name and output file optional in gen\_params function
* make name and output file optional
* allow multiple type directives
* add test multiple dihedrals
* proper expansion of diehdral types from topology
* Fix typo in LIBRARY.md (links to martini3 PTMA and dextran)
* Add HEA, PAM, PMAM (gromos2016H66) to LIBRARY.md; done
* fix indentation
* add support for older python versions
* (finally) Working tests
* Add more 2016H66 to LIBRARY.md
* Add all the M3 models to LIBRARY.md
* Add all the M2 models to the LIBRARY.md file
* Partially working tests
* add extension check for user provided files
* Add link to LIBRARY.md in main README.md
* All the models as in Supp. Table 1 of the NatCommun polyply paper
* Add column with full polymer name to LIBRARY table
* Add draft of library table (summarizing available models)
* Rename PTMA.customexcl.ibi.ff -> PTMA.CGM3.ibi.ff
* Add PTMA CG IBI model to polyply library [arXiv:2209.02072]
* Add test for PTMA M3 model (part 2/2)
* Add test for PTMA M3 model
* Name in citations.bib need to be {Surname, Last Name}
* Add PTMA CG M3 model to polyply library [arXiv:2209.02072]
* Add PTMA AA FF to polyply library [arXiv:2209.02072]

v1.4.0
------

* Update polyply/src/topology.py
* Update topology.py
* Update topology.py
* Update topology.py
* Update polyply/src/topology.py
* sort graph nodes of meta-mol node attribute by index when reading positions
* fix bug in topology reading and add test
* fix bug in topology reading
* address comments
* Update polyply/src/apply\_links.py
* Update polyply/src/apply\_links.py
* Update .github/ISSUE\_TEMPLATE/parameter-submission.md
* Update issue templates
* Update python-app.yml
* add development branch to CI
* Fix failing tests (now really)
* Fix failing tests
* small fixes
* revert accidental commits
* add buildfile parsing functionality
* add buildfile parsing functionality
* Update .github/CONTRIBUTING.md
* Update .github/CONTRIBUTING.md
* Update .github/CONTRIBUTING.md
* Update .github/CONTRIBUTING.md
* Update .github/CONTRIBUTING.md
* Update issue templates
* Create CONTRIBUTING.md
* add TXT FASTA and IG format to gen\_params help text
* Add test
* Only parse known file extensions
* count num fragments instead of getting it from length of list
* more efficient parameter removal
* add integral test that nodes can be scheduled for removal
* add test that nodes can be scheduled for removal
* fix bug and implement option for removing nodes
* make sure self-links are applied
* make volume code cleaner to read by removing continue statement
* add test file with missing cog coords
* raise warning if meta-mol coordinates are incomplete
* fix typos
* add test for two single residue mol multiblocks
* remove prints
* fix multi-block for single residue
* add error message details and test for when multiblock doesn't match resgraph sequence
* fix multiblock input
* add tests for template and volume parsing
* debug build file parser
* fix generate templates
* take care to rename self.\_gen\_temp to self.get\_temp
* add volumes as class attribute to topology
* update and clean generate templates
* compute volume upon parsing
* update doc-string and clean compute volume function
* fix typo
* cosmetic change to if elif else
* fix bug in gen\_coords, add test for backmap only gen\_coords
* fix bug in gen\_coords, add infrastruct for gen\_coord testing
* add more clear error message
* only have bonds and constraints make edges
* Fix 242
* fix type in test
* address comment
* address comments + map template from COG
* handle already present volumes/templates
* linting and implement check for defined templates/volumes
* add parsing of volumes
* add parsing of templates
* add backmap key in all relevant places
* use backmap attribute instead of build in backmap processor
* add test for only meta-molecule coordinates
* add test for only meta-molecule coordinates
* allow parsing of meta\_molecule coordinates in gen\_coords and bin/polyply
* allow parsing of meta\_molecule coordinates
* update topology tests
* Update polyply/src/gen\_seq.py
* Update polyply/src/gen\_coords.py
* Update polyply/src/gen\_coords.py
* Update polyply/src/gen\_coords.py
* Update polyply/src/gen\_coords.py
* Update polyply/src/gen\_coords.py
* Update polyply/src/gen\_coords.py
* Update polyply/src/gen\_coords.py
* Update polyply/src/gen\_coords.py
* Update polyply/src/gen\_seq.py
* Update polyply/src/gen\_itp.py
* Update README.md
* Update polyply/src/gen\_seq.py
* Update polyply/src/gen\_seq.py
* Update polyply/src/gen\_itp.py
* Update polyply/src/gen\_coords.py
* Update polyply/src/gen\_coords.py
* Update polyply/src/gen\_coords.py
* Update bin/polyply

