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Commit 74f30614 authored by Studer Gabriel's avatar Studer Gabriel
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mmcif writer: produces first valid mmcif files!

parent 97710d19
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modules/io/pymod/export_mmcif_io.cc
+ 1
− 1
View file @ 74f30614
......@@ -77,7 +77,7 @@ void export_mmcif_io()
;
class_<MMCifWriter, boost::noncopyable>("MMCifWriter", init<const String&, const IOProfile&>())
.def("Process_atom_site", &MMCifWriter::Process_atom_site)
.def("SetEntity", &MMCifWriter::SetEntity)
.def("Write", &MMCifWriter::Write)
;
......
modules/io/src/mol/mmcif_writer.cc
+ 371
− 27
View file @ 74f30614
......@@ -70,12 +70,133 @@ namespace {
std::vector<int> indices;
};
// internal object with all info to fill chem_comp_ category
struct CompInfo {
String type;
};
inline String chem_class_to_chem_comp_type(char chem_class) {
String type = "";
switch(chem_class) {
case 'P': {
type = "peptide linking";
break;
}
case 'D': {
type = "D-peptide linking";
break;
}
case 'L': {
type = "L-peptide linking";
break;
}
case 'R': {
type = "RNA linking";
break;
}
case 'S': {
type = "DNA linking";
break;
}
case 'N': {
type = "non-polymer";
break;
}
case 'X': {
type = "L-saccharide";
break;
}
case 'Y': {
type = "D-saccharide";
break;
}
case 'Z': {
type = "saccharide";
break;
}
case 'W': {
type = "non-polymer";
break;
}
case 'U': {
type = "non-polymer";
break;
}
default: {
std::stringstream err;
err << "Invalid chem class: "<<chem_class;
throw ost::io::IOException(err.str());
}
}
return type;
}
inline String chem_class_to_entity_poly_type(char chem_class) {
String type = "";
switch(chem_class) {
case 'P': {
type = "polypeptide(L)";
break;
}
case 'D': {
type = "polypeptide(D)";
break;
}
case 'L': {
type = "polypeptide(L)";
break;
}
case 'R': {
type = "polyribonucleotide";
break;
}
case 'S': {
type = "polydeoxyribonucleotide";
break;
}
case 'X': {
type = "polysaccharide(L)";
break;
}
case 'Y': {
type = "polysaccharide(D)";
break;
}
default: {
type = "other";
}
}
return type;
}
void Setup_chem_comp_(const ost::mol::ResidueHandleList& res_list,
std::map<String, CompInfo>& comp_infos) {
for(auto res: res_list) {
String res_name = res.GetName();
String type = chem_class_to_chem_comp_type(res.GetChemClass());
auto it = comp_infos.find(res_name);
if(it != comp_infos.end()) {
// check whether type is consistent
if(it->second.type != type) {
throw ost::io::IOException("There can be only one");
}
} else {
CompInfo info;
info.type = type;
comp_infos[res_name] = info;
}
}
}
// internal object with all info to fill entity_, struct_asym_,
// entity_poly_seq_ categories
struct EntityInfo {
char chem_class; // all residues of this entity have this ChemClass
String poly_type; // relevant for _entity_poly
std::vector<String> asym_ids; // relevant for _struct_asym.id
std::vector<String> mon_ids; // relevant for _entity_poly_seq.mon_id
bool is_poly; // in principle mon_ids.size() > 1
};
int Setup_entity_(const String& asym_chain_name,
......@@ -97,6 +218,8 @@ namespace {
entity_infos.back().chem_class = ost::mol::ChemClass::WATER;
entity_infos.back().asym_ids.push_back(asym_chain_name);
entity_infos.back().mon_ids.push_back("HOH");
entity_infos.back().poly_type = "";
entity_infos.back().is_poly = false;
return entity_idx;
}
