Skip to content

Commit

Permalink
More robust parsing of atom symbols.
Browse files Browse the repository at this point in the history
  • Loading branch information
@johnmay
johnmay committed Oct 19, 2016
1 parent c887ff3 commit f65dcc9
Showing 1 changed file with 29 additions and 49 deletions.
78 changes: 29 additions & 49 deletions storage/pdb/src/main/java/org/openscience/cdk/io/PDBReader.java
View file
Expand Up @@ -104,8 +104,6 @@ public class PDBReader extends DefaultChemObjectReader {
*/
private List<IBond> bondsFromConnectRecords;

private static AtomTypeFactory pdbFactory;

/**
* A mapping between HETATM 3-letter codes + atomNames to CDK atom type
* names; for example "RFB.N13" maps to "N.planar3".
Expand Down Expand Up @@ -139,7 +137,6 @@ public PDBReader(InputStream oIn) {
public PDBReader(Reader oIn) {
_oInput = new BufferedReader(oIn);
initIOSettings();
pdbFactory = null;
hetDictionary = null;
cdkAtomTypeFactory = null;
}
Expand Down Expand Up @@ -194,16 +191,6 @@ public boolean accepts(Class<? extends IChemObject> classObject) {
@Override
public <T extends IChemObject> T read(T oObj) throws CDKException {
if (oObj instanceof IChemFile) {
if (pdbFactory == null) {
try {
pdbFactory = AtomTypeFactory.getInstance("org/openscience/cdk/config/data/pdb_atomtypes.xml",
((IChemFile) oObj).getBuilder());
} catch (Exception exception) {
logger.debug(exception);
throw new CDKException("Could not setup list of PDB atom types! " + exception.getMessage(),
exception);
}
}
return (T) readChemFile((IChemFile) oObj);
} else {
throw new CDKException("Only supported is reading of ChemFile objects.");
Expand Down Expand Up @@ -483,7 +470,7 @@ else if ("HELIX ".equalsIgnoreCase(cCol)) {
} // ignore all other commands
}
} while (_oInput.ready() && (cRead != null));
} catch (IOException | IllegalArgumentException e) {
} catch (IOException | IllegalArgumentException | CDKException e) {
logger.error("Found a problem at line:");
logger.error(cRead);
logger.error("01234567890123456789012345678901234567890123456789012345678901234567890123456789");
Expand Down Expand Up @@ -559,6 +546,20 @@ private boolean createBondsWithRebondTool(IAtomContainer molecule) {
return true;
}

private static boolean isUpper(char c) {
return c >= 'A' && c <= 'Z';
}

private String parseAtomSymbol(String str) {
if (str == null || str.isEmpty())
return null;
int pos = 0;
final int len = str.length();
while (pos < len && isUpper(str.charAt(pos)))
pos++;
return str.substring(0, pos);
}

/**
* Creates an <code>Atom</code> and sets properties to their values from
* the ATOM or HETATM record. If the line is shorter than 80 characters, the
Expand All @@ -569,7 +570,7 @@ private boolean createBondsWithRebondTool(IAtomContainer molecule) {
* @return the <code>Atom</code> created from the record.
* @throws RuntimeException if the line is too short (less than 59 characters).
*/
private PDBAtom readAtom(String cLine, int lineLength) {
private PDBAtom readAtom(String cLine, int lineLength) throws CDKException {
// a line can look like (two in old format, then two in new format):
//
// 1 2 3 4 5 6 7
Expand All @@ -586,62 +587,41 @@ private PDBAtom readAtom(String cLine, int lineLength) {
if (lineLength < 59) {
throw new RuntimeException("PDBReader error during readAtom(): line too short");
}
String elementSymbol;
if (cLine.length() > 78) {
elementSymbol = cLine.substring(76, 78).trim();
if (elementSymbol.length() == 0) {
elementSymbol = cLine.substring(12, 14).trim();
}
} else {
elementSymbol = cLine.substring(12, 14).trim();
}

if (elementSymbol.length() == 2) {
// ensure that the second char is lower case
if (Character.isDigit(elementSymbol.charAt(0))) {
elementSymbol = elementSymbol.substring(1);
} else {
elementSymbol = elementSymbol.charAt(0) + elementSymbol.substring(1).toLowerCase();
}
}
boolean isHetatm = cLine.substring(0, 6).equals("HETATM");
String atomName = cLine.substring(12, 16).trim();
String resName = cLine.substring(17, 20).trim();
String symbol = parseAtomSymbol(atomName);

String rawAtomName = cLine.substring(12, 16).trim();
String resName = cLine.substring(17, 20).trim();
boolean isHetatm;
try {
IAtomType type = pdbFactory.getAtomType(resName + "." + rawAtomName);
elementSymbol = type.getSymbol();
isHetatm = false;
} catch (NoSuchAtomTypeException e) {
logger.error("Did not recognize PDB atom type: " + resName + "." + rawAtomName);
isHetatm = true;
}
PDBAtom oAtom = new PDBAtom(elementSymbol, new Point3d(Double.parseDouble(cLine.substring(30, 38)),
if (symbol == null)
handleError("Cannot parse symbol from " + atomName);

PDBAtom oAtom = new PDBAtom(symbol, new Point3d(Double.parseDouble(cLine.substring(30, 38)),
Double.parseDouble(cLine.substring(38, 46)), Double.parseDouble(cLine.substring(46, 54))));
if (useHetDictionary.isSet() && isHetatm) {
String cdkType = typeHetatm(resName, rawAtomName);
String cdkType = typeHetatm(resName, atomName);
oAtom.setAtomTypeName(cdkType);
if (cdkType != null) {
try {
cdkAtomTypeFactory.configure(oAtom);
} catch (CDKException cdke) {
logger.warn("Could not configure", resName, " ", rawAtomName);
logger.warn("Could not configure", resName, " ", atomName);
}
}
}

oAtom.setRecord(cLine);
oAtom.setSerial(Integer.parseInt(cLine.substring(6, 11).trim()));
oAtom.setName(rawAtomName.trim());
oAtom.setName(atomName.trim());
oAtom.setAltLoc(cLine.substring(16, 17).trim());
oAtom.setResName(resName);
oAtom.setChainID(cLine.substring(21, 22).trim());
oAtom.setResSeq(cLine.substring(22, 26).trim());
oAtom.setICode(cLine.substring(26, 27).trim());
if (useHetDictionary.isSet() && isHetatm) {
oAtom.setID(oAtom.getResName() + "." + rawAtomName);
oAtom.setID(oAtom.getResName() + "." + atomName);
} else {
oAtom.setAtomTypeName(oAtom.getResName() + "." + rawAtomName);
oAtom.setAtomTypeName(oAtom.getResName() + "." + atomName);
}
if (lineLength >= 59) {
String frag = cLine.substring(54, Math.min(lineLength, 60)).trim();
Expand Down

0 comments on commit f65dcc9

Please sign in to comment.