General Fragment Syntax¶

Overview¶

CGsmiles supports the representation of molecular structures at different resolutions through a fragment replacement syntax. This allows users to specify more detailed molecular structures connected to a coarse graph representation.

Fragment Graphs¶

The notation for a fragment graph starts with a ‘#’ followed by the label of the coarser-resolution node and an ‘=’ sign. Each fragment name must be unique to ensure unambiguous identification. Fragments graphs use the same general graph syntax as outlined before, however, it is permitted to use OpenSMILES syntax to define an atomic resolution fragment.

Example: Bezene as single fragment
"{#BENZ}.{#BENZ=c1ccccc1}"

Bond Operators¶

To define how two consecutive fragments at a finer resolution are connected, CGsmiles builds upon the bonding connector syntax established in BigSMILES to avoid ambiguity. Any node or atom that connects to a neighboring fragment is followed by one of four bonding connectors (‘$’, ‘>’, ‘<’, ‘!’) enclosed in square brackets. In addition, any operator may be combined with an alphanumeric label to distinguish non-equivalent operators of the same type.

Undirected Bonding Operator $. The undirected bonding operator ‘$’ connects to any other ‘$’ operator in connected fragments, as specified in the coarser resolution graph. An undirected bonding operator may be followed by an alphanumeric label, ensuring that only operators with matching labels are connected.
```
Example: PEO can connect to any other PEO on the first or second carbon
{[#PEO=[$]COC[$]}
```
Directed Bonding Operators > and < A directed bonding operator can only pair with its complementary counterpart to ensure the correct connectivity in asymmetric fragments. These bonding operators can also be annotated with an alphanumeric label for further specificity.
```
Example: Polystyrene, where the CH2 group always connects to the CH group
{[#PS=[>]CC[<]c1ccccc1]}
```
Shared Bonding Operator ! To address a common scenario in CG force fields where an atom is distributed between two finer resolution nodes, CGsmiles introduces the shared bonding operator ‘!’. In the case of toluene represented at the Martini 3 level, some of the ring atoms are shared between the two CG beads. When two fragments are connected using the shared bonding operator, the atoms at the connection point are merged into a single atom, retaining the bonds from both fragments.
```
Example: Martini3 Toluene where some of the carbon atoms in Toluene are
shared between beads
{[#SC4]1[#TC5][#TC5]1}.{#SC4=Cc(c[!])c[!],#TC5=[!]ccc[!]}
```

Valency¶

CGSimles does not enforce valency rules for atoms or nodes, allowing any atom to be followed by multiple bonding operators. In the case of all-atom fragments, the hydrogen count is determined only after the molecule’s full connection is established. In cases where a bond of higher order needs to be represented, a bond order symbol should be placed between the node and bonding operator in both fragments. For example, splitting 2-pentene into two fragments results in {[#A][#B]}.{#A=CC=[$],#B=[$]=CCC}, where the bond order symbol ‘=’ indicates a double bond between ethane and propane fragment.

Updated Bonding Descriptors Lookup Table¶

This table now includes the squash descriptor, summarizing all the bonding descriptors used in CGsmiles:

Descriptor	Symbol	Description
Indiscriminate	[$]	Connects to any matching $ descriptor.
Forward bond	[>]	Must connect with a bonding descriptor of type <.
Backward bond	[<]	Designed to connect with a descriptor of type >.
Alphanumeric	[descriptor]alphanumeric	Adds specificity to descriptors, requiring exact matches.
Squash	[!]	Indicates overlapping mappings; connected atoms are identical.