Documentation
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Index ¶
- func AssignPDBxCategories(dataItems []converterUtils.PDBxItem) map[string][]converterUtils.PDBxItem
- func ConversionTableReadColumn(path string, column string) ([]string, error)
- func CreteMetadataCif(nameMapper map[string]string, PDBxItems map[string][]cU.PDBxItem, ...) (string, error)
- func EMDBconvert(scientificMetadata map[string]any, metadataLevelNameInJson string, ...) (string, error)
- func FromJson(jsonContent map[string]any, mapAll *map[string][]string, ...) error
- func LoopDataEntry(scanner *bufio.Scanner, category string) (map[string]string, string, uint32, string)
- func PDBconvertFromPath(scientificMetadata map[string]any, metadataLevelNameInJson string, ...) (string, error)
- func PDBconvertFromReader(scientificMetadata map[string]any, metadataLevelNameInJson string, ...) (string, error)
- func PDBxDict(path string, relevantNames []string) ([]converterUtils.PDBxItem, error)
- func SupplementCoordinates(nameMapper map[string]string, PDBxItems map[string][]cU.PDBxItem, ...) (string, error)
- func SupplementCoordinatesFromPath(nameMapper map[string]string, PDBxItems map[string][]cU.PDBxItem, ...) (string, error)
- func WriteCif(mmCIFText string, mmCIFOutputPath string) error
Constants ¶
This section is empty.
Variables ¶
This section is empty.
Functions ¶
func AssignPDBxCategories ¶
func AssignPDBxCategories(dataItems []converterUtils.PDBxItem) map[string][]converterUtils.PDBxItem
func ConversionTableReadColumn ¶
ConversionTableReadColumn return a slice of column values in a table. It takes a path to a CSV file and column name as an argument.
func CreteMetadataCif ¶ added in v1.1.1
func CreteMetadataCif(nameMapper map[string]string, PDBxItems map[string][]cU.PDBxItem, valuesMap map[string][]string, OSCEMunits map[string][]string) (string, error)
CreteMetadataCif creates and mmCIF file content as a string. This function only converts metadata in the required format. Meant for EMDB depositions where no other existing mmCIF is available
func EMDBconvert ¶ added in v1.1.1
func LoopDataEntry ¶ added in v1.1.2
func LoopDataEntry(scanner *bufio.Scanner, category string) (map[string]string, string, uint32, string)
return the categories, same as long string, the length and next category
func PDBconvertFromPath ¶ added in v1.1.1
func PDBconvertFromReader ¶ added in v1.1.6
func PDBxDict ¶
func PDBxDict(path string, relevantNames []string) ([]converterUtils.PDBxItem, error)
PDBxDict parses full dictionary and returns a map, where key is data category name and value is slice of structs ordered the same way as in the dictionary. This struct contains relevant properties of a data item in the dictionary. PDBx contains a few thousands of data items. For a single experiment done with a certain technique it is redundant no keep track of most of data items as they are highly specific to this technique. To avoid that relevantNames argument makes this function record only data items references in the slice.
func SupplementCoordinates ¶ added in v1.1.6
func SupplementCoordinates(nameMapper map[string]string, PDBxItems map[string][]cU.PDBxItem, valuesMap map[string][]string, OSCEMunits map[string][]string, mmCIFpath io.Reader) (string, error)
Given an mmCIF file create a new one with added scientific Metadata. Meant for PDB depositions
func SupplementCoordinatesFromPath ¶ added in v1.1.1
func SupplementCoordinatesFromPath(nameMapper map[string]string, PDBxItems map[string][]cU.PDBxItem, valuesMap map[string][]string, OSCEMunits map[string][]string, mmCIFpath string) (string, error)
Given an mmCIF file path, open it and create a new one with added scientific Metadata. Meant for PDB depositions
Types ¶
This section is empty.
Source Files