Adding hydrogens and bond orders to structures without them

From BlueObelisk

Contents 1 Adding hydrogens and bond orders to structures without them 1.1 Data (PATTY expert system) 1.2 Algorithm 2 Other starting points 3 Open discussion

Adding hydrogens and bond orders to structures without them

Data (PATTY expert system)

• JOELib
  • implicitValence.txt
  • phmodel.txt
• OpenBabel
  • atomtyp.txt (see IMPVAL entries, only)
  • phmodel.txt

Algorithm

• CDK
  • Java source code

Other starting points

• Atomic Composition
• Total Charge
• Coordinates
• Conventional Framework
• Bond Orders
• Localized Charges

Open discussion

• For creating bonds for unconnected atoms, see e.g. ConnectionHelper
• IMHO a free [PATTY] definition is the most general way to define and change a protonation model and makes the software more general and robust against user specifications. JKW,2006-05-28,10:03