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java.lang.Objectorg.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.cifpdb.CifReader
public class CifReader
A true line-free CIF file reader for CIF and mmCIF files.
http://www.iucr.org/iucr-top/cif/ http://www.iucr.org/iucr-top/cif/standard/cifstd5.html
Field Summary | |
---|---|
private static byte |
ADP_TYPE
|
private static byte |
ALT_ID
|
private static byte |
ANISO_B11
|
private static byte |
ANISO_B12
|
private static byte |
ANISO_B13
|
private static byte |
ANISO_B22
|
private static byte |
ANISO_B23
|
private static byte |
ANISO_B33
|
private static byte |
ANISO_Beta_11
|
private static byte |
ANISO_Beta_12
|
private static byte |
ANISO_Beta_13
|
private static byte |
ANISO_Beta_22
|
private static byte |
ANISO_Beta_23
|
private static byte |
ANISO_Beta_33
|
private static byte |
ANISO_LABEL
|
private static byte |
ANISO_MMCIF_ID
|
private static byte |
ANISO_MMCIF_U11
|
private static byte |
ANISO_MMCIF_U12
|
private static byte |
ANISO_MMCIF_U13
|
private static byte |
ANISO_MMCIF_U22
|
private static byte |
ANISO_MMCIF_U23
|
private static byte |
ANISO_MMCIF_U33
|
private static byte |
ANISO_U11
|
private static byte |
ANISO_U12
|
private static byte |
ANISO_U13
|
private static byte |
ANISO_U22
|
private static byte |
ANISO_U23
|
private static byte |
ANISO_U33
|
private static byte |
ASYM_ID
|
private static byte |
ATOM_TYPE_OXIDATION_NUMBER
|
private static byte |
ATOM_TYPE_SYMBOL
|
private static String[] |
atomFields
|
private static String[] |
atomTypeFields
|
private Hashtable |
atomTypes
|
private static byte |
AUTH_ATOM
|
private static byte |
B_ISO
|
private static byte |
BEG_ASYM_ID
|
private static byte |
BEG_INS_CODE
|
private static byte |
BEG_SEQ_ID
|
private static byte |
CARTN_X
|
private static byte |
CARTN_Y
|
private static byte |
CARTN_Z
|
static String[] |
cellParamNames
|
private static byte |
CHEM_COMP_ID
|
private static byte |
CHEM_COMP_NAME
|
private static String[] |
chemCompFields
|
private String |
chemicalName
|
private static byte |
COMP_ID
|
private static byte |
CONF_TYPE_ID
|
private String |
data
|
private static byte |
DISORDER_GROUP
|
private static byte |
DUMMY_ATOM
|
private static byte |
END_ASYM_ID
|
private static byte |
END_INS_CODE
|
private static byte |
END_SEQ_ID
|
(package private) String |
field
|
private byte[] |
fieldOf
|
private char |
firstChar
|
private static byte |
FRACT_X
|
private static byte |
FRACT_Y
|
private static byte |
FRACT_Z
|
private static byte |
GEOM_BOND_ATOM_SITE_LABEL_1
|
private static byte |
GEOM_BOND_ATOM_SITE_LABEL_2
|
private static byte |
GEOM_BOND_SITE_SYMMETRY_2
|
private static String[] |
geomBondFields
|
private static byte |
GROUP_PDB
|
private static byte |
HELIX_CLASS
|
private String[] |
hetatmData
optional nonloop format -- see 1jsa.cif |
private Hashtable |
htHetero
|
private Hashtable |
htSites
|
private boolean |
iHaveDesiredModel
|
private static byte |
INS_CODE
|
private boolean |
isPDB
|
private String |
key
|
private static byte |
LABEL
|
private static byte |
MODEL_NO
|
private static byte |
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 |
OCCUPANCY
|
private int |
propertyCount
|
private int[] |
propertyOf
|
private static byte |
SEQ_ID
|
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 static byte |
SYM_EQUIV_XYZ
|
private static String[] |
symmetryOperationsFields
|
private static byte |
SYMOP_XYZ
|
private String |
thisDataSetName
|
private String |
thisFormula
|
private String |
thisStructuralFormula
|
private CifDataReader |
tokenizer
|
private static String[] |
TransformFields
|
private static byte |
TYPE_SYMBOL
|
private static byte |
U_ISO_OR_EQUIV
|
Constructor Summary | |
---|---|
CifReader()
|
Method Summary | |
---|---|
private void |
addHetero(String groupName,
String hetName)
|
void |
applySymmetryAndSetTrajectory()
|
private void |
disableField(int fieldIndex)
used for turning off fractional or nonfractional coord. |
private int |
fieldProperty(int i)
|
protected void |
finalizeReader()
|
private boolean |
getData()
|
void |
initializeReader()
|
private static boolean |
isMatch(String str1,
String str2)
|
private void |
parseLoopParameters(String[] fields)
sets up arrays and variables for tokenizer.getData() |
(package private) boolean |
processAtomSiteLoopBlock()
reads atom data in any order |
private void |
processAtomTypeLoopBlock()
reads the oxidation number and associates it with an atom name, which can then later be associated with the right atom indirectly. |
private void |
processCellParameter()
unit cell parameters -- two options, so we use MOD 6 |
private void |
processChemCompLoopBlock()
a general name definition field. |
private void |
processChemicalInfo(String type)
reads some of the more interesting info into specific atomSetAuxiliaryInfo elements |
private void |
processDataParameter()
initialize a new atom set |
private void |
processGeomBondLoopBlock()
reads bond data -- N_ijk symmetry business is ignored, so we only indicate bonds within the unit cell to just the original set of atoms. |
private void |
processLoopBlock()
processes loop_ blocks of interest or skips the data |
private void |
processNonpolyData()
|
private void |
processNonpolyLoopBlock()
a HETERO name definition field. |
private void |
processStructConfLoopBlock()
identifies ranges for HELIX and TURN |
private void |
processStructSheetRangeLoopBlock()
identifies sheet ranges |
private void |
processStructSiteBlock()
identifies structure sites |
