amsr 0.1.6

Another molecular string representation

AMSR

Another Molecular String Representation, inspired by

• H. Hiz, "A Linearization of Chemical Graphs," J. Chem. Doc. 4, 173-180 (1964)
• SMILES
• PATTY
• DeepSMILES
• SELFIES

Demo

amsr.harrystern.org

Installing

uv pip install .
uv pip install ".[gpu]" # for GPU support

Usage

import amsr

amsr.ToMol("CNcncc5cNcN6C.oC.o") # caffeine

taxol_smi = "CC1=C2[C@@]([C@]([C@H]([C@@H]3[C@]4([C@H](OC4)C[C@@H]([C@]3(C(=O)[C@@H]2OC(=O)C)C)O)OC(=O)C)OC(=O)c5ccccc5)(C[C@@H]1OC(=O)[C@H](O)[C@@H](NC(=O)c6ccccc6)c7ccccc7)O)(C)C"

amsr.FromSmiles(taxol_smi)
# CccCC`C`C`C'C`OC4.CC'C'6coC`8[OAc].C.O....[OAc].O[Bz].CC`6OcoC`O.C'N[Bz].[Ph]....O.C.C

amsr.FromSmiles(taxol_smi, useGroups=False)
# CccCC`C`C`C'C`OC4.CC'C'6coC`8OcoC..C.O....OcoC..Ococccccc6......CC`6OcoC`O.C'Ncocccccc6......cccccc6.........O.C.C

Description

A molecular string representation in which every sequence of tokens generates a "reasonable" molecule. You may have different ideas about what constitutes a reasonable molecule than this string representation.

Atoms

Atoms are represented by their symbol enclosed in square brackets, as in SMILES. For a one-letter symbol, brackets may be omitted. Atoms are assumed to have a fixed valence that limits the number of covalently-bonded neighbors. If an atom makes fewer bonds than its valence, hydrogens are assumed.

AMSR	molecule
C	methane
O	water
[Cl]	hydrochloric acid

Chains

Each atom in a chain is bonded to the most recently added atom that can still make bonds, according to its valence. Hydrogens may be added explicitly like any other atom. In the example below, the fluorines are added to the second carbon; the chlorine is then added to the first carbon, since the second can no longer bond.

AMSR	molecule
CCFFF[Cl]	2-chloro-1,1,1-trifluoroethane

Branches

Branches are formed automatically when atoms can no longer make bonds. They can also be made by "capping" or "saturating" an atom with hydrogens, using a period . (capping hydrogens are applied to the most recently-added atom that can still make bonds). New atoms will then be bonded to those added earlier, forming a branch.

AMSR	molecule
CCC.C	isobutane
CC.CC.C.C	2,2-dimethylbutane

Rings

Rings are denoted by a single digit (or two or more digits enclosed in square brackets) giving the size of the ring. A new bond is formed between the two most recently-added atoms that can make bonds and when bonded will form a ring of that size.

AMSR	molecule
CCO3	oxirane
CCCCCC6	cyclohexane
CCCCCCCCCCCC[12]	cyclododecane

Double bonds (sp² centers)

Atoms making a double bond are indicated by changing the symbol to lowercase (note that lowercase does not mean "aromatic"; merely, "atom having one fewer neighbor than its valence.") Double bonds are assigned by a matching algorithm. If a perfect matching cannot be found (for instance, in the case of an odd number of contiguous lowercase symbols) a maximal matching is chosen, non-matched atoms remain singly bonded, and hydrogens are added.

AMSR	molecule
co	formaldehyde
cccccc6	benzene
cco	acetaldehyde (only one double bond added)

Note that an oxygen with two neighbors or a nitrogen with three in an aromatic ring is still denoted by a capital (not a lowercase) symbol, although sp²-hybridized, since its coordination number is still equal to its valence.

AMSR	molecule
ccccO5	furan
ccccN5	pyrrole

Ring selection

When more than one ring of a given size can be formed, one or more @ signs immediately after the digit will make ring-forming bonds with atoms appearing earlier in the string, rather than the most recent.

AMSR	molecule
ccOcc5cccc6	benzofuran
ccOcc5cccc6@	isobenzofuran

Triple bonds (sp centers)

Atoms with two fewer neighbors than their valence are designated by a trailing colon : can make triple bonds (or more than one double bond).

AMSR	molecule
C:N:	hydrogen cyanide
oC:o	carbon dioxide

Hypervalent atoms

Atoms denoted by their symbol alone are assumed to have their lowest possible valence (for instance, two for sulfur). Higher valences are denoted by one or more exclamation points !.

