SYBYL

Molecule:

Fully connected set of atoms.

Substructure:

Most often a functional group in the traditional chemical sense, e.g.

• amino acid monomers of a protein
• phenyl ring
• t-butyl, etc.

Atoms & Bonds:

Defined in the traditional manner.
32 (103) atom types, new types can be defined.
Single, double, triple, amide and aromatic bond types.

Rings:

• Internal: within substructures.
  e.g. a phenyl ring as part of phenylalanine.
• External: crossing substructure boundaries.
  e.g. a disulfide bridge between two cysteines.

Feature:

Miscellaneous information.
Examples:

• center of mass,
• plane,
• normal of a plane,
• vector,
• aggregate,
• rotatable bond,
• anchor atom,
• constraint,
• unit cell parameters,
• spacegroup, etc.

Set:

Collection of objects, like substructures, atoms or bonds.
Offers a shorthand notation for often referenced objects.

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