Syntax Examples¶

This page collects examples of CGsmiles string of increasing complexity. They are seperated into the following categories:

CGsmiles without fragments
CGsmiles with all-atom fragments
CGsmiles with coarse-grained fragments

CGsmiles without fragments¶

If one just seeks to describe a graph at abitrary level of complexity CGsmiles notation can be used. Each of the smiles listed below can be read and converted using the read_cgsmiles function of the package:

simple linear graph with three nodes
```
"{[#nodeA][#nodeB][#nodeC]}"
```
simple linear graph of 10 nodes of B and three other nodes neighborung it
```
"{[#nodeA][#nodeB]|10[#nodeC]}"
```

simple ring of six nodes

"{[#nodeA]1[#nodeB][#nodeC][#nodeD][#nodeE][#nodeD]1}

rhombic graph with four nodes

"{[#nodeA]1[#nodeB]2[#nodeC]1[#nodeD]2}

linear sequence with branch

"{[#nodeA]([#nodeAB][#nodeAB])[#nodeC][#nodeD]}

linear sequence with regular branching pattern; this is equivalent to a graft polymer. Note that this results into 5 nodes A connected to each other each with an AB branch of two units.
```
"{[#nodeA]([#nodeAB][#nodeAB])|5}"
```

CGsmiles with all-atom fragments¶

simple linear graph describing PEO with two OH end-groups
```
"{[#OH][#PEO][#OH]}.{#OH=[$]O,#PEO=[$]COC[$]}"
```

same as above but now with 10 residues.

"{[#OH][#PEO]|10[#OH]}.{#OH=[$]O,#PEO=[$]COC[$]}"

simple ring describing crwon ether

"{[#PEO]1[#PEO]|4[#PEO]1}.{#PEO=[$]COC[$]}"

mPEG acrylate with 5 residues .. code:

"{[#PMA]([#PEO]|3)|5}.{#PMA=[>]CC[<](C(=O)OC[$]),#PEO=[$]COC[$]}"