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Descriptions of common industry-standard formats for representing reactions and molecules.
Fixed list-type pseudoatom handling. Note: in list [H,C], "C" is treated
as methyl, not alkyl.
Major overhaul of the python code. Added command-line interface to
pddl generator and image generator. Partially implemented pddl
generator; current challenge: existentials in the preconditions;
parameters and effects are working well.
Fix to previous commit; these are the latest versions.
Cleanup.
Added Readme.
Precondition now works with (single-atom) r-groups and pseudoatoms.
Non-parameter atoms are now properly quantified. It remains to add
explicit inequality of atoms of the same type.
Added explicit inequalities between same-type atoms.
Catalysts are still not handled.
Added catalysts into preconditions. Warning: multi-atom catalysts are
not working correctly due to not having atom-to-atom mapping numbers.
Proposed solution: once the generic reaction is created, count the
maximum possible number of atoms any instance of the reaction may ever
have, and enumerate catalyst atoms starting from max+1. Problem with
proposed solution: arbitrary alkyls can be arbitrarily long. Alternative
solution: enumerate catalyst atoms while ignoring r-groups, and then
change r-group enumeration to account for that.
Removed questionable characters from reaction name.
Some rules for git - helps dealing with files that should not be
committed, like bytecode or logs.
Milti-atom catalysts are now handled correctly in PDDL.
Warning: these changes need to be tested wrt reaction.getInstance().
Minor updates to command line interface; minor bug fixes.
Added (almost) full periodic table nomenclature. But we still lack in
atom group names, i.e. halogen, alkali_metal, etc.
Replacing "Halogen" with "X" in reaction file. It seem that "X" is the
standard and "Halogen" was put there manually.
Removed trailing space from directory name.
Now, rxn parser replaces rxn AAM numbers with new ones, resulting in
a consistent, continuous numbering of reactant/product atoms AND
catalyst atoms, which is necessary for instantiation of R-groups and
pseudoatoms.
Minor updates.