v1.3.1
------

* change argument type for grid spacing from int to float
* fix variable names in gen\_coords
* update seq and param tests
* change argument destination macros to macro\_strings to avoid conflict in gen\_seq
* fix bugs in top-level programs
* parse args as func variables not class attributes to gen\_coords
* parse args as func variables not class attributes to gen\_seq
* parse args as func variables not class attributes to gen\_itp
* improve test gen\_params for missing edges
* Update polyply/src/graph\_utils.py
* remove missing\_edges from gen\_params; update test for missing edges
* add test for missing edges
* move missing links to graph utils
* Add files via upload
* Add files via upload
* Add files via upload
* Add files via upload
* Add files via upload
* Add files via upload
* Update PPE.itp
* Update citations.bib
* Add files via upload
* Delete PPE.martini3.ff
* Delete PPEter.martini3.ff
* Delete PPEinit.martini3.ff
* Update PPE.itp
* Delete PPE\_20mers.itp
* Add files via upload
* Add files via upload
* Update command
* Add files via upload
* Update test\_lib\_files.py
* Update test\_lib\_files.py
* Add files via upload
* Create command
* Delete test2
* Add files via upload
* Delete test
* Delete PPE\_20mers.itp
* Create test2
* Add files via upload
* Create test
* Update citations.bib
* Update PPE.martini3.ff
* Update citations.bib
* Update citations.bib
* Add files via upload
* Add files via upload
* Add files via upload
* Small improv error message top\_parser
* FixType2016H66

v1.3.0
------

* Update vermouth dependency
* fix typo
* add test for logger warning
* use read\_itp instead of read\_polyply; difference is edges are now only made from bonds, angles, constraints
* use read\_itp instead of read\_polyply; difference is edges are now only made from bonds, angles, constraints
* add doc\_strings
* better record of missing links
* add comments
* test logging of warning
* fix branched test
* fix persistence error message
* use real path not edge-list for making end-to-end dsitances
* update pair/exclusion in test for PS
* update pair/exclusion in block PS
* change resnames to macros in links for better control
* remove incorrect dihedrals from head-tail-head PEO polyvinyl arrangement
* add pairs of CH3 to PMMA and PMAM
* add mPEG
* Update persistence.py
* Update persistence.py
* update links
* add PMAM; fix pair in PMMA
* look at actual persistence length distribution before raising error/warning
* add ig test case which fails
* update json doc-strings
* update doc-strings
* add test for failure to read ig due to missing terminal digit
* Update meta\_molecule.py
* Delete test.csv
* Update test\_simple\_seq\_parsers.py
* Update meta\_molecule.py
* drop csv support
* fix doc-string point
* add test for unkown file extension error
* change file\_handle to file\_path as variable name in parse\_sequence\_files
* fix termini also for RNA
* change error message to FileFormatError instead if IOError
* add doc-strings; and raise error when file-format is unkown
* add test covering failure when default resids cannot be assigned
* address style, and lint comments; clear up ig function
* Update polyply/src/simple\_seq\_parsers.py
* Update polyply/src/simple\_seq\_parsers.py
* Update polyply/src/simple\_seq\_parsers.py
* Update polyply/src/simple\_seq\_parsers.py
* Update polyply/src/meta\_molecule.py
* add charges to DT3
* Update polyply/src/meta\_molecule.py
* fix the linktype circle attribute
* update doc-strings
* fix178
* add second sequence to trigger warning
* merge upstream
* raise warnings through Logger
* add test files for simple sequence file formats
* add test for RNA
* remove fasta ig support of AAs
* debug ig for circle format; add test ig circle
* rename test to prevent overwriting
* fix leftover commenting
* fix test; improve error message
* add tests for simple-seq parsers; fix bug in ig format
* fix ig format; patch DNA terminii; add docstring to DNARNA identifier
* include edge parsing into the json parser
* incooperate parsers with main MetaMolecule workflow creating a more general constructor method
* reorganize meta\_molecule constructor
* init draft for fasta, ig, csv, txt, plain
* add DNA citations
* test remove comment
* add version and put comment
* reduce print
* add backbone side chain angles; update exclusions
* fix test
* wMerge branch 'master' into news\_section
* change # as polyply is already taken
* change branched test
* add library test for M2 ssDNA
* Correct use of pytest.approx
* Remove unneeded (invalid?) staticmethod decorators
* Add News section

