From 68899ae1d7285159c1c1e3025558fb9c8abf5803 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Thu, 16 May 2024 15:46:53 +0200
Subject: [PATCH] fix: SCHWED-6274 read SEQRES from entity_poly_seq
This commit additional drops more side-effects of the presence of a
seqres record by moving all the logic to the GetSeqRes function, rather
than being generated on the fly during parsing.
---
CHANGELOG.txt | 3 +
modules/io/doc/mmcif.rst | 26 +--
modules/io/pymod/__init__.py | 3 +-
modules/io/pymod/export_mmcif_io.cc | 6 +-
modules/io/src/mol/mmcif_info.hh | 3 +-
modules/io/src/mol/mmcif_reader.cc | 187 ++++++++----------
modules/io/src/mol/mmcif_reader.hh | 43 +---
modules/io/src/mol/mmcif_str.cc | 1 -
modules/io/tests/test_mmcif_reader.cc | 64 ------
.../io/tests/testfiles/mmcif/atom_site.mmcif | 9 +
.../alg/tests/testfiles/align_to_seqres.mmcif | 82 +++++++-
.../validate_segres_aln_breakage.mmcif | 81 +++++++-
.../validate_seqres_aln_connected.mmcif | 83 +++++++-
13 files changed, 364 insertions(+), 227 deletions(-)
diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index f3f863c14..0864bb6e6 100644
--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
@@ -8,6 +8,9 @@ Changes in Release x.x.x
* Added 'full_bs_search' argument in ligand scoring to optionally speed up
computations in large complexes.
the number of model binding sites
+ * SEQRES information is now read from the entity_poly_seq category in mmCIF.
+ The canonical as well as semi-canonical (with 3 letter-codes in bracket)
+ SEQRES are now available from the MMCifInfo object.
* Several bug fixes and improvements.
Changes in Release 2.7.0
diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index 91d6cda1f..43618968f 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -65,8 +65,7 @@ Notes:
It is added as string property named "pdb_auth_chain_name" to the
:class:`~ost.mol.ChainHandle`. The mapping is also stored in
:class:`MMCifInfo` as :meth:`~MMCifInfo.GetMMCifPDBChainTr` and
- :meth:`~MMCifInfo.GetPDBMMCifChainTr` if a non-empty SEQRES record exists for
- that chain (this should exclude ligands and water).
+ :meth:`~MMCifInfo.GetPDBMMCifChainTr` (the latter only for polymer chains).
* Molecular entities in mmCIF are identified by an ``entity.id``, which is
extracted from ``atom_site.label_entity_id`` for the first atom of the chain.
It is added as string property named "entity_id" to the
@@ -1417,16 +1416,21 @@ of the annotation available.
:class:`str`
- .. attribute:: seqres
+ .. attribute:: seqres_canonical
- SEQRES with gentle preprocessing - empty string if entity is not of type
- "polymer". By default, the :class:`ost.io.MMCifReader` reads the value of the
- ``_entity_poly.pdbx_seq_one_letter_code`` token. Copies all letters but
- searches a :class:`ost.conop.CompoundLib` for compound names in brackets.
- *seqres* gets an 'X' if no compound is found or the respective compound has
- one letter code '?'. Uses the one letter code of the found compound
- otherwise. So it's basically a canonical SEQRES with exactly one character
- per residue.
+ Canonical SEQRES - empty string if entity is not of type "polymer".
+ This contains the canonical sequence extracted from the
+ ``_entity_poly.pdbx_seq_one_letter_code_can`` data item.
+
+ :type: :class:`str`
+
+ .. attribute:: seqres_pdbx
+
+ PDBx SEQRES - empty string if entity is not of type "polymer".
+ This contains the sequence extracted from the
+ ``_entity_poly.pdbx_seq_one_letter_code`` data item.
+ Modifications and non-standard amino acids are represented by
+ their three letter code in brackets, e.g. "(MSE)"
:type: :class:`str`
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index 89c1c3c8e..66a518def 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -430,8 +430,7 @@ def LoadMMCIF(filename, fault_tolerant=None, calpha_only=None,
try:
ent = mol.CreateEntity()
reader = MMCifReader(filename, ent, prof)
