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Fix for issue 517 #541

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Merged
andreasprlic merged 5 commits into from
Jul 28, 2016
Merged

Fix for issue 517 #541

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bdca0e1
Now testing seqres groups in roundtrip
josemduarte Jul 26, 2016
e4cf7f8
Fixing #517
josemduarte Jul 27, 2016
fefb03d
Merge branch 'master' into fixIssue517
josemduarte Jul 27, 2016
4fa6833
Fixing issue introduced in PR #537
josemduarte Jul 27, 2016
347a8fc
Replacing the very old 1tap.pdb so that test logs aren't so long
josemduarte Jul 28, 2016
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Fixing issue introduced in PR #537
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@josemduarte
josemduarte committed Jul 27, 2016
commit 4fa68339c0a2893f0cc7496176d75a5cfd3ecdbf
9 changes: 8 additions & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1836,6 +1836,7 @@ private void pdb_ATOM_Handler(String line) {
logger.warn("Element column was empty for atom {} {}. Assigning atom element "
+ "from Chemical Component Dictionary information", fullname.trim(), pdbnumber);
} else {

try {
element = Element.valueOfIgnoreCase(elementSymbol);
guessElement = false;
Expand Down Expand Up @@ -1863,7 +1864,13 @@ private void pdb_ATOM_Handler(String line) {
logger.warn("Atom name {} was not found in the Chemical Component Dictionary information of {}. "
+ "Assigning generic element R to it", fullname.trim(), currentGroup.getPDBName());
} else {
element = Element.valueOfIgnoreCase(elementSymbol);
try {
element = Element.valueOfIgnoreCase(elementSymbol);
} catch (IllegalArgumentException e) {
// this can still happen for cases like UNK
logger.warn("Element symbol {} found in chemical component dictionary for Atom {} {} could not be recognised as a known element. "
+ "Assigning generic element R to it", elementSymbol, fullname.trim(), pdbnumber);
}
}
} else {
logger.warn("Chemical Component Dictionary information was not found for Atom name {}. "
Expand Down