v1.2.1
------

* fix year in polyply citation
* Update README.md
* update polyply citation
* update M3 citation
* update polyply citations
* Update README.md
* add polyply citations
* update README
* add martini3 citation
* fix #148
* add m3beta citation
* add Horta citation
* Update README.md
* Fix small typo (vinly --> vinyl); cosmetic
* change open to deffered\_open in gen\_params
* fix change in deferred file writing
* Update run\_pylint.py
* print from run\_pyling
* Patch PSS files

v1.2.0
------

* skip  unused molecules in residue check
* disable unfixable pylint warnings
* some lint in bin/polyply
* some lint
* remove tutorial files
* remove unused imports
* remove print
* add molnames
* add logging to source file
* fix bug in logging test; add additional test for IOerror in restraints
* remove logging from rw, add test for restraint error in parser; fix test 1
* logging tests for build file
* add warnings and Errors to build file parser
* raise Error if block is not part of the library
* remove atype check as this will mess with the PEO of UA FFs
* implement residue check test
* implement residue check
* relax restraint check; allow for branched molecules in principle
* Bug fix regarding the use of ligand annotator
* fix test
* fix docstrings and nitpick
* fix issue 160
* address comments
* add additional dihedrals to test-file
* update test file
* remove print
* update dih function; improve template gen
* use double dih
* simplify compute average step length
* implement tolerance for cycles
* implement tolerance for distance restraints
* completly remove pos-res
* add error for non-linear cyclic molecules
* deal with cycles; move to gen\_coords
* deal with cycles bug-fix
* deal with cycles
* use bfs-tree path in random-walk
* fix error raising in restraint
* move \_find\_starting\_node
* adjust persistence tests
* adjust restraint tests
* use bfs tree with restraints
* add citations
* adjust DNA test
* rename DNA ff; update links for cycle; add chirality defs
* light linting in polyply
* light linting
* adjust tests
* add error when multiresidue block is not already in meta-molecule
* add defined path to tests for restraints
* add defined path to persistence module
* typo fix in parser
* set restraints along a defined path
* don't compute distances on infinities
* some linting
* fix docstrings; address comments batch3
* add some warnings for persistence
* Fix multiple blocks from itp
* test if error is raised
* fix return in set\_restraints
* use topology.molecules for restraints and build systeme
* raise warnings and errors
* fix minor comments
* store restraints with topology; tests for restraints; bug fixes
* adjust tests
* refactor apply\_restraints part3
* refactor apply\_restraints part2
* refactor apply\_restraints
* fix nameing error
* implement other nucleobases
* implement DT
* change relative resid
* test for milestone check; remove print from test presistence
* tests for restraints and lp sampling; bug fixes
* update test build file parser
* remove needless statement
* some debugging
* implement presistence sampling part II
* implement presistence sampling
* refactoring restraint code
* uncomment tests
* clean up dihedral pattern matching; add more patterns
* add VS1 to top-parser method dict
* init draft
* add amber patterns to bonded interactions
* update top-parser
* Add test for OPLS PEO
* fix one incorrect dihedral in end-residues
* add amber DNA test
* add amber DNA ff-file
* only check mass if reference file contains it
* make library test stricter for dihedrals
* clean comments for angle links
* correct mass for P3HT in martini3
* add format specifier to disconnected molecule logging warning
* include chirality/links for HEA
* fix charge assignment for neutral and charged AAs
* fix tests apply links for patterns and non-edges
* address comments
* add edge to VS to remove warning
* add tests for patterns and non-edges
* add data files for protein test
* implement patterns and M3 protein test
* implement M3 disordered proteins
* implement molmeta keyword and non-edge matching
* support single residues
* add parsing for non-edge directive
* remove PPO from resnames in links
* clean chiral-links
* add correct masses to vinyl ether links
* add correct masses to PEO
* add pairs for PAM equilibriation
* clean
* Add badges
* Address comments
* Make the readme more streamline
* Fix vermouth dependency error
* add masses to library test
* add masses to it
* fix mass problem
* fix mass problem; add PAM
* fix wrong comment
* add PAM to polyvinyls
* fix mass problem polyethers; implement PPO

