diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index 4af329c284532452ba627e246fe7ff17299ddc0f..18831c0465b34eab6a6450bed00018e95dfe79cd 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -898,8 +898,7 @@ namespace {
for(int i = 0; i < N; ++i) {
symbols.insert(data[i*desc_size + type_symbol_idx].GetValue());
}
- std::vector<ost::io::StarWriterValue> atom_type_data;
- atom_type_data.push_back(ost::io::StarWriterValue::FromString(""));
+ std::vector<ost::io::StarWriterValue> atom_type_data(1);
for(auto symbol: symbols) {
atom_type_data[0] = ost::io::StarWriterValue::FromString(symbol);
atom_type_ptr->AddData(atom_type_data);
@@ -914,14 +913,10 @@ namespace {
ost::io::MMCifWriterEntity& entity_info,
const T& res_list) {
- std::vector<ost::io::StarWriterValue> data;
- data.push_back(ost::io::StarWriterValue::FromString(label_asym_id));
- data.push_back(ost::io::StarWriterValue::FromInt(label_entity_id));
- data.push_back(ost::io::StarWriterValue::FromString(""));
- data.push_back(ost::io::StarWriterValue::FromInt(0));
- data.push_back(ost::io::StarWriterValue::FromString(""));
- data.push_back(ost::io::StarWriterValue::FromInt(0));
- data.push_back(ost::io::StarWriterValue::FromString(""));
+ std::vector<ost::io::StarWriterValue> data(7);
+ // processing chain by chain, label_asym_id and label_entity_id are constant
+ data[0] = ost::io::StarWriterValue::FromString(label_asym_id);
+ data[1] = ost::io::StarWriterValue::FromInt(label_entity_id);
int asym_idx = entity_info.GetAsymIdx(label_asym_id);
const std::vector<String>& aln = entity_info.asym_alns[asym_idx];
@@ -979,6 +974,7 @@ namespace {
int asym_idx = entity_info.GetAsymIdx(label_asym_id);
const std::vector<String>& aln = entity_info.asym_alns[asym_idx];
int label_seq_id = 0; // 0-based index
+ std::vector<ost::io::StarWriterValue> at_data(17);
for(auto res: res_list) {
String comp_id = res.GetName();
@@ -1004,49 +1000,48 @@ namespace {
}
for(auto at: at_list) {
- std::vector<ost::io::StarWriterValue> at_data;
// group_PDB
if(at.IsHetAtom()) {
- at_data.push_back(ost::io::StarWriterValue::FromString("HETATM"));
+ at_data[0] = ost::io::StarWriterValue::FromString("HETATM");
} else {
- at_data.push_back(ost::io::StarWriterValue::FromString("ATOM"));
+ at_data[0] = ost::io::StarWriterValue::FromString("ATOM");
}
// type_symbol
- at_data.push_back(ost::io::StarWriterValue::FromString(at.GetElement()));
+ at_data[1] = ost::io::StarWriterValue::FromString(at.GetElement());
// label_atom_id
- at_data.push_back(ost::io::StarWriterValue::FromString(at.GetName()));
+ at_data[2] = ost::io::StarWriterValue::FromString(at.GetName());
// label_comp_id
- at_data.push_back(ost::io::StarWriterValue::FromString(comp_id));
+ at_data[3] = ost::io::StarWriterValue::FromString(comp_id);
// label_asym_id
- at_data.push_back(ost::io::StarWriterValue::FromString(label_asym_id));
+ at_data[4] = ost::io::StarWriterValue::FromString(label_asym_id);
// label_entity_id
- at_data.push_back(ost::io::StarWriterValue::FromInt(label_entity_id));
+ at_data[5] = ost::io::StarWriterValue::FromInt(label_entity_id);
// label_seq_id
if(entity_info.is_poly) {
- at_data.push_back(ost::io::StarWriterValue::FromInt(label_seq_id+1));
+ at_data[6] = ost::io::StarWriterValue::FromInt(label_seq_id+1);
