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Commit 352335f1 authored by Studer Gabriel's avatar Studer Gabriel
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mmcif writer: write _entity, _struct_asym, _entity_poly_seq categories

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modules/io/src/mol/mmcif_writer.cc
+ 292
− 88
View file @ 352335f1
......@@ -70,6 +70,208 @@ namespace {
int n_chain_names;
std::vector<int> indices;
};
// 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
std::vector<String> asym_ids; // relevant for _struct_asym.id
std::vector<String> mon_ids; // relevant for _entity_poly_seq.mon_id
};
int Setup_entity_(const String& asym_chain_name,
char chem_class,
const ost::mol::ResidueHandleList& res_list,
std::vector<EntityInfo>& entity_infos) {
std::vector<String> mon_ids;
for(auto res : res_list) {
mon_ids.push_back(res.GetName());
}
// check whether we already have that entity
// right now we're just looking for exact matches in chem_class and
// mon_ids (i.e. sequence).
int entity_idx = -1;
for(size_t i = 0; i < entity_infos.size(); ++i) {
if(entity_infos[i].chem_class == chem_class &&
entity_infos[i].mon_ids == mon_ids) {
entity_idx = i;
break;
}
}
if(entity_idx != -1) {
entity_infos[entity_idx].asym_ids.push_back(asym_chain_name);
} else {
entity_idx = entity_infos.size();
entity_infos.push_back(EntityInfo());
entity_infos.back().chem_class = chem_class;
entity_infos.back().asym_ids.push_back(asym_chain_name);
entity_infos.back().mon_ids = mon_ids;
}
return entity_idx;
}
ost::io::StarLoop* Setup_atom_site_ptr() {
ost::io::StarLoopDesc desc;
desc.SetCategory("_atom_site");
desc.Add("group_PDB");
desc.Add("type_symbol");
desc.Add("label_atom_id");
desc.Add("label_comp_id");
desc.Add("label_asym_id");
desc.Add("label_entity_id");
desc.Add("label_seq_id");
desc.Add("label_alt_id");
desc.Add("Cartn_x");
desc.Add("Cartn_y");
desc.Add("Cartn_z");
desc.Add("occupancy");
desc.Add("B_iso_or_equiv");
desc.Add("auth_seq_id");
desc.Add("auth_asym_id");
desc.Add("id");
ost::io::StarLoop* sl = new ost::io::StarLoop(desc);
return sl;
}
ost::io::StarLoop* Setup_entity_ptr() {
ost::io::StarLoopDesc desc;
desc.SetCategory("_entity");
desc.Add("id");
desc.Add("type");
ost::io::StarLoop* sl = new ost::io::StarLoop(desc);
return sl;
}
ost::io::StarLoop* Setup_struct_asym_ptr() {
ost::io::StarLoopDesc desc;
desc.SetCategory("_struct_asym");
desc.Add("id");
desc.Add("entity_id");
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");
desc.Add("entity_id");
desc.Add("mon_id");
desc.Add("num");
ost::io::StarLoop* sl = new ost::io::StarLoop(desc);
return sl;
}
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) {
int label_seq_id = 1;
for(auto res: res_list) {
String comp_id = res.GetName();
ost::mol::AtomHandleList at_list = res.GetAtomList();
String auth_asym_id = res.GetChain().GetName();
String auth_seq_id = res.GetNumber().AsString();
for(auto at: at_list) {
std::vector<ost::io::StarLoopDataItemDO> at_data;
// group_PDB
if(at.IsHetAtom()) {
at_data.push_back(ost::io::StarLoopDataItemDO("HETATM"));
} else {
at_data.push_back(ost::io::StarLoopDataItemDO("ATOM"));
}
// type_symbol
at_data.push_back(ost::io::StarLoopDataItemDO(at.GetElement()));
// label_atom_id
at_data.push_back(ost::io::StarLoopDataItemDO(at.GetName()));