v1.1.0
------

* Update pypi\_deploy.yml
* some light lint on random\_lin\_comb
* make central repro for M3 parameters
* rename test\_itp\_files
* rename gen\_itp to gen\_params in library test
* rename gen\_itp data folder
* remove backed up files
* frename test\_gen\_itp to test\_gen\_params
* change gen\_itp to gen\_params
* add all tutorial files
* remove assert True
* fix bug; and check meta value of interactions
* add ifdef TI statement
* add Dextran test to library check
* add Dextran to m3 polymers
* add links for PEGylated lipids and PS PEO
* Update P3HT.itp for test (added the FLEXIBLE ifs)
* Add ifdef FLEXIBLE to M3 P3HT
* add PVA
* implement PSS assuming bond-lengths are not affected too much by COG mapping
* add parameters for PMMA
* Update command for gromos53A6 P3HT test
* Add test for gromos53A6 P3HT
* Rename polyply/data folder to gromos53A6
* Rename oplsaa LigParGen data folder (in line with newer data folder names)
* Fix P3HT.martini3.ff (now everything works) and add reference P3HT.itp for test
* reorganize angles in PE
* update tests PS
* add FLEXIBLE option for PS
* add test M3 PE
* implement M3 PE
* HEA input
* Fix centeral-->central typo
* Convert P3HT.martini3.itp to P3HT.martini3.ff
* Create PMA.martini3.ff
* Update polyply
* Update polyply
* Add missing column to atom\_types and LigParGen citations
* Update fudge factors
* Add OPLS-AA LigParGen PEO to the library (ff, links, etc.)
* Update polyply/src/meta\_molecule.py
* remove leftover files
* move lib tests from gen\_itp to libtest
* fix lib-file test; automatically give resids to json graphs; test, error, and warning when resids not provided
* complete merge master
* small nit-pick
* add M3 P3HT; add tests for M3
* add M3 polymers; rename martini libraries
* reduce gromos to minimum
* Add decorator install criterion
* address comments
* Add {version: x} to AA P3HT links.ff for multiple multiplicities
* make WEIGHTS dict
* comments; clean up and extend map to molecule tests
* Switch to .ff format for P3HT G53A6; add citations
* Add DOIs to Martini 2 citations and fix typo in gen\_itp.py
* c
* complete merge
* remove conflict
* mix up node\_keys as additional check
* remove dependancy of links on node keys
* put multiresidue test back in
* fix comments
* Update polyply/src/gen\_itp.py
* add warning for disconnected molecules
* implement acrylates; update library; more tests
* address comments
* implementd stricter success criterion on the minimizer
* update doc-string
* adjust test input files
* fix bugs and implement new mapping in workflow
* improve map to molecule to recognize proteins etc. draft
* fix test
* add logger to gen\_itp
* add citation infrastructure
* add test cases for AA-charmm; flat-dih
* increase angle/dih tolerance to 5
* update doc-string
* update compute\_dihedral function
* adjust comment
* address comments and add test
* Rename H termini residues as Hter (instead of P3HT)
* add test-files for GROMOS
* add check for number of terms must be equal
* add missing angle in CH3ter
* update GROMOS library
* infrastructure for testing library files
* add error messages
* remove proper dihedrals from structure generation
* Implement AA P3HT (the first GROMOS 53A6 polymer)
* merge maste
* print gen\_itp command to file
* typo
* remove nproc form polyply
* small nitpicks
* fix edge making in links
* fix/107
* address comments on docstring
* change make edges to positive criterion
* fix logger in generate templates
* remove processor arg from backmap call
* choose random initial rotation for molecules
* Small fixes to the main README file
* Add test for PEO-PE block copolymer generation
* Add one more link to allow building of PEO-PE block copolymers
* address comments
* change summation in norm\_matrix
* rebuilt tree once when positions are removed
* remove n-proc from test of backmapping
* address simple comments
* subclass ff-parser to parse edge attribtues
* remove crude timing feature
* use edge attributes in applying links
* address comments
* rebuild tree instead of looping over
* Update pyproject.toml
* implement Logger
* Fix deploy
* Update setup.py
* delete version
* Update setup.py
* Fix version in metadata
* Update pypi\_deploy.yml
* fix deploy to run with new release
* Update actions
* Update pypi\_deploy.yml
* Deploy workflow
* lint only with one python version
* add pylint
* Update python-app.yml
* Update python-app.yml
* GH actions for testing
* make 1level shallow copy of each molecule in system; max coords 12Mio
* test for gen\_seq
* get rid of need to copy nb\_matrix
* adjust naming for PC/PE lipid head group
* small bugs
* testing for PEGylated lipids; PEO in martini2
* remove memory trakcing
* fast, linear scaleing and accurate backmapping
* keep dihedrals from making edges
* temp commit for rudimentary monitoring
* much faster backmapping algorithm
* add find edges from residue graph method
* add new tags argument in test
* fix bug in gen\_seq
* remove topology attribute from molecule and only store neccessary information
* linear scaling backmap
* fast backmap
* infra structure for chirality
* add link which doesn't apply
* fix logic
* filter links by resname before using graph matching
* fix splitting function; properly generates new resids