- reader.read_seqres = seqres
-
+
# NOTE: to speed up things, we could introduce a restrict_chains parameter
# similar to the one in LoadPDB. Here, it would have to be a list/set
# of chain-name-strings.
diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index fa09b5bfa..aa6595bc2 100644
--- a/modules/io/pymod/export_mmcif_io.cc
+++ b/modules/io/pymod/export_mmcif_io.cc
@@ -107,7 +107,6 @@ void export_mmcif_io()
class_<MMCifReader, boost::noncopyable>("MMCifReader", init<const String&, EntityHandle&, const IOProfile&>())
.def("Parse", &MMCifReader::Parse)
.def("SetRestrictChains", &MMCifReader::SetRestrictChains)
- .def("SetReadCanonicalSeqRes", &MMCifReader::SetReadCanonicalSeqRes)
.def("GetSeqRes", &MMCifReader::GetSeqRes)
.def("GetInfo", make_function(&MMCifReader::GetInfo,
return_value_policy<copy_const_reference>()))
@@ -116,8 +115,6 @@ void export_mmcif_io()
return_value_policy<copy_const_reference>()),
&MMCifReader::SetRestrictChains)
.add_property("seqres", &MMCifReader::GetSeqRes)
- .add_property("read_seqres", &MMCifReader::GetReadSeqRes,
- &MMCifReader::SetReadSeqRes)
.add_property("info", make_function(&MMCifReader::GetInfo,
return_value_policy<copy_const_reference>()))
;
@@ -493,7 +490,8 @@ void export_mmcif_io()
.add_property("entity_poly_type", &MMCifEntityDesc::entity_poly_type)
.add_property("branched_type", &MMCifEntityDesc::branched_type)
.add_property("details", &MMCifEntityDesc::details)
- .add_property("seqres", &MMCifEntityDesc::seqres)
+ .add_property("seqres_canonical", &MMCifEntityDesc::seqres_canonical)
+ .add_property("seqres_pdbx", &MMCifEntityDesc::seqres_pdbx)
.add_property("mon_ids", &MMCifEntityDesc::mon_ids)
.add_property("hetero_num", &MMCifEntityDesc::hetero_num)
.add_property("hetero_ids", &MMCifEntityDesc::hetero_ids)
diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh
index c658af2b5..2892ae7c6 100644
--- a/modules/io/src/mol/mmcif_info.hh
+++ b/modules/io/src/mol/mmcif_info.hh
@@ -957,7 +957,8 @@ typedef struct {
String entity_poly_type; ///< value of _entity_poly.type
String branched_type; ///< value of _pdbx_entity_branch.type
String details; ///< description of this entity
- String seqres; ///< chain of monomers
+ String seqres_canonical; ///< _entity_poly.pdbx_seq_one_letter_code_can
+ String seqres_pdbx; ///< _entity_poly.pdbx_seq_one_letter_code
std::vector<String> mon_ids; ///< list of monomer names from _entity_poly_seq
std::vector<int> hetero_num; ///< res num of heterogeneous compounds
std::vector<String> hetero_ids;///< names of heterogeneous compounds
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 6ad799100..2a3fed856 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -59,15 +59,11 @@ void MMCifReader::Init()
atom_count_ = 0;
residue_count_ = 0;
auth_chain_id_ = false;
- seqres_can_ = false;
has_model_ = false;
restrict_chains_ = "";
subst_res_id_ = "";
curr_chain_ = mol::ChainHandle();
curr_residue_ = mol::ResidueHandle();
- seqres_ = seq::CreateSequenceList();
- read_seqres_ = true;
- warned_rule_based_ = false;
info_ = MMCifInfo();
}
@@ -80,7 +76,6 @@ void MMCifReader::ClearState()
atom_count_ = 0;
category_ = DONT_KNOW;
warned_name_mismatch_ = false;
- seqres_ = seq::CreateSequenceList();
info_ = MMCifInfo();
entity_desc_map_.clear();
authors_map_.clear();
@@ -737,7 +732,8 @@ MMCifEntityDescMap::iterator MMCifReader::GetEntityDescMapIterator(
.entity_poly_type = "",
.branched_type = "",
.details="",
- .seqres="",
+ .seqres_canonical="",
+ .seqres_pdbx="",
.mon_ids=std::vector<String>(),
.hetero_num=std::vector<int>(),
.hetero_ids=std::vector<String>()};
@@ -785,93 +781,17 @@ void MMCifReader::ParseEntityPoly(const std::vector<StringRef>& columns)
edm_it->second.entity_poly_type = columns[indices_[EP_TYPE]].str();
}
- // store seqres
- if (edm_it->second.seqres.length() > 0) {
- throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
- "entity_poly.pdbx_seq_one_letter_code[_can] clash: sequence for entry '" +
- columns[indices_[ENTITY_ID]].str() +
- "' is already set to '" +