......@@ -114,6 +237,8 @@ namespace {
entity_infos.back().chem_class = ost::mol::ChemClass::NON_POLYMER;
entity_infos.back().asym_ids.push_back(asym_chain_name);
entity_infos.back().mon_ids.push_back(res_list[0].GetName());
entity_infos.back().poly_type = "";
entity_infos.back().is_poly = false;
return entity_idx;
}
......@@ -131,6 +256,8 @@ namespace {
entity_infos.back().chem_class = ost::mol::ChemClass::UNKNOWN;
entity_infos.back().asym_ids.push_back(asym_chain_name);
entity_infos.back().mon_ids.push_back(res_list[0].GetName());
entity_infos.back().poly_type = "";
entity_infos.back().is_poly = false;
return entity_idx;
}
......@@ -165,10 +292,20 @@ namespace {
entity_infos.back().chem_class = chem_class;
entity_infos.back().asym_ids.push_back(asym_chain_name);
entity_infos.back().mon_ids = mon_ids;
entity_infos.back().poly_type = chem_class_to_entity_poly_type(chem_class);
entity_infos.back().is_poly = entity_infos.back().mon_ids.size() > 1;
}
return entity_idx;
}
ost::io::StarLoop* Setup_atom_type_ptr() {
ost::io::StarLoopDesc desc;
desc.SetCategory("_atom_type");
desc.Add("symbol");
ost::io::StarLoop* sl = new ost::io::StarLoop(desc);
return sl;
}
ost::io::StarLoop* Setup_atom_site_ptr() {
ost::io::StarLoopDesc desc;
desc.SetCategory("_atom_site");
......@@ -193,6 +330,20 @@ namespace {
return sl;
}
ost::io::StarLoop* Setup_pdbx_poly_seq_scheme_ptr() {
ost::io::StarLoopDesc desc;
desc.SetCategory("_pdbx_poly_seq_scheme");
desc.Add("asym_id");
desc.Add("entity_id");
desc.Add("mon_id");
desc.Add("seq_id");
desc.Add("pdb_strand_id");
desc.Add("pdb_seq_num");
desc.Add("pdb_ins_code");
ost::io::StarLoop* sl = new ost::io::StarLoop(desc);
return sl;
}
ost::io::StarLoop* Setup_entity_ptr() {
ost::io::StarLoopDesc desc;
desc.SetCategory("_entity");
......@@ -211,6 +362,15 @@ namespace {
return sl;
}
ost::io::StarLoop* Setup_entity_poly_ptr() {
ost::io::StarLoopDesc desc;
desc.SetCategory("_entity_poly");
desc.Add("entity_id");
desc.Add("type");
ost::io::StarLoop* sl = new ost::io::StarLoop(desc);
return sl;
}
ost::io::StarLoop* Setup_entity_poly_seq_ptr() {
ost::io::StarLoopDesc desc;
desc.SetCategory("_entity_poly_seq");
......@@ -221,10 +381,72 @@ namespace {
return sl;
}
ost::io::StarLoop* Setup_chem_comp_ptr() {
ost::io::StarLoopDesc desc;
desc.SetCategory("_chem_comp");
desc.Add("id");
desc.Add("type");
ost::io::StarLoop* sl = new ost::io::StarLoop(desc);
return sl;
}
void Feed_atom_type_(ost::io::StarLoop* atom_type_ptr,
ost::io::StarLoop* atom_site_ptr) {
// we're just extracting every type_symbol that we observed
// in atom_site (this is a bit of circular stupidity...)
std::set<String> symbols;
int desc_size = atom_site_ptr->GetDesc().GetSize();
int type_symbol_idx = atom_site_ptr->GetDesc().GetIndex("type_symbol");
int N = atom_site_ptr->GetN();
const std::vector<ost::io::StarLoopDataItemDO>& data = atom_site_ptr->GetData();
for(int i = 0; i < N; ++i) {
symbols.insert(data[i*desc_size + type_symbol_idx].GetValue());
}
std::vector<ost::io::StarLoopDataItemDO> atom_type_data;
atom_type_data.push_back(ost::io::StarLoopDataItemDO(""));
for(auto symbol: symbols) {
atom_type_data[0] = ost::io::StarLoopDataItemDO(symbol);
atom_type_ptr->AddData(atom_type_data);
}
}
void Feed_pdbx_poly_seq_scheme(ost::io::StarLoop* pdbx_poly_seq_scheme_ptr,
const String& label_asym_id,
int label_entity_id,
