schrodinger.application.peptide_workflow.clustering module

class schrodinger.application.peptide_workflow.clustering.BasicCluster(clustering_cutoff=1.0)

Bases: object

__init__(clustering_cutoff=1.0)

calculateRMSD(peptide1, peptide2)

withinCluster(peptide1, peptide2)

class schrodinger.application.peptide_workflow.clustering.InterfaceBackboneRMSDCluster(recep_st, clustering_cutoff=1.0)

Bases: BasicCluster

Use interface backbone RMSD to cluster peptides

__init__(recep_st, clustering_cutoff=1.0)

calculateRMSD(peptide1, peptide2)

class schrodinger.application.peptide_workflow.clustering.BackboneTorsionRMSDCluster(clustering_cutoff=1.0)

Bases: BasicCluster

calculateRMSD(peptide1, peptide2)

Calculate the backbone torsion RMSD in degrees, this is useful to compare peptide conformers without receptor This RMSD is often larger than the RMSD in 3D cartesian coordinates. RMSD within 10 degrees is often considered as close enough