org.jmol.adapter.readers.cifpdb
Class CifReader
public
class
CifReader
extends AtomSetCollectionReader
private static final byte ADP_TYPE
private static final byte ALT_ID
private static final byte ANISO_B11
private static final byte ANISO_B12
private static final byte ANISO_B13
private static final byte ANISO_B22
private static final byte ANISO_B23
private static final byte ANISO_B33
private static final byte ANISO_Beta_11
private static final byte ANISO_Beta_12
private static final byte ANISO_Beta_13
private static final byte ANISO_Beta_22
private static final byte ANISO_Beta_23
private static final byte ANISO_Beta_33
private static final byte ANISO_LABEL
private static final byte ANISO_MMCIF_U11
private static final byte ANISO_MMCIF_U12
private static final byte ANISO_MMCIF_U13
private static final byte ANISO_MMCIF_U22
private static final byte ANISO_MMCIF_U23
private static final byte ANISO_MMCIF_U33
private static final byte ANISO_U11
private static final byte ANISO_U12
private static final byte ANISO_U13
private static final byte ANISO_U22
private static final byte ANISO_U23
private static final byte ANISO_U33
private static final byte ASYM_ID
private static final byte ATOM_TYPE_OXIDATION_NUMBER
private static final byte ATOM_TYPE_SYMBOL
private static final byte AUTH_ATOM
private static final String[] atomFields
private static final String[] atomTypeFields
private Hashtable atomTypes
private static final byte BEG_ASYM_ID
private static final byte BEG_INS_CODE
private static final byte BEG_SEQ_ID
private static final byte B_ISO
public static final String[] cellParamNames
private static final String[] chemCompFields
private String chemicalName
private static final byte CARTN_X
private static final byte CARTN_Y
private static final byte CARTN_Z
private static final byte CHEM_COMP_ID
private static final byte CHEM_COMP_NAME
private static final byte COMP_ID
private static final byte CONF_TYPE_ID
private String data
private static final byte DISORDER_GROUP
private static final byte DUMMY_ATOM
private static final byte END_ASYM_ID
private static final byte END_INS_CODE
private static final byte END_SEQ_ID
String field
int fieldCount
private byte[] fieldOf
private char firstChar
private static final byte FRACT_X
private static final byte FRACT_Y
private static final byte FRACT_Z
private static final String[] geomBondFields
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 byte GROUP_PDB
private String[] hetatmData
optional nonloop format -- see 1jsa.cif
private Hashtable htHetero
private Hashtable htSites
private static final byte INS_CODE
private String key
String[] loopData
private static final byte LABEL
private static final byte MODEL_NO
private static final String[] nonpolyFields
private static final byte NONE
private static final byte NONPOLY_COMP_ID
private static final byte NONPOLY_ENTITY_ID
private static final byte NONPOLY_NAME
private static final byte OCCUPANCY
private int propertyCount
private int[] propertyOf
private int siteNum
private static final String[] structConfFields
private static final String[] structSheetRangeFields
private static final String[] structSiteRangeFields
private static final String[] symmetryOperationsFields
private static final byte SEQ_ID
private static final byte SITE_ASYM_ID
private static final byte SITE_COMP_ID
private static final byte SITE_ID
private static final byte SITE_INS_CODE
private static final byte SITE_SEQ_ID
private static final byte SYMOP_XYZ
private static final byte SYM_EQUIV_XYZ
private String thisDataSetName
private String thisFormula
private String thisStructuralFormula
private static final String[] TransformFields
private static final byte TYPE_SYMBOL
private static final byte U_ISO_OR_EQUIV
private void addHetero(String groupName, String hetName)
private void disableField(int fieldIndex)
used for turning off fractional or nonfractional coord.
Parameters: fieldIndex
private int fieldProperty(int i)
private boolean getData()
Returns: TRUE if data, even if ''; FALSE if '.' or '?' or eof.
Throws: Exception
private static boolean isMatch(String str1, String str2)
Parameters: str1 str2
Returns: TRUE if a match
private void parseLoopParameters(String[] fields)
sets up arrays and variables for tokenizer.getData()
Parameters: fields
Throws: Exception
boolean processAtomSiteLoopBlock()
reads atom data in any order
Returns: TRUE if successful; FALS if EOF encountered
Throws: Exception
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.
Throws: Exception
private void processCellParameter()
unit cell parameters -- two options, so we use MOD 6
Throws: Exception
private void processChemCompLoopBlock()
a general name definition field. Not all hetero
Throws: Exception
private void processChemicalInfo(String type)
reads some of the more interesting info
into specific atomSetAuxiliaryInfo elements
Parameters: type "name" "formula" etc.
Throws: Exception
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. "connect" script or "set forceAutoBond"
will override these values.
Throws: Exception
private void processLoopBlock()
processes loop_ blocks of interest or skips the data
Throws: Exception
private void processNonpolyData()
private void processNonpolyLoopBlock()
a HETERO name definition field. Maybe not all hetero? nonpoly?
Throws: Exception
private void processStructConfLoopBlock()
identifies ranges for HELIX and TURN
Throws: Exception
private void processStructSheetRangeLoopBlock()
identifies sheet ranges
Throws: Exception
private void processStructSiteBlock()
identifies structure sites
Throws: Exception
private void processSymmetryOperationsLoopBlock()
retrieves symmetry operations
Throws: Exception
private void processSymmetrySpaceGroupName()
done by AtomSetCollectionReader
Throws: Exception
private void processUnitCellTransformMatrix()
the PDB transformation matrix cartesian --> fractional
Throws: Exception
private void skipLoop()
skips all associated loop data
Throws: Exception