Revision: 5172
Author: hansonr
Date: 2006-05-25 08:17:47 -0700 (Thu, 25 May 2006)
ViewCVS: http://svn.sourceforge.net/jmol/?rev=5172&view=rev
Log Message:
-----------
10.3 CIF reader fix and alignment with 10.x.
--properly read 5hvp.cif
Only two small sections different now between 10.x and 10.3,
both having to do with symmetry and unit cells, which 10.2 doesn't do anyway.
-- see references to "10.x")
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/smarter/CifReader.java
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/CifReader.java 2006-05-25
14:51:25 UTC (rev 5171)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/CifReader.java 2006-05-25
15:17:47 UTC (rev 5172)
@@ -24,10 +24,9 @@
package org.jmol.adapter.smarter;
import java.io.BufferedReader;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.Map;
+// attempt to use 10.x in rollback
+
/**
* CIF file reader for CIF and mmCIF files.
*
@@ -40,69 +39,112 @@
*/
class CifReader extends AtomSetCollectionReader {
- float[] notionalUnitcell;
+ int[] unitCells = new int[3];
+ int desiredModelNumber;
+ int modelNumber = 0;
+ boolean normalize = true;
+ boolean iHaveAppliedSymmetry = false;
BufferedReader reader;
String line;
- RidiculousFileFormatTokenizer tokenizer =
- new RidiculousFileFormatTokenizer();
- Map strandsMap;
+ RidiculousFileFormatTokenizer tokenizer = new
RidiculousFileFormatTokenizer();
void initialize() {
+ desiredModelNumber = -1;
+ unitCells[0] = unitCells[1] = unitCells[2] = 0;
+ }
+
+ void initialize(int[] params) {
+ initialize();
+ if (params == null)
+ return;
+ int ipt = 0;
+ if (params.length == 1 || params.length == 4)
+ desiredModelNumber = params[ipt++];
+ if (params.length < ipt + 3)
+ return;
+ unitCells[0] = params[ipt++];
+ unitCells[1] = params[ipt++];
+ unitCells[2] = params[ipt++];
+ }
+
+ boolean iHaveUnitCell = false;
+ float[] notionalUnitcell;
+ String spaceGroup;
+ boolean coordinatesAreFractional;
+
+ void initializeUnitcell() {
+ iHaveUnitCell = false;
notionalUnitcell = new float[6];
- for (int i = 6; --i >= 0; )
+ for (int i = 6; --i >= 0;)
notionalUnitcell[i] = Float.NaN;
+ spaceGroup = "unspecified";
+ coordinatesAreFractional = false;
}
- AtomSetCollection readAtomSetCollection(BufferedReader reader) throws
Exception {
+ AtomSetCollection readAtomSetCollection(BufferedReader reader)
+ throws Exception {
this.reader = reader;
atomSetCollection = new AtomSetCollection("cif");
- strandsMap = new Hashtable();
-
+
// this loop is a little tricky
// the CIF format seems to generate lots of problems for parsers
// the top of this loop should be ready to process the current line
// pay careful attention to the 'break' and 'continue' sequence
// or you will get stuck in an infinite loop
line = reader.readLine();
+ initializeUnitcell();
+ modelNumber = 0;
+ boolean skipping = false;
+ boolean iHaveDesiredModel = false;
+ boolean inSemicolonString = false;
while (line != null) {
- if (line.startsWith("loop_")) {
- processLoopBlock();
- // there is already an unprocessed line in the firing chamber
+ if (line.startsWith(";"))
+ inSemicolonString = !inSemicolonString;
+ if (inSemicolonString) {
+ line = reader.readLine();
continue;
+ }
+ if (line.startsWith("loop_")) {
+ if (!skipping) {
+ processLoopBlock();
+ // there is already an unprocessed line in the firing chamber
+ continue;
+ }
} else if (line.startsWith("data_")) {
- processDataParameter();
+ if (iHaveDesiredModel)
+ break;
+ skipping = (++modelNumber != desiredModelNumber && desiredModelNumber
> 0);
+ if (!skipping) {
+ processDataParameter();
+ initializeUnitcell();
+ iHaveDesiredModel = (desiredModelNumber > 0);
+ }
+ } else if (line.startsWith("_chemical_name ")) {
+ processChemicalName();
} else if (line.startsWith("_cell_") || line.startsWith("_cell.")) {
- processCellParameter();
- } else if (line.startsWith("_symmetry_space_group_name_H-M")) {
- processSymmetrySpaceGroupNameHM();
- } else if (line.startsWith("_struct_asym")) {
- processStructAsymBlock();
+ if (!skipping)
+ processCellParameter();
+ } else if (line.startsWith("_symmetry_space_group_name_H-M")
+ || line.startsWith("_symmetry.space_group_name_H-M")) {
+ if (!skipping)
+ processSymmetrySpaceGroupNameHM();
}
line = reader.readLine();
}
- checkUnitcell();
- logger.log("Done reading... Found these strands:");
- Iterator strands = strandsMap.values().iterator();
- while (strands.hasNext()) {
- Strand strand = (Strand)strands.next();
- logger.log(strand.toString());
- }
return atomSetCollection;
}
-
final static boolean isMatch(String str1, String str2) {
int cch = str1.length();
if (str2.length() != cch)
return false;
- for (int i = cch; --i >= 0; ) {
+ for (int i = cch; --i >= 0;) {
char ch1 = str1.charAt(i);
char ch2 = str2.charAt(i);
if (ch1 == ch2)
continue;
- if ((ch1 == '_' || ch1 == '.') &&
- (ch2 == '_' || ch2 == '.'))
+ if ((ch1 == '_' || ch1 == '.') && (ch2 == '_' || ch2 == '.'))
continue;
if (ch1 <= 'Z' && ch1 >= 'A')
ch1 += 'a' - 'A';
@@ -113,85 +155,115 @@
}
return true;
}
-
+ String thisDataSetName = "";
+
void processDataParameter() {
- String collectionName = line.substring(5).trim();
- if (collectionName.length() > 0)
- atomSetCollection.collectionName = collectionName;
+ thisDataSetName = (line.length() < 6 ? "" : line.substring(5).trim());
+ if (thisDataSetName.length() > 0) {
+ if (atomSetCollection.currentAtomSetIndex >= 0) {
+ // note that there can be problems with multi-data mmCIF sets each with
+ // multiple models; and we could be loading multiple files!