- edm_it->second.seqres + "'.",
- this->GetCurrentLinenum()));
+ // store canonical seqres
+ if (indices_[PDBX_SEQ_ONE_LETTER_CODE_CAN] != -1) {
+ StringRef seqres_can=columns[indices_[PDBX_SEQ_ONE_LETTER_CODE_CAN]];
+ edm_it->second.seqres_canonical = seqres_can.str_no_whitespace();
}
- if (read_seqres_) {
- StringRef seqres;
- if (seqres_can_) {
- if (indices_[PDBX_SEQ_ONE_LETTER_CODE_CAN] != -1) {
- seqres=columns[indices_[PDBX_SEQ_ONE_LETTER_CODE_CAN]];
- edm_it->second.seqres = seqres.str_no_whitespace();
- } else {
- throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
- "'entity_poly.pdbx_seq_one_letter_code_can' not available.'",
- this->GetCurrentLinenum()));
- }
- } else if (indices_[PDBX_SEQ_ONE_LETTER_CODE] != -1) {
- seqres=columns[indices_[PDBX_SEQ_ONE_LETTER_CODE]];
-
- conop::CompoundLibBasePtr comp_lib=conop::Conopology::Instance()
- .GetDefaultLib();
- if (!comp_lib) {
- if (!warned_rule_based_) {
- LOG_WARNING("SEQRES import requires a valid compound library to "
- "handle non standard compounds. Their One letter "
- "codes will be set to X.");
- }
- warned_rule_based_=true;
- comp_lib = conop::CompoundLibBasePtr(new ost::conop::MinimalCompoundLib);
- }
- edm_it->second.seqres = this->ConvertSEQRES(seqres.str_no_whitespace(),
- comp_lib);
- } else {
- throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
- "'entity_poly.pdbx_seq_one_letter_code' not available.'",
- this->GetCurrentLinenum()));
- }
- }
-}
-
-String MMCifReader::ConvertSEQRES(const String& seqres,
- conop::CompoundLibBasePtr comp_lib)
-{
- String can_seqres;
- for (String::const_iterator i=seqres.begin(), e=seqres.end(); i!=e; ++i) {
- if (*i=='(') {
- bool found_end_paren=false;
- String tlc;
- tlc.reserve(3);
- while ((++i)!=seqres.end()) {
- if (*i==')') {
- found_end_paren=true;
- break;
- }
- tlc.push_back(*i);
- }
- if (!found_end_paren) {
- throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
- "'entity_poly.pdbx_seq_one_letter_code' contains "
- "unmatched '('", this->GetCurrentLinenum()));
- }
- conop::CompoundPtr compound=comp_lib->FindCompound(tlc,
- conop::Compound::PDB);
- if (!compound) {
- if (tlc!="UNK") {
- LOG_WARNING("unknown residue '" << tlc << "' in SEQRES record. "
- "Setting one-letter-code to 'X'");
- }
- can_seqres.push_back('X');
- continue;
- }
- if (compound->GetOneLetterCode()=='?') {
- can_seqres.push_back('X');
- } else {
- can_seqres.push_back(compound->GetOneLetterCode());
- }
-
- } else {
- can_seqres.push_back(*i);
+ // store non canonical seqres
+ if (indices_[PDBX_SEQ_ONE_LETTER_CODE] != -1) {
+ StringRef seqres_pdbx=columns[indices_[PDBX_SEQ_ONE_LETTER_CODE]];
+ edm_it->second.seqres_pdbx = seqres_pdbx.str_no_whitespace();
}
- }
- return can_seqres;
}
void MMCifReader::ParseCitation(const std::vector<StringRef>& columns)
@@ -1943,11 +1863,13 @@ void MMCifReader::OnEndData()
if (edm_it != entity_desc_map_.end()) {
editor.SetChainType(css->first, edm_it->second.type);
editor.SetChainDescription(css->first, edm_it->second.details);
- if (edm_it->second.seqres.length() > 0) {
- seqres_.AddSequence(seq::CreateSequence(css->first.GetName(),
- edm_it->second.seqres));
- pdb_auth_chain_name = css->first.GetStringProp("pdb_auth_chain_name");
- info_.AddMMCifPDBChainTr(css->first.GetName(), pdb_auth_chain_name);
+ // Add chain mapping for all chains
+ pdb_auth_chain_name = css->first.GetStringProp("pdb_auth_chain_name");
+ info_.AddMMCifPDBChainTr(css->first.GetName(), pdb_auth_chain_name);
+
+ if (edm_it->second.entity_type=="polymer") {
+ // PDB -> mmCIF chain mapping only for polymers
+ // This is not a 1:1 mapping because of ligands
info_.AddPDBMMCifChainTr(pdb_auth_chain_name, css->first.GetName());
} else if (edm_it->second.entity_type=="non-polymer") {
mol::ChainHandle chain=css->first;
@@ -1959,7 +1881,8 @@ void MMCifReader::OnEndData()
}
} else {
LOG_WARNING("No entity description found for atom_site.label_entity_id '"
- << css->second << "'");
+ << css->second << "'. SEQRES, chain mapping and ligand "