} else {
- at_data.push_back(ost::io::StarWriterValue::FromString("."));
+ at_data[6] = ost::io::StarWriterValue::FromString(".");
}
// label_alt_id
- at_data.push_back(ost::io::StarWriterValue::FromString("."));
+ at_data[7] = ost::io::StarWriterValue::FromString(".");
// Cartn_x
- at_data.push_back(ost::io::StarWriterValue::FromFloat(at.GetPos().GetX(), 3));
+ at_data[8] = ost::io::StarWriterValue::FromFloat(at.GetPos().GetX(), 3);
// Cartn_y
- at_data.push_back(ost::io::StarWriterValue::FromFloat(at.GetPos().GetY(), 3));
+ at_data[9] = ost::io::StarWriterValue::FromFloat(at.GetPos().GetY(), 3);
// Cartn_z
- at_data.push_back(ost::io::StarWriterValue::FromFloat(at.GetPos().GetZ(), 3));
+ at_data[10] = ost::io::StarWriterValue::FromFloat(at.GetPos().GetZ(), 3);
// occupancy
- at_data.push_back(ost::io::StarWriterValue::FromFloat(at.GetOccupancy(), 2));
+ at_data[11] = ost::io::StarWriterValue::FromFloat(at.GetOccupancy(), 2);
// B_iso_or_equiv
- at_data.push_back(ost::io::StarWriterValue::FromFloat(at.GetBFactor(), 2));
+ at_data[12] = ost::io::StarWriterValue::FromFloat(at.GetBFactor(), 2);
// auth_seq_id
- at_data.push_back(ost::io::StarWriterValue::FromString(auth_seq_id));
+ at_data[13] = ost::io::StarWriterValue::FromString(auth_seq_id);
// auth_asym_id
- at_data.push_back(ost::io::StarWriterValue::FromString(auth_asym_id));
+ at_data[14] = ost::io::StarWriterValue::FromString(auth_asym_id);
// id
- at_data.push_back(ost::io::StarWriterValue::FromInt(atom_site_ptr->GetN()));
+ at_data[15] = ost::io::StarWriterValue::FromInt(atom_site_ptr->GetN());
// pdbx_PDB_ins_code
- at_data.push_back(ost::io::StarWriterValue::FromString(ins_code));
+ at_data[16] = ost::io::StarWriterValue::FromString(ins_code);
atom_site_ptr->AddData(at_data);
}
++label_seq_id;
@@ -1055,21 +1050,21 @@ namespace {
void Feed_entity(ost::io::StarWriterLoopPtr entity_ptr,
const std::vector<ost::io::MMCifWriterEntity>& entity_info) {
+ std::vector<ost::io::StarWriterValue> ent_data(2);
for(size_t entity_idx = 0; entity_idx < entity_info.size(); ++entity_idx) {
- std::vector<ost::io::StarWriterValue> ent_data;
- ent_data.push_back(ost::io::StarWriterValue::FromInt(entity_idx));
- ent_data.push_back(ost::io::StarWriterValue::FromString(entity_info[entity_idx].type));
+ ent_data[0] = ost::io::StarWriterValue::FromInt(entity_idx);
+ ent_data[1] = ost::io::StarWriterValue::FromString(entity_info[entity_idx].type);
entity_ptr->AddData(ent_data);
}
}
void Feed_struct_asym(ost::io::StarWriterLoopPtr struct_asym_ptr,
const std::vector<ost::io::MMCifWriterEntity>& entity_info) {
+ std::vector<ost::io::StarWriterValue> asym_data(2);
for(size_t entity_idx = 0; entity_idx < entity_info.size(); ++entity_idx) {
for(auto asym_id : entity_info[entity_idx].asym_ids) {
- std::vector<ost::io::StarWriterValue> asym_data;
- asym_data.push_back(ost::io::StarWriterValue::FromString(asym_id));
- asym_data.push_back(ost::io::StarWriterValue::FromInt(entity_idx));
+ asym_data[0] = ost::io::StarWriterValue::FromString(asym_id);
+ asym_data[1] = ost::io::StarWriterValue::FromInt(entity_idx);
struct_asym_ptr->AddData(asym_data);
}
}
@@ -1077,12 +1072,7 @@ namespace {
void Feed_entity_poly_seq(ost::io::StarWriterLoopPtr entity_poly_seq_ptr,
