test_class.file: singa-structure/src/test/java/bio/singa/structure/parser/pdb/ligands/CifFileParserTest.java
test_class.identifier: CifFileParserTest
test_case.body: @Test
      void shouldParseSingleBondLigandSkeleton() {
          LeafSkeleton leafSkeleton = LigandParserService.parseLeafSkeleton("OH");
          Map<Pair<String>, CovalentBondType> bonds = leafSkeleton.getBonds();
          assertEquals(1, bonds.size());
      }
test_case.class_method_signature: CifFileParserTest.shouldParseSingleBondLigandSkeleton()
test_case.full_signature: @Test void shouldParseSingleBondLigandSkeleton()
test_case.identifier: shouldParseSingleBondLigandSkeleton
test_case.invocations: parseLeafSkeleton getBonds assertEquals size
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void shouldParseSingleBondLigandSkeleton()
focal_class.declarator: logger = LoggerFactory.getLogger(CifFileParser.class)
focal_class.modifier: private static final
focal_class.original_string: private static final Logger logger = LoggerFactory.getLogger(CifFileParser.class);
focal_class.type: Logger
focal_class.var_name: logger
focal_class.declarator: DEFAULT_VALUE_PATTERN = Pattern.compile("([\\w.]+)\\s+(.+)")
focal_class.modifier: private static final
focal_class.original_string: private static final Pattern DEFAULT_VALUE_PATTERN = Pattern.compile("([\\w.]+)\\s+(.+)");
focal_class.type: Pattern
focal_class.var_name: DEFAULT_VALUE_PATTERN
focal_class.declarator: quotationPattern = Pattern.compile("([\"'])(?:(?=(\\\\?))\\2.)*?\\1")
focal_class.modifier: private static final
focal_class.original_string: private static final Pattern quotationPattern = Pattern.compile("([\"'])(?:(?=(\\\\?))\\2.)*?\\1");
focal_class.type: Pattern
focal_class.var_name: quotationPattern
focal_class.declarator: lines
focal_class.modifier: private final
focal_class.original_string: private final List<String> lines;
focal_class.type: List<String>
focal_class.var_name: lines
focal_class.declarator: atomLines
focal_class.modifier: private final
focal_class.original_string: private final List<String> atomLines;
focal_class.type: List<String>
focal_class.var_name: atomLines
focal_class.declarator: bondLines
focal_class.modifier: private final
focal_class.original_string: private final List<String> bondLines;
focal_class.type: List<String>
focal_class.var_name: bondLines
focal_class.declarator: atoms
focal_class.modifier: private final
focal_class.original_string: private final Map<String, OakAtom> atoms;
focal_class.type: Map<String, OakAtom>
focal_class.var_name: atoms
focal_class.declarator: defaultCoordinates
focal_class.modifier: private final
focal_class.original_string: private final Map<String, Vector3D> defaultCoordinates;
focal_class.type: Map<String, Vector3D>
focal_class.var_name: defaultCoordinates
focal_class.declarator: idealCoordinates
focal_class.modifier: private final
focal_class.original_string: private final Map<String, Vector3D> idealCoordinates;
focal_class.type: Map<String, Vector3D>
focal_class.var_name: idealCoordinates
focal_class.declarator: bonds
focal_class.modifier: private final
focal_class.original_string: private final Map<Pair<String>, CovalentBondType> bonds;
focal_class.type: Map<Pair<String>, CovalentBondType>
focal_class.var_name: bonds
focal_class.declarator: defaultIncomplete
focal_class.modifier: private
focal_class.original_string: private boolean defaultIncomplete;
focal_class.type: boolean
focal_class.var_name: defaultIncomplete
focal_class.declarator: idealIncomplete
focal_class.modifier: private
focal_class.original_string: private boolean idealIncomplete;
focal_class.type: boolean
focal_class.var_name: idealIncomplete
focal_class.declarator: name
focal_class.modifier: private
focal_class.original_string: private String name;
focal_class.type: String
focal_class.var_name: name
focal_class.declarator: type
focal_class.modifier: private
focal_class.original_string: private String type;
focal_class.type: String
focal_class.var_name: type
focal_class.declarator: oneLetterCode
focal_class.modifier: private
focal_class.original_string: private String oneLetterCode;
focal_class.type: String
focal_class.var_name: oneLetterCode
focal_class.declarator: threeLetterCode
focal_class.modifier: private
focal_class.original_string: private String threeLetterCode;
focal_class.type: String
focal_class.var_name: threeLetterCode
focal_class.declarator: parent
focal_class.modifier: private
focal_class.original_string: private String parent;
focal_class.type: String
focal_class.var_name: parent
focal_class.declarator: inchi
focal_class.modifier: private
focal_class.original_string: private String inchi;
focal_class.type: String
focal_class.var_name: inchi
focal_class.declarator: singleAtom