+ atomSetCollection.newAtomSet();
+ atomSetCollection.setCollectionName("<collection of "
+ + (atomSetCollection.currentAtomSetIndex + 1) + " models>");
+ } else {
+ atomSetCollection.setCollectionName(thisDataSetName);
+ }
+ }
+ logger.log(line);
}
-
+
+ void processChemicalName() {
+ if (line.length() < 16)
+ return;
+ thisDataSetName += " " + line.substring(15).trim();
+ logger.log(line);
+ }
+
void processSymmetrySpaceGroupNameHM() {
- atomSetCollection.spaceGroup = line.substring(29).trim();
+ tokenizer.setString(line.substring(30).trim());
+ spaceGroup = tokenizer.nextToken();
}
- final static String[] cellParamNames =
- {"_cell_length_a", "_cell_length_b", "_cell_length_c",
- "_cell_angle_alpha", "_cell_angle_beta", "_cell_angle_gamma"};
-
+ final static String[] cellParamNames = { "_cell_length_a", "_cell_length_b",
+ "_cell_length_c", "_cell_angle_alpha", "_cell_angle_beta",
+ "_cell_angle_gamma", "_cell.length_a", "_cell.length_b",
+ "_cell.length_c", "_cell.angle_alpha", "_cell.angle_beta",
+ "_cell.angle_gamma" };
+
void processCellParameter() {
// logger.log("processCellParameter() line:" + line);
String cellParameter = parseToken(line);
- for (int i = cellParamNames.length; --i >= 0; )
+ for (int i = cellParamNames.length; --i >= 0;)
if (isMatch(cellParameter, cellParamNames[i])) {
- notionalUnitcell[i] = parseFloat(line, ichNextParse);
+ notionalUnitcell[i % 6] = parseFloat(line, ichNextParse);
// logger.log("value=" + notionalUnitcell[i]);
+ iHaveUnitCell = true;
return;
}
// logger.log("NOT");
}
-
- void checkUnitcell() {
- for (int i = 6; --i >= 0; ) {
- if (Float.isNaN(notionalUnitcell[i]))
- return;
- }
- atomSetCollection.notionalUnitcell = notionalUnitcell;
- }
-
+
private void processLoopBlock() throws Exception {
// logger.log("processLoopBlock()-------------------------");
line = reader.readLine().trim();
// logger.log("trimmed line:" + line);
- if (line.startsWith("_atom_site")) {
+ if (line.startsWith("_atom_site_") || line.startsWith("_atom_site.")) {
processAtomSiteLoopBlock();
+ atomSetCollection.setAtomSetName(thisDataSetName);
+ /* 10.x functionality only
+
atomSetCollection.setCoordinatesAreFractional(coordinatesAreFractional);
+ if (iHaveUnitCell
+ && atomSetCollection.setNotionalUnitcell(notionalUnitcell, logger)) {
+ atomSetCollection.setAtomSetSpaceGroup(spaceGroup);
+ if (atomSetCollection.haveSymmetry()) {
+ atomSetCollection.applySymmetry(normalize, unitCells);
+ iHaveAppliedSymmetry = true;
+ } else {
+ //mmCIF -- unit cell and spacegroup,
+ //but no symmetry info, not fractional coordinates
+ }
+ }
+ */
return;
}
- if (line.startsWith("_struct_asym")) {
- processStructAsymBlock();
- return;
- }
if (line.startsWith("_geom_bond")) {
+ if (iHaveAppliedSymmetry) {
+ line = reader.readLine();
+ return;
+ }
processGeomBondLoopBlock();
return;
}
- if (line.startsWith("_struct_conf") &&
- !line.startsWith("_struct_conf_type")) {
+ if (line.startsWith("_struct_conf")
+ && !line.startsWith("_struct_conf_type")) {
processStructConfLoopBlock();
return;
}
- if (line.startsWith("_pdbx_poly_seq_scheme")) {
- processPolySeqSchemeLoopBlock();
+ if (line.startsWith("_struct_sheet_range")) {
+ processStructSheetRangeLoopBlock();
return;
}
- if (line.startsWith("_pdbx_nonpoly_scheme")) {
- processNonPolySchemeLoopBlock();
- return;
- }
if (line.startsWith("_struct_sheet_range")) {
processStructSheetRangeLoopBlock();
return;
}
+ if (line.startsWith("_symmetry_equiv_pos")
+ || line.startsWith("space_group_symop")) {
+ processSymmetryOperationsLoopBlock();
+ return;
+ }
+
// logger.log("Skipping loop block:" + line);
skipLoopHeaders();
skipLoopData();
}
-
+
private void skipLoopHeaders() throws Exception {
// skip everything that begins with _
- while (line != null &&
- (line = line.trim()).length() > 0 &&
- line.charAt(0) == '_') {
+ while (line != null && (line = line.trim()).length() > 0
+ && line.charAt(0) == '_') {
line = reader.readLine();
}
}
@@ -200,67 +272,62 @@
// skip everything until empty line, or comment line
// or start of a new loop_ or data_
char ch;
- while (line != null &&
- (line = line.trim()).length() > 0 &&
- (ch = line.charAt(0)) != '_' &&
- ch != '#' &&
- ! line.startsWith("loop_") &&
- ! line.startsWith("data_")) {
- // logger.log("skipLoopData just discarded:" + line);
+ while (line != null) {
+ line = line.trim();
+ if (line.length() != 0
+ && ((ch = line.charAt(0)) == '_' || ch == '#'
+ || line.startsWith("loop_") || line.startsWith("data_")))
+ break;
line = reader.readLine();
}
}
-
+
////////////////////////////////////////////////////////////////
// atom data
////////////////////////////////////////////////////////////////
- final static byte NONE = 0;
+ final static byte NONE = 0;
final static byte TYPE_SYMBOL = 1;
- final static byte LABEL = 2;
- final static byte FRACT_X = 3;
- final static byte FRACT_Y = 4;
- final static byte FRACT_Z = 5;
- final static byte CARTN_X = 6;
- final static byte CARTN_Y = 7;
- final static byte CARTN_Z = 8;
- final static byte OCCUPANCY = 9;
- final static byte B_ISO = 10;
- final static byte COMP_ID = 11;
- final static byte ASYM_ID = 12;
- final static byte SEQ_ID = 13;
- final static byte INS_CODE = 14;
- final static byte ALT_ID = 15;
- final static byte GROUP_PDB = 16;
- final static byte SITE_ID = 17;
- final static byte MODEL_NO = 18;