+ << " annotation will be missing.");
}
// find
blm_it = entity_branch_link_map_.find(css->second);
@@ -2075,19 +1998,19 @@ void MMCifReader::OnEndData()
}
// conclude EntityDesc (add entity_poly_seq if present) and add to MMCifInfo
- for(auto entity_it: entity_desc_map_) {
+ for(auto &entity_it: entity_desc_map_) {
if(entity_poly_seq_map_.find(entity_it.first) != entity_poly_seq_map_.end()) {
int max_num = 1;
- for(auto seqres_it: entity_poly_seq_map_[entity_it.first]) {
+ for(auto &seqres_it: entity_poly_seq_map_[entity_it.first]) {
max_num = std::max(max_num, seqres_it.first);
}
entity_it.second.mon_ids.assign(max_num, "?");
- for(auto seqres_it: entity_poly_seq_map_[entity_it.first]) {
+ for(auto &seqres_it: entity_poly_seq_map_[entity_it.first]) {
entity_it.second.mon_ids[seqres_it.first-1] = seqres_it.second;
}
}
if(entity_poly_seq_h_map_.find(entity_it.first) != entity_poly_seq_h_map_.end()) {
- for(auto hetero_it: entity_poly_seq_h_map_[entity_it.first]) {
+ for(auto &hetero_it: entity_poly_seq_h_map_[entity_it.first]) {
entity_it.second.hetero_num.push_back(hetero_it.first);
entity_it.second.hetero_ids.push_back(hetero_it.second);
}
@@ -2163,4 +2086,68 @@ String OSTBondOrderToMMCifValueOrder(const unsigned char bond_order)
return String("");
}
+seq::SequenceList MMCifReader::GetSeqRes() const {
+ std::map<String, String> entity_seqres_map; // Map entity_id -> seqres
+ seq::SequenceList seqres_list = seq::CreateSequenceList();
+
+ // We need a compound lib for the conversion
+ conop::CompoundLibBasePtr comp_lib=conop::Conopology::Instance()
+ .GetDefaultLib();
+ if (!comp_lib) {
+ LOG_WARNING("SEQRES requires a valid compound library to "
+ "handle non standard compounds. Their One letter "
+ "codes will be set to X.");
+ comp_lib = conop::CompoundLibBasePtr(new ost::conop::MinimalCompoundLib);
+ }
+
+ // Generate the SEQRES for every entity
+ for(auto const &entity_it: entity_desc_map_) {
+ if (entity_it.second.entity_type == "polymer") {
+ entity_seqres_map[entity_it.first] = "";
+ auto mon_ids = entity_it.second.mon_ids;
+// if (mon_ids.size() == 0) {
+// // We hit this if there was an _entity_poly category but no _entity_poly_seq
+// LOG_WARNING("No SEQRES found for entity '"
+// << entity_it.first << "'.");
+// }
+ entity_seqres_map[entity_it.first].reserve(mon_ids.size());
+ for (auto const &mon_id: mon_ids) {
+ conop::CompoundPtr compound=comp_lib->FindCompound(mon_id, conop::Compound::PDB);
+ if (!compound) {
+ if (mon_id != "UNK") {
+ LOG_WARNING("unknown residue '" << mon_id << "' in SEQRES record. "
+ "Setting one-letter-code to 'X'");
+ }
+ entity_seqres_map[entity_it.first].push_back('X');
+ continue;
+ }
+ if (compound->GetOneLetterCode()=='?') {
+ entity_seqres_map[entity_it.first].push_back('X');
+ } else {
+ entity_seqres_map[entity_it.first].push_back(compound->GetOneLetterCode());
+ }
+ }
+ }
+ }
+
+ // Assign
+ for (auto const &css: chain_id_pairs_) {
+ auto entity_seqres_map_it = entity_seqres_map.find(css.second);
+ if (entity_seqres_map_it != entity_seqres_map.end()) {
+ if (entity_seqres_map_it->second == "") {
+ // We hit this if there was an _entity_poly category but no _entity_poly_seq
+ LOG_WARNING("No SEQRES found for chain '"
+ << css.first << "'. Most likely the entity_poly_seq "
+ << "category was missing from the input file.");
+ } else {
+ seqres_list.AddSequence(seq::CreateSequence(css.first.GetName(),
+ entity_seqres_map_it->second));
+ }
+ }
+ // else: either non polymer chain, or no entity_poly was available (this
+ // triggered a warning before)
+ }
+ return seqres_list;
+}
+
}}
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index 28798a49f..cc61e9ca3 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -89,16 +89,6 @@ public:
/// \param restrict_chains chain name
void SetRestrictChains(const String& restrict_chains);
- /// \brief Toggle reading of canonical sequence residues
- /// (entity_poly.pdbx_seq_one_letter_code_can instead of
- /// entity_poly.pdbx_seq_one_letter_code). This flag is exclusive.