focal_class.modifier: private
focal_class.original_string: private boolean singleAtom;
focal_class.type: boolean
focal_class.var_name: singleAtom
focal_class.declarator: singleBond
focal_class.modifier: private
focal_class.original_string: private boolean singleBond;
focal_class.type: boolean
focal_class.var_name: singleBond
focal_class.file: singa-structure/src/main/java/bio/singa/structure/parser/pdb/ligands/CifFileParser.java
focal_class.identifier: CifFileParser
focal_class.class_method_signature: CifFileParser.CifFileParser(List<String> lines)
focal_class.full_signature: private  CifFileParser(List<String> lines)
focal_class.identifier: CifFileParser
focal_class.modifiers: private
focal_class.parameters: (List<String> lines)
focal_class.signature:  CifFileParser(List<String> lines)
focal_class.class_method_signature: CifFileParser.parseLeafSubstructure(List<String> lines)
focal_class.full_signature: public static LeafSubstructure<?> parseLeafSubstructure(List<String> lines)
focal_class.identifier: parseLeafSubstructure
focal_class.modifiers: public static
focal_class.parameters: (List<String> lines)
focal_class.return: LeafSubstructure<?>
focal_class.signature: LeafSubstructure<?> parseLeafSubstructure(List<String> lines)
focal_class.class_method_signature: CifFileParser.parseLeafSkeleton(List<String> lines)
focal_class.full_signature: public static LeafSkeleton parseLeafSkeleton(List<String> lines)
focal_class.identifier: parseLeafSkeleton
focal_class.modifiers: public static
focal_class.parameters: (List<String> lines)
focal_class.return: LeafSkeleton
focal_class.signature: LeafSkeleton parseLeafSkeleton(List<String> lines)
focal_class.class_method_signature: CifFileParser.extractValue(String line)
focal_class.full_signature: private static String extractValue(String line)
focal_class.identifier: extractValue
focal_class.modifiers: private static
focal_class.parameters: (String line)
focal_class.return: String
focal_class.signature: String extractValue(String line)
focal_class.class_method_signature: CifFileParser.replaceQuotation(String quotedString)
focal_class.full_signature: private static String replaceQuotation(String quotedString)
focal_class.identifier: replaceQuotation
focal_class.modifiers: private static
focal_class.parameters: (String quotedString)
focal_class.return: String
focal_class.signature: String replaceQuotation(String quotedString)
focal_class.class_method_signature: CifFileParser.collectLines()
focal_class.full_signature: private void collectLines()
focal_class.identifier: collectLines
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void collectLines()
focal_class.class_method_signature: CifFileParser.processBondBlock(ListIterator<String> lineIterator)
focal_class.full_signature: private void processBondBlock(ListIterator<String> lineIterator)
focal_class.identifier: processBondBlock
focal_class.modifiers: private
focal_class.parameters: (ListIterator<String> lineIterator)
focal_class.return: void
focal_class.signature: void processBondBlock(ListIterator<String> lineIterator)
focal_class.class_method_signature: CifFileParser.processAtomBlock(ListIterator<String> lineIterator)
focal_class.full_signature: private void processAtomBlock(ListIterator<String> lineIterator)
focal_class.identifier: processAtomBlock
focal_class.modifiers: private
focal_class.parameters: (ListIterator<String> lineIterator)
focal_class.return: void
focal_class.signature: void processAtomBlock(ListIterator<String> lineIterator)
focal_class.class_method_signature: CifFileParser.addAtom(String indexString, String atomNameString, String elementString, String charge)
focal_class.full_signature: private void addAtom(String indexString, String atomNameString, String elementString, String charge)
focal_class.identifier: addAtom
focal_class.modifiers: private
focal_class.parameters: (String indexString, String atomNameString, String elementString, String charge)
focal_class.return: void
focal_class.signature: void addAtom(String indexString, String atomNameString, String elementString, String charge)
focal_class.class_method_signature: CifFileParser.addIdealCoordinates(String atomName, String x, String y, String z)
focal_class.full_signature: private void addIdealCoordinates(String atomName, String x, String y, String z)
focal_class.identifier: addIdealCoordinates
focal_class.modifiers: private
focal_class.parameters: (String atomName, String x, String y, String z)
focal_class.return: void
focal_class.signature: void addIdealCoordinates(String atomName, String x, String y, String z)
focal_class.class_method_signature: CifFileParser.addDefaultCoordinates(String atomName, String x, String y, String z)
focal_class.full_signature: private void addDefaultCoordinates(String atomName, String x, String y, String z)