- final static byte AUTH_SEQ_ID = 19;
- final static byte ATOM_PROPERTY_MAX = 20;
-
+ final static byte LABEL = 2;
+ final static byte FRACT_X = 3;
+ final static byte FRACT_Y = 4;
+ final static byte FRACT_Z = 5;
+ final static byte CARTN_X = 6;
+ final static byte CARTN_Y = 7;
+ final static byte CARTN_Z = 8;
+ final static byte OCCUPANCY = 9;
+ final static byte B_ISO = 10;
+ final static byte COMP_ID = 11;
+ final static byte ASYM_ID = 12;
+ final static byte SEQ_ID = 13;
+ final static byte INS_CODE = 14;
+ final static byte ALT_ID = 15;
+ final static byte GROUP_PDB = 16;
+ final static byte MODEL_NO = 17;
+ final static byte DUMMY_ATOM = 18;
+ final static byte ATOM_PROPERTY_MAX = 19;
- final static String[] atomFields = {
- "_atom_site_type_symbol",
- "_atom_site_label", "_atom_site_label_atom_id",
- "_atom_site_fract_x", "_atom_site_fract_y", "_atom_site_fract_z",
- "_atom_site.Cartn_x", "_atom_site.Cartn_y", "_atom_site.Cartn_z",
- "_atom_site_occupancy",
- "_atom_site.b_iso_or_equiv",
- "_atom_site.label_comp_id", "_atom_site.label_asym_id",
- "_atom_site.label_seq_id", "_atom_site.pdbx_PDB_ins_code",
- "_atom_site.label_alt_id",
- "_atom_site.group_PDB", "_atom_site.id",
- "_atom_site.pdbx_PDB_model_num","_atom_site.auth_seq_id"
- };
+ final static String[] atomFields = { "_atom_site_type_symbol",
+ "_atom_site_label", "_atom_site_auth_atom_id", "_atom_site_fract_x",
+ "_atom_site_fract_y", "_atom_site_fract_z", "_atom_site.Cartn_x",
+ "_atom_site.Cartn_y", "_atom_site.Cartn_z", "_atom_site_occupancy",
+ "_atom_site.b_iso_or_equiv", "_atom_site.auth_comp_id",
+ "_atom_site.auth_asym_id", "_atom_site.auth_seq_id",
+ "_atom_site.pdbx_PDB_ins_code", "_atom_site.label_alt_id",
+ "_atom_site.group_PDB", "_atom_site.pdbx_PDB_model_num",
+ "_atom_site_calc_flag", };
- final static byte[] atomFieldMap = {
- TYPE_SYMBOL,
- LABEL, LABEL,
- FRACT_X, FRACT_Y, FRACT_Z,
- CARTN_X, CARTN_Y, CARTN_Z,
- OCCUPANCY, B_ISO,
- COMP_ID, ASYM_ID, SEQ_ID, INS_CODE,
- ALT_ID, GROUP_PDB, SITE_ID, MODEL_NO, AUTH_SEQ_ID
- };
+ /* to: [EMAIL PROTECTED]
+ * from: Zukang Feng [EMAIL PROTECTED]
+ * re: Two mmCIF issues
+ * date: 4/18/2006 10:30 PM
+ * "You should always use _atom_site.auth_asym_id for PDB chain IDs."
+ *
+ *
+ */
+ final static byte[] atomFieldMap = { TYPE_SYMBOL, LABEL, LABEL, FRACT_X,
+ FRACT_Y, FRACT_Z, CARTN_X, CARTN_Y, CARTN_Z, OCCUPANCY, B_ISO, COMP_ID,
+ ASYM_ID, SEQ_ID, INS_CODE, ALT_ID, GROUP_PDB, MODEL_NO, DUMMY_ATOM };
static {
if (atomFieldMap.length != atomFields.length)
@@ -270,21 +337,20 @@
void processAtomSiteLoopBlock() throws Exception {
// logger.log("processAtomSiteLoopBlock()-------------------------");
int currentModelNO = -1;
- int missingSequenceNumber = 0;
- int atomSerial = 0;
+ boolean isPDB = false;
int[] fieldTypes = new int[100]; // should be enough
boolean[] atomPropertyReferenced = new boolean[ATOM_PROPERTY_MAX];
- int fieldCount = parseLoopParameters(atomFields,
- atomFieldMap,
- fieldTypes,
- atomPropertyReferenced);
+ int fieldCount = parseLoopParameters(atomFields, atomFieldMap, fieldTypes,
+ atomPropertyReferenced);
// now that headers are parsed, check to see if we want
// cartesian or fractional coordinates;
+
if (atomPropertyReferenced[CARTN_X]) {
+ coordinatesAreFractional = false;
for (int i = FRACT_X; i < FRACT_Z; ++i)
disableField(fieldCount, fieldTypes, i);
} else if (atomPropertyReferenced[FRACT_X]) {
- atomSetCollection.coordinatesAreFractional = true;
+ coordinatesAreFractional = true;
for (int i = CARTN_X; i < CARTN_Z; ++i)
disableField(fieldCount, fieldTypes, i);
} else {
@@ -294,33 +360,30 @@
return;
}
+ char alternateLocationID = '0';
for (; line != null; line = reader.readLine()) {
int lineLength = line.length();
if (lineLength == 0)
break;
char chFirst = line.charAt(0);
- if (chFirst == '#' ||
- chFirst == '_' ||
- line.startsWith("loop_") ||
- line.startsWith("data_"))
+ if (chFirst == '#' || chFirst == '_' || line.startsWith("loop_")
+ || line.startsWith("data_"))
break;
if (chFirst == ' ') {
int i;
- for (i = lineLength; --i >= 0 && line.charAt(i) == ' '; ) {
+ for (i = lineLength; --i >= 0 && line.charAt(i) == ' ';) {
}
if (i < 0)
break;
}
// logger.log("line:" + line);
// logger.log("of length = " + line.length());
- if (line.length() == 1)
- logger.log("char value is " + (chFirst + 0));
tokenizer.setString(line);
// logger.log("reading an atom");
Atom atom = new Atom();
- for (int i = 0; i < fieldCount; ++i) {
- if (! tokenizer.hasMoreTokens())
- tokenizer.setString(reader.readLine());
+ out: for (int i = 0; i < fieldCount; ++i) {
+ if (!tokenizer.hasMoreTokens())
+ tokenizer.setStringNextLine(reader);
String field = tokenizer.nextToken();
if (field == null)
logger.log("field == null!");
@@ -358,8 +421,8 @@
break;
case OCCUPANCY:
float floatOccupancy = parseFloat(field);
- if (! Float.isNaN(floatOccupancy))
- atom.occupancy = (int)(floatOccupancy * 100);
+ if (!Float.isNaN(floatOccupancy))
+ atom.occupancy = (int) (floatOccupancy * 100);
break;
case B_ISO:
atom.bfactor = parseFloat(field);
@@ -370,43 +433,13 @@
case ASYM_ID:
if (field.length() > 1)
logger.log("Don't know how to deal with chains more than 1 char",
- field);
- atom.chainID = getChainIdFromStrandMap(field.charAt(0));
- logger.log(atomSerial + atom.group3+" asym_id "+atom.chainID + " " +
field.charAt(0));
- //ok to assign ' ' when blank?
