Uses of Class
org.proteinshader.structure.io.exceptions.PDBFieldExtractorException

Packages that use PDBFieldExtractorException

org.proteinshader.structure.io

Holds the classes needed for reading Protein Data Bank structure files.

Uses of PDBFieldExtractorException in org.proteinshader.structure.io

Methods in org.proteinshader.structure.io that throw PDBFieldExtractorException

String	PDBAtomFieldExtractor.extractAltLocation(String line) Obtains the alternate location from (altLoc field: 17), or returns an empty String if it is not found (this field is usually blank).
String	PDBAtomFieldExtractor.extractAtomID(String line) Obtains the atomID from (name field: 13-16).
int	PDBAtomFieldExtractor.extractAtomSerialNo(String line) Obtains the atom serial number from (serial field: 7-11).
AtomEnum	PDBAtomFieldExtractor.extractAtomType(String line) Obtains the atom type (chemical element) from an ATOM or HETATM record.
String	PDBBetaStrandFieldExtractor.extractBetaStrandNumber(String line) Obtains the betaStrandNumber from (strandNo field: 8-10).
String	PDBBetaStrandFieldExtractor.extractChainID(String line) Obtains the chainID from (initChainID field: 22).
String	PDBHelixFieldExtractor.extractChainID(String line) Obtains the chainID from (initChainID field: 20).
String	PDBAtomFieldExtractor.extractChainID(String line) Obtains the chainID from (chainID field: 22 ) if it is present.
int	PDBAtomFieldExtractor.extractCharge(String line) Obtains the charge from (charge field: 79-80), or sets it to 0 if the field is only whitespace.
List<Integer>	PDBConnectFieldExtractor.extractDstAtomSerialNo(String line) Obtains destination Atom serial number(s) from field 1 = (serial field: 12-16) field 2 = (serial field: 17-21) field 3 = (serial field: 22-26) field 4 = (serial field: 27-31) It is legal for any (or even all 4) of these fields to be blank, as the CONECT record may be used to specify salt bridges or hydrogen bonds that are found in other fields.
String	PDBBetaStrandFieldExtractor.extractEndResidueID(String line) Obtains the endResidueID by combining (endResName field: 29-31), (endSeqNum field: 34-37), and the optional (endICode field: 38).
String	PDBHelixFieldExtractor.extractEndResidueID(String line) Obtains the endResidueID by combining (endResName field: 28-30), (endSeqNum field: 34-37), and the optional (endICode field: 38).
String	PDBHelixFieldExtractor.extractHelixID(String line) Obtains the helixID from (helixID field: 12-14).
double	PDBAtomFieldExtractor.extractOccupancy(String line) Obtains the occupancy from (occupancy field: 55-60).
String	PDBAtomFieldExtractor.extractResidueID(String line) Obtains the residueID by combining (resName field: 18-20), (resSeq field: 23-26), and the optional (icode field: 27).
String	PDBAtomFieldExtractor.extractResidueName(String line) Obtains the Residue name from (resName field: 18-20).
int	PDBBetaStrandFieldExtractor.extractSense(String line) Obtains the sense (orientation) from (sense field: 39-40).
String	PDBHelixFieldExtractor.extractSerialNo(String line) Obtains the helix serial number from (serial field: 8-10).
String	PDBBetaStrandFieldExtractor.extractSheetID(String line) Obtains the sheetID from (sheetID field: 12-14).
int	PDBConnectFieldExtractor.extractSrcAtomSerialNo(String line) Obtains the source Atom serial number from (serial field: 7-11)
String	PDBBetaStrandFieldExtractor.extractStartResidueID(String line) Obtains the startResidueID by combining (initResName field: 18-20), (initSeqNum field: 23-26), and the optional (initICode field: 27).
String	PDBHelixFieldExtractor.extractStartResidueID(String line) Obtains the startResidueID by combining (initResName field: 16-18), (initSeqNum field: 22-25), and the optional (initICode field: 26).
int	PDBBetaStrandFieldExtractor.extractStrandsInSheet(String line) Obtains the number of strands in the sheet from (numStrands field: 15-16).
double	PDBAtomFieldExtractor.extractTemperature(String line) Obtains the temperature from (tempFactor field: 61-66).
HelixEnum	PDBHelixFieldExtractor.extractType(String line) Extracts the helix type from (helixClass field: 39-40).
double	PDBAtomFieldExtractor.extractX(String line) Obtains the x-coordinate from (x field: 31-38 ).
double	PDBAtomFieldExtractor.extractY(String line) extractY() - obtains the y-coordinate from (y field: 39-46 ).
double	PDBAtomFieldExtractor.extractZ(String line) extractZ() - obtains the z-coordinate from (z field: 47-54 ).