SMARTSってなんやねん(化学)
参考:
要は
SMILES
SMARTS
- SMILESを検索クエリ用に拡張
- ワイルドカードで表記できる
- 同一記法でもSMILESとは意味が異なる可能性あり
「SMILE語」の文法を学ぶ
語学を学ぶには最低限の文法理解は必要, ということで以下のテーブルをざっくり理解。
原子表記(atomic primitives)
Symbol | Symbol name | Atomic property requirements | Default |
---|---|---|---|
* | wildcard | any atom | (no default) |
a | aromatic | aromatic | (no default) |
A | aliphatic | aliphatic | (no default) |
D<n> | degree | <n> explicit connections | exactly one |
H<n> | total-H-count | <n> attached hydrogens | exactly one1 |
h<n> | implicit-H-count | <n> implicit hydrogens | at least one |
R<n> | ring membership | in <n> SSSR rings | any ring atom |
r<n> | ring size | in smallest SSSR ring of size <n> | any ring atom2 |
v<n> | valence | total bond order <n> | exactly one2 |
X<n> | connectivity | <n> total connections | exactly one2 |
x<n> | ring connectivity | <n> total ring connections | at least one2 |
- <n> | negative charge | -<n> charge | -1 charge (-- is -2, etc) |
+<n> | positive charge | +<n> formal charge | +1 charge (++ is +2, etc) |
#n | atomic number | atomic number <n> | (no default)2 |
@ | chirality | anticlockwise | anticlockwise, default class2 |
@@ | chirality | clockwise | clockwise, default class2 |
@<c><n> | chirality | chiral class <c> chirality <n> | (nodefault) |
@<c><n>? | chiral or unspec | chirality <c><n> or unspecified | (no default) |
<n> | atomic mass | explicit atomic mass | unspecified mass |
原子表記の例
C |
aliphatic carbon atom |
|
c |
aromatic carbon atom |
|
a |
aromatic atom | |
[#6] |
carbon atom |
|
[Ca] |
calcium atom |
|
[++] |
atom with a +2 charge |
|
[R] |
atom in any ring |
|
[D3] |
atom with 3 explicit bonds (implicit H's don't count) |
|
[X3] |
atom with 3 total bonds (includes implicit H's) |
|
[v3] |
atom with bond orders totaling 3 (includes implicit H's) |
|
C[C@H](F)O |
match chirality (H-F-O anticlockwise viewed from C) |
|
C[C@?H](F)O |
matches if chirality is as specified or is not specified |
結合表記(bond primitive)
こっちは原子表記より少ないので楽
Symbol | Atomic property requirements |
---|---|
- | single bond (aliphatic) |
/ | directional bond "up"1 |
\ | directional bond "down"1 |
/? | directional bond "up or unspecified" |
\? | directional bond "down or unspecified" |
= | double bond |
# | triple bond |
: | aromatic bond |
~ | any bond (wildcard) |
@ | any ring bond1 |
結合表記の例:
C | any aliphatic carbon |
cc | any pair of attached aromatic carbons |
c:c | aromatic carbons joined by an aromatic bond |
c-c | aromatic carbons joined by a single bond (e.g. biphenyl) |
省略されると
引用元:
SMARTS官能基当てクイズ
Q:
- [CX4]
- [CX3]=[OX1]
- [NX3][CX3](=[OX1])[#6]
A:
- 4つ結合がある脂肪族炭素
⇒ アルキル基 - (3つ結合がある脂肪族炭素)二重結合(結合を一つもつ酸素)
⇒ カルボニル基 - (3つ結合がある窒素)(3つ結合がある炭素)(=二重結合(結合を一つもつ酸素))(原子番号6の原子)
⇒ アミド基
あとは適宜わからんのが出てきたら学ぶ。
引用:
SMARTSを可視化する
大量に可視化したい場合はRDkitなどを使う必要があるのだろうが, ひとまず以下のサイトでお手軽に可視化できる。