pwem.viewers.viewer_localres module

class pwem.viewers.viewer_localres.ChimeraAttributeViewer(**kwargs)[source]

Bases: ProtocolViewer

Viewer for attributes of a SetOfAtomStruct or AtomStruct. Includes visualization in chimera and in histograms

createAttributesFile(cifFile, chiEleId)[source]

getAtomStructObject()[source]

getColors()[source]

getValuesRange()[source]

class pwem.viewers.viewer_localres.LocalResolutionViewer(*args, **kwargs)[source]

Bases: ProtocolViewer

Visualization tools for local resolution results.

binaryCondition = '(colorMap == 6) '

createChimeraScript(scriptFile, fnResVol, fnOrigMap, sampRate, numColors=13, lowResLimit=None, highResLimit=None, showAxis=True)[source]

getImgData(imgFile, minMaskValue=0.1, maxMaskValue=None)[source]

getSlice(index, volumeData)[source]

getSliceImage(volumeData, sliceNumber, dataAxis)[source]

pwem.viewers.viewer_localres.chimeraInstalled()[source]

pwem.viewers.viewer_localres.getChimeraError()[source]

pwem.viewers.viewer_localres.getCifKeyName(cifDic, keyBase)[source]

pwem.viewers.viewer_localres.getResidueAverage(atomValues, atomSpec)[source]

pwem.viewers.viewer_localres.getResiduePositions(attrSpecs, attrValues, chainName)[source]

pwem.viewers.viewer_localres.getStructureRecipient(cifDic, attrName)[source]: Returns a list with the names of the attributes of the output object

pwem.viewers.viewer_localres.makeResidueValuesDic(cifDic, attrName)[source]

pwem.viewers.viewer_localres.replaceOcuppancyWithAttribute(cifFile, attrName, outFile=None)[source]: Instead of defining the atribute in a defattr file, switch it with the occupancy and color by it. It notably speeds up chimera colouring