ample.ensembler.subcluster module¶

Subcluster core module

class 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

generate_distance_matrix(pdb_list)[source]¶

Run cctbx to generate the distance distance_matrix

class 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

generate_distance_matrix(pdb_list)[source]¶

class 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

generate_distance_matrix(pdb_list, purge=False)[source]¶

class 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

calc_rmsd(model1, model2, nresidues=None, logfile=’lsqkab.out’, purge=False)[source]¶

generate_distance_matrix(models, purge=True, metric=’qscore’)[source]¶

parse_lsqkab_output(output_file)[source]¶

class 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

generate_distance_matrix(pdb_list)[source]¶

Run maxcluster to generate the distance distance_matrix

class 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

calculate_score(cluster)[source]¶

Given a list of indices of a cluster, calculate the rmsd we want to give to phaser

cluster_by_radius(radius)[source]¶

Return a list of pdbs clustered by the given radius

dump_pdb_matrix(file_name=’score.matrix’, offset=0)[source]¶

dump_raw_matrix(file_name)[source]¶

generate_distance_matrix(*args, **kwargs)[source]¶