continuousflex.protocols.protocol_structure_mapping module¶

class continuousflex.protocols.protocol_structure_mapping.FlexProtStructureMapping(**kwargs)[source]¶

Bases: continuousflex.protocols.pdb.protocol_pseudoatoms_base.FlexProtConvertToPseudoAtomsBase, continuousflex.protocols.protocol_nma_base.FlexProtNMABase

A quantitive analysis of dissimilarities (distances) among the EM maps that placing the entire set of density maps in to a common space of comparison.The approach is based on statistical analysis of distance among elastically aligned EM maps, and results in visualizing those maps as points in a lower dimensional distance space.

alignVolumeStep(refFn, inVolFn, outVolFn, volId)[source]¶

elasticAlignmentStep(nVoli, Ts, nVolj, fnAlignedVolj)[source]¶

gatherResultsStep()[source]¶

gatherSingleVolumeStep()[source]¶

managingOutputFilesStep()[source]¶

continuousflex.protocols.protocol_structure_mapping.mds(d, dimensions=2)[source]¶: Multidimensional Scaling - Given a matrix of interpoint distances, find a set of low dimensional points that have similar interpoint distances.