const ost::mol::ResidueHandleList& res_list) {
std::vector<ost::io::StarLoopDataItemDO> data;
data.push_back(ost::io::StarLoopDataItemDO(label_asym_id));
data.push_back(ost::io::StarLoopDataItemDO(label_entity_id));
data.push_back(ost::io::StarLoopDataItemDO(""));
data.push_back(ost::io::StarLoopDataItemDO(0));
data.push_back(ost::io::StarLoopDataItemDO(""));
data.push_back(ost::io::StarLoopDataItemDO(0));
data.push_back(ost::io::StarLoopDataItemDO(""));
int label_seq_id = 1;
for(auto res: res_list) {
data[2] = ost::io::StarLoopDataItemDO(res.GetName());
data[3] = ost::io::StarLoopDataItemDO(label_seq_id);
data[4] = ost::io::StarLoopDataItemDO(res.GetChain().GetName());
data[5] = ost::io::StarLoopDataItemDO(res.GetNumber().GetNum());
char ins_code = res.GetNumber().GetInsCode();
if(ins_code == '\0') {
data[6] = ost::io::StarLoopDataItemDO("");
} else {
String tmp = " ";
tmp[0] = ins_code;
data[6] = ost::io::StarLoopDataItemDO(tmp);
}
pdbx_poly_seq_scheme_ptr->AddData(data);
label_seq_id += 1;
}
}
void Feed_atom_site_(ost::io::StarLoop* atom_site_ptr,
const String& label_asym_id,
int label_entity_id,
const ost::mol::ResidueHandleList& res_list) {
const ost::mol::ResidueHandleList& res_list,
bool is_poly) {
int label_seq_id = 1;
for(auto res: res_list) {
String comp_id = res.GetName();
......@@ -250,7 +472,11 @@ namespace {
// label_entity_id
at_data.push_back(ost::io::StarLoopDataItemDO(label_entity_id));
// label_seq_id
at_data.push_back(ost::io::StarLoopDataItemDO(label_seq_id));
if(is_poly) {
at_data.push_back(ost::io::StarLoopDataItemDO(label_seq_id));
} else {
at_data.push_back(ost::io::StarLoopDataItemDO("."));
}
// label_alt_id
at_data.push_back(ost::io::StarLoopDataItemDO("."));
// Cartn_x
......@@ -319,22 +545,50 @@ namespace {
void Feed_entity_poly_seq_(ost::io::StarLoop* entity_poly_seq_ptr,
const std::vector<EntityInfo>& entity_info) {
// reuse data vector for efficiency
std::vector<ost::io::StarLoopDataItemDO> mon_data;
mon_data.push_back(ost::io::StarLoopDataItemDO(0));
mon_data.push_back(ost::io::StarLoopDataItemDO("ALA"));
mon_data.push_back(ost::io::StarLoopDataItemDO(1));
std::vector<ost::io::StarLoopDataItemDO> entity_poly_seq_data;
entity_poly_seq_data.push_back(ost::io::StarLoopDataItemDO(0));
entity_poly_seq_data.push_back(ost::io::StarLoopDataItemDO("ALA"));
entity_poly_seq_data.push_back(ost::io::StarLoopDataItemDO(1));
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;
for(size_t mon_idx = 0; mon_idx < mon_ids.size(); ++mon_idx) {
entity_poly_seq_data[0] = ost::io::StarLoopDataItemDO(entity_idx);
entity_poly_seq_data[1] = ost::io::StarLoopDataItemDO(mon_ids[mon_idx]);
entity_poly_seq_data[2] = ost::io::StarLoopDataItemDO(mon_idx+1);
entity_poly_seq_ptr->AddData(entity_poly_seq_data);
}
}
}
}
void Feed_entity_poly_(ost::io::StarLoop* entity_poly_ptr,
const std::vector<EntityInfo>& entity_info) {
// reuse data vector for efficiency
std::vector<ost::io::StarLoopDataItemDO> entity_poly_data;
entity_poly_data.push_back(ost::io::StarLoopDataItemDO(0));
entity_poly_data.push_back(ost::io::StarLoopDataItemDO("other"));
for(size_t entity_idx = 0; entity_idx < entity_info.size(); ++entity_idx) {
const std::vector<String>& mon_ids = entity_info[entity_idx].mon_ids;
for(size_t mon_idx = 0; mon_idx < mon_ids.size(); ++mon_idx) {
mon_data[0] = ost::io::StarLoopDataItemDO(entity_idx);