+ field);
+ char firstChar = field.charAt(0);
+ if (firstChar != '?' && firstChar != '.')
+ atom.chainID = firstChar;
break;
- case AUTH_SEQ_ID:
- if (atom.sequenceNumber >= 0)
- break;
- logger.log("assigning #"+atomSerial + " group3=" + atom.group3 + "
as " + field);
- /*
- * The idea is that it is better to err on the side of consistency
- * with PDB files than to leave this blank. See 1bkx, where this
- * now allows the rna monomer (and not all the H2O as well)
- * to be identified as RNA.
- *
- * Bob Hanson 2006/04/14
- *
- */
case SEQ_ID:
atom.sequenceNumber = parseInt(field);
- if (atom.sequenceNumber == Integer.MIN_VALUE) {
- logger.log("Warning! mmCIF ERROR: Missing SEQ_ID in mmCIF file for
#"+atomSerial + " group3=" + atom.group3);
- atom.sequenceNumber = --missingSequenceNumber;
- }
- /*
- * 1d66.cif is missing this information, causing Jmol to
- * improperly assign "CD" to HOH as group3 in HETATM records.
- *
- * interestingly, this fix allows for
- *
- * select -3
- *
- * but I wouldn't publicize that.
- *
- * -- Bob Hanson 206/04/14
- *
- */
break;
case INS_CODE:
char insCode = field.charAt(0);
@@ -414,30 +447,16 @@
atom.chainID = insCode;
break;
case ALT_ID:
- char alternateLocationID = field.charAt(0);
- if (alternateLocationID != '?' && alternateLocationID != '.')
- atom.alternateLocationID = alternateLocationID;
+ alternateLocationID = field.charAt(0);
+ if (alternateLocationID == '?' || alternateLocationID == '.')
+ break;
+ atom.alternateLocationID = alternateLocationID;
break;
case GROUP_PDB:
+ isPDB = true;
if ("HETATM".equals(field))
atom.isHetero = true;
break;
- case SITE_ID:
- //atom.atomSerial = parseInt(field);
- /*
- * I considered the above, but then decided there might be
- * a reason we aren't assigning a serial number for atoms in
- * a CIF file, maybe to do with the fact that in CIF files we
- * are using mapped atom names, whereas in PDB files we are not
- * Egon?
- *
- * So this assignment for now is just for internal purposes.
- *
- * -- Bob Hanson
- *
- */
- atomSerial = parseInt(field);
- break;
case MODEL_NO:
int modelNO = parseInt(field);
if (modelNO != currentModelNO) {
@@ -445,90 +464,39 @@
currentModelNO = modelNO;
}
break;
+ case DUMMY_ATOM:
+ //see http://www.iucr.org/iucr-top/cif/cifdic_html/
+ // 1/cif_core.dic/Iatom_site_calc_flag.html
+ if ("dum".equals(field)) {
+ atom.x = Float.NaN;
+ continue out;
+ }
+ break;
}
}
if (Float.isNaN(atom.x) || Float.isNaN(atom.y) || Float.isNaN(atom.z))
- logger.log("atom " + atom.atomName +
- " has invalid/unknown coordinates");
- else
+ logger
+ .log("atom " + atom.atomName + " has invalid/unknown coordinates");
+ else {
atomSetCollection.addAtomWithMappedName(atom);
+ }
}
+ if (isPDB)
+ atomSetCollection.setAtomSetAuxiliaryInfo("isPDB", new Boolean(isPDB));
}
- char getChainIdFromStrandMap(char chainChar) {
- /*
- * the problem (see 1pgb.cif) was that while the atom chainIDs
- * were being set using this function, the STRUCTURE chainIDs were
- * not, so then later the structures were taken to be in different
- * chains than the atoms, and no structures were determined.
- *
- * this method is called by helix/turn, by sheet, and by atoms!
- *
- * more problems here also with 1bkx.cif. RNA fragment being given
- * 0 instead of B. Why? In the CIF file we have
- *
- * Bob Hanson 2006/04/14
- *
- */
-
- if (chainChar == '?' || chainChar == '.')
- return ' ';
- String chainID = "" + chainChar;
- if (!strandsMap.containsKey(chainID))
- return chainChar;
- Strand strand = (Strand) strandsMap.get(chainID);
- // OK, here is the if/else construct that Wayne send me
- if (strand.isBlank.booleanValue())
- return ' '; // no author provided ID
- if (strand.authorID != null)
- // not pretty, but let's just assume the string only has one char
- return strand.authorID.charAt(0);
- return ' ';
- /*
- * Egon:
- *
- * Should last return be chainChar?
- * Is mapping supposed to mean "author's or nothing? Or is there ever
- * a time when a mapped mmCIF-given chain ID should be used?
- *
- * _struct_asym.id
- * _struct_asym.pdbx_blank_PDB_chainid_flag
- * _struct_asym.pdbx_modified
- * _struct_asym.entity_id
- * _struct_asym.details
- * A N N 1 ?
- * B N N 2 ?
- * C N N 3 ?
- *
- * So they aren't modified and they aren't blank.
- * Doesn't that indicate that none should be blank?
- * Part of the problem may be that the RNA piece here
- * is being classified in mmCIF as HETATM but in PDB as ATOM
- * and I think there is a flaw in the mmCIF generator for HETATM
- * returning ? when it should not be.