- ///
- /// \param flag True for reading canonical sequences.
- void SetReadCanonicalSeqRes(bool flag)
- {
- seqres_can_ = flag;
- }
-
const String& GetRestrictChains() const
{
return restrict_chains_;
@@ -141,25 +131,7 @@ public:
/// \brief Return sequences
///
/// \return List of sequences
- seq::SequenceList GetSeqRes() const {
- return seqres_;
- }
-
- /// \brief Toggle reading of SEQRES
- ///
- /// \param flag True enables, False disables reading SEQRES
- void SetReadSeqRes(bool flag)
- {
- read_seqres_ = flag;
- }
-
- /// \brief Check if reading of SEQRES is enabled
- ///
- /// \return True if reading of SEQRES is enabled
- bool GetReadSeqRes() const
- {
- return read_seqres_;
- }
+ seq::SequenceList GetSeqRes() const;
/// \brief Get additional information of the mmCIF file.
///
@@ -232,15 +204,7 @@ protected:
void ParseCitation(const std::vector<StringRef>& columns);
const MMCifInfoStructRefs& GetStructRefs() const { return struct_refs_; }
- /// \brief convert the seqres data item to canonical form.
- ///
- /// The seqres sequence lists non-standard residues in parenthesis. For
- /// proper handling of our sequence classes, these need to be converted to
- /// one-letter-codes. Ideally, we would use the canonical SEQRES. This is
- /// not possible, however, since the PDB assigns multiple one letter codes
- /// to some of the residues. To be consistent, we have to do the conversion
- /// on our own.
- String ConvertSEQRES(const String& seqres, conop::CompoundLibBasePtr compound_lib);
+
/// \brief Fetch mmCIF citation_author information
///
/// \param columns data row
@@ -717,7 +681,6 @@ private:
mol::EntityHandle& ent_handle_;
String restrict_chains_;
bool auth_chain_id_; ///< use chain IDs given by authors rather than pdb
- bool seqres_can_; ///< read canonical 1-letter residues?
mol::ChainHandle curr_chain_;
mol::ResidueHandle curr_residue_;
int chain_count_;
@@ -731,8 +694,6 @@ private:
std::vector<std::pair<mol::ChainHandle, String> > chain_id_pairs_;
///< chain and label_entity_id
MMCifEntityDescMap entity_desc_map_; ///< stores entity items
- seq::SequenceList seqres_;
- bool read_seqres_;
MMCifInfo info_; ///< info container
MMCifCitationAuthorMap authors_map_;
MMCifBioUAssemblyVector bu_assemblies_;
diff --git a/modules/io/src/mol/mmcif_str.cc b/modules/io/src/mol/mmcif_str.cc
index 6fde265e4..604af0d2d 100644
--- a/modules/io/src/mol/mmcif_str.cc
+++ b/modules/io/src/mol/mmcif_str.cc
@@ -50,7 +50,6 @@ MMCifStringToEntity(const String& mmcif, const IOProfile& profile, bool process)
std::stringstream stream(mmcif);
mol::EntityHandle ent = mol::CreateEntity();
MMCifReader reader(stream, ent, profile);
- reader.SetReadSeqRes(true);
reader.Parse();
if(profile.processor && process) {
profile.processor->Process(ent);
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index 6d81b4603..4670b815a 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -65,10 +65,7 @@ public:
using MMCifReader::ParsePdbxEntityBranchLink;
using MMCifReader::TryStoreIdx;
using MMCifReader::SetRestrictChains;
- using MMCifReader::SetReadSeqRes;
- using MMCifReader::SetReadCanonicalSeqRes;
using MMCifReader::ClearState;