// label_comp_id
at_data.push_back(ost::io::StarLoopDataItemDO(comp_id));
// label_asym_id
at_data.push_back(ost::io::StarLoopDataItemDO(label_asym_id));
// 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));
// label_alt_id
at_data.push_back(ost::io::StarLoopDataItemDO("."));
// Cartn_x
at_data.push_back(ost::io::StarLoopDataItemDO(at.GetPos().GetX(), 3));
// Cartn_y
at_data.push_back(ost::io::StarLoopDataItemDO(at.GetPos().GetY(), 3));
// Cartn_z
at_data.push_back(ost::io::StarLoopDataItemDO(at.GetPos().GetZ(), 3));
// occupancy
at_data.push_back(ost::io::StarLoopDataItemDO(at.GetOccupancy(), 2));
// B_iso_or_equiv
at_data.push_back(ost::io::StarLoopDataItemDO(at.GetBFactor(), 2));
// auth_seq_id
at_data.push_back(ost::io::StarLoopDataItemDO(auth_seq_id));
// auth_asym_id
at_data.push_back(ost::io::StarLoopDataItemDO(auth_asym_id));
// id
at_data.push_back(ost::io::StarLoopDataItemDO(atom_site_ptr->GetN()));
atom_site_ptr->AddData(at_data);
}
++label_seq_id;
}
}
void Feed_entity_(ost::io::StarLoop* entity_ptr,
const std::vector<EntityInfo>& entity_info) {
for(size_t entity_idx = 0; entity_idx < entity_info.size(); ++entity_idx) {
std::vector<ost::io::StarLoopDataItemDO> ent_data;
// id
ent_data.push_back(ost::io::StarLoopDataItemDO(entity_idx));
// type
ost::mol::ChemClass chem_class(entity_info[entity_idx].chem_class);
if(chem_class.IsPeptideLinking() || chem_class.IsNucleotideLinking()) {
ent_data.push_back(ost::io::StarLoopDataItemDO("polymer"));
} else if(chem_class.IsWater()) {
ent_data.push_back(ost::io::StarLoopDataItemDO("water"));
} else if(chem_class == ost::mol::ChemClass::NON_POLYMER) {
ent_data.push_back(ost::io::StarLoopDataItemDO("non-polymer"));
} else if(chem_class.IsSaccharide()) {
// I doubt that this is correct
ent_data.push_back(ost::io::StarLoopDataItemDO("branched"));
} else {
throw ost::io::IOException("Entity type issue");
}
entity_ptr->AddData(ent_data);
}
}
void Feed_struct_asym_(ost::io::StarLoop* struct_asym_ptr,
const std::vector<EntityInfo>& entity_info) {
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::StarLoopDataItemDO> asym_data;
asym_data.push_back(ost::io::StarLoopDataItemDO(asym_id));
asym_data.push_back(ost::io::StarLoopDataItemDO(entity_idx));
struct_asym_ptr->AddData(asym_data);
}
}
}
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));
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);
}
}
}
}
namespace ost { namespace io {
......@@ -77,17 +279,47 @@ namespace ost { namespace io {
MMCifWriter::MMCifWriter(const String& filename, const IOProfile& profile):
StarWriter(filename),
profile_(profile),
atom_site_(NULL) { }
atom_site_(NULL),
entity_(NULL),
struct_asym_(NULL),
entity_poly_seq_(NULL) { }
MMCifWriter::~MMCifWriter() {
if(atom_site_ != NULL) {
delete atom_site_;
}
if(entity_ != NULL) {
delete entity_;
}
if(struct_asym_ != NULL) {
delete struct_asym_;
}
if(entity_poly_seq_ != NULL) {
delete entity_poly_seq_;
}
}
void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
this->Setup_atom_site_();
// tabula rasa
if(atom_site_ != NULL) {
delete atom_site_;
}
if(entity_ != NULL) {
delete entity_;
}
if(struct_asym_ != NULL) {
delete struct_asym_;
}
if(entity_poly_seq_ != NULL) {
delete entity_poly_seq_;
}
atom_site_ = Setup_atom_site_ptr();
entity_ = Setup_entity_ptr();