mon_data[1] = ost::io::StarLoopDataItemDO(mon_ids[mon_idx]);
mon_data[2] = ost::io::StarLoopDataItemDO(mon_idx+1);
entity_poly_seq_ptr->AddData(mon_data);
if(entity_info[entity_idx].is_poly) {
entity_poly_data[0] = ost::io::StarLoopDataItemDO(entity_idx);
entity_poly_data[1] = ost::io::StarLoopDataItemDO(entity_info[entity_idx].poly_type);
entity_poly_ptr->AddData(entity_poly_data);
}
}
}
void Feed_chem_comp_(ost::io::StarLoop* chem_comp_ptr,
const std::map<String, CompInfo>& comp_infos) {
std::vector<ost::io::StarLoopDataItemDO> comp_data;
comp_data.push_back(ost::io::StarLoopDataItemDO("ALA"));
comp_data.push_back(ost::io::StarLoopDataItemDO("L-peptide linking"));
for(auto it = comp_infos.begin(); it != comp_infos.end(); ++it) {
comp_data[0] = it->first;
comp_data[1] = it->second.type;
chem_comp_ptr->AddData(comp_data);
}
}
}
namespace ost { namespace io {
......@@ -342,47 +596,78 @@ namespace ost { namespace io {
MMCifWriter::MMCifWriter(const String& filename, const IOProfile& profile):
StarWriter(filename),
profile_(profile),
atom_type_(NULL),
atom_site_(NULL),
pdbx_poly_seq_scheme_(NULL),
entity_(NULL),
struct_asym_(NULL),
entity_poly_seq_(NULL) { }
entity_poly_(NULL),
entity_poly_seq_(NULL),
chem_comp_(NULL) { }
MMCifWriter::~MMCifWriter() {
if(atom_type_ != NULL) {
delete atom_type_;
}
if(atom_site_ != NULL) {
delete atom_site_;
}
if(pdbx_poly_seq_scheme_ != NULL) {
delete pdbx_poly_seq_scheme_;
}
if(entity_ != NULL) {
delete entity_;
}
if(struct_asym_ != NULL) {
delete struct_asym_;
}
if(entity_poly_ != NULL) {
delete entity_poly_;
}
if(entity_poly_seq_ != NULL) {
delete entity_poly_seq_;
}
if(chem_comp_ != NULL) {
delete chem_comp_;
}
}
void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
void MMCifWriter::SetEntity(const ost::mol::EntityHandle& ent) {
// tabula rasa
if(atom_type_ != NULL) {
delete atom_type_;
}
if(atom_site_ != NULL) {
delete atom_site_;
}
if(pdbx_poly_seq_scheme_ != NULL) {
delete pdbx_poly_seq_scheme_;
}
if(entity_ != NULL) {
delete entity_;
}
if(struct_asym_ != NULL) {
delete struct_asym_;
}
if(entity_poly_ != NULL) {
delete entity_poly_;
}
if(entity_poly_seq_ != NULL) {
delete entity_poly_seq_;
}
}
if(chem_comp_ != NULL) {
delete chem_comp_;
}
atom_type_ = Setup_atom_type_ptr();
atom_site_ = Setup_atom_site_ptr();
pdbx_poly_seq_scheme_ = Setup_pdbx_poly_seq_scheme_ptr();
entity_ = Setup_entity_ptr();
struct_asym_ = Setup_struct_asym_ptr();
entity_poly_ = Setup_entity_poly_ptr();
entity_poly_seq_ = Setup_entity_poly_seq_ptr();
chem_comp_ = Setup_chem_comp_ptr();
std::vector<std::vector<ost::mol::ResidueHandle> > L_chains; // L_PEPTIDE_LINKING
std::vector<std::vector<ost::mol::ResidueHandle> > D_chains; // D_PEPTIDE_LINKING
......@@ -394,16 +679,18 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
std::vector<std::vector<ost::mol::ResidueHandle> > W_chains; // WATER
std::vector<ost::mol::ResidueHandle> N_chains; // NON_POLYMER (1 res per chain)
std::vector<ost::mol::ResidueHandle> U_chains; // UNKNOWN (1 res per chain)
std::map<String, CompInfo> comp_infos;
ost::mol::ChainHandleList chain_list = ent.GetChainList();
for(auto ch: chain_list) {
ost::mol::ResidueHandleList res_list = ch.GetResidueList();
Setup_chem_comp_(res_list, comp_infos);
// we don't just go for chain type here...
// just think of PDB entries that have a polypeptide, water and a ligand
// in the same chain...
