No sorry, I don't understand. What is "the element with value 1"?
Do you want to find all i,j such that Aij == 1, Aij == Aji, and i != j?
Or do you want to "mask" the matrix? In that case you can multiply it by cond:
cond
#> V1 V2 V3 V4 V5
#> [1,] FALSE TRUE TRUE FALSE FALSE
#> [2,] TRUE FALSE TRUE FALSE TRUE
#> [3,] TRUE TRUE FALSE TRUE TRUE
#> [4,] FALSE FALSE TRUE FALSE FALSE
#> [5,] FALSE TRUE TRUE FALSE FALSE
A
#> V1 V2 V3 V4 V5
#> [1,] 0 0 1 0 1
#> [2,] 0 0 0 1 0
#> [3,] 1 0 0 0 1
#> [4,] 1 0 0 0 0
#> [5,] 0 0 1 1 0
cond*A
#> V1 V2 V3 V4 V5
#> [1,] 0 0 1 0 0
#> [2,] 0 0 0 0 0
#> [3,] 1 0 0 0 1
#> [4,] 0 0 0 0 0
#> [5,] 0 0 1 0 0
notice how in A*cond the element [1,5] has become 0, as A[1,5] != A[5,1].