struct_asym_ = Setup_struct_asym_ptr();
entity_poly_seq_ = Setup_entity_poly_seq_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
......@@ -229,53 +461,86 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
}
ChainNameGenerator chain_name_gen;
std::vector<EntityInfo> entity_info;
// process L_PEPTIDE_LINKING
for(auto res_list: L_chains) {
String chain_name = chain_name_gen.Get();
Feed_atom_site_(chain_name, 0, res_list);
int entity_id = Setup_entity_(chain_name,
ost::mol::ChemClass::L_PEPTIDE_LINKING,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
}
// process D_PEPTIDE_LINKING
for(auto res_list: D_chains) {
String chain_name = chain_name_gen.Get();
Feed_atom_site_(chain_name, 0, res_list);
int entity_id = Setup_entity_(chain_name,
ost::mol::ChemClass::D_PEPTIDE_LINKING,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
}
// process PEPTIDE_LINKING
for(auto res_list: P_chains) {
String chain_name = chain_name_gen.Get();
Feed_atom_site_(chain_name, 0, res_list);
int entity_id = Setup_entity_(chain_name,
ost::mol::ChemClass::PEPTIDE_LINKING,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
}
// process RNA_LINKING
for(auto res_list: R_chains) {
String chain_name = chain_name_gen.Get();
Feed_atom_site_(chain_name, 0, res_list);
int entity_id = Setup_entity_(chain_name,
ost::mol::ChemClass::RNA_LINKING,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
}
// process DNA_LINKING
for(auto res_list: S_chains) {
String chain_name = chain_name_gen.Get();
Feed_atom_site_(chain_name, 0, res_list);
int entity_id = Setup_entity_(chain_name,
ost::mol::ChemClass::DNA_LINKING,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
}
// process L_SACHARIDE
for(auto res_list: X_chains) {
String chain_name = chain_name_gen.Get();
Feed_atom_site_(chain_name, 0, res_list);
int entity_id = Setup_entity_(chain_name,
ost::mol::ChemClass::L_SACCHARIDE,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
}
// process D_SACHARIDE
for(auto res_list: Y_chains) {
String chain_name = chain_name_gen.Get();
Feed_atom_site_(chain_name, 0, res_list);
int entity_id = Setup_entity_(chain_name,
ost::mol::ChemClass::D_SACCHARIDE,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
}
// process WATER
for(auto res_list: W_chains) {
String chain_name = chain_name_gen.Get();
Feed_atom_site_(chain_name, 0, res_list);
int entity_id = Setup_entity_(chain_name,
ost::mol::ChemClass::WATER,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
}
// process NON_POLYMER
......@@ -283,7 +548,11 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
ost::mol::ResidueHandleList res_list;
res_list.push_back(res);
String chain_name = chain_name_gen.Get();
Feed_atom_site_(chain_name, 0, res_list);
int entity_id = Setup_entity_(chain_name,
ost::mol::ChemClass::NON_POLYMER,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
}
// process UNKNOWN
......@@ -291,87 +560,22 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
ost::mol::ResidueHandleList res_list;
res_list.push_back(res);
String chain_name = chain_name_gen.Get();
Feed_atom_site_(chain_name, 0, res_list);
int entity_id = Setup_entity_(chain_name,
ost::mol::ChemClass::UNKNOWN,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
}
Feed_entity_(entity_, entity_info);
Feed_struct_asym_(struct_asym_, entity_info);
