class

Chem::Templates::Builder

Inherits Reference / Object

TODO: add docs (include checks)

Constructors

new(spec_aliases : Hash(String, String) | Nil = nil)

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Class methods

guess_root(atoms : Array(Atom), bonds : Array(Bond), link_bond : Bond | Nil) : String

Returns the atom with the highest bonding complexity.

The bonding complexity of an atom depends on the nature of the atom, the bonds, and the bonds of its neighbors.

First, carbon atoms are the most frequent so they have the lowest complexity (0), followed by non-carbon atoms (+1), and then non-organic (not CHON) atoms (+2). Hydrogen atoms are ignored.

The complexity is further increased by the number of bonds with other heavy atoms, i.e., bonds X-H are ignored.

The total complexity of an atom is computed as the sum of its complexity and the complexities of the bonded atoms.

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Instance methods

build

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code(char : Char) : self

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description(name : String) : self

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link_adjacent_by(bond_spec : String) : self

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name(*names : String) : self

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names(names : Enumerable(String)) : self

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names(*names : String) : self

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root(atom_name : String) : self

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spec(spec : String) : self

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symmetry(pairs : Enumerable(Tuple(String, String))) : self

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symmetry(*pairs : Tuple(String, String)) : self

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type(type : ResidueType) : self

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