I have two dataframes (nodes and edges). nodes data frame contains x and y coordinaates for nodes (which are essentially atoms) and atom numbers. edges dataframe contains x_start x_end and y_start y_end for edges to connect specific atoms (i.e. bonds). I am wondering if there is any way using R to tell which atoms (which atom numbers) belong to the ring.
For example in the plot, atoms 6,4,5,8,19,18 and 9,7,2,20,24,21 form the ring. Because I have coordinates of thousands of molecules, instead of manually checking I was wondering if there is a way to detect which atoms belong to the ring structure. Rings can be different in size than example plot (e.g. different number of atoms) and different composition (not necessarily carbons)
any help will be much appreciated, thanks in advance
edges <- structure(list(edge_from = c(2L, 3L, 4L, 5L, 9L, 10L, 11L, 12L,
13L, 14L, 15L, 16L, 17L, 19L, 20L, 21L, 22L, 23L, 18L, 6L, 6L,
7L, 7L, 8L, 8L, 18L, 18L, 24L, 24L, 21L, 21L), edge_to = c(1L,
6L, 5L, 16L, 7L, 1L, 1L, 1L, 3L, 3L, 3L, 22L, 7L, 8L, 2L, 24L,
23L, 17L, 6L, 4L, 4L, 2L, 2L, 5L, 5L, 19L, 19L, 20L, 20L, 9L,
9L), n_bonds = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L), x_start = c(3.789674, -4.197826, -2.872826,
-2.872826, 5.114674, 0.952174, 1.239674, 2.197974, -4.193726,
-2.947826, -5.443726, -1.535326, 2.460474, -5.527026, 5.114674,
6.439674, -0.210326, 1.127174, -5.527026, -4.197826, -4.27811279554577,
3.789674, 4.029008, -4.197826, -4.27846455694268, -5.527026,
-5.287692, 6.439674, 6.35974852787204, 6.439674, 6.35903544305732
), y_start = c(-2.181736, 3.964064, 1.651564, 0.118264, 0.126564,
-2.381736, -3.656736, -4.535936, 5.347464, 4.959964, 4.968264,
-0.656736, 0.126564, 0.118264, -2.948436, -0.648436, 0.118264,
-0.648436, 1.651564, 2.422464, 2.26341679554577, -0.648436, -0.648436,
-0.656736, -0.498040556942684, 1.651564, 1.651564, -2.181736,
-2.02232747212796, -0.648436, -0.807131443057316), x_end = c(2.452174,
-4.197826, -2.872826, -1.535326, 3.789674, 2.452174, 2.452174,
2.452174, -4.197826, -4.197826, -4.197826, -0.210326, 3.789674,
-4.197826, 3.789674, 6.439674, 1.127174, 2.460474, -4.197826,
-2.872826, -2.95311279554577, 3.789674, 4.029008, -2.872826,
-2.95346455694268, -5.527026, -5.287692, 5.114674, 5.03474852787204,
5.114674, 5.03403544305732), y_end = c(-2.948436, 2.422464, 0.118264,
-0.656736, -0.648436, -2.948436, -2.948436, -2.948436, 3.964064,
3.964064, 3.964064, 0.118264, -0.648436, -0.656736, -2.181736,
-2.181736, -0.648436, 0.126564, 2.422464, 1.651564, 1.49251679554577,
-2.181736, -2.181736, 0.118264, 0.276959443057316, 0.118264,
0.118264, -2.948436, -2.78902747212796, 0.126564, -0.0321314430573162
)), row.names = c(NA, -31L), class = "data.frame")
nodes <- structure(list(X = c(2.452174, 3.789674, -4.197826, -2.872826,
-2.872826, -4.197826, 3.789674, -4.197826, 5.114674, 0.952174,
1.239674, 2.197974, -4.193726, -2.947826, -5.443726, -1.535326,
2.460474, -5.527026, -5.527026, 5.114674, 6.439674, -0.210326,
1.127174, 6.439674), Y = c(-2.948436, -2.181736, 3.964064, 1.651564,
0.118264, 2.422464, -0.648436, -0.656736, 0.126564, -2.381736,
-3.656736, -4.535936, 5.347464, 4.959964, 4.968264, -0.656736,
0.126564, 1.651564, 0.118264, -2.948436, -0.648436, 0.118264,
-0.648436, -2.181736), atom = c("C", "C", "C", "N", "C", "C",
"C", "N", "N", "F", "F", "F", "F", "F", "F", "N", "N", "C", "C",
"C", "C", "C", "C", "C"), atom_n = 1:24), class = "data.frame", row.names = c(NA,
-24L))
library(ggplot2)
ggplot(data = nodes, aes(x = X, y = Y))+
geom_text(aes(label = atom_n, size = 3), color = "red", show.legend = F)+
geom_segment(data = edges, aes(x = x_start, y = y_start, xend = x_end, yend = y_end))+
theme_void()