v1.0.0
------

* add new restricted scope token

v0.0.1
------

* add new token and update pypi ref
* address comment
* Update README.md
* Update Readme for first release
* replace logging in \_\_init\_\_ by print for the moment
* introduce vermouth version; delete numba requirement
* comment; make density and box argument required but mutually exclusive
* set cut-off dynamically
* more tests; build file parser
* complete test
* add pypi test release feature
* line linting
* address final comments; in lieu of missing logger clean up printing
* address final comments
* merge master
* address comments
* last comments
* adjust rewind function
* remove hard-wall check
* put treshold in compute volume
* address old test comments
* address old rw comments
* make numba optional everywhere; import from \_\_init\_\_
* old comments and lint
* lint and comments topology gen\_coords
* lint random-walk; comments; test for graph-utils
* lint polyply exe
* address comments; new rw push option
* address comments; more testing
* fix meta\_mol expansion; add check for branching
* fix meta\_mol expansion; add check for branching
* address more comments
* set build attribute by default; migrate check to helper function
* redo split molecule; delte copy method
* tests for gen\_coords
* small fix; reduce gen\_coords
* address comments re. nonbond\_engine
* rename nonbond\_matrix to nonbond\_engine
* rework and test build system
* expose fudge factor for backmapping
* expose rewind number
* complete merge master
* more tests and address comments
* test for nb engine
* test reverse link
* minor linting
* sane way of adding edges
* more doc-strings and comment
* fix small bug in VS handeling when generating bonded interactions
* address comments
* add tqdm package to install requirements tests
* add tqdm package to install requirements
* move neighbourhood to graph utils
* rename res-fragment attribute in meta\_molecule
* graph-matcher based apply links
* fix bug in polyply parser; now links get edges
* make isomorphism based link matching
* only update interactions after we have found all replaced ones
* make apply links much faster by only searching atoms in residues
* create new MetaMolecules when parsing top; this is more memory efficent than a true deep-copy
* add progress bar to links processor
* address comments
* comments and higher code-cov
* fix comment
* inital tests for system builder
* make numba compatible with codecov LJforce
* make numba compatible with codecov
* tests for build file parser
* remove prints and add comments
* testing for annotate ligands and copy for metamol
* more testing for random walk
* adjust test for minimzer
* add numba to install requirements
* deep copy of meta-molecule
* rewrite and testing of annotate ligands
* exclude not defined atomtype tokens from typing
* add martini amber and charmm tests for top-parser
* test dir for files related to system builder
* start for testing system builder
* add the topology as argument to gentemplate processor
* type the tests in linalg as floats so numba works
* add nproc argument to backmapping
* updated randomwalk geometrical constraints
* tests for random walk processor
* add magic sclaing for backmapping
* parallel split residues
* store command
* geometrical restriction also for starting nodes
* numba linalg; improved template generation for AA
* backmap parallel option exposed to CLI
* fix exclusions
* backmap parallel
* use set of trees instead of single tree; also numba improve nonbonded
* numba and set cKDTree to unbalanced for speed
* set proper defaults for start option
* implement PBC for RW
* implement build file with geometrical constraints and cylinder and sphere
* implement build file with geometrical constraints
* parser for build file
* have start option; fix bug in rewind
* fix line-breaks in test\_topology
* change minimizer to take inter\_types; swithc of printing in random walk
* test skipping of directives for real and make sure something is actually parsed
* adjust parsing of atomtypes according to comment; add test for fail
