Subcluster core module
CctbxClusterer
(executable=None, nproc=1)[source]¶Bases: ample.ensembler.subcluster.SubClusterer
Class to cluster files with maxcluster
Methods
calculate_score (cluster) |
Given a list of indices of a cluster, calculate the rmsd we want to give to phaser |
cluster_by_radius (radius) |
Return a list of pdbs clustered by the given radius |
generate_distance_matrix (pdb_list) |
Run cctbx to generate the distance distance_matrix |
dump_pdb_matrix | |
dump_raw_matrix |
FpcClusterer
(executable=None, nproc=1)[source]¶Bases: ample.ensembler.subcluster.SubClusterer
Class to cluster files with fast_protein_clusterer
Methods
calculate_score (cluster) |
Given a list of indices of a cluster, calculate the rmsd we want to give to phaser |
cluster_by_radius (radius) |
Return a list of pdbs clustered by the given radius |
dump_pdb_matrix | |
dump_raw_matrix | |
generate_distance_matrix |
GesamtClusterer
(executable=None, nproc=1)[source]¶Bases: ample.ensembler.subcluster.SubClusterer
Class to cluster files with Gesamt
Methods
calculate_score (cluster) |
Given a list of indices of a cluster, calculate the rmsd we want to give to phaser |
cluster_by_radius (radius) |
Return a list of pdbs clustered by the given radius |
dump_pdb_matrix | |
dump_raw_matrix | |
generate_distance_matrix |
LsqkabClusterer
(executable=None, nproc=1)[source]¶Bases: ample.ensembler.subcluster.SubClusterer
Class to cluster files with Lsqkab
Methods
calculate_score (cluster) |
Given a list of indices of a cluster, calculate the rmsd we want to give to phaser |
cluster_by_radius (radius) |
Return a list of pdbs clustered by the given radius |
calc_rmsd | |
dump_pdb_matrix | |
dump_raw_matrix | |
generate_distance_matrix | |
parse_lsqkab_output |
MaxClusterer
(executable=None, nproc=1)[source]¶Bases: ample.ensembler.subcluster.SubClusterer
Class to cluster files with maxcluster
Methods
calculate_score (cluster) |
Given a list of indices of a cluster, calculate the rmsd we want to give to phaser |
cluster_by_radius (radius) |
Return a list of pdbs clustered by the given radius |
generate_distance_matrix (pdb_list) |
Run maxcluster to generate the distance distance_matrix |
dump_pdb_matrix | |
dump_raw_matrix |
SubClusterer
(executable=None, nproc=1)[source]¶Bases: object
Base class for clustering pdbs by distance Sub-classes just need to provide a generate_distance_matrix class
Methods
calculate_score (cluster) |
Given a list of indices of a cluster, calculate the rmsd we want to give to phaser |
cluster_by_radius (radius) |
Return a list of pdbs clustered by the given radius |
dump_pdb_matrix | |
dump_raw_matrix | |
generate_distance_matrix |