{"shas":[["aa77d685b6bacf9ade79d15034ac3564a74ffe53","d2efaa4c3e5af267960de800d4d586f2bce0207f@mit.edu","Sidebar now contains links to website sections on all pages.\n\nThis is done by placing the HTML defining the links in the base.html\ntemplate, so that they always appear. You can now use the sidebar_items\nblock to add custom items to the sidebar; they will appear below the\nlogo but above these links.\n\nThe styles that define the sidebar links were moved to default.css so that\nthey would be available on every page.\n\nCloses #12.","Josh Allen"],["cca771e1f55f4ab2b506a18e998200a9a4c124f3","d2efaa4c3e5af267960de800d4d586f2bce0207f@mit.edu","Added generateReactions() function to database tools.\n\nThis function collects the code for querying RMG-Py and RMG-Java for\nreactions and associated kinetics, as we use this functionality in multiple\nplaces (specifically kineticsData and kineticsResults). Before I had\nupdated only the former with a more thorough algorithm, leading to the\nwebsite displaying a different number of results in the two views. Now they\nuse the same code, and therefore generate the same number of results.\n\nCloses #8.","Josh Allen"],["6be129e10f6d19ac46acf259b813ce441d5d758f","d2efaa4c3e5af267960de800d4d586f2bce0207f@mit.edu","Convert ArrheniusEP kinetics to Arrhenius in kinetics search results.\n\nSince we are searching for real reactions, we have access to the reactants\nand products, and therefore can compute the thermo needed for the enthalpy\nof reaction, and can do this conversion. This allows for easy comparison to\nthe other search results, especially for cases where alpha is nonzero\n(which is not very often in our current set of rules, but it happens once\nin a while).\n\nWe also needed to do this because you can't generate the reverse of\nArrheniusEP kinetics, and the kinetics search would try to do so if the\nrule was in the reverse direction of what you were searching for.","Josh Allen"],["f36c0f2aca11c401225dda633208d97579ca18c7","d2efaa4c3e5af267960de800d4d586f2bce0207f@mit.edu","reactionMatchesReactants() now handles the A + A --> products checking.\n\nBefore this, you would get the A --> products reactions in the wrong\ndirection because it was checking for A + A due to the search for\nA + A --> products reactions. Two changes were needed for this: (1) make\na new list of the bimolecular reactants A + A to avoid trampling over the\noriginal, and (2) allow for the case of one reactant passed as a parameter\nbut two products in the reaction when using reactionMatchesReactants(). In\nthe latter we require that *both* products are the specified reactant in\norder to return True.\n\nCloses #16.","Josh Allen"],["f097bdb42c1b8cd44ee7c3a16995bb7e264eaaff","d2efaa4c3e5af267960de800d4d586f2bce0207f@mit.edu","generateReactions() returns Python and Java results as separate lists.\n\nThe kineticsData view relies on having a separate list of the kinetics from\nRMG-Java in order to handle those in a special way. Thus we need to return\nthem separately from generateReactions(). This function now returns two\nlists; the first contains the reactions generated from RMG-Py only, the\nsecond the reactions from RMG-Java only.","Josh Allen"],["5244064583b5a8dabd18cbe08ba0b840db34d23d","d2efaa4c3e5af267960de800d4d586f2bce0207f@mit.edu","Improved implementation of searchReaction() in parsing RMG-Java search results.\n\nThe previous implementation assumed that we were searching with both\nreactants and products specified. This caused the RMG-Java results to appear\nin only on the kineticsData view, not on the kineticsResults view, which\nwas another reason the number of search results was incorrect.","Josh Allen"]],"ref":"refs/heads/master","size":6,"head":"5244064583b5a8dabd18cbe08ba0b840db34d23d","push_id":36951933}