* add comment and lint
* add exclusions for nodes that have been tagged with exclude option
* enable merge of blocks with different nrecl
* split syntax
* first draft for ligand placement
* interpret OPLS bond-types accurately
* parse complete atomtype directive
* add split option to structure builder
* test for skip star comments in topology file
* skip star comments in topology file
* add more tests for replace; address comments
* fix exclude for molecules with no positions
* implement exclude option to system building
* find proper starting node in random walk when positions are present
* implement build res for membrane complition
* add rewind option
* progress bar and implement rectangular box
* implement rectangular box
* exclude particles from volume calculation when exactly in center
* expose variables of structure building to CLI
* test for skip directives
* skip gen-born directive
* add test for raising error when no bondedtype can be matched
* add virtual\_sitesn to be excluded when doing gne\_bonded; remove prints
* exclude files which are not defined
* some more testing for generation of bonded pairs
* implement generic dihedraltypes
* generate bonded interactions; this makes charmm topologies work
* keep pairs and exclusions from making edges
* part2 of add push option
* add push option
* do not random-walk molecules that are complete
* fix multi component systems
* merge master
* address last comments
* address comments and lint
* address comments
* Update polyply/tests/test\_optimize\_geometry.py
* small bug fixes
* Update polyply/src/backmap.py
* Update polyply/src/backmap.py
* Update polyply/src/topology.py
* adopt random-walk and built-system
* adopt random walk to work with nonbondmatrix object
* store all information for nonbonded interaction handling in single object called NonBondInteractionMatrix
* init draft fast method
* init-draft
* resolve conflict from merge
* adjust tolarance
* cleaner logic for finding reference atoms and tests
* add tests for geometry optimizaer
* reset all VS after optimization; fixes compliance with scipy 1.5.x
* use deferred file-writer
* update tests
* remove ill conversion of node to resid
* update docstring
* expose max\_opt flag for generating template part2
* expose max\_opt flag for generating template
* comments and linitng
* use deferred file-writer
* remove tqdm
* fix CLI
* Update polyply/src/generate\_templates.py
* Update polyply/src/backmap.py
* Update polyply/src/backmap.py
* adjust tests
* set build attribute at metamol level; zero resids
* make backmapping residue based and more efficient
* add virtual sites for edges
* add residue based building
* add virtual-sites3/2/3 for edge building
* fix expand init coords for real
* fix expand init coords
* fix test random walk; fix doc-string
* only generate template once per residue
* improve initial guess of template
* take restarting into account
* introduce fudge factor
* orient templates incl. AA prev
* actually fix all merge remains
* test more than one molecule in pdb
* add appropiate test
* fix reading of complete coordinate files and pdb reading of multiple molecules
* use single random seed; linting; strip edges correctly
* address comments
* add appropiate test
* fix reading of complete coordinate files and pdb reading of multiple molecules
* update polyply
* add modifications for termini
* cleaning of gen\_seq
* cleaning of bin/polyply
* improve the sequence generator
* add correct reference file
* update some arguments in bin
* split up gen\_seq; add more unit tests
* add test for random polymers
* some test data for the sequence generator
* small edit to meta\_molecule
* daft for tests
* add sequence generation tool
* input files for M2 PEGylated lipids and OHTer or PEO residue
* lint; remove except
* add replace syntax to links
* Fix few typos in README.md
* fix key error in topology preprocess
* reduce step-length to 1.1 of rvdw
* fix calculation of radius of gyration
* fix conversion of C6/C12 to sigma epsilon and add test
