Thanks to visit codestin.com
Credit goes to github.com

Skip to content

Check string bounds on PDB COMPND line. Fixes #870 #871

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 1 commit into from
Jul 13, 2022
Merged

Check string bounds on PDB COMPND line. Fixes #870 #871

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 5 additions & 2 deletions storage/pdb/src/main/java/org/openscience/cdk/io/PDBReader.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -394,8 +394,11 @@ private IChemFile readChemFile(IChemFile oFile) {
logger.warn("REMARK line found without any comment!");
}
} else if ("COMPND".equalsIgnoreCase(cCol)) {
String title = cRead.substring(10).trim();
oFile.setProperty(CDKConstants.TITLE, title);
if (cRead.length() > 10) {
String title = cRead.substring(10).trim();
if (!title.isEmpty())
oFile.setProperty(CDKConstants.TITLE, title);
}
}

/* ***********************************************************
Expand Down
18 changes: 18 additions & 0 deletions storage/pdb/src/test/java/org/openscience/cdk/io/PDBReaderTest.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -124,6 +124,24 @@ public void oldFormatNewFormatTest() throws Exception {
Assert.assertEquals("H", acNew.getAtom(0).getSymbol());
}

@Test
public void emptyFields() throws Exception {
String data = "HEADER\n" +
"TITLE\n" +
"COMPND\n" +
"KEYWDS\n" +
"EXPDTA\n" +
"AUTHOR\n" +
"REVDAT\n" +
"HET 1 13\n" +
"HETNAM\n" +
"FORMUL\n" +
"END\n";
IChemFile chemFile = getChemFileFromString(data);
IAtomContainer atomContainer = getFirstAtomContainer(chemFile, 1, 1, 1);
}


@Test
public void testAccepts() {
PDBReader reader = new PDBReader();
Expand Down