const std::vector<ost::io::MMCifWriterEntity>& entity_info) {
- // reuse data vector for efficiency
- std::vector<ost::io::StarWriterValue> entity_poly_seq_data;
- entity_poly_seq_data.push_back(ost::io::StarWriterValue::FromInt(0));
- entity_poly_seq_data.push_back(ost::io::StarWriterValue::FromString("ALA"));
- entity_poly_seq_data.push_back(ost::io::StarWriterValue::FromInt(1));
-
+ std::vector<ost::io::StarWriterValue> entity_poly_seq_data(3);
for(size_t entity_idx = 0; entity_idx < entity_info.size(); ++entity_idx) {
if(entity_info[entity_idx].is_poly) {
const std::vector<String>& mon_ids = entity_info[entity_idx].mon_ids;
@@ -1098,12 +1088,7 @@ namespace {
void Feed_entity_poly(ost::io::StarWriterLoopPtr entity_poly_ptr,
const std::vector<ost::io::MMCifWriterEntity>& entity_info) {
- // reuse data vector for efficiency
- std::vector<ost::io::StarWriterValue> entity_poly_data;
- entity_poly_data.push_back(ost::io::StarWriterValue::FromInt(0));
- entity_poly_data.push_back(ost::io::StarWriterValue::FromString("other"));
- entity_poly_data.push_back(ost::io::StarWriterValue::FromString("A"));
- entity_poly_data.push_back(ost::io::StarWriterValue::FromString("A"));
+ std::vector<ost::io::StarWriterValue> entity_poly_data(4);
for(size_t entity_idx = 0; entity_idx < entity_info.size(); ++entity_idx) {
if(entity_info[entity_idx].is_poly) {
entity_poly_data[0] = ost::io::StarWriterValue::FromInt(entity_idx);
@@ -1133,9 +1118,7 @@ namespace {
void Feed_chem_comp(ost::io::StarWriterLoopPtr chem_comp_ptr,
const std::map<String, ost::io::MMCifWriterComp>& comp_infos) {
- std::vector<ost::io::StarWriterValue> comp_data;
- comp_data.push_back(ost::io::StarWriterValue::FromString("ALA"));
- comp_data.push_back(ost::io::StarWriterValue::FromString("L-PEPTIDE LINKING"));
+ std::vector<ost::io::StarWriterValue> comp_data(2);
for(auto it = comp_infos.begin(); it != comp_infos.end(); ++it) {
comp_data[0] = ost::io::StarWriterValue::FromString(it->first);
comp_data[1] = ost::io::StarWriterValue::FromString(it->second.type);
@@ -1145,9 +1128,7 @@ namespace {
void Feed_pdbx_entity_branch(ost::io::StarWriterLoopPtr pdbx_entity_branch_ptr,
const std::vector<ost::io::MMCifWriterEntity>& entity_infos) {
- std::vector<ost::io::StarWriterValue> branch_data;
- branch_data.push_back(ost::io::StarWriterValue::FromInt(0));
- branch_data.push_back(ost::io::StarWriterValue::FromString("oligosaccharide"));
+ std::vector<ost::io::StarWriterValue> branch_data(2);
for(size_t i = 0; i < entity_infos.size(); ++i) {
if(entity_infos[i].type == "branched") {
branch_data[0] = ost::io::StarWriterValue::FromInt(i);
diff --git a/modules/io/src/mol/star_writer.hh b/modules/io/src/mol/star_writer.hh
index dd8cb5a2acf1feaa27154eb5c6101b4c9908882b..49728fcb77d93a2e183ba0667556ceca33ff1470 100644
--- a/modules/io/src/mol/star_writer.hh
+++ b/modules/io/src/mol/star_writer.hh
@@ -88,6 +88,9 @@ public:
class DLLEXPORT_OST_IO StarWriterValue{
public:
+
+ StarWriterValue() { }
+
static StarWriterValue FromInt(int int_value) {
StarWriterValue value;
value.value_ = std::to_string(int_value);
@@ -123,8 +126,6 @@ public:
}
const String& GetValue() const { return value_; }
private:
-// force construction through static members
-StarWriterValue() { }
String value_;
};