cms_n_common_contacts
- mdtools.structure.cms_n_common_contacts(cms)[source]
Get the number of contacts common in all contact matrices.
- Parameters:
cms (
tuple
orlist
) – List of contact matrices as e.g. generated withmdtools.structure.contact_matrices()
. The contact matrices can be given either asNumPy arrays
or asSciPy sparse matrices
. A mix ofNumPy arrays
andSciPy sparse matrices
is not possible.- Returns:
n_bound_in_all_cms (
int
) – Number of non-zero elements of the product of all arrays in cms (i.e. the number of non-zero elements that are common in all arrays in cms).
See also
mdtools.structure.contact_matrix()
Construct a boolean contact matrix for two MDAnalysis
AtomGroups
mdtools.structure.contact_matrices()
Construct a contact matrix for each frame in a trajectory
mdtools.structure.cms_n_contacts()
Get the number of contacts per contact matrix and the number of contacts common in all contact matrices
Examples
NumPy arrays
as input:>>> cm0 = np.array([[ True, True, False], ... [False, True, True]]) >>> cm1 = np.array([[ True, False, False], ... [False, False, True]]) >>> cm2 = np.array([[ True, True, False], ... [False, False, True]]) >>> mdt.strc.cms_n_common_contacts([cm0,]) 4 >>> cms = [cm0, cm1, cm2] >>> mdt.strc.cms_n_common_contacts(cms) 2
SciPy sparse matrices
as input:>>> from scipy import sparse >>> cms = [sparse.csr_matrix(cm) for cm in cms] >>> mdt.strc.cms_n_common_contacts([cms[0],]) 4 >>> mdt.strc.cms_n_common_contacts(cms) 2