Package org.biojava.nbio.structure.io.density
package org.biojava.nbio.structure.io.density
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ClassDescriptionShared machinery for the concrete density map providers: cache lookup, download with validation, size limiting and format sanity checking.Recognises CCP4/MRC map files by their header.Where cached density files live on disk.The file format a density map was delivered in.Downloads and caches electron density and cryo-EM maps, trying several sources in turn until one produces a map.The kind of density map being requested, i.e. what the values in the grid mean.Fetches density maps from one particular service.A request for a density map, describing what is wanted and how hard to look for it.Builder for
DensityMapRequest.A density map that was successfully obtained, together with everything a caller needs to know in order to use it.A remote service that density data can be fetched from.Thrown when a density map exceeds the configured download size limit.The few facts about an EMDB entry's primary map that matter when fetching and displaying it.Finds the EMDB entry, if any, associated with a PDB entry, and reads the few facts about its map that are needed to fetch and display it.Fetches the full-resolution primary map of an EMDB entry.Thrown when no enabled source could supply a density map for an entry.Fetches PDBe's pre-computed CCP4 maps.Expands the named placeholders used in the configurable density-server URL templates.Fetches downsampled volume slices from a Mol* density server.Which density server to talk to.Fetches the map coefficients published alongside the wwPDB validation reports.