focal_class.identifier: addDefaultCoordinates
focal_class.modifiers: private
focal_class.parameters: (String atomName, String x, String y, String z)
focal_class.return: void
focal_class.signature: void addDefaultCoordinates(String atomName, String x, String y, String z)
focal_class.class_method_signature: CifFileParser.addBond(String firstAtom, String secondAtom, CovalentBondType bond)
focal_class.full_signature: private void addBond(String firstAtom, String secondAtom, CovalentBondType bond)
focal_class.identifier: addBond
focal_class.modifiers: private
focal_class.parameters: (String firstAtom, String secondAtom, CovalentBondType bond)
focal_class.return: void
focal_class.signature: void addBond(String firstAtom, String secondAtom, CovalentBondType bond)
focal_class.class_method_signature: CifFileParser.extractAtoms()
focal_class.full_signature: private void extractAtoms()
focal_class.identifier: extractAtoms
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void extractAtoms()
focal_class.class_method_signature: CifFileParser.extractBonds()
focal_class.full_signature: private void extractBonds()
focal_class.identifier: extractBonds
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void extractBonds()
focal_class.class_method_signature: CifFileParser.extractInformation(String line)
focal_class.full_signature: private void extractInformation(String line)
focal_class.identifier: extractInformation
focal_class.modifiers: private
focal_class.parameters: (String line)
focal_class.return: void
focal_class.signature: void extractInformation(String line)
focal_class.class_method_signature: CifFileParser.parseCompleteLeafSubstructure()
focal_class.full_signature: private OakLeafSubstructure<?> parseCompleteLeafSubstructure()
focal_class.identifier: parseCompleteLeafSubstructure
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: OakLeafSubstructure<?>
focal_class.signature: OakLeafSubstructure<?> parseCompleteLeafSubstructure()
focal_class.class_method_signature: CifFileParser.createLeafSubstructure(LeafIdentifier leafIdentifier)
focal_class.full_signature: private OakLeafSubstructure<?> createLeafSubstructure(LeafIdentifier leafIdentifier)
focal_class.identifier: createLeafSubstructure
focal_class.modifiers: private
focal_class.parameters: (LeafIdentifier leafIdentifier)
focal_class.return: OakLeafSubstructure<?>
focal_class.signature: OakLeafSubstructure<?> createLeafSubstructure(LeafIdentifier leafIdentifier)
focal_class.class_method_signature: CifFileParser.parseLeafSkeleton()
focal_class.full_signature: private LeafSkeleton parseLeafSkeleton()
focal_class.identifier: parseLeafSkeleton
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: LeafSkeleton
focal_class.signature: LeafSkeleton parseLeafSkeleton()
focal_class.class_method_signature: CifFileParser.createLeafSkeleton()
focal_class.full_signature: private LeafSkeleton createLeafSkeleton()
focal_class.identifier: createLeafSkeleton
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: LeafSkeleton
focal_class.signature: LeafSkeleton createLeafSkeleton()
focal_class.class_method_signature: CifFileParser.isNucleotide()
focal_class.full_signature: private boolean isNucleotide()
focal_class.identifier: isNucleotide
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: boolean
focal_class.signature: boolean isNucleotide()
focal_class.class_method_signature: CifFileParser.isAminoAcid()
focal_class.full_signature: private boolean isAminoAcid()
focal_class.identifier: isAminoAcid
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: boolean
focal_class.signature: boolean isAminoAcid()
focal_class.class_method_signature: CifFileParser.connectAtoms(OakLeafSubstructure<?> leafWithAtoms)
focal_class.full_signature: private void connectAtoms(OakLeafSubstructure<?> leafWithAtoms)
focal_class.identifier: connectAtoms
focal_class.modifiers: private
focal_class.parameters: (OakLeafSubstructure<?> leafWithAtoms)
focal_class.return: void
focal_class.signature: void connectAtoms(OakLeafSubstructure<?> leafWithAtoms)
focal_method.body: public static LeafSkeleton parseLeafSkeleton(List<String> lines) {
          CifFileParser parser = new CifFileParser(lines);
          return parser.parseLeafSkeleton();
      }
focal_method.class_method_signature: CifFileParser.parseLeafSkeleton(List<String> lines)
focal_method.full_signature: public static LeafSkeleton parseLeafSkeleton(List<String> lines)
focal_method.identifier: parseLeafSkeleton
focal_method.invocations: parseLeafSkeleton
focal_method.modifiers: public static
focal_method.parameters: (List<String> lines)
focal_method.return: LeafSkeleton
focal_method.signature: LeafSkeleton parseLeafSkeleton(List<String> lines)