From e8db20b697ceb79accea34d6d7041951e3670931 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Mon, 10 Sep 2018 11:07:42 +0200
Subject: [PATCH] mmCIF reader fix: removed restrictions on data block
identifier.
---
modules/io/src/mol/mmcif_reader.cc | 16 +---------------
modules/io/src/mol/mmcif_reader.hh | 10 +---------
modules/io/tests/test_mmcif_reader.cc | 24 ------------------------
3 files changed, 2 insertions(+), 48 deletions(-)
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 905e28442..b473c96ca 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -97,26 +97,12 @@ void MMCifReader::SetRestrictChains(const String& restrict_chains)
restrict_chains_ = restrict_chains;
}
-bool MMCifReader::IsValidPDBIdent(const StringRef& pdbid)
-{
- if (pdbid.length() == PDBID_LEN && isdigit(pdbid[0])) {
- return true;
- }
- return false;
-}
-
bool MMCifReader::OnBeginData(const StringRef& data_name)
{
LOG_DEBUG("MCIFFReader: " << profile_);
Profile profile_import("MMCifReader::OnBeginData");
- // check for PDB id
- if (!this->IsValidPDBIdent(data_name)) {
- throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
- "No valid PDB id found for data block, read instead \'"
- + data_name.str() + "\'",
- this->GetCurrentLinenum()));
- }
+ // IDs in mmCIF files can be any string, so no restrictions here
this->ClearState();
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index edd249f38..163972b60 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -187,13 +187,6 @@ protected:
}
} // tested
- /// \brief Check a PDB id to be of length 4 and start with a digit
- ///
- /// \param pdbid putative PDB id
- ///
- /// \return true for a valid id, false otherwise
- bool IsValidPDBIdent(const StringRef& pdbid);
-
/// \brief fetch values identifying atoms
///
/// \param[in] columns data row
@@ -353,8 +346,7 @@ protected:
private:
/// \enum magic numbers of this class
typedef enum {
- PDBID_LEN=4, ///< length of a PDB id
- MAX_ITEMS_IN_ROW=18, ///< count for possible items in a loop row
+ MAX_ITEMS_IN_ROW=18 ///< count for possible items in a loop row
} MMCifMagicNos;
/// \enum items of the atom_site category
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index 69210a1b9..e4129c2ab 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -51,7 +51,6 @@ public:
using MMCifReader::OnBeginLoop;
using MMCifReader::OnEndData;
- using MMCifReader::IsValidPDBIdent;
using MMCifReader::ParseAtomIdent;
using MMCifReader::ParseAndAddAtom;
using MMCifReader::ParseEntity;
@@ -113,29 +112,6 @@ conop::CompoundLibPtr SetDefaultCompoundLib() {
BOOST_AUTO_TEST_SUITE( io );
-BOOST_AUTO_TEST_CASE(mmcif_isvalidpdbident)
-{
- mol::EntityHandle eh=mol::CreateEntity();
-
- // on changing the tests for a PDB id in mmcif files, extend this unit test
- BOOST_TEST_MESSAGE(" Running mmcif_isvalidpdbident tests...");
- std::ifstream s("testfiles/mmcif/atom_site.mmcif");
- TestMMCifReaderProtected tmmcif_p(s, eh);
- StringRef id = StringRef("1FOO", 4);
- BOOST_TEST_MESSAGE(" Testing valid id ('"+ id.str() +"')...");
- BOOST_CHECK(tmmcif_p.IsValidPDBIdent(id));
- BOOST_TEST_MESSAGE(" done.");
- id = StringRef("this is to long for a PDB id", 28);
- BOOST_TEST_MESSAGE(" Testing oversized PDB id ('"+ id.str() +"')...");
- BOOST_CHECK(!tmmcif_p.IsValidPDBIdent(id));
- BOOST_TEST_MESSAGE(" done.");
- id = StringRef("nFOO", 4);
- BOOST_TEST_MESSAGE(" Testing PDB id with missing number ('"
- + id.str() + "')...");
- BOOST_CHECK(!tmmcif_p.IsValidPDBIdent(id));
- BOOST_TEST_MESSAGE(" done.");
-}
-
BOOST_AUTO_TEST_CASE(mmcif_trystoreidx)
{
mol::EntityHandle eh = mol::CreateEntity();
--
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