- using MMCifReader::ConvertSEQRES;
using MMCifReader::GetInfo;
using MMCifReader::DetermineSecStructType;
using MMCifReader::MMCifSecStructElement;
@@ -128,23 +125,6 @@ BOOST_AUTO_TEST_CASE(mmcif_trystoreidx)
BOOST_CHECK_NO_THROW(tmmcif_p.TryStoreIdx(0, "bar", mmcif_h));
}
-BOOST_AUTO_TEST_CASE(mmcif_convert_seqres)
-{
- conop::CompoundLibPtr compound_lib = SetDefaultCompoundLib();
- if (!compound_lib) {
- std::cout << "WARNING: skipping mmcif_convert_seqres unit test. "
- << "Compound library is required" << std::endl;
- return;
- }
-
- mol::EntityHandle eh=mol::CreateEntity();
-
- TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
- BOOST_CHECK_EQUAL(tmmcif_p.ConvertSEQRES("A(MSE)Y", compound_lib), "AMY");
- BOOST_CHECK_THROW(tmmcif_p.ConvertSEQRES("A(MSEY", compound_lib),
- IOException);
-}
-
BOOST_AUTO_TEST_CASE(mmcif_onbeginloop)
{
mol::EntityHandle eh=mol::CreateEntity();
@@ -404,7 +384,6 @@ BOOST_AUTO_TEST_CASE(mmcif_entity_poly_tests)
mol::EntityHandle eh = mol::CreateEntity();
MMCifReader mmcif_p("testfiles/mmcif/atom_site.mmcif", eh, profile);
- mmcif_p.SetReadSeqRes(true);
mmcif_p.Parse();
seq::SequenceList seqres = mmcif_p.GetSeqRes();
@@ -414,7 +393,6 @@ BOOST_AUTO_TEST_CASE(mmcif_entity_poly_tests)
BOOST_TEST_MESSAGE(" testing type recognition...");
{
TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
- tmmcif_p.SetReadSeqRes(false);
std::vector<StringRef> columns;
// create corresponding entity entry
@@ -493,46 +471,7 @@ columns.push_back(StringRef("polydeoxyribonucleotide/polyribonucleotide hybrid",
columns.push_back(StringRef("1", 1));
columns.push_back(StringRef("other", 5));
columns.push_back(StringRef("ABRND", 5));
- tmmcif_p.SetReadSeqRes(true);
- tmmcif_p.SetReadCanonicalSeqRes(true);
- BOOST_CHECK_THROW(tmmcif_p.ParseEntityPoly(columns), IOException);
- tmmcif_p.SetReadCanonicalSeqRes(false);
BOOST_CHECK_NO_THROW(tmmcif_p.ParseEntityPoly(columns));
- BOOST_CHECK_THROW(tmmcif_p.ParseEntityPoly(columns), IOException);
- }
- BOOST_TEST_MESSAGE(" done.");
- BOOST_TEST_MESSAGE(" testing pdbx_seq_one_letter_code_can "
- "reading...");
- {
- TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
- std::vector<StringRef> columns;
-
- tmmcif_h.Clear();
- tmmcif_h.SetCategory(StringRef("entity", 6));
- tmmcif_h.Add(StringRef("id", 2));
- tmmcif_h.Add(StringRef("type", 4));
- tmmcif_p.OnBeginLoop(tmmcif_h);
- columns.push_back(StringRef("1", 1));
- columns.push_back(StringRef("polymer", 7));
- tmmcif_p.ParseEntity(columns);
- columns.pop_back();
- columns.pop_back();
-
- tmmcif_h.Clear();
- tmmcif_h.SetCategory(StringRef("entity_poly", 11));
- tmmcif_h.Add(StringRef("entity_id", 9));
- tmmcif_h.Add(StringRef("type", 4));
- tmmcif_h.Add(StringRef("pdbx_seq_one_letter_code_can", 28));
- tmmcif_p.OnBeginLoop(tmmcif_h);
- tmmcif_p.SetReadCanonicalSeqRes(false);
- columns.push_back(StringRef("1", 1));
- columns.push_back(StringRef("other", 5));
- columns.push_back(StringRef("ABRND", 5));
- tmmcif_p.SetReadSeqRes(true);
- BOOST_CHECK_THROW(tmmcif_p.ParseEntityPoly(columns), IOException);
- tmmcif_p.SetReadCanonicalSeqRes(true);
- BOOST_CHECK_NO_THROW(tmmcif_p.ParseEntityPoly(columns));