AMSR	molecule
CSC	dimethyl sulfide
Cs!oC	dimethyl sulfoxide
S!!FFFFFF	sulfur hexafluoride

Formal charges, radical electrons, isotopes

Positive/negative formal charges are designated by one or more of +/-. Radical electrons are denoted by one or more asterisks *. An isotopic mass is denoted by a number prefix before the atomic symbol (in which case square brackets must be used even for a one-letter symbol).

AMSR	molecule
[Mg++];S!!:ooO-O-	magnesium sulfate
CC.C.CCCCC.C.N6O*	(2,2,6,6-Tetramethylpiperidin-1-yl)oxyl or TEMPO
[2H]O[2H]	heavy water

Tetrahedral stereochemistry

Tetrahedral stereochemistry is denoted by a single quote ' meaning "clockwise" or a backtick ` meaning "counterclockwise," referring to the first three neighbors of a stereocenter atoms as they appear in the string, with the last neighbor (or implicit hydrogen) in back.

AMSR	molecule
C`C.FO	(1S)-1-fluoroethanol
C'C.FO	(1R)-1-fluoroethanol

E/Z stereochemistry

Stereochemistry for a double bond is denoted by an underscore _ meaning "trans" or E, or caret ^ meaning "cis" or Z, between the two atoms making the bond, where the reference neighboring atoms are those that appear earliest in the string.

AMSR	molecule
c[Br][Cl]_c[Cl]	(E)-1-bromo-1,2-dichloroethene
c[Br][Cl]^c[Cl]	(Z)-1-Bromo-1,2-dichloroethene

Groups

The following abbreviations may be used to represent various functional groups:

(5aN), (5aNbN), (5aNbO), (5aNbS), (5aNcN), (5aNcO), (5aNcS), (5aNdN), (5aNdO), (5aNdS), (5aNeN), (5aNeO), (5aNeS), (5aO), (5aS), (5bN), (5bNaN), (5bNaO), (5bNaS), (5bNcN), (5bNcO), (5bNcS), (5bNdN), (5bNdO), (5bNdS), (5bNeN), (5bNeO), (5bNeS), (5bO), (5bS), (5cN), (5cNaN), (5cNaO), (5cNaS), (5cNbN), (5cNbO), (5cNbS), (5cNdN), (5cNdO), (5cNdS), (5cNeN), (5cNeO), (5cNeS), (5cO), (5cS), (5dN), (5dNaN), (5dNaO), (5dNaS), (5dNbN), (5dNbO), (5dNbS), (5dNcN), (5dNcO), (5dNcS), (5dNeN), (5dNeO), (5dNeS), (5dO), (5dS), (5eN), (5eNaN), (5eNaO), (5eNaS), (5eNbN), (5eNbO), (5eNbS), (5eNcN), (5eNcO), (5eNcS), (5eNdN), (5eNdO), (5eNdS), (5eO), (5eS), (6), (6aN), (6abN), (6abcN), (6abdN), (6abeN), (6abfN), (6acN), (6acdN), (6aceN), (6acfN), (6adN), (6adeN), (6adfN), (6aeN), (6aefN), (6afN), (6bN), (6bcN), (6bcdN), (6bceN), (6bcfN), (6bdN), (6bdeN), (6bdfN), (6beN), (6befN), (6bfN), (6cN), (6cdN), (6cdeN), (6cdfN), (6ceN), (6cefN), (6cfN), (6dN), (6deN), (6defN), (6dfN), (6eN), (6efN), (6fN), [Ac], [Bn], [Boc], [Bz], [CCl3], [CF3], [CHO], [CN], [COO-], [COOEt], [COOH], [COOMe], [Cbz], [Cy], [Et], [Ms], [NC], [NHAc], [NHMe], [NMe2], [NO2], [OAc], [OEt], [OMe], [OiBu], [PO3], [Ph], [Piv], [SMe], [SO3], [Tf], [Tol], [Ts], [iBu], [iPr], [nBu], [nDec], [nHept], [nHex], [nNon], [nOct], [nPent], [nPr], [sBu], [tBu]

AMSR	molecule
N+C'[Bn][COO-]	L-phenylalanine
cccccc6[iBu]..CC.[COOH]	ibuprofen
C[Ph][Et]coNcoNco6	phenobarbital

Multiple molecules

More than one molecule may be specified by separating with ;.

AMSR	molecule
ocC.O(6)[COOH];CcoN(6)..O	aspirin and acetaminophen

Developing

uv pip install ".[dev]"
pre-commit install