From 5dcc9da4fee66d931d5e7319a6a836c2eea30ec9 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Thu, 27 Jul 2017 19:47:35 +0200
Subject: [PATCH] SCHWED-2589: improved error handling for messed up mmCIF
files.
---
modules/io/src/mol/mmcif_reader.cc | 14 +++++++++++---
1 file changed, 11 insertions(+), 3 deletions(-)
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 1c971ee2f..9d0fac194 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -357,6 +357,10 @@ bool MMCifReader::OnBeginLoop(const StarLoopDesc& header)
indices_[PARH_ORDINAL] = header.GetIndex("ordinal");
// TOCHECK: shouldn't ordinal be mandatory??
his_revision_ordinal_avail_ = (indices_[PARH_ORDINAL] != -1);
+ if (!his_revision_ordinal_avail_) {
+ LOG_WARNING("No 'pdbx_audit_revision_history.ordinal' items "
+ "found! The revision history will not have status entries!");
+ }
cat_available = true;
} else if (header.GetCategory()=="pdbx_audit_revision_details") {
// THIS IS FOR mmCIF versions >= 5
@@ -367,6 +371,10 @@ bool MMCifReader::OnBeginLoop(const StarLoopDesc& header)
indices_[PARD_REVISION_ORDINAL] = header.GetIndex("revision_ordinal");
// TOCHECK: shouldn't ordinal be mandatory??
det_revision_ordinal_avail_ = (indices_[PARD_REVISION_ORDINAL] != -1);
+ if (!det_revision_ordinal_avail_) {
+ LOG_WARNING("No 'pdbx_audit_revision_details.revision_ordinal' items "
+ "found! The revision history will not have status entries!");
+ }
cat_available = true;
} else if (header.GetCategory()=="pdbx_database_status") {
// THIS IS FOR mmCIF versions >= 5
@@ -1413,7 +1421,7 @@ void MMCifReader::ParsePdbxAuditRevisionHistory(
} else if (revision_dates_.empty()) {
num = 0;
} else {
- num = revision_dates_.begin()->first + 1;
+ num = revision_dates_.rbegin()->first + 1;
}
// get date
date = columns[indices_[PARH_REVISION_DATE]];
@@ -1432,7 +1440,7 @@ void MMCifReader::ParsePdbxAuditRevisionDetails(
} else if (revision_types_.empty()) {
num = 0;
} else {
- num = revision_types_.begin()->first + 1;
+ num = revision_types_.rbegin()->first + 1;
}
// get type
type = columns[indices_[PARD_TYPE]];
@@ -1797,7 +1805,7 @@ void MMCifReader::OnEndData()
// add revision history for new style mmCIFs (only if no old data there)
if (!database_PDB_rev_added_) {
- std::map<int, String>::const_iterator rd_it, rt_it;
+ std::map<int, String>::const_iterator rd_it;
for (rd_it = revision_dates_.begin(); rd_it != revision_dates_.end();
++rd_it) {
// look for status
--
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