From 640bb00efa2330ea4bab131488d4adc8f713fde3 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Fri, 23 Jan 2015 11:33:06 +0100
Subject: [PATCH] Dealing with PDB setting some mmCIF values to ?
---
modules/io/src/mol/mmcif_reader.cc | 33 ++++++++++++++++++++++--------
1 file changed, 24 insertions(+), 9 deletions(-)
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 52cd7e1ae..d6af7a258 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -750,13 +750,18 @@ void MMCifReader::ParseCitation(const std::vector<StringRef>& columns)
// just add info
cit.SetID(columns[indices_[CITATION_ID]].str());
if (indices_[ABSTRACT_ID_CAS] != -1) {
- cit.SetCAS(columns[indices_[ABSTRACT_ID_CAS]].str());
+ if (columns[indices_[ABSTRACT_ID_CAS]][0]!='?') {
+ cit.SetCAS(columns[indices_[ABSTRACT_ID_CAS]].str());
+ }
}
if (indices_[BOOK_ID_ISBN] != -1) {
- cit.SetISBN(columns[indices_[BOOK_ID_ISBN]].str());
+ if (columns[indices_[BOOK_ID_ISBN]][0]!='?') {
+ cit.SetISBN(columns[indices_[BOOK_ID_ISBN]].str());
+ }
}
if (indices_[BOOK_TITLE] != -1) {
- if (columns[indices_[BOOK_TITLE]] != StringRef(".", 1)) {
+ if ((columns[indices_[BOOK_TITLE]] != StringRef(".", 1)) &&
+ (columns[indices_[BOOK_TITLE]][0]!='?')) {
cit.SetPublishedIn(columns[indices_[BOOK_TITLE]].str());
}
}
@@ -774,16 +779,24 @@ void MMCifReader::ParseCitation(const std::vector<StringRef>& columns)
}
}
if (indices_[JOURNAL_VOLUME] != -1) {
- cit.SetVolume(columns[indices_[JOURNAL_VOLUME]].str());
+ if (columns[indices_[JOURNAL_VOLUME]][0]!='?') {
+ cit.SetVolume(columns[indices_[JOURNAL_VOLUME]].str());
+ }
}
if (indices_[PAGE_FIRST] != -1) {
- cit.SetPageFirst(columns[indices_[PAGE_FIRST]].str());
+ if (columns[indices_[PAGE_FIRST]][0]!='?') {
+ cit.SetPageFirst(columns[indices_[PAGE_FIRST]].str());
+ }
}
if (indices_[PAGE_LAST] != -1) {
- cit.SetPageLast(columns[indices_[PAGE_LAST]].str());
+ if (columns[indices_[PAGE_LAST]][0]!='?') {
+ cit.SetPageLast(columns[indices_[PAGE_LAST]].str());
+ }
}
if (indices_[PDBX_DATABASE_ID_DOI] != -1) {
- cit.SetDOI(columns[indices_[PDBX_DATABASE_ID_DOI]].str());
+ if (columns[indices_[PDBX_DATABASE_ID_DOI]][0]!='?') {
+ cit.SetDOI(columns[indices_[PDBX_DATABASE_ID_DOI]].str());
+ }
}
if (indices_[PDBX_DATABASE_ID_PUBMED] != -1) {
if (columns[indices_[PDBX_DATABASE_ID_PUBMED]][0]!='?') {
@@ -1072,8 +1085,10 @@ void MMCifReader::ParseStruct(const std::vector<StringRef>& columns)
}
if (indices_[PDBX_FORMULA_WEIGHT] != -1) {
- details.SetMass(this->TryGetReal(columns[indices_[PDBX_FORMULA_WEIGHT]],
- "struct.pdbx_formula_weight"));
+ if (columns[indices_[PDBX_FORMULA_WEIGHT]][0] != '?') {
+ details.SetMass(this->TryGetReal(columns[indices_[PDBX_FORMULA_WEIGHT]],
+ "struct.pdbx_formula_weight"));
+ }
}
if (indices_[PDBX_FORMULA_WEIGHT_METHOD] != -1) {
--
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