- *
- * Bob
- *
- */
- }
-
void disableField(int fieldCount, int[] fieldTypes, int fieldIndex) {
- for (int i = fieldCount; --i >= 0; )
+ for (int i = fieldCount; --i >= 0;)
if (fieldTypes[i] == fieldIndex)
fieldTypes[i] = 0;
}
- int parseLoopParameters(String[] fields,
- byte[] fieldMap,
- int[] fieldTypes,
+ int parseLoopParameters(String[] fields, byte[] fieldMap, int[] fieldTypes,
boolean[] propertyReferenced) throws Exception {
int fieldCount = 0;
- outer_loop:
- for (; line != null &&
- (line = line.trim()).length() > 0 &&
- line.charAt(0) == '_';
- ++fieldCount, line = reader.readLine()) {
- for (int i = fields.length; --i >= 0; )
+ outer_loop: for (; line != null && (line = line.trim()).length() > 0
+ && line.charAt(0) == '_'; ++fieldCount, line = reader.readLine()) {
+ for (int i = fields.length; --i >= 0;)
if (isMatch(line, fields[i])) {
int iproperty = fieldMap[i];
propertyReferenced[iproperty] = true;
@@ -540,103 +508,51 @@
return fieldCount;
}
- Object[] parseAndProcessStructParameters(
- String[] fields,
- byte[] fieldMap,
- int[] fieldTypes,
- boolean[] propertyReferenced) throws Exception {
- int fieldCount = 0;
- Strand struct = new Strand();
- for (; line != null &&
- (line = line.trim()).length() > 0 &&
- line.charAt(0) == '_';
- ++fieldCount, line = reader.readLine()) {
- logger.log("Processing line: ", line);
- for (int i = fields.length; --i >= 0; ) {
- tokenizer.setString(line);
- String key = tokenizer.nextToken();
- // take this valid mmCIF into account:
- // _struct_asym.id A
- String value = null;
- if (isMatch(key, fields[i])) {
- if (tokenizer.hasMoreTokens()) {
- value = tokenizer.nextToken();
- if (fields[i].equals(structAsymNames[STRUCT_ASYM_ID-1]))
- struct.chainID = value;
- if (fields[i].equals(structAsymNames[STRUCT_BLANK_CHAIN_ID-1]))
- struct.isBlank = "Y".equals(value) ? Boolean.TRUE :
Boolean.FALSE;
- logger.log("struct", struct);
- } else {
- struct = null;
- }
- int iproperty = fieldMap[i];
- propertyReferenced[iproperty] = true;
- fieldTypes[fieldCount] = iproperty;
- i = -1;
- }
- }
- }
- logger.log("parseLoopParameters sees fieldCount=" + fieldCount);
- logger.log("parsed struct -> " + struct);
- Object[] results = new Object[2];
- results[0] = new Integer(fieldCount);
- results[1] = struct;
- return results;
- }
-
////////////////////////////////////////////////////////////////
// bond data
////////////////////////////////////////////////////////////////
final static byte GEOM_BOND_ATOM_SITE_LABEL_1 = 1;
final static byte GEOM_BOND_ATOM_SITE_LABEL_2 = 2;
- final static byte GEOM_BOND_SITE_SYMMETRY_2 = 3;
+ final static byte GEOM_BOND_SITE_SYMMETRY_2 = 3;
// final static byte GEOM_BOND_DISTANCE = 4;
-
- final static byte GEOM_BOND_PROPERTY_MAX = 4;
- final static String[] geomBondFields = {
- "_geom_bond_atom_site_label_1",
- "_geom_bond_atom_site_label_2",
- "_geom_bond_site_symmetry_2",
- // "_geom_bond_distance",
+ final static byte GEOM_BOND_PROPERTY_MAX = 4;
+
+ final static String[] geomBondFields = { "_geom_bond_atom_site_label_1",
+ "_geom_bond_atom_site_label_2", "_geom_bond_site_symmetry_2",
+ // "_geom_bond_distance",
};
- final static byte[] geomBondFieldMap = {
- GEOM_BOND_ATOM_SITE_LABEL_1,
- GEOM_BOND_ATOM_SITE_LABEL_2,
- GEOM_BOND_SITE_SYMMETRY_2,
- // GEOM_BOND_DISTANCE,
+ final static byte[] geomBondFieldMap = { GEOM_BOND_ATOM_SITE_LABEL_1,
+ GEOM_BOND_ATOM_SITE_LABEL_2, GEOM_BOND_SITE_SYMMETRY_2,
+ // GEOM_BOND_DISTANCE,
};
void processGeomBondLoopBlock() throws Exception {
int[] fieldTypes = new int[100]; // should be enough
boolean[] propertyReferenced = new boolean[GEOM_BOND_PROPERTY_MAX];
- int fieldCount = parseLoopParameters(geomBondFields,
- geomBondFieldMap,
- fieldTypes,
- propertyReferenced);
- for (int i = GEOM_BOND_PROPERTY_MAX; --i > 0; ) // only > 0, not >= 0
- if (! propertyReferenced[i]) {
+ int fieldCount = parseLoopParameters(geomBondFields, geomBondFieldMap,
+ fieldTypes, propertyReferenced);
+ for (int i = GEOM_BOND_PROPERTY_MAX; --i > 0;)
+ // only > 0, not >= 0
+ if (!propertyReferenced[i]) {
logger.log("?que? missing _geom_bond property:" + i);
skipLoopData();
return;
}
- for (; line != null &&
- (line = line.trim()).length() > 0 &&
- line.charAt(0) != '#' &&
- line.charAt(0) != '_' &&
- !line.startsWith("loop_") &&
- !line.startsWith("data_");
- line = reader.readLine()) {
+ for (; line != null && (line = line.trim()).length() > 0
+ && line.charAt(0) != '#' && line.charAt(0) != '_'
+ && !line.startsWith("loop_") && !line.startsWith("data_"); line =
reader
+ .readLine()) {
tokenizer.setString(line);
int atomIndex1 = -1;
int atomIndex2 = -1;
String symmetry = null;
for (int i = 0; i < fieldCount; ++i) {
- if (! tokenizer.hasMoreTokens())
- tokenizer.setString(reader.readLine());
+ if (!tokenizer.hasMoreTokens())
+ tokenizer.setStringNextLine(reader);
String field = tokenizer.nextToken();
switch (fieldTypes[i]) {
case NONE:
@@ -669,57 +585,46 @@
// helix and turn structure data
////////////////////////////////////////////////////////////////
- final static byte CONF_TYPE_ID = 1;
- final static byte BEG_ASYM_ID = 2;
- final static byte BEG_SEQ_ID = 3;
- final static byte BEG_INS_CODE = 4;
- final static byte END_ASYM_ID = 5;
- final static byte END_SEQ_ID = 6;
- final static byte END_INS_CODE = 7;
+ final static byte CONF_TYPE_ID = 1;
+ final static byte BEG_ASYM_ID = 2;
+ final static byte BEG_SEQ_ID = 3;
+ final static byte BEG_INS_CODE = 4;
+ final static byte END_ASYM_ID = 5;
+ final static byte END_SEQ_ID = 6;
+ final static byte END_INS_CODE = 7;
final static byte STRUCT_CONF_PROPERTY_MAX = 8;
- final static String[] structConfFields = {
- "_struct_conf.conf_type_id",
+ final static String[] structConfFields = { "_struct_conf.conf_type_id",
- "_struct_conf.beg_auth_asym_id",
- "_struct_conf.beg_auth_seq_id",
- "_struct_conf.pdbx_beg_PDB_ins_code",
-
- "_struct_conf.end_auth_asym_id",
- "_struct_conf.end_auth_seq_id",
- "_struct_conf.pdbx_end_PDB_ins_code",
- };
