From 3cbc89aa757c388877771a47b8bd84aa1440fe9c Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Fri, 16 Sep 2011 23:15:53 +0200
Subject: [PATCH] fixes and cleanups for mmCIF parser
---
modules/io/src/mol/mmcif_reader.cc | 14 +++++++-------
modules/io/src/mol/mmcif_reader.hh | 2 +-
2 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 1c2ae5a2d..cf4221f3b 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -181,7 +181,7 @@ bool MMCifParser::OnBeginLoop(const StarLoopDesc& header)
indices_[ABSTRACT_ID_CAS] = header.GetIndex("abstract_id_CAS");
indices_[BOOK_ID_ISBN] = header.GetIndex("book_id_ISBN");
indices_[BOOK_TITLE] = header.GetIndex("book_title");
- indices_[JOURNAL_FULL] = header.GetIndex("journal_full");
+ indices_[JOURNAL_ABBREV] = header.GetIndex("journal_abbrev");
indices_[YEAR] = header.GetIndex("year");
indices_[TITLE] = header.GetIndex("title");
indices_[JOURNAL_VOLUME] = header.GetIndex("journal_volume");
@@ -645,7 +645,7 @@ String MMCifParser::ConvertSEQRES(const String& seqres,
if (tlc!="UNK") {
LOG_WARNING("unknown residue '" << tlc << "' in SEQRES record. "
- "Setting one-letter-code to '?'");
+ "Setting one-letter-code to 'X'");
}
can_seqres.push_back('X');
continue;
@@ -680,16 +680,16 @@ void MMCifParser::ParseCitation(const std::vector<StringRef>& columns)
cit.SetPublishedIn(columns[indices_[BOOK_TITLE]].str());
}
}
- if (indices_[JOURNAL_FULL] != -1) {
- if (columns[indices_[JOURNAL_FULL]] != StringRef(".", 1)) {
+ if (indices_[JOURNAL_ABBREV] != -1) {
+ if (columns[indices_[JOURNAL_ABBREV]] != StringRef(".", 1)) {
if (cit.GetPublishedIn().length() > 0) {
throw IOException(this->FormatDiagnostic(STAR_DIAG_WARNING,
"citation.book_title already occupies the 'published_in' field of this citation, cannot add " +
- columns[indices_[JOURNAL_FULL]].str() +
+ columns[indices_[JOURNAL_ABBREV]].str() +
".",
this->GetCurrentLinenum()));
} else {
- cit.SetPublishedIn(columns[indices_[JOURNAL_FULL]].str());
+ cit.SetPublishedIn(columns[indices_[JOURNAL_ABBREV]].str());
}
}
}
@@ -713,7 +713,7 @@ void MMCifParser::ParseCitation(const std::vector<StringRef>& columns)
}
if (indices_[YEAR] != -1) {
if (columns[indices_[YEAR]][0]!='?') {
- cit.SetPubMed(this->TryGetInt(columns[indices_[YEAR]], "citation.year"));
+ cit.SetYear(this->TryGetInt(columns[indices_[YEAR]], "citation.year"));
}
}
if (indices_[TITLE] != -1) {
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index 740a93132..ee63212a7 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -320,7 +320,7 @@ private:
ABSTRACT_ID_CAS, ///< CAS identifier
BOOK_ID_ISBN, ///< ISBN code assigned, if book cited
BOOK_TITLE, ///< title of book storing the citation
- JOURNAL_FULL, ///< full journal title for articles
+ JOURNAL_ABBREV, ///< abbreviated journal title for articles
JOURNAL_VOLUME, ///< volume of cited journal
PAGE_FIRST, ///< first page of citation
PAGE_LAST, ///< last page of citation
--
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