Read Rigid Body Files in Flex-EM format

class RigidBodyParser.RBParser[source]

A class to read Rigid Body files

static RBfileToRBlist(file_in)[source]

Read a rigid body files in Flex-EM format (text file) using residue numbers in a list of segments. Each line describes one rigid body by specifying the initial and final residue of each of the segments in that rigid body (eg, ‘2 6 28 30’ means that residues 2-6 and 28-30 will be included in the same rigid body). We recommend to use the RIBFIND server for accurately identifying Rigid Bodies in a protein structures.

Arguments:
file_in
Rigid Body File in Flex EM format
list_out

Return a list of segments (each line in the file). The list of rigid body is defined as:

[[riA,rfA],..,[riB,rfB]]

where :

riA is the starting residues number of segment A. rfA is the final residues number of segment A.
static read_FlexEM_RIBFIND_files(file_in, structure_instance, list_out=True)[source]

Read a rigid body files in Flex-EM format (text file) using residue numbers in a structure instance. Each line describes one rigid body by specifying the initial and final residue of each of the segments in that rigid body (eg, ‘2 6 28 30’ means that residues 2-6 and 28-30 will be included in the same rigid body). We recommend to use the RIBFIND server for accurately identifying Rigid Bodies in a protein structures.

Arguments:
file_in
Rigid Body File in Flex EM format
structure_instance
Structure Instance to manipulate
list_out
True return a list of the Rigid Bodies structure instances (each line in the file). False will print them separately.