public class MMCifReader extends Object implements MMCifInterface
Modifier and Type | Field and Description |
---|---|
private String[] |
assem |
private static byte |
ASSEM_ID |
private static byte |
ASSEM_LIST |
private static byte |
ASSEM_OPERS |
private static String[] |
assemblyFields |
private Map<String,BS> |
assemblyIdAtoms |
private static byte |
BEG_ASYM_ID |
private static byte |
BEG_INS_CODE |
private static byte |
BEG_SEQ_ID |
private boolean |
byChain |
private boolean |
bySymop |
private int[] |
chainAtomCount |
private Map<String,int[]> |
chainAtomCounts |
private Map<String,javajs.util.P3> |
chainAtomMap |
private javajs.util.P3 |
chainSum |
private static byte |
CHEM_COMP_BOND_AROMATIC_FLAG |
private static byte |
CHEM_COMP_BOND_ATOM_ID_1 |
private static byte |
CHEM_COMP_BOND_ATOM_ID_2 |
private static byte |
CHEM_COMP_BOND_VALUE_ORDER |
private static byte |
CHEM_COMP_ID |
private static byte |
CHEM_COMP_NAME |
private static String[] |
chemCompBondFields |
private static String[] |
chemCompFields |
private static byte |
CONF_TYPE_ID |
private CifReader |
cr |
private String |
data |
private static byte |
END_ASYM_ID |
private static byte |
END_INS_CODE |
private static byte |
END_SEQ_ID |
private String |
field |
private int[] |
fieldOf |
private char |
firstChar |
private static byte |
HELIX_CLASS |
private String[] |
hetatmData
optional nonloop format -- see 1jsa.cif
|
private Map<String,javajs.util.M4> |
htBiomts |
private Map<String,String> |
htHetero |
private Map<String,Map<String,Object>> |
htSites |
private boolean |
isBiomolecule |
private boolean |
isCourseGrained |
private String |
key |
private static int |
NONE |
private static byte |
NONPOLY_COMP_ID |
private static byte |
NONPOLY_ENTITY_ID |
private static byte |
NONPOLY_NAME |
private static String[] |
nonpolyFields |
private static byte |
OPER_ID |
private static byte |
OPER_XYZ |
private static String[] |
operFields |
private int |
propertyCount |
private static byte |
SERIAL_NO |
private static byte |
SHEET_ID |
private static byte |
SITE_ASYM_ID |
private static byte |
SITE_COMP_ID |
private static byte |
SITE_ID |
private static byte |
SITE_INS_CODE |
private static byte |
SITE_SEQ_ID |
private static byte |
STRAND_ID |
private static byte |
STRUCT_ID |
private static String[] |
structConfFields |
private static String[] |
structSheetRangeFields |
private static String[] |
structSiteRangeFields |
private Map<String,Object> |
thisBiomolecule |
private int |
thisChain |
private javajs.util.List<Map<String,Object>> |
vBiomolecules |
Constructor and Description |
---|
MMCifReader() |
Modifier and Type | Method and Description |
---|---|
private void |
addAssembly() |
private void |
addHetero(String groupName,
String hetName) |
boolean |
checkAtom(Atom atom,
String assemblyId,
int index) |
private void |
createParticle(String id) |
private String |
crossBinary(String ops1,
String ops2) |
private String |
decodeAssemblyOperators(String ops) |
private int |
fieldProperty(int i) |
void |
finalizeReader(int nAtoms) |
private javajs.util.M4 |
getOpMatrix(String ops) |
boolean |
initialize(CifReader r) |
private void |
parseLoopParameters(String[] fields) |
private boolean |
processAssemblyGenBlock() |
private boolean |
processChemCompLoopBlock()
a general name definition field.
|
void |
processData(String key) |
private void |
processDataAssemblyGen() |
private void |
processDataNonpoly() |
private boolean |
processLigandBondLoopBlock() |
private boolean |
processNonpolyLoopBlock()
a HETERO name definition field.
|
boolean |
processPDBLoops(String str) |
private boolean |
processStructConfLoopBlock()
identifies ranges for HELIX and TURN
|
private boolean |
processStructOperListBlock() |
private boolean |
processStructSheetRangeLoopBlock()
identifies sheet ranges
|
private boolean |
processStructSiteBlock()
identifies structure sites
|
private void |
setBiomolecules(Map<String,Object> biomolecule) |
private CifReader cr
private boolean isBiomolecule
private boolean byChain
private boolean bySymop
private boolean isCourseGrained
private static final int NONE
private int thisChain
private javajs.util.P3 chainSum
private int[] chainAtomCount
private static final byte OPER_ID
private static final byte OPER_XYZ
private static final String[] operFields
private static final byte ASSEM_ID
private static final byte ASSEM_OPERS
private static final byte ASSEM_LIST
private static final String[] assemblyFields
private String[] assem
private String data
private String key
private static final byte NONPOLY_ENTITY_ID
private static final byte NONPOLY_NAME
private static final byte NONPOLY_COMP_ID
private static final String[] nonpolyFields
private String[] hetatmData
private String field
private char firstChar
private static final byte CHEM_COMP_ID
private static final byte CHEM_COMP_NAME
private static final String[] chemCompFields
private int propertyCount
private int[] fieldOf
private static final byte CONF_TYPE_ID
private static final byte BEG_ASYM_ID
private static final byte BEG_SEQ_ID
private static final byte BEG_INS_CODE
private static final byte END_ASYM_ID
private static final byte END_SEQ_ID
private static final byte END_INS_CODE
private static final byte STRUCT_ID
private static final byte SERIAL_NO
private static final byte HELIX_CLASS
private static final String[] structConfFields
private static final byte SHEET_ID
private static final byte STRAND_ID
private static final String[] structSheetRangeFields
private static final byte SITE_ID
private static final byte SITE_COMP_ID
private static final byte SITE_ASYM_ID
private static final byte SITE_SEQ_ID
private static final byte SITE_INS_CODE
private static final String[] structSiteRangeFields
private static final byte CHEM_COMP_BOND_ATOM_ID_1
private static final byte CHEM_COMP_BOND_ATOM_ID_2
private static final byte CHEM_COMP_BOND_VALUE_ORDER
private static final byte CHEM_COMP_BOND_AROMATIC_FLAG
private static final String[] chemCompBondFields
public boolean initialize(CifReader r)
initialize
in interface MMCifInterface
public void finalizeReader(int nAtoms) throws Exception
finalizeReader
in interface MMCifInterface
Exception
public void processData(String key) throws Exception
processData
in interface MMCifInterface
Exception
private boolean processAssemblyGenBlock() throws Exception
Exception
private boolean processStructOperListBlock() throws Exception
Exception
private boolean processChemCompLoopBlock() throws Exception
Exception
private boolean processNonpolyLoopBlock() throws Exception
Exception
private boolean processStructConfLoopBlock() throws Exception
Exception
private boolean processStructSheetRangeLoopBlock() throws Exception
Exception
private void parseLoopParameters(String[] fields) throws Exception
Exception
private boolean processStructSiteBlock() throws Exception
Exception
private int fieldProperty(int i)
private void createParticle(String id)
private javajs.util.M4 getOpMatrix(String ops)
private boolean processLigandBondLoopBlock() throws Exception
Exception
public boolean checkAtom(Atom atom, String assemblyId, int index)
checkAtom
in interface MMCifInterface
public boolean processPDBLoops(String str) throws Exception
processPDBLoops
in interface MMCifInterface
Exception