private void |
processSymmetryOperationsLoopBlock()
retrieves symmetry operations |
private void |
processSymmetrySpaceGroupName()
done by AtomSetCollectionReader |
private void |
processUnitCellTransformMatrix()
the PDB transformation matrix cartesian --> fractional |
String |
readLine()
|
private void |
skipLoop()
skips all associated loop data |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
private CifDataReader tokenizer
private String thisDataSetName
private String chemicalName
private String thisStructuralFormula
private String thisFormula
private boolean iHaveDesiredModel
private boolean isPDB
private Hashtable htHetero
public static final String[] cellParamNames
private static final String[] TransformFields
private String key
private String data
private Hashtable atomTypes
private static final byte ATOM_TYPE_SYMBOL
private static final byte ATOM_TYPE_OXIDATION_NUMBER
private static final String[] atomTypeFields
private static final byte NONE
private static final byte TYPE_SYMBOL
private static final byte LABEL
private static final byte AUTH_ATOM
private static final byte FRACT_X
private static final byte FRACT_Y
private static final byte FRACT_Z
private static final byte CARTN_X
private static final byte CARTN_Y
private static final byte CARTN_Z
private static final byte OCCUPANCY
private static final byte B_ISO
private static final byte COMP_ID
private static final byte ASYM_ID
private static final byte SEQ_ID
private static final byte INS_CODE
private static final byte ALT_ID
private static final byte GROUP_PDB
private static final byte MODEL_NO
private static final byte DUMMY_ATOM
private static final byte DISORDER_GROUP
private static final byte ANISO_LABEL
private static final byte ANISO_MMCIF_ID
private static final byte ANISO_U11
private static final byte ANISO_U22
private static final byte ANISO_U33
private static final byte ANISO_U12
private static final byte ANISO_U13
private static final byte ANISO_U23
private static final byte ANISO_MMCIF_U11
private static final byte ANISO_MMCIF_U22
private static final byte ANISO_MMCIF_U33
private static final byte ANISO_MMCIF_U12
private static final byte ANISO_MMCIF_U13
private static final byte ANISO_MMCIF_U23
private static final byte U_ISO_OR_EQUIV
private static final byte ANISO_B11
private static final byte ANISO_B22
private static final byte ANISO_B33
private static final byte ANISO_B12
private static final byte ANISO_B13
private static final byte ANISO_B23
private static final byte ANISO_Beta_11
private static final byte ANISO_Beta_22
private static final byte ANISO_Beta_33
private static final byte ANISO_Beta_12
private static final byte ANISO_Beta_13
private static final byte ANISO_Beta_23
private static final byte ADP_TYPE
private static final String[] atomFields
private static final byte GEOM_BOND_ATOM_SITE_LABEL_1
private static final byte GEOM_BOND_ATOM_SITE_LABEL_2
private static final byte GEOM_BOND_SITE_SYMMETRY_2
private static final String[] geomBondFields
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 static final byte CHEM_COMP_ID
private static final byte CHEM_COMP_NAME
private static final String[] chemCompFields
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 Hashtable htSites
private static final byte SYMOP_XYZ
private static final byte SYM_EQUIV_XYZ
private static final String[] symmetryOperationsFields
String field
private char firstChar
private int[] propertyOf
private byte[] fieldOf
private int propertyCount
Constructor Detail |
---|
public CifReader()
Method Detail |
---|
public void initializeReader() throws Exception
initializeReader
in class AtomSetCollectionReader
Exception
protected void finalizeReader() throws Exception
finalizeReader
in class AtomSetCollectionReader
Exception
public void applySymmetryAndSetTrajectory() throws Exception
applySymmetryAndSetTrajectory
in class AtomSetCollectionReader
Exception
private void processDataParameter()
private void processChemicalInfo(String type) throws Exception
type
- "name" "formula" etc.
Exception
private void processSymmetrySpaceGroupName() throws Exception
Exception
private void processCellParameter() throws Exception
Exception
private void processUnitCellTransformMatrix() throws Exception
Exception
private boolean getData() throws Exception
Exception
private void processLoopBlock() throws Exception
Exception
private void processAtomTypeLoopBlock() throws Exception
Exception
boolean processAtomSiteLoopBlock() throws Exception
Exception
private void processGeomBondLoopBlock() throws Exception
Exception
private void processNonpolyData()
private void processChemCompLoopBlock() throws Exception
Exception
private void processNonpolyLoopBlock() throws Exception
Exception
private void addHetero(String groupName, String hetName)
private void processStructConfLoopBlock() throws Exception
Exception
private void processStructSheetRangeLoopBlock() throws Exception
Exception
private void processStructSiteBlock() throws Exception
Exception
private void processSymmetryOperationsLoopBlock() throws Exception
Exception
private int fieldProperty(int i)
private void parseLoopParameters(String[] fields) throws Exception
fields
-
Exception
public String readLine() throws Exception
readLine
in interface JmolLineReader
readLine
in class AtomSetCollectionReader
Exception
private void disableField(int fieldIndex)
fieldIndex
- private void skipLoop() throws Exception
Exception
private static boolean isMatch(String str1, String str2)
str1
- str2
-
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