From 2cd8c57eba4c97951669ad84eb10be172a40763e Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Thu, 10 May 2012 20:06:40 +0200
Subject: [PATCH] store original pdb chain name as generic property
---
modules/io/src/mol/mmcif_reader.cc | 32 ++++++++++++++-------------
modules/io/src/mol/mmcif_reader.hh | 3 ++-
modules/io/tests/test_mmcif_reader.cc | 12 +++++-----
3 files changed, 26 insertions(+), 21 deletions(-)
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index c58c14c8d..d4a9e3140 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -342,7 +342,8 @@ mol::ResNum to_res_num(int num, char ins_code)
}
bool MMCifReader::ParseAtomIdent(const std::vector<StringRef>& columns,
- String& chain_name,
+ String& auth_chain_name,
+ String& cif_chain_name,
StringRef& res_name,
mol::ResNum& resnum,
bool& valid_res_num,
@@ -357,13 +358,11 @@ bool MMCifReader::ParseAtomIdent(const std::vector<StringRef>& columns,
}
}
// CHAIN ID
- if (auth_chain_id_) { // unit test different IDs
- chain_name = columns[indices_[AUTH_ASYM_ID]].str();
- } else {
- chain_name = columns[indices_[LABEL_ASYM_ID]].str();
- }
+ auth_chain_name = columns[indices_[AUTH_ASYM_ID]].str();
+ cif_chain_name = columns[indices_[LABEL_ASYM_ID]].str();
+
if (restrict_chains_.size() > 0 &&
- restrict_chains_.find(chain_name) == String::npos) {
+ restrict_chains_.find(cif_chain_name) == String::npos) {
return false;
}
@@ -398,7 +397,8 @@ void MMCifReader::ParseAndAddAtom(const std::vector<StringRef>& columns)
{
mol::XCSEditor editor=ent_handle_.EditXCS(mol::BUFFERED_EDIT); // potbl
char alt_loc=0;
- String chain_name;
+ String auth_chain_name;
+ String cif_chain_name;
StringRef res_name, atom_name;
mol::ResNum res_num(0);
bool valid_res_num = false;
@@ -416,7 +416,8 @@ void MMCifReader::ParseAndAddAtom(const std::vector<StringRef>& columns)
}
if (!this->ParseAtomIdent(columns,
- chain_name,
+ auth_chain_name,
+ cif_chain_name,
res_name,
res_num,
valid_res_num,
@@ -460,7 +461,7 @@ void MMCifReader::ParseAndAddAtom(const std::vector<StringRef>& columns)
if(!curr_chain_) { // unit test
update_chain=true;
update_residue=true;
- } else if(curr_chain_.GetName() != chain_name) { // unit test
+ } else if(curr_chain_.GetName() != cif_chain_name) { // unit test
update_chain=true;
update_residue=true;
}
@@ -471,12 +472,12 @@ void MMCifReader::ParseAndAddAtom(const std::vector<StringRef>& columns)
if (indices_[AUTH_SEQ_ID] != -1 &&
indices_[PDBX_PDB_INS_CODE] != -1) {
if (subst_res_id_ !=
- chain_name +
+ cif_chain_name +
columns[indices_[AUTH_SEQ_ID]].str() +
columns[indices_[PDBX_PDB_INS_CODE]].str()) {
update_residue=true;
- subst_res_id_ = chain_name +
+ subst_res_id_ = cif_chain_name +
columns[indices_[AUTH_SEQ_ID]].str() +
columns[indices_[PDBX_PDB_INS_CODE]].str();
}
@@ -490,10 +491,11 @@ void MMCifReader::ParseAndAddAtom(const std::vector<StringRef>& columns)
}
if(update_chain) { // unit test
- curr_chain_ = ent_handle_.FindChain(chain_name);
