A contact matrix is an \(N \times N\) matrix in which the \(i\)th, \(j\)th element tells you whether or not the \(i\)th and \(j\)th atoms/molecules from a set of \(N\) atoms/molecules are adjacent or not. There are various ways of definining whether a pair of atoms/molecules are adjacent or not. For example we can say two atoms are adjacent if the distance between them is less than some cutoff. Alternatively, if we have a have a pair of molecules, we might state they are adjacent if their centre's of mass are within a certain cutoff and if the two molecules have the same orientation. Two electronegative atoms might be said to be adjacent if there is a hydrogen bond between them. For these reasons then PLUMED contains all of the following methods for calculating an adjacency matrix

ALIGNED_MATRIX	Adjacency matrix in which two molecule are adjacent if they are within a certain cutoff and if they have the same orientation.
CONTACT_MATRIX	Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff.
HBOND_MATRIX	Adjacency matrix in which two atoms are adjacent if there is a hydrogen bond between them.

Once you have calculated an adjacency matrix you can then perform any one of the following operations on this object in order to reduce it to a scalar number.

COLUMNSUMS	Sum the columns of a contact matrix
DFSCLUSTERDIAMETER	Find the connected components in an adjacency matrix and then output the maximum radius.
DFSCLUSTERING	Find the various connected components in an adjacency matrix and then output averageproperties of the atoms in those connected components.
DFSCLUSTERING_WITHSURFACE	Find the various connected components in an adjacency matrix and then output averageproperties of the atoms in those connected components.
DFSMAXCLUSTER	Find the connected components and determine the maximum size of the clusters in your system using a smooth function
DFSNUMEROFCLUSTERS	Find the number of connected components that have a size larger than a certain critical threshold.
DFSOUTPUT
ROWSUMS	Sum the rows of a contact matrix
SPRINT	Calculate SPRINT topological variables from an adjacency matrix.