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It was proposed that additional features should be allowed in the medium table format. Currently the medium table format consists of 4 column (2 required, 2 optional), specifying compound ID, compartment, lower bound and upper bound. With this proposal, additional user defined properties should be allowed after the four existing columns.
The user defined properties should be parsed and be made accessible through the API. For example, with a user defined property "class":
compound compartment lower upper class
akg e 0 400 carbon-source
glcD e -10 - carbon-source
This would require that a header be added to the medium table format so that a key can be specified for each property. It would also change the format of the table file to be strictly tab-separated instead of being space-separated as it is now. A new class MediumEntry can be defined so that the additional user defined properties can be held. The properties can be made available from the NativeModel through parse_medium() which would iterate over MediumEntry objects instead of tuples.
The text was updated successfully, but these errors were encountered:
It was proposed that additional features should be allowed in the medium table format. Currently the medium table format consists of 4 column (2 required, 2 optional), specifying compound ID, compartment, lower bound and upper bound. With this proposal, additional user defined properties should be allowed after the four existing columns.
The user defined properties should be parsed and be made accessible through the API. For example, with a user defined property "class":
This would require that a header be added to the medium table format so that a key can be specified for each property. It would also change the format of the table file to be strictly tab-separated instead of being space-separated as it is now. A new class
MediumEntry
can be defined so that the additional user defined properties can be held. The properties can be made available from theNativeModel
throughparse_medium()
which would iterate overMediumEntry
objects instead of tuples.The text was updated successfully, but these errors were encountered: