 Adam Husar
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80bad6b5b3
Fixed handling of newline cancellation '\' followed by Windows newline
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3 年之前 |
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Adam Husar
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c25d773f0d
Fixed time when a new molecule is created in case when a tranparent
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3 年之前 |
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Adam Husar
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dc743aa703
Made sure that the num_instantiations is set to 0 for new species
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3 年之前 |
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Adam Husar
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bb06fa93c1
Renamed .inc files to a more common extension .inl
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3 年之前 |
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Adam Husar
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5b056b55f4
Support for conversion of release sites into BNGL's seed species
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3 年之前 |
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Adam Husar
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ea22b3cb08
Fixed case where a reused surface reactant changes orientation such as
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3 年之前 |
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Adam Husar
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cfc85d0597
Fixed orinetation handling for rxns where the surface molecule is
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3 年之前 |
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Adam Husar
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7add1710c7
Handling of compartments in Introspection.get_molecule_ids
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3 年之前 |
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Adam Husar
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a0afc02ca7
Minor comment cleanup
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3 年之前 |
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Adam Husar
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19623d2047
Added support for updating compartment when crossing transparent walls
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3 年之前 |
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Adam Husar
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91c5b595d3
Fixed handling of molecule counts for patterns that use primary surface
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3 年之前 |
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Adam Husar
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ef9d049b7d
Fixed Cplx::matches_complex_fully_ignore_orientation - checking that
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3 年之前 |
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Adam Husar
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439fcbdfcc
Fixed assignment of orientation to reactions in the form S + V -> S.V
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3 年之前 |
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Adam Husar
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1471141fc3
Added support for creating products where compartment of the reactant
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3 年之前 |
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Adam Husar
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a828d978c6
Preparation for unbinding for rxn with unspecified compartment
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3 年之前 |
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Adam Husar
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a71f9162ca
Added a python script that generates a BNGL function from a data file
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3 年之前 |
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Adam Husar
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3c85b4f85e
Setting compartments for products of rxn rules where their compartments
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3 年之前 |
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Adam Husar
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a3cac16f5d
Added check for invalid combination of compartments in rxn
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3 年之前 |
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Adam Husar
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c13d828373
Minor refactorization of update_compartment in Partition, all tests pass
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3 年之前 |
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Adam Husar
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801bab3b77
Code cleanup
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3 年之前 |
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Adam Husar
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69a999df0b
Removed utility function is_nonprintable_compartment_id
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3 年之前 |
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Adam Husar
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aff67ef4a1
Fixed reusing of reactant that is also present as a product - it must be
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3 年之前 |
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Adam Husar
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ce2f080f41
Observables now use directly patterns with compartments, 3 tests are
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3 年之前 |
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Adam Husar
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626993c3f0
Disabled debug dumps
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3 年之前 |
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Adam Husar
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d8263b6a85
Initial step towards rework of observables with compartments, test that
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3 年之前 |
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Adam Husar
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b2a453d5ff
Fixed parsing of BNGL rxn A -> 0
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3 年之前 |
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Adam Husar
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5e95042d0b
Fixed check in is_used_compartment used for data model to pymcell4
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3 年之前 |
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Adam Husar
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b9728e725e
Fixed case where data model -> pymcell4 conversion did not know that an
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3 年之前 |
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Adam Husar
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5d4adf5c28
Assigning specific compartments to rxn products
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3 年之前 |
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Adam Husar
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e7b9af4f01
Handling ':' in rxn name generation from data model
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3 年之前 |
