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Copy file name to clipboardExpand all lines: docs/reactions.rst
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@@ -1065,8 +1065,8 @@ How a Corpus Row Composes
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table, ``reactions.tsv``, and one id space. It is keyed by the name ``reaction=`` selects on, and each
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value is that name's whole **family** of rows: ``amidation`` holds one per acyl source and N-H partner.
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A row does not carry a SMIRKS string of its own: it names **slots** by the functional-group name they
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take, out of ``functional.tsv``, and its ``product`` column patches the atoms those groups number. The template is composed from the two lazily, and cached for the
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table as a whole.
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take, out of ``functional.tsv``, and its ``product`` column patches the atoms those groups number. The
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template is composed from the two lazily, and cached for the table as a whole.
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A group leaves its **leaving group unnumbered**, so the atoms it numbers are the ones it means to keep --
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and keeping them is the product side's job, deletion being by absence. Adding an atom to a group
@@ -1314,8 +1314,9 @@ An unknown name raises ``ValueError`` listing every name ``protective.tsv`` has.
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An ester reports its alcohol half as a ``carboxyl_*`` group -- ``CC(=O)OC(C)(C)C`` is ``carboxyl_tbu``,
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revealing acetic acid -- and the ether of the same group stays ``hydroxyl_*``. Where the acyl half is
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itself a protecting group the larger row claims the ester, a tie falling to file order: tert-butyl
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benzoate is ``hydroxyl_benzoate``, benzyl benzoate is ``carboxyl_benzyl``.
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itself a protecting group the alkyl half still claims the ester, which reads as a protected acid:
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tert-butyl benzoate is ``carboxyl_tbu``, methyl pivalate ``hydroxyl_methyl``, benzyl acetate
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``carboxyl_benzyl``.
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**The enumeration unit is the site, not the rule**, because chemistry is not deterministic: a reagent
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that *can* cleave every Boc does not thereby cleave every Boc, and controlled mono-cleavage of a
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