+ "_struct_conf.beg_auth_asym_id", "_struct_conf.beg_auth_seq_id",
+ "_struct_conf.pdbx_beg_PDB_ins_code",
- final static byte[] structConfFieldMap = {
- CONF_TYPE_ID,
- BEG_ASYM_ID, BEG_SEQ_ID, BEG_INS_CODE,
- END_ASYM_ID, END_SEQ_ID, END_INS_CODE,
- };
+ "_struct_conf.end_auth_asym_id", "_struct_conf.end_auth_seq_id",
+ "_struct_conf.pdbx_end_PDB_ins_code", };
+ final static byte[] structConfFieldMap = { CONF_TYPE_ID, BEG_ASYM_ID,
+ BEG_SEQ_ID, BEG_INS_CODE, END_ASYM_ID, END_SEQ_ID, END_INS_CODE, };
+
void processStructConfLoopBlock() throws Exception {
int[] fieldTypes = new int[100]; // should be enough
boolean[] propertyReferenced = new boolean[STRUCT_CONF_PROPERTY_MAX];
- int fieldCount = parseLoopParameters(structConfFields,
- structConfFieldMap,
- fieldTypes,
- propertyReferenced);
- for (int i = STRUCT_CONF_PROPERTY_MAX; --i > 0; ) // only > 0, not >= 0
- if (! propertyReferenced[i]) {
+ int fieldCount = parseLoopParameters(structConfFields, structConfFieldMap,
+ fieldTypes, propertyReferenced);
+ for (int i = STRUCT_CONF_PROPERTY_MAX; --i > 0;)
+ // only > 0, not >= 0
+ if (!propertyReferenced[i]) {
logger.log("?que? missing _struct_conf property:" + i);
skipLoopData();
return;
}
- for (; line != null &&
- (line = line.trim()).length() > 0 &&
- line.charAt(0) != '#';
- line = reader.readLine()) {
+ for (; line != null && (line = line.trim()).length() > 0
+ && line.charAt(0) != '#'; line = reader.readLine()) {
tokenizer.setString(line);
Structure structure = new Structure();
-
for (int i = 0; i < fieldCount; ++i) {
- if (! tokenizer.hasMoreTokens())
- tokenizer.setString(reader.readLine());
+ if (!tokenizer.hasMoreTokens())
+ tokenizer.setStringNextLine(reader);
String field = tokenizer.nextToken();
char firstChar = field.charAt(0);
switch (fieldTypes[i]) {
@@ -734,24 +639,26 @@
structure.structureType = "none";
break;
case BEG_ASYM_ID:
- structure.startChainID = getChainIdFromStrandMap(firstChar);
+ structure.startChainID = (firstChar == '.' || firstChar == '?') ? ' '
+ : firstChar;
break;
case BEG_SEQ_ID:
structure.startSequenceNumber = parseInt(field);
break;
case BEG_INS_CODE:
- structure.startInsertionCode =
- (firstChar == '.' || firstChar == '?') ? ' ' : firstChar;
+ structure.startInsertionCode = (firstChar == '.' || firstChar ==
'?') ? ' '
+ : firstChar;
break;
case END_ASYM_ID:
- structure.endChainID = getChainIdFromStrandMap(firstChar);
+ structure.endChainID = (firstChar == '.' || firstChar == '?') ? ' '
+ : firstChar;
break;
case END_SEQ_ID:
structure.endSequenceNumber = parseInt(field);
break;
case END_INS_CODE:
- structure.endInsertionCode =
- (firstChar == '.' || firstChar == '?') ? ' ' : firstChar;
+ structure.endInsertionCode = (firstChar == '.' || firstChar == '?')
? ' '
+ : firstChar;
break;
}
}
@@ -766,69 +673,65 @@
// note that the conf_id is not used
final static byte STRUCT_SHEET_RANGE_PROPERTY_MAX = 8;
+ //auth not label!
+
final static String[] structSheetRangeFields = {
- "_struct_sheet_range.beg_label_asym_id",
- "_struct_sheet_range.beg_label_seq_id",
- "_struct_sheet_range.pdbx_beg_PDB_ins_code",
-
- "_struct_sheet_range.end_label_asym_id",
- "_struct_sheet_range.end_label_seq_id",
- "_struct_sheet_range.pdbx_end_PDB_ins_code",
- };
+ "_struct_sheet_range.beg_auth_asym_id",
+ "_struct_sheet_range.beg_auth_seq_id",
+ "_struct_sheet_range.pdbx_beg_PDB_ins_code",
- final static byte[] structSheetRangeFieldMap = {
- BEG_ASYM_ID, BEG_SEQ_ID, BEG_INS_CODE,
- END_ASYM_ID, END_SEQ_ID, END_INS_CODE,
- };
+ "_struct_sheet_range.end_auth_asym_id",
+ "_struct_sheet_range.end_auth_seq_id",
+ "_struct_sheet_range.pdbx_end_PDB_ins_code", };
+ final static byte[] structSheetRangeFieldMap = { BEG_ASYM_ID, BEG_SEQ_ID,
+ BEG_INS_CODE, END_ASYM_ID, END_SEQ_ID, END_INS_CODE, };
+
void processStructSheetRangeLoopBlock() throws Exception {
int[] fieldTypes = new int[100]; // should be enough
- boolean[] propertyReferenced =
- new boolean[STRUCT_SHEET_RANGE_PROPERTY_MAX];
+ boolean[] propertyReferenced = new
boolean[STRUCT_SHEET_RANGE_PROPERTY_MAX];
int fieldCount = parseLoopParameters(structSheetRangeFields,
- structSheetRangeFieldMap,
- fieldTypes,
- propertyReferenced);
- for (int i = STRUCT_SHEET_RANGE_PROPERTY_MAX; --i > 1; )
- if (! propertyReferenced[i]) {
+ structSheetRangeFieldMap, fieldTypes, propertyReferenced);
+ for (int i = STRUCT_SHEET_RANGE_PROPERTY_MAX; --i > 1;)
+ if (!propertyReferenced[i]) {
logger.log("?que? missing _struct_conf property:" + i);
skipLoopData();
return;
}
- for (; line != null &&
- (line = line.trim()).length() > 0 &&
- line.charAt(0) != '#';
- line = reader.readLine()) {
+ for (; line != null && (line = line.trim()).length() > 0
+ && line.charAt(0) != '#'; line = reader.readLine()) {
tokenizer.setString(line);
Structure structure = new Structure();
structure.structureType = "sheet";
-
+
for (int i = 0; i < fieldCount; ++i) {
- if (! tokenizer.hasMoreTokens())
- tokenizer.setString(reader.readLine());
+ if (!tokenizer.hasMoreTokens())
+ tokenizer.setStringNextLine(reader);
String field = tokenizer.nextToken();
char firstChar = field.charAt(0);
switch (fieldTypes[i]) {
case BEG_ASYM_ID:
- structure.startChainID = getChainIdFromStrandMap(firstChar);
+ structure.startChainID = (firstChar == '.' || firstChar == '?') ? ' '
+ : firstChar;
break;
case BEG_SEQ_ID:
structure.startSequenceNumber = parseInt(field);
break;
case BEG_INS_CODE:
- structure.startInsertionCode =
- (firstChar == '.' || firstChar == '?') ? ' ' : firstChar;
+ structure.startInsertionCode = (firstChar == '.' || firstChar ==
'?') ? ' '
+ : firstChar;
break;
case END_ASYM_ID:
- structure.endChainID = getChainIdFromStrandMap(firstChar);
+ structure.endChainID = (firstChar == '.' || firstChar == '?') ? ' '
+ : firstChar;
break;
case END_SEQ_ID:
structure.endSequenceNumber = parseInt(field);
break;
case END_INS_CODE:
- structure.endInsertionCode =
- (firstChar == '.' || firstChar == '?') ? ' ' : firstChar;
+ structure.endInsertionCode = (firstChar == '.' || firstChar == '?')