- BOOST_CHECK_THROW(tmmcif_p.ParseEntityPoly(columns), IOException);
}
BOOST_TEST_MESSAGE(" done.");
@@ -1323,9 +1262,6 @@ BOOST_AUTO_TEST_CASE(mmcif_test_chain_mappings)
std::ifstream s("testfiles/mmcif/atom_site.mmcif");
IOProfile profile;
MMCifReader mmcif_p(s, eh, profile);
- if (compound_lib_available) {
- mmcif_p.SetReadSeqRes(true);
- }
BOOST_REQUIRE_NO_THROW(mmcif_p.Parse());
const MMCifInfo& info = mmcif_p.GetInfo();
diff --git a/modules/io/tests/testfiles/mmcif/atom_site.mmcif b/modules/io/tests/testfiles/mmcif/atom_site.mmcif
index 9bd8159d6..e01cf812a 100644
--- a/modules/io/tests/testfiles/mmcif/atom_site.mmcif
+++ b/modules/io/tests/testfiles/mmcif/atom_site.mmcif
@@ -26,6 +26,15 @@ _entity_poly.nstd_linkage no
_entity_poly.nstd_monomer no
_entity_poly.pdbx_seq_one_letter_code 'VTI'
+loop_
+_entity_poly_seq.entity_id
+_entity_poly_seq.num
+_entity_poly_seq.mon_id
+_entity_poly_seq.hetero
+1 1 VAL n
+1 2 THR n
+1 3 ILE n
+
loop_
_citation.id
_citation.abstract_id_CAS
diff --git a/modules/seq/alg/tests/testfiles/align_to_seqres.mmcif b/modules/seq/alg/tests/testfiles/align_to_seqres.mmcif
index 177b53a64..9fce63c4b 100644
--- a/modules/seq/alg/tests/testfiles/align_to_seqres.mmcif
+++ b/modules/seq/alg/tests/testfiles/align_to_seqres.mmcif
@@ -20,7 +20,87 @@ _entity_poly.nstd_monomer no
_entity_poly.pdbx_seq_one_letter_code MYTNSDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGKK
_entity_poly.pdbx_seq_one_letter_code_can MYTNSDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGKK
_entity_poly.pdbx_strand_id A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V
-#
+#
+loop_
+_entity_poly_seq.entity_id
+_entity_poly_seq.num
+_entity_poly_seq.mon_id
+_entity_poly_seq.hetero
+1 1 MET n
+1 2 TYR n
+1 3 THR n
+1 4 ASN n
+1 5 SER n
+1 6 ASP n
+1 7 PHE n
+1 8 VAL n
+1 9 VAL n
+1 10 ILE n
+1 11 LYS n
+1 12 ALA n
+1 13 LEU n
+1 14 GLU n
+1 15 ASP n
+1 16 GLY n
+1 17 VAL n
+1 18 ASN n
+1 19 VAL n
+1 20 ILE n
+1 21 GLY n
+1 22 LEU n
+1 23 THR n
+1 24 ARG n
+1 25 GLY n
+1 26 ALA n
+1 27 ASP n
+1 28 THR n
+1 29 ARG n
+1 30 PHE n
+1 31 HIS n
+1 32 HIS n
+1 33 SER n
+1 34 GLU n
+1 35 LYS n
+1 36 LEU n
+1 37 ASP n
+1 38 LYS n
+1 39 GLY n
+1 40 GLU n
+1 41 VAL n
+1 42 LEU n
+1 43 ILE n
+1 44 ALA n
+1 45 GLN n
+1 46 PHE n
+1 47 THR n
+1 48 GLU n
+1 49 HIS n
+1 50 THR n
+1 51 SER n
+1 52 ALA n
+1 53 ILE n
+1 54 LYS n
+1 55 VAL n
+1 56 ARG n
+1 57 GLY n
+1 58 LYS n
+1 59 ALA n
+1 60 TYR n
+1 61 ILE n
+1 62 GLN n
+1 63 THR n
+1 64 ARG n
+1 65 HIS n
+1 66 GLY n
+1 67 VAL n
+1 68 ILE n
+1 69 GLU n
+1 70 SER n
+1 71 GLU n
+1 72 GLY n
+1 73 LYS n
+1 74 LYS n
+#
loop_
_atom_site.group_PDB
_atom_site.id
diff --git a/modules/seq/alg/tests/testfiles/validate_segres_aln_breakage.mmcif b/modules/seq/alg/tests/testfiles/validate_segres_aln_breakage.mmcif
index 0d66b8fa2..57d45b9df 100644
--- a/modules/seq/alg/tests/testfiles/validate_segres_aln_breakage.mmcif
+++ b/modules/seq/alg/tests/testfiles/validate_segres_aln_breakage.mmcif
@@ -19,7 +19,86 @@ _entity_poly.nstd_linkage no
_entity_poly.nstd_monomer no
_entity_poly.pdbx_seq_one_letter_code MYTNSDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEKK
_entity_poly.pdbx_seq_one_letter_code_can MYTNSDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEKK
-_entity_poly.pdbx_strand_id A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V
+_entity_poly.pdbx_strand_id A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V
+#
+loop_
+_entity_poly_seq.entity_id
+_entity_poly_seq.num
+_entity_poly_seq.mon_id
+_entity_poly_seq.hetero
+1 1 MET n
+1 2 TYR n
+1 3 THR n
+1 4 ASN n
+1 5 SER n
+1 6 ASP n
+1 7 PHE n
+1 8 VAL n
+1 9 VAL n
+1 10 ILE n
+1 11 LYS n
+1 12 ALA n
+1 13 LEU n
+1 14 GLU n
+1 15 ASP n
+1 16 GLY n
+1 17 VAL n
+1 18 ASN n
+1 19 VAL n
+1 20 ILE n
+1 21 GLY n
+1 22 LEU n
+1 23 THR n
+1 24 ARG n
+1 25 GLY n
+1 26 ALA n
+1 27 ASP n
+1 28 THR n
+1 29 ARG n
+1 30 PHE n
+1 31 HIS n
+1 32 HIS n
+1 33 SER n
+1 34 GLU n
+1 35 LYS n
+1 36 LEU n
+1 37 ASP n
+1 38 LYS n
+1 39 GLY n
+1 40 GLU n
+1 41 VAL n
+1 42 LEU n
+1 43 ILE n
+1 44 ALA n
+1 45 GLN n
+1 46 PHE n
+1 47 THR n
+1 48 GLU n
+1 49 HIS n
+1 50 THR n
+1 51 SER n
+1 52 ALA n
+1 53 ILE n
+1 54 LYS n
+1 55 VAL n
+1 56 ARG n
+1 57 GLY n
+1 58 LYS n
+1 59 ALA n
+1 60 TYR n
+1 61 ILE n
+1 62 GLN n
+1 63 THR n
+1 64 ARG n
+1 65 HIS n
+1 66 GLY n
+1 67 VAL n
+1 68 ILE n
+1 69 GLU n
+1 70 SER n
+1 71 GLU n
+1 72 LYS n
+1 73 LYS n
#
loop_
_atom_site.group_PDB
diff --git a/modules/seq/alg/tests/testfiles/validate_seqres_aln_connected.mmcif b/modules/seq/alg/tests/testfiles/validate_seqres_aln_connected.mmcif
index 2e76cf323..fb3a0807f 100644
--- a/modules/seq/alg/tests/testfiles/validate_seqres_aln_connected.mmcif
+++ b/modules/seq/alg/tests/testfiles/validate_seqres_aln_connected.mmcif
@@ -19,7 +19,88 @@ _entity_poly.nstd_linkage no
_entity_poly.nstd_monomer no
_entity_poly.pdbx_seq_one_letter_code MYTNSDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGGKK
_entity_poly.pdbx_seq_one_letter_code_can MYTNSDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGGKK
-_entity_poly.pdbx_strand_id A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V
+_entity_poly.pdbx_strand_id A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V
+#
+loop_
+_entity_poly_seq.entity_id
+_entity_poly_seq.num
+_entity_poly_seq.mon_id
+_entity_poly_seq.hetero
+1 1 MET n
+1 2 TYR n
+1 3 THR n
+1 4 ASN n
+1 5 SER n
+1 6 ASP n
+1 7 PHE n
+1 8 VAL n
+1 9 VAL n
+1 10 ILE n
+1 11 LYS n
+1 12 ALA n
+1 13 LEU n
+1 14 GLU n
+1 15 ASP n
+1 16 GLY n
+1 17 VAL n
+1 18 ASN n
+1 19 VAL n
+1 20 ILE n
+1 21 GLY n
+1 22 LEU n
+1 23 THR n
+1 24 ARG n
+1 25 GLY n
+1 26 ALA n
+1 27 ASP n
+1 28 THR n
+1 29 ARG n
+1 30 PHE n
+1 31 HIS n
+1 32 HIS n
+1 33 SER n
+1 34 GLU n
+1 35 LYS n
+1 36 LEU n
+1 37 ASP n
+1 38 LYS n
+1 39 GLY n
+1 40 GLU n
+1 41 VAL n
+1 42 LEU n
+1 43 ILE n
+1 44 ALA n
+1 45 GLN n
+1 46 PHE n
+1 47 THR n
+1 48 GLU n
+1 49 HIS n
+1 50 THR n
+1 51 SER n
+1 52 ALA n
+1 53 ILE n
+1 54 LYS n
+1 55 VAL n
+1 56 ARG n
+1 57 GLY n
+1 58 LYS n
+1 59 ALA n
+1 60 TYR n
+1 61 ILE n
+1 62 GLN n
+1 63 THR n
+1 64 ARG n
+1 65 HIS n
+1 66 GLY n
+1 67 VAL n
+1 68 ILE n
+1 69 GLU n
+1 70 SER n
+1 71 GLU n
+1 72 GLY n
+1 73 GLY n
+1 74 LYS n
+1 75 LYS n
#
loop_
_atom_site.group_PDB
--
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