Welcome, What's New

Release 2.0.1

I have decided to begin a blog detailing the new features, updates, and bug fixes with each consecutive version released.

• Stereochemistry support Support is now in place for creation of, naming of, and reactions with molecules containing chiral stereocenters. The stereochemistry support is a mode than may be turned on and off, depending on the user's preferences. In off mode, chiral centers will not be named and enantiomers will not be considered separate molecules. Reactions will not target molecules with specific stereochemistry. In on mode, chiral centers will be named and enantiomers will be considered separate molecules. Stereospecific reactions will only react with molecules with the targeted stereochemistry.
  Standards - IUPAC nomenclature will be followed. Cahn Ingold Prelog priority rules are followed for assigning R/S designation of stereocenters. Atoms are displayed on 3 levels along the z axis: flush with the plane of the molecule, directed into the page (represented by a dashed line), and directed out of the page (represented by a solid triangle).
  Controls - Stereochemistry support mode may be toggled on and off by clicking on the hide/show chirality button. This will control all aspects of stereochemistry support: nomenclature, molecule display, and reaction pathways. Stereochemistry for a specific stereocenter may be toggled by clicking on the stereocenter.
  Future considerations - E/Z nomenclature will be assigned around unsaturated carbon-carbon bonds. Optical activity dextrorotatory/levorotatory (+/-) designations will be linked to official IUPAC names as common names.

• Additions: Inorganic Phosphate polyatomic ion support addedThe user may now create molecules containing a Pi group for inorganic Phosphate. The impetus being to allow support for molecules found in common biochemical metabolism pathways such as glycolysis, oxidative respiration, and the Calvin cycle.
  Standards - IUPAC nomenclature will be applied.
  Controls - The additions section may now be paged, similar to the skeleton section, to add phosphate ions.
  Future considerations - The workspace will likely include functionality to expand polyatomic ions to view all atoms.

• Dedicated Pathways page The detailed description of a proposed/generated pathway has now been given a dedicated page as opposed to the prior implementation of displaying a modal on top of the pathway/molecule design page. This dedicated page contains the following details of each step in the pathway: IUPAC names of the reactant and product, display of product and reactant, primary enzyme used in step, step monetary cost, calculation source, step running time, step energy expenditure, and verification data. All but the last three details are currently data-driven and live.
  The new pathways page also provides an index view to be used for viewing pathways by category. Currently included is a portion of the Calvin cycle used in the Photosynthesis process of plants: the steps fixating CO₂ to the molcule ribulose-5-phosphate.
  Standards - IUPAC nomenclature will be applied. In fact, currently all constituents of the steps listed in the Calvin cycle are named by IUPAC nomenclature as opposed to more common names. For example, in the place of glycerate 3-phosphate, we are using the IUPAC name (2R)-2-Hydroxy-3-phosphonooxypropanoic acid. Note: Full rules for nomenclature of Phosphorous containing compounds have not yet been implemented in the nomenclature engine. For now in some cases we are using a generated IUPAC approximation.
  Controls - The user may click on any molecule name to open the molecule in the molecule design page view. The user may also click on the enzyme/substrate used in a pathway step or the vendor used for addition information and a link to the vendor. Finally, upon reviewing the pathway steps for a given pathway, the user may approve or reject the pathway using a digital signature and optional notes. This feature is not yet implemented.
  Future considerations - Full support for Phosphorous containing compounds in the nomenclature engine will be implemented. Support for common molecule names in addition to IUPAC names will also be implemented for sake of clarity and readability. The additional details of each pathway step will be wired to be data-driven and live. The data points will be updated at regular intervals. The pathway index view will be expanded to include other known biochemical pathways including the TCA cycle, glycolysis, gluconeogenesis, and oxidation of fatty acids, among others. Approval/Rejection of proposed/generated pathways will be fully implemented. These pathways will then be visible from the pathway index view.
  

• Sitewide navigationImportant now with introduction of specialized pages.