Implementation of the GEN_FF workflow#383

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fgrunewald wants to merge 107 commits intomasterfrom gen_ff_clean

+5,248-282

Commits on Aug 15, 2024

init draft itp to ff
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imporve graph matching
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fragment finder with prints
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add tests for fragment finder
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add test for 100% coverage
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refactor graph matchin post isomorph check
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add check on node naming
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add pysmiles to tests
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tests for ffoutput
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use tmp-file for testing ffoutput
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modify extract block and use in itp_to_ff
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add isomorphism naming
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properly check if interactions are equal
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read itp files
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draft round robin tests
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fix input types
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add test print
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clean up output
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methods to deal with charges
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methods to deal with charges
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methods to deal with charges
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adjust test
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resolve
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small fix
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allow for charged residues and make pysmiles optional import
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make mass optional
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add doc-strings and rename equalize_charge
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remove print
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remove martini2 from ffoutput test as it fails on GH
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add test for extract links
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add test for extract links with redundant interaction
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test for charge balancing
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test for charge balancing
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implement tolerances for charge balancing
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add integration tests itp_to_ff and adjust CLI
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fix bug in integration tests itp_to_ff
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complex integration test itp_to_ff plus charged mol
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use top file for ACOL test and fix bug in test
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fix toplevel itp_to_ff parser
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bigsmile_draft
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have charge balancing for itps but raise error when bond length is missing
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infrastructure for big smile parsing
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optional dep. for pysmiles
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add a processor that reads a big smile string and returns a full metamolecule including edges.
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atest-big-smile parsing part I
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fix hcount for single atom; fix nexted branches
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tests for smile iter and test nested branches
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add tests for bonding descriptor evaluation
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add tests for big smile molecule prc
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allow multiple bonding per atom; fix bugs
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remove mpl import
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add changed tests for multiple bonding per atom
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delete old processor file
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add closing bracket to special characters
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only balance charges for blocks with at least 2 atoms
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refactor fragment finder
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refactor fragment itp_to_ff
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change input for itp_to_ff to allow bigmsiles
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take most central fragment
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add special links for terminal modifications
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type the charges to float in itp to ff
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read provided ff file and use these blocks instead of making new ones
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skip termini mods if none atoms are different
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account for explicit hydrogen in the smiles string input
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test accounting for explicit hydrogen in the smiles string input
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adjust doc string
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redo hydrogen based on valency not based on how many bonding descriptors are leftover
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fix tests
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Apply suggestions from code review

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pckroon
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allow nested branch expansion
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test branch expansion
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add comments all over residue expansion functions
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address comments
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allow for ionic bonds with . syntax
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fix previous issue with link appending
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update itp_to_ff tests
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update tests for fragment finder
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remove leftover files
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add versions if bonded interactions within a block occur more than once
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add bond orders for connecting edges
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allow missing atom_num in topology file
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replace all bonded interaction if atomtype change is detected
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fix bug in hcount function
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fix order attributes and hcounting
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fix top_parser
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increase charge tolerance requirement and add elements
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sort hydrogen atoms after replacing unconsumed bond ids
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fix counting of hydrogens
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remove bigsmiles
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remove bigsmiles
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resolve
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move simple sequence interpreter to appropiate file
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resolve
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base on cgsmiles
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fix cgsmiles bug
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add liscence text
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add changed license text
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rename and add changed license text
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temp removal of OPLS test due to problematic atype naming in OPLS
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rename gen_ff in file
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put proper license in tests
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change setup
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remove leftovers
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fix OPLS ligpargen atomtypes
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resolve merge issue
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remove 3.7 support
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Commits on Aug 16, 2024

fix small bug
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