Feed_entity_poly_seq_(entity_poly_seq_, entity_info);
// finalize
this->Push(entity_);
this->Push(struct_asym_);
this->Push(entity_poly_seq_);
this->Push(atom_site_);
}
void MMCifWriter::Setup_atom_site_() {
StarLoopDesc desc;
desc.SetCategory("_atom_site");
desc.Add("group_PDB");
desc.Add("type_symbol");
desc.Add("label_atom_id");
desc.Add("label_comp_id");
desc.Add("label_asym_id");
desc.Add("label_entity_id");
desc.Add("label_seq_id");
desc.Add("label_alt_id");
desc.Add("Cartn_x");
desc.Add("Cartn_y");
desc.Add("Cartn_z");
desc.Add("occupancy");
desc.Add("B_iso_or_equiv");
desc.Add("auth_seq_id");
desc.Add("auth_asym_id");
desc.Add("id");
atom_site_ = new StarLoop(desc);
}
void MMCifWriter::Feed_atom_site_(const String& label_asym_id,
int label_entity_id,
const ost::mol::ResidueHandleList& res_list) {
int label_seq_id = 1;
for(auto res: res_list) {
String comp_id = res.GetName();
ost::mol::AtomHandleList at_list = res.GetAtomList();
String auth_asym_id = res.GetChain().GetName();
String auth_seq_id = res.GetNumber().AsString();
for(auto at: at_list) {
std::vector<StarLoopDataItemDO> at_data;
// group_PDB
if(at.IsHetAtom()) {
at_data.push_back(StarLoopDataItemDO("HETATM"));
} else {
at_data.push_back(StarLoopDataItemDO("ATOM"));
}
// type_symbol
at_data.push_back(StarLoopDataItemDO(at.GetElement()));
// label_atom_id
at_data.push_back(StarLoopDataItemDO(at.GetName()));
// label_comp_id
at_data.push_back(StarLoopDataItemDO(comp_id));
// label_asym_id
at_data.push_back(StarLoopDataItemDO(label_asym_id));
// label_entity_id
at_data.push_back(StarLoopDataItemDO(label_entity_id));
// label_seq_id
at_data.push_back(StarLoopDataItemDO(label_seq_id));
// label_alt_id
at_data.push_back(StarLoopDataItemDO("."));
// Cartn_x
at_data.push_back(StarLoopDataItemDO(at.GetPos().GetX(), 3));
// Cartn_y
at_data.push_back(StarLoopDataItemDO(at.GetPos().GetY(), 3));
// Cartn_z
at_data.push_back(StarLoopDataItemDO(at.GetPos().GetZ(), 3));
// occupancy
at_data.push_back(StarLoopDataItemDO(at.GetOccupancy(), 2));
// B_iso_or_equiv
at_data.push_back(StarLoopDataItemDO(at.GetBFactor(), 2));
// auth_seq_id
at_data.push_back(StarLoopDataItemDO(auth_seq_id));
// auth_asym_id
at_data.push_back(StarLoopDataItemDO(auth_asym_id));
// id
at_data.push_back(StarLoopDataItemDO(atom_site_->GetN()));
atom_site_->AddData(at_data);
}
++label_seq_id;
}
}
}} // ns
modules/io/src/mol/mmcif_writer.hh
+ 8
− 5
View file @ 352335f1
......@@ -36,17 +36,20 @@ public:
virtual ~MMCifWriter();
// initializes
// atom_site_
// entity_
// struct_asym_
// entity_poly_seq_
void Process_atom_site(const ost::mol::EntityHandle& ent);
private:
void Setup_atom_site_();
void Feed_atom_site_(const String& label_asym_id,
int label_entity_id,
const ost::mol::ResidueHandleList& res_list);
IOProfile profile_;
StarLoop* atom_site_;
StarLoop* entity_;
StarLoop* struct_asym_;
StarLoop* entity_poly_seq_;
};
......
modules/mol/base/src/chem_class.hh
+ 7
− 0
View file @ 352335f1
......@@ -79,6 +79,13 @@ struct DLLEXPORT ChemClass {
operator char() const {
return chem_class_;
}
bool IsSaccharide() const {
return (chem_class_==ChemClass::SACCHARIDE ||
chem_class_==ChemClass::L_SACCHARIDE ||
chem_class_==ChemClass::D_SACCHARIDE);
}
private:
char chem_class_;
};
......
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