bool has_l_peptide_linking = false;
bool has_d_peptide_linking = false;
bool has_peptide_linking = false;
......@@ -533,7 +820,12 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
ost::mol::ChemClass::L_PEPTIDE_LINKING,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
entity_info[entity_id].is_poly);
if(entity_info[entity_id].is_poly) {
Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme_, chain_name,
entity_id, res_list);
}
}
// process D_PEPTIDE_LINKING
......@@ -543,7 +835,12 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
ost::mol::ChemClass::D_PEPTIDE_LINKING,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
entity_info[entity_id].is_poly);
if(entity_info[entity_id].is_poly) {
Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme_, chain_name,
entity_id, res_list);
}
}
// process PEPTIDE_LINKING
......@@ -553,7 +850,12 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
ost::mol::ChemClass::PEPTIDE_LINKING,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
entity_info[entity_id].is_poly);
if(entity_info[entity_id].is_poly) {
Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme_, chain_name,
entity_id, res_list);
}
}
// process RNA_LINKING
......@@ -563,7 +865,12 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
ost::mol::ChemClass::RNA_LINKING,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
entity_info[entity_id].is_poly);
if(entity_info[entity_id].is_poly) {
Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme_, chain_name,
entity_id, res_list);
}
}
// process DNA_LINKING
......@@ -573,7 +880,12 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
ost::mol::ChemClass::DNA_LINKING,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
entity_info[entity_id].is_poly);
if(entity_info[entity_id].is_poly) {
Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme_, chain_name,
entity_id, res_list);
}
}
// process L_SACHARIDE
......@@ -583,7 +895,12 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
ost::mol::ChemClass::L_SACCHARIDE,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
entity_info[entity_id].is_poly);
if(entity_info[entity_id].is_poly) {
Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme_, chain_name,
entity_id, res_list);
}
}
// process D_SACHARIDE
......@@ -593,7 +910,12 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
ost::mol::ChemClass::D_SACCHARIDE,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
entity_info[entity_id].is_poly);
if(entity_info[entity_id].is_poly) {
Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme_, chain_name,
entity_id, res_list);
}
}
// process WATER
......@@ -603,7 +925,12 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
ost::mol::ChemClass::WATER,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
entity_info[entity_id].is_poly);
if(entity_info[entity_id].is_poly) {
Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme_, chain_name,
entity_id, res_list);
}
}
// process NON_POLYMER
......@@ -615,7 +942,12 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
ost::mol::ChemClass::NON_POLYMER,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
entity_info[entity_id].is_poly);
if(entity_info[entity_id].is_poly) {
Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme_, chain_name,
entity_id, res_list);
}
}
// process UNKNOWN
......@@ -627,17 +959,29 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
ost::mol::ChemClass::UNKNOWN,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
entity_info[entity_id].is_poly);
if(entity_info[entity_id].is_poly) {
Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme_, chain_name,
entity_id, res_list);
}
}
Feed_entity_(entity_, entity_info);
Feed_struct_asym_(struct_asym_, entity_info);
Feed_entity_poly_(entity_poly_, entity_info);
Feed_entity_poly_seq_(entity_poly_seq_, entity_info);
Feed_chem_comp_(chem_comp_, comp_infos);
Feed_atom_type_(atom_type_, atom_site_);
// finalize
this->Push(chem_comp_);
this->Push(entity_);
this->Push(struct_asym_);
this->Push(entity_poly_);
this->Push(entity_poly_seq_);
this->Push(pdbx_poly_seq_scheme_);
this->Push(atom_type_);
this->Push(atom_site_);
}
......
modules/io/src/mol/mmcif_writer.hh
+ 6
− 9
View file @ 74f30614
......@@ -36,23 +36,20 @@ public:
virtual ~MMCifWriter();
// initializes
// atom_site_
// entity_
// struct_asym_
// entity_poly_seq_
void Process_atom_site(const ost::mol::EntityHandle& ent);
void SetEntity(const ost::mol::EntityHandle& ent);
private:
IOProfile profile_;
StarLoop* atom_type_;
StarLoop* atom_site_;
StarLoop* pdbx_poly_seq_scheme_;
StarLoop* entity_;
StarLoop* struct_asym_;
StarLoop* entity_poly_;
StarLoop* entity_poly_seq_;
StarLoop* chem_comp_;
};
}} // ns
#endif
\ No newline at end of file
#endif
modules/io/src/mol/star_base.hh
+ 17
− 1
View file @ 74f30614
......@@ -232,9 +232,21 @@ public:
// - special characters in strings (put in quotation marks)
// - long strings (semicolon based syntax)
// see https://mmcif.wwpdb.org/docs/tutorials/mechanics/pdbx-mmcif-syntax.html
bool has_space = false;
for(char c: value) {
if(isspace(c)) {
has_space = true;
break;
}
}
if(value == "") {
value_ = ".";
} else {
} else if(has_space) {
value_ = "'" + value + "'";
}
else {
value_ = value;
}
}
......@@ -272,6 +284,8 @@ public:
desc_ = desc;
}
const StarLoopDesc& GetDesc() { return desc_; }
void AddData(const std::vector<StarLoopDataItemDO>& data) {
if(data.size() != desc_.GetSize()) {
throw ost::io::IOException("Invalid data size when adding to StarLoop");
......@@ -279,6 +293,8 @@ public:
data_.insert(data_.end(), data.begin(), data.end());
}
const std::vector<StarLoopDataItemDO>& GetData() { return data_; }
int GetN() {
return data_.size() / desc_.GetSize();
}
......
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