? ' '
+ : firstChar;
break;
}
}
@@ -837,256 +740,71 @@
}
////////////////////////////////////////////////////////////////
- // strand data
+ // symmetry operations
////////////////////////////////////////////////////////////////
- final static byte STRUCT_ASYM_ID = 1;
- final static byte STRUCT_BLANK_CHAIN_ID = 2;
- final static byte STRUCT_PROPERTY_MAX = 3;
+ final static byte SYMOP_XYZ = 1;
+ final static byte SYM_EQUIV_XYZ = 2;
+ final static byte SYMMETRY_OPERATIONS_PROPERTY_MAX = 3;
- final static String[] structAsymNames =
- {"_struct_asym.id", "_struct_asym.pdbx_blank_PDB_chainid_flag"};
+ final static String[] symmetryOperationsFields = {
+ "_space_group_symop_operation_xyz", "_symmetry_equiv_pos_as_xyz", };
- final static byte[] structAsymMap = {
- STRUCT_ASYM_ID, STRUCT_BLANK_CHAIN_ID
- };
+ final static byte[] symmetryOperationsFieldMap = { SYMOP_XYZ, SYM_EQUIV_XYZ,
};
- static {
- if (structAsymMap.length != structAsymNames.length)
- structAsymNames[100] = "explode";
- }
-
- private void addOrUpdateStrandInfo(Strand strand) {
- logger.log("Found only one chain", strand.chainID);
- if (strandsMap.containsKey(strand.chainID)) {
- Strand prevStrand = (Strand)strandsMap.get(strand.chainID);
- if (strand.authorID != null) prevStrand.authorID = strand.authorID;
- if (prevStrand.isBlank != null) prevStrand.isBlank = strand.isBlank;
- } else {
- strandsMap.put(strand.chainID, strand);
+ void processSymmetryOperationsLoopBlock() throws Exception {
+ int[] fieldTypes = new int[100]; // should be enough
+ boolean[] propertyReferenced = new
boolean[SYMMETRY_OPERATIONS_PROPERTY_MAX];
+ int fieldCount = parseLoopParameters(symmetryOperationsFields,
+ symmetryOperationsFieldMap, fieldTypes, propertyReferenced);
+ int nRefs = 0;
+ for (int i = SYMMETRY_OPERATIONS_PROPERTY_MAX; --i > 1;)
+ if (propertyReferenced[i])
+ nRefs++;
+ if (nRefs != 1) {
+ logger
+ .log("?que? _symmetry_equiv or _space_group_symop property not
found");
+ skipLoopData();
+ return;
}
- }
- private void processStructAsymBlock() throws Exception {
- // logger.log("processAtomSiteLoopBlock()-------------------------");
- int[] fieldTypes = new int[10]; // should be enough
- boolean[] structPropertyReferenced = new boolean[STRUCT_PROPERTY_MAX];
- Object[] results = parseAndProcessStructParameters(
- structAsymNames, structAsymMap,
- fieldTypes, structPropertyReferenced);
- int fieldCount = ((Integer)results[0]).intValue();
- Strand struct = ((Strand)results[1]);
- // now that headers are parsed, check to see if we want
- // cartesian or fractional coordinates;
- if (struct != null) {
- /* Then this syntax was found:
- * _struct_asym.id A
- * _struct_asym.pdbx_blank_PDB_chainid_flag Y
- * _struct_asym.pdbx_modified N
- * _struct_asym.entity_id 1
- * _struct_asym.details ?
- * #
- */
- addOrUpdateStrandInfo(struct);
- } else {
- /* Then the 'normal' _loop format was found. */
- logger.log("Found multiple chains... parsing them now");
- for (; line != null; line = reader.readLine()) {
- int lineLength = line.length();
- if (lineLength == 0)
- break;
- char chFirst = line.charAt(0);
- if (chFirst == '#' ||
- chFirst == '_' ||
- line.startsWith("loop_") ||
- line.startsWith("data_"))
- break;
- if (chFirst == ' ') {
- int i;
- for (i = lineLength; --i >= 0 && line.charAt(i) == ' '; ) {
- }
- if (i < 0)
- break;
+ for (; line != null; line = reader.readLine()) {
+ int lineLength = line.length();
+ if (lineLength == 0)
+ break;
+ char chFirst = line.charAt(0);
+ if (chFirst == '#' || chFirst == '_' || line.startsWith("loop_")
+ || line.startsWith("data_"))
+ break;
+ if (chFirst == ' ') {
+ int i;
+ for (i = lineLength; --i >= 0 && line.charAt(i) == ' ';) {
}
- // logger.log("line:" + line);
- // logger.log("of length = " + line.length());
- if (line.length() == 1)
- logger.log("char value is " + (chFirst + 0));
- tokenizer.setString(line);
- // logger.log("reading an atom");
- struct = new Strand();
- for (int i = 0; i < fieldCount; ++i) {
- if (! tokenizer.hasMoreTokens())
- tokenizer.setString(reader.readLine());
- String field = tokenizer.nextToken();
- if (field == null)
- logger.log("field == null!");
- switch (fieldTypes[i]) {
- case STRUCT_ASYM_ID:
- struct.chainID = field;
- break;
- case STRUCT_BLANK_CHAIN_ID:
- struct.isBlank = "Y".equals(field) ? Boolean.TRUE : Boolean.FALSE;
- break;
- }
- }
- addOrUpdateStrandInfo(struct);
+ if (i < 0)
+ break;
}
- }
- }
-
- ////////////////////////////////////////////////////////////////
- // poly sequence scheme data
- ////////////////////////////////////////////////////////////////
-
- final static byte POLYSEQ_ASYM_ID = 1;
- final static byte POLYSEQ_PDB_STRAND_ID = 2;
- final static byte POLYSEQ_PROPERTY_MAX = 3;
-
- final static String[] polySeqFields =
- {"_pdbx_poly_seq_scheme.asym_id",
- "_pdbx_poly_seq_scheme.pdb_strand_id"};
-
- final static byte[] polySeqMap = {
- POLYSEQ_ASYM_ID, POLYSEQ_PDB_STRAND_ID
- };
-
- static {
- if (polySeqMap.length != polySeqFields.length)
- polySeqFields[100] = "explode";
- }
-
- private void processPolySeqSchemeLoopBlock() throws Exception {