* Fix identical error in tests
* Fix multi-residue detection in map\_to\_molecule
* Add nargs='+' to -seq flag for multi-part polymers
* Typo and small addition
* add data files
* Update README.md
* Update README.md
* updateminimal README
* install vermouth for pylint test
* exclude tests from pylint; lower pylint on score to 8
* remove doc building form CI for the moment
* add docs requirements
* remove python3.5-dev
* remove python3.5 and remove ordering issue in test\_links
* address comments
* add test data variable
* install vermouth develop for testing; update setup.cfg and requirements
* add vermouth to requirements for tests
* setup everything fir CI and pbr
* edit setup files to work with pbr
* make backmapping and extract\_block dependent on atom-name instead of node-key, more tests
* remove links form replace defines
* address some comments
* update setup.py
* some linting
* use np.average in vs builder
* introduce explicit preprocess function to topology; raise IOError when reading Buckingham potential
* reanming to snake-case; comments on unitsphere
* test multiple defines in single interaction
* raise Error if molecule or residue is disconnected
* fix counting of atoms in backmapping
* last comments
* fix backmap and tests
* add license and fix order issue in backmap
* add license
* small bug fixes; P3HT lysoPEG PMMA work
* implements GROMACS VS
* move replace\_defines to topology parser
* replace combination rule in random-walk with the one in topology
* merge master
* adding doc-string for all structure related functions
* restart minimizer upon failed optimization
* address comments
* implement gen-pairs, set default nb to LJ sig-eps, some comments
* merge master
* remove sorting of edges
* fix ordering
* update exec
* add newline
* liniting of tests
* address comments
* add License
* PEP8
* address comments
* address comments
* remove advanced links
* lint test
* reintorduce file lost in merge
* merge master
* implement #else statements
* unmerge
* fix issues in readme
* Update README.md
* Update README.md
* add License text
* Add LICENSE to polyply
* initial README
* implement fix for graph matching at res level
* more tests for top-parser
* comments linalg
* comments topology
* comments top\_parser/polyply\_parser/polyply/meta\_mol
* merge upstream; enforce sorting of json graphs
* enforce rigorous sorting when reading graphs from json
* Update meta\_molecule.py
* fix ordering issue
* structure generator
* updating gitignore
* updating gitignore
* some cleaning of tests; tests for topology
* testing for topology parser
* testing for load\_library
* reorder parser infrastructure
* new constructor meta\_molecule.py
* add new arguments to polyply exec
* fix comments
* fix multi-residue molecule
* change library infr.-struct
* fix library import
* some cleaning
* fix making residues up reading ppy files
* fix comments; slimmer block-to-res-graph method
* new ff loader
* fix #ifdef in this branch
* small fixs
* reorganzie filegroup
* add itp parser for meta\_molecule
* graph from itp file for metamol
* exclusive arguments -seq -seqf
* fix incorrecct ref itp file
* some linting on tests
* fix review comments
* review changes & lyinting of test
* improved multi exe
* some linting
* fix: vermouth order taken correctly into account
* refactoring of apply links
* move list-blocks and list-ffs to toplevel of parser
* use sub-commands in executable and write integral tests for itp generator
* Review of apply\_links
* convert executable into subcommands
* remove pychache
* remove html\_cov and add to gitignore
* final commit before pushing to GH
* some cleaninng and travis, codecov etc
* some cleaninng
* treat mutliresidue as expected
* add gitignore
* all basic tests covered
* secondd complete polyply run
* first complete polyply run
* fix on apply links
* refactor and apply links
* apply link processor that replaces DoLinks from vermouth
* meta\_molecule tests, json creator
* parser and meta\_molecule fixs
* fully working initial draft for single molecule
