atomstructutils.protocols.protocol_atomStructs_rmsd module¶

class atomstructutils.protocols.protocol_atomStructs_rmsd.ProtRMSDAtomStructs(**kwargs)[source]¶

Bases: pwem.protocols.protocol.EMProtocol

Protocol to calculate the RMSD between all pairs of atom structures in a set of them. It calculates the overall RMSD for all of them and for each of their residues to validate their associated volume

averageRMSDs = []¶

calculateRMSDStep(combo)[source]¶

combinedResRMSDs = []¶

convertInputStep()[source]¶

createOutputStep()[source]¶

getConvertedFile(inFile)[source]¶

getInputFileNames()[source]¶

getInputVolume()[source]¶

getRMSDAtoms()[source]¶

getRMSDAttributeDic()[source]¶: Return a dictionary with {spec: value} “spec” should be a chimera specifier

atomstructutils.protocols.protocol_atomStructs_rmsd.get_coordinates(filename, hydrogen, chain=None, backbone=None, weight=1.0)[source]¶: Get coordinates from the first chain in a pdb file and return a vectorset with all the coordinates.

atomstructutils.protocols.protocol_atomStructs_rmsd.rmsd(V, W)[source]¶: Calculate Root-mean-square deviation from two sets of vectors V and W.