- int[] fieldTypes = new int[100]; // should be enough
- boolean[] propertyReferenced =
- new boolean[POLYSEQ_PROPERTY_MAX];
- int fieldCount = parseLoopParameters(polySeqFields,
- polySeqMap, fieldTypes, propertyReferenced);
- for (int i = POLYSEQ_PROPERTY_MAX; --i > 1; )
- if (! propertyReferenced[i]) {
- logger.log("?que? missing _pdbx_poly_seq_scheme property:" + i);
- skipLoopData();
- return;
- }
-
- String lastChainID = "XXXXX";
- for (; line != null &&
- (line = line.trim()).length() > 0 &&
- line.charAt(0) != '#';
- line = reader.readLine()) {
tokenizer.setString(line);
- Strand strand = new Strand();
+
for (int i = 0; i < fieldCount; ++i) {
- if (! tokenizer.hasMoreTokens())
- tokenizer.setString(reader.readLine());
+ if (!tokenizer.hasMoreTokens())
+ tokenizer.setStringNextLine(reader);
String field = tokenizer.nextToken();
+ if (field == null)
+ logger.log("field == null!");
switch (fieldTypes[i]) {
- case POLYSEQ_ASYM_ID:
- strand.chainID = field;
- break;
- case POLYSEQ_PDB_STRAND_ID:
- if (field.charAt(0) == '?') {
- strand.authorID = null;
- } else {
- strand.authorID = field;
- }
- break;
+ case SYMOP_XYZ:
+ case SYM_EQUIV_XYZ:
+/* 10.x only
+ * if (!atomSetCollection.addSymmetry(field))
+ logger.log("Skipping symmetry operation " + field);
+*/
+break;
}
}
- // OK, we're only interested in the chain IDs
- // hence we only parse the first AA in a chain
- if (lastChainID.equals(strand.chainID)) {
- // skip
- } else {
- addOrUpdateStrandInfo(strand);
- lastChainID = strand.chainID;
- }
}
- logger.log("Done reading _loop Poly Seq Scheme");
- Iterator strands = strandsMap.values().iterator();
- while (strands.hasNext()) {
- Strand strand = (Strand)strands.next();
- logger.log(strand.toString());
- }
}
////////////////////////////////////////////////////////////////
- // non poly scheme data
- ////////////////////////////////////////////////////////////////
-
- final static byte NONPOLY_ASYM_ID = 1;
- final static byte NONPOLY_PDB_STRAND_ID = 2;
- final static byte NONPOLY_PROPERTY_MAX = 3;
-
- final static String[] nonPolyFields =
- {"_pdbx_nonpoly_scheme.asym_id",
- "_pdbx_nonpoly_scheme.pdb_strand_id"};
-
- final static byte[] nonPolyMap = {
- POLYSEQ_ASYM_ID, POLYSEQ_PDB_STRAND_ID
- };
-
- static {
- if (nonPolyMap.length != nonPolyFields.length)
- nonPolyFields[100] = "explode";
- }
-
- private void processNonPolySchemeLoopBlock() throws Exception {
- int[] fieldTypes = new int[100]; // should be enough
- boolean[] propertyReferenced =
- new boolean[NONPOLY_PROPERTY_MAX];
- int fieldCount = parseLoopParameters(nonPolyFields,
- polySeqMap, fieldTypes, propertyReferenced);
- for (int i = NONPOLY_PROPERTY_MAX; --i > 1; )
- if (! propertyReferenced[i]) {
- logger.log("?que? missing _pdbx_nonpoly_scheme property:" + i);
- skipLoopData();
- return;
- }
-
- String lastChainID = "XXXXX";
- for (; line != null &&
- (line = line.trim()).length() > 0 &&
- line.charAt(0) != '#';
- line = reader.readLine()) {
- tokenizer.setString(line);
- Strand strand = new Strand();
- for (int i = 0; i < fieldCount; ++i) {
- if (! tokenizer.hasMoreTokens())
- tokenizer.setString(reader.readLine());
- String field = tokenizer.nextToken();
- switch (fieldTypes[i]) {
- case NONPOLY_ASYM_ID:
- strand.chainID = field;
- break;
- case NONPOLY_PDB_STRAND_ID:
- if (field.charAt(0) == '?') {
- strand.authorID = null;
- } else {
- strand.authorID = field;
- }
- break;
- }
- }
- // OK, we're only interested in the chain IDs
- // hence we only parse the first AA in a chain
- if (lastChainID.equals(strand.chainID)) {
- // skip
- } else {
- addOrUpdateStrandInfo(strand);
- lastChainID = strand.chainID;
- }
- }
- logger.log("Done reading _loop NonPoly Scheme");
- Iterator strands = strandsMap.values().iterator();
- while (strands.hasNext()) {
- Strand strand = (Strand)strands.next();
- logger.log(strand.toString());
- }
- }
-
-
- ////////////////////////////////////////////////////////////////
// special tokenizer class
////////////////////////////////////////////////////////////////
@@ -1142,7 +860,7 @@
* Specifications," J. Chem. Info. Comp. Sci., 34, 505-508.
*</p>
*/
-
+
static class RidiculousFileFormatTokenizer {
String str;
int ich;
@@ -1156,6 +874,27 @@
ich = 0;
}
+ void setStringNextLine(BufferedReader reader) throws Exception {
+ String str = reader.readLine();
+ if (str == null)
+ str = "";
+
+ if (str.length() > 0 && str.charAt(0) == ';') {
+
+ String newline = '\1' + str.substring(1);
+ str = "";
+ while (newline != null) {
+ if (newline.startsWith(";")) {
+ str += newline.substring(1) + '\1';
+ break;
+ }
+ str += newline + "\n";
+ newline = reader.readLine();
+ }
+ }
+ setString(str);
+ }
+
boolean hasMoreTokens() {
char ch;
while (ich < cch && ((ch = str.charAt(ich)) == ' ' || ch == '\t'))
@@ -1171,7 +910,7 @@
return null;
int ichStart = ich;
char ch = str.charAt(ichStart);
- if (ch != '\'' && ch != '"') {
+ if (ch != '\'' && ch != '"' && ch != '\1') {
while (ich < cch && (ch = str.charAt(ich)) != ' ' && ch != '\t')
++ich;
return str.substring(ichStart, ich);
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