Chemical Modelling using Matab

I'm aiming to model clusters as molecules in 3D space using .xyz file, clusterid, clusterinfo n typeofatoms where bond order if <1.35 is single bond and >1.35 is double bond. id here refers to Atom Id. In the excel sheets and the .txt file, we have 4000 numbers(d's) which represents atom indices. 1, 5, 9 ...3997 and 2, 6, 10...3998 are C and 3, 7, 11...3999 and 4,8, 12...4000 are Hs. Using clustering code, we found out how these atoms (ids) are connected to each other. In clusterinfo file, the bond order values, charge of id_1 and lonepairelctrons of id_1 are given. I want to have a code where I can have all these molecules are listed in 2D/3D using the .txt file (which provides position of the atoms in the space) and then they have the bonds (single /double) based on the bond order value and their corresponding charge and lone pair electons respectively. I would be grateful if someone can help me model these clusters.