The lower-case single character i is
used as an annotation dictionary key
that points to one or more other atomic nodes within a CurlySMILES
notation. For each component (subnotation) of a CurlySMILES notation,
atomic nodes are counted from left-to right by starting with number 1
at the first atom.
The value of i is composed by entries, which
can be in any of the following formats:
any of the following
Format |
Meaning |
n |
single integer pointing to an atomic node by taking
atomic node with number 1 as a reference |
n-m |
integer range (n<m) pointing to consecutive atomic
nodes by taking atomic node with number 1 as a reference
|
-n |
negative integer pointing to an atomic node by taking
the anchor atom as a reference and formally moving to
the left by n nodes
|
By default, the numbers of an entry refer to the atoms in the same
component in which their anchor atom is located. To point to atoms
of another component, the character #
followed by the component number is appended to the entry.
Multiple entries a separated by semicolon.
For example, if i=2-4,-3,7#1 is a
key/value pair occurring in an annotation anchored at the ninth
atom of the second component, then i
is pointing to atoms 2, 3, 4, and 6 in this component and to
atom 7 in the first component.
The following notation, which encodes a cyclic dimer of two
benzoic acid molecules built by intermolecular hydrogen bonding,
illustrates the use of i in a
multi-component CurlySMILES notation:
c1ccccc1C(=O)O{!Hi=3#2}.O{!Hi=8#1}C(=O)c1ccccc1
The annotation {!Hi=3#2} at the hydroxy
group in the first component indicates that the group's H-acceptor
atom is the third atom in the second component. The annotation
{!Hi=8#1} at the hydroxy group in the
second component indicates that the acceptor atom is the eighth
atom in the first component.
|