Hypotheses in Catalyst

Introduction to hypotheses

How do I . . .

• Create a hypothesis
• Generate a hypothesis automatically from a set of training molecules
• Prepare for hypothesis generation?
• Generate a hypothesis?
• Construct a hypothesis manually
• Add fragments and functions from the Feature Dictionary?
• Convert a molecule into a hypothesis?
• Use a template molecule?
• Edit a hypothesis
• Delete parts of a hypothesis?
• Merge separate features into one hypothesis?
• Set atom and bond specifications
  • Specify elements for an atom
  • Specify other attributes (charge, valence...)?
  • Specify bond type?
• Define geometric objects
• Add a centroid?
• Add a vector?
• Add a hydrogen-bond acceptor vector?
• Add a hydrogen-bond donor vector?
• Add a best-fit plane?
  
• Specify and modify constraints
  • Add location constraints?
  • Add distance constraints?
  • Add angle constraints?
  • Add torsion constraints?
  • Add excluded-volume constraints?
  • Set feature weights?
  • Display constraint names and values?
  • Change constraint names or values?
  • Change the display style of constraints?
• Refine a hypothesis
• Specify alternatives (the feature can be x or y)
  • Add alternative features to a hypothesis?
  • Add more alternative features?
  • Modify alternative features?
• Specify exclusions (but the feature cannot be z)
• Specify exclusions to alternative features?
• Add more exclusions?
• View the different mappings of an exclusion?
• View all exclusions to an alternative feature?
• Specify associations among alternatives
• Use associations to summarize matching features?
• Set associations for alternatives?
• View associations?
• Delete associations?
• Combine hypotheses
• Merge features from two hypotheses?
• Integrate a shape into a hypothesis?
• Cluster hypotheses?
• Evaluate and use hypotheses
• Measure distances within hypotheses?
• Score a hypothesis?
• Search a database with a hypothesis?
• Use a hypothesis to search for 1D property data?
• Regress a hypothesis?
• Estimate the activity of a molecule with a hypothesis?
• Compare/Fit a molecule to a hypothesis?
• Compare two hypotheses?