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Fix #703: Recover from empty structure files in PDB_CACHE_DIR #774

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Merged
sbliven merged 11 commits into from
Jun 18, 2018
Merged

Fix #703: Recover from empty structure files in PDB_CACHE_DIR #774

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5c1a335
Improving CathInstallation logging
sbliven Jun 4, 2018
4785d57
Add test for #703
sbliven Jun 4, 2018
c3cec91
Support initial comments in MMCif files (e.g. those generated by PyMOL)
sbliven Jun 8, 2018
b207d34
Make tests for #703 fail with an assertion
sbliven Jun 8, 2018
6ea9ae7
Re-download empty structure or chemical component structures
sbliven Sep 4, 2017
62fb2a4
Set and restore the ChemCompGroupFactory singleton
sbliven Jun 8, 2018
f5b325f
Incorporating suggestions from @josemduarte
sbliven Jun 12, 2018
13f267c
Add GlobalsHelper class to manage our global state
sbliven Jun 14, 2018
c1c3c30
Fix NullPointer when restoring global state
sbliven Jun 14, 2018
0c10a2e
Fix test failure due to PDB change
sbliven Jun 15, 2018
08ab3e1
Revert fix for mmcif files without auth_seq_id column
sbliven Jun 18, 2018
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Support initial comments in MMCif files (e.g. those generated by PyMOL)
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@sbliven
sbliven committed Jun 8, 2018
commit c3cec9187eae380878a462495cbb98dbfdcdce5e
3 changes: 3 additions & 0 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
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Original file line number Diff line number Diff line change
Expand Up @@ -212,6 +212,9 @@ public void parse(BufferedReader buf)

// the first line is a data_PDBCODE line, test if this looks like a mmcif file
line = buf.readLine();
while( line != null && (line.isEmpty() || line.startsWith(COMMENT_CHAR))) {
line = buf.readLine();
}
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@josemduarte josemduarte Jun 8, 2018

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Nice to handle comments in first line!

Is an empty first line also valid CIF?

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@sbliven sbliven Jun 12, 2018

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I think blank lines are permitted anywhere in CIF, but I could be wrong. I try to write permissive parsers. It seems like it shouldn't break the spec so we might as well be robust to it either way.

if (line == null || !line.startsWith(MMCIF_TOP_HEADER)){
logger.error("This does not look like a valid mmCIF file! The first line should start with 'data_', but is: '" + line+"'");
triggerDocumentEnd();
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