From 352335f134c90006fe9787acdfb603fda4d7e9f2 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 22 Nov 2023 09:32:32 +0100
Subject: [PATCH] mmcif writer: write _entity, _struct_asym, _entity_poly_seq
categories
---
modules/io/src/mol/mmcif_writer.cc | 380 ++++++++++++++++++++++-------
modules/io/src/mol/mmcif_writer.hh | 13 +-
modules/mol/base/src/chem_class.hh | 7 +
3 files changed, 307 insertions(+), 93 deletions(-)
diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index c266d01c2..6abcd266d 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -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
diff --git a/modules/io/src/mol/mmcif_writer.hh b/modules/io/src/mol/mmcif_writer.hh
index f5b5ece37..d5f1e01bd 100644
--- a/modules/io/src/mol/mmcif_writer.hh
+++ b/modules/io/src/mol/mmcif_writer.hh
@@ -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_;
};
diff --git a/modules/mol/base/src/chem_class.hh b/modules/mol/base/src/chem_class.hh
index efd838679..aa4033e7f 100644
--- a/modules/mol/base/src/chem_class.hh
+++ b/modules/mol/base/src/chem_class.hh
@@ -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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