+ curr_chain_ = ent_handle_.FindChain(cif_chain_name);
if(!curr_chain_.IsValid()) { // unit test
- LOG_DEBUG("new chain " << chain_name);
- curr_chain_=editor.InsertChain(chain_name);
+ LOG_DEBUG("new chain " << cif_chain_name);
+ curr_chain_=editor.InsertChain(cif_chain_name);
+ curr_chain_.SetStringProp("pdb_auth_chain_name", auth_chain_name);
++chain_count_;
// store entity id
chain_id_pairs_.push_back(std::pair<mol::ChainHandle,String>(curr_chain_,
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index 06215f56b..e9ff3b893 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -202,7 +202,8 @@ protected:
/// \param[out] atom_name corresponds to label_atom_id
/// \param[out] alt_loc gets first letter of atom_site.label_alt_id
bool ParseAtomIdent(const std::vector<StringRef>& columns,
- String& chain_name,
+ String& auth_chain_name,
+ String& cif_chain_name,
StringRef& res_name,
mol::ResNum& resnum,
bool& valid_res_num,
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index b2294ba90..fff6bbb2e 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -644,7 +644,7 @@ BOOST_AUTO_TEST_CASE(mmcif_struct_ref)
BOOST_CHECK_EQUAL(seqs[1]->GetDBEnd(), 49);
MMCifInfoStructRefSeqDifs diffs=seqs[0]->GetDifs();
BOOST_CHECK_EQUAL(diffs.size(), 1);
- BOOST_CHECK_EQUAL(diffs[0]->GetRNum(), 91);
+ BOOST_CHECK_EQUAL(diffs[0]->GetSeqRNum(), 91);
BOOST_CHECK_EQUAL(diffs[0]->GetDetails(), "ENGINEERED MUTATION");
}
@@ -1091,7 +1091,8 @@ BOOST_AUTO_TEST_CASE(mmcif_parseatomident)
StarLoopDesc tmmcif_h;
TestMMCifReaderProtected tmmcif_p(s, eh, profile);
std::vector<StringRef> columns;
- String chain_name;
+ String cif_chain_name;
+ String auth_chain_name;
StringRef res_name;
mol::ResNum resnum(0);
bool valid_res_num = false;
@@ -1099,7 +1100,6 @@ BOOST_AUTO_TEST_CASE(mmcif_parseatomident)
StringRef atom_name;
BOOST_MESSAGE(" testing valid line");
- //tmmcif_p.ParseAtomIdent();
BOOST_MESSAGE(" done.");
// negative
//cols.push_back(StringRef("ATOM", 4));
@@ -1148,7 +1148,8 @@ BOOST_AUTO_TEST_CASE(mmcif_parseatomident)
columns.push_back(StringRef("25.369", 6)); // Cartn_x
columns.push_back(StringRef("30.691", 6)); // Cartn_y
columns.push_back(StringRef("11.795", 6)); // Cartn_z
- BOOST_CHECK_EQUAL(tmmcif_p.ParseAtomIdent(columns, chain_name, res_name,
+ BOOST_CHECK_EQUAL(tmmcif_p.ParseAtomIdent(columns, auth_chain_name,
+ cif_chain_name, res_name,
resnum, valid_res_num, atom_name,
alt_loc), true);
columns.pop_back();
@@ -1167,7 +1168,8 @@ BOOST_AUTO_TEST_CASE(mmcif_parseatomident)
columns.push_back(StringRef("25.369", 6)); // Cartn_x
columns.push_back(StringRef("30.691", 6)); // Cartn_y
columns.push_back(StringRef("11.795", 6)); // Cartn_z
- BOOST_CHECK_EQUAL(tmmcif_p.ParseAtomIdent(columns, chain_name, res_name,
+ BOOST_CHECK_EQUAL(tmmcif_p.ParseAtomIdent(columns, auth_chain_name,
+ cif_chain_name, res_name,
resnum, valid_res_num, atom_name,
alt_loc), false);
}
--
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