From d72c2972d102bb50e0b8ebca5d6a707790418a68 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 5 Jan 2024 16:23:32 +0100
Subject: [PATCH] mmcif writer: enable _pdbx_entity_branch category
---
modules/io/src/mol/mmcif_writer.cc | 58 +++++++++++++++++++++++++++---
modules/io/src/mol/mmcif_writer.hh | 4 +++
2 files changed, 57 insertions(+), 5 deletions(-)
diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index 2c5490ea4..4af329c28 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -154,6 +154,16 @@ namespace {
return "other";
}
+ // template to allow ost::mol::ResidueHandleList and ost::mol::ResidueViewList
+ template<class T>
+ String GuessEntityBranchType(const T& res_list) {
+ // guesses _pdbx_entity_branch.type based on residue chem classes
+ //
+ // Thats a hard one... only allowed value according to mmcif_pdbx_v50.dic:
+ // oligosaccharide
+ return "oligosaccharide";
+ }
+
// template to allow ost::mol::ResidueHandleList and ost::mol::ResidueViewList
template<class T>
String GuessEntityType(const T& res_list) {
@@ -612,13 +622,14 @@ namespace {
int SetupEntity(const String& asym_chain_name,
const String& type,
const String& poly_type,
+ const String& branch_type,
const T& res_list,
bool resnum_alignment,
std::vector<ost::io::MMCifWriterEntity>& entity_infos) {
bool is_poly = type == "polymer";
- if(!is_poly && res_list.size() != 1 && type != "water") {
+ if(!is_poly && res_list.size() != 1 && type != "water" && type != "branched") {
std::stringstream ss;
ss << "Cannot setup entity with " << res_list.size() << " residues ";
ss << "but is of type: " << type;
@@ -632,7 +643,8 @@ namespace {
return i;
}
if(entity_infos[i].type == type &&
- entity_infos[i].poly_type == poly_type) {
+ entity_infos[i].poly_type == poly_type &&
+ entity_infos[i].branch_type == branch_type) {
if(is_poly && resnum_alignment) {
if(MatchEntityResnum(res_list, entity_infos[i])) {
AddAsymResnum(asym_chain_name, res_list, entity_infos[i]);
@@ -718,6 +730,7 @@ namespace {
entity_infos.push_back(ost::io::MMCifWriterEntity());
entity_infos.back().type = type;
entity_infos.back().poly_type = poly_type;
+ entity_infos.back().branch_type = branch_type;
entity_infos.back().mon_ids = mon_ids;
entity_infos.back().seq_olcs = seq;
entity_infos.back().seq_can_olcs = seq_can;
@@ -746,7 +759,12 @@ namespace {
if(is_poly) {
poly_type = GuessEntityPolyType(res_list);
}
- return SetupEntity(asym_chain_name, type, poly_type, res_list,
+ bool is_branched = type == "branched";
+ String branch_type = "";
+ if(is_branched) {
+ branch_type = GuessEntityBranchType(res_list);
+ }
+ return SetupEntity(asym_chain_name, type, poly_type, branch_type, res_list,
resnum_alignment, entity_infos);
}
@@ -765,7 +783,12 @@ namespace {
if(is_poly) {
poly_type = ost::mol::EntityPolyTypeFromChainType(chain_type);
}
- return SetupEntity(asym_chain_name, type, poly_type, res_list,
+ bool is_branched = type == "branched";
+ String branch_type = "";
+ if(is_branched) {
+ branch_type = ost::mol::BranchedTypeFromChainType(chain_type);
+ }
+ return SetupEntity(asym_chain_name, type, poly_type, branch_type, res_list,
resnum_alignment, entity_infos);
}
@@ -855,6 +878,14 @@ namespace {
return sl;
}
+ ost::io::StarWriterLoopPtr Setup_pdbx_entity_branch_ptr() {
+ ost::io::StarWriterLoopDesc desc("_pdbx_entity_branch");
+ desc.Add("entity_id");
+ desc.Add("type");
+ ost::io::StarWriterLoopPtr sl(new ost::io::StarWriterLoop(desc));
+ return sl;
+ }
+
void Feed_atom_type(ost::io::StarWriterLoopPtr atom_type_ptr,
ost::io::StarWriterLoopPtr atom_site_ptr) {
// we're just extracting every type_symbol that we observed
@@ -1112,6 +1143,20 @@ 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"));
+ for(size_t i = 0; i < entity_infos.size(); ++i) {
+ if(entity_infos[i].type == "branched") {
+ branch_data[0] = ost::io::StarWriterValue::FromInt(i);
+ branch_data[1] = ost::io::StarWriterValue::FromString(entity_infos[i].branch_type);
+ pdbx_entity_branch_ptr->AddData(branch_data);
+ }
+ }
+ }
+
// template to allow ost::mol::ResidueHandleList and ost::mol::ResidueViewList
template<class T>
void ProcessEntmmCIFify(const std::vector<T>& res_lists,
@@ -1418,6 +1463,7 @@ void MMCifWriter::Setup() {
entity_poly_ = Setup_entity_poly_ptr();
entity_poly_seq_ = Setup_entity_poly_seq_ptr();
chem_comp_ = Setup_chem_comp_ptr();
+ pdbx_entity_branch_ = Setup_pdbx_entity_branch_ptr();
}
void MMCifWriter::Finalize() {
@@ -1433,7 +1479,8 @@ void MMCifWriter::Finalize() {
Feed_entity_poly(entity_poly_, entity_info_);
Feed_entity_poly_seq(entity_poly_seq_, entity_info_);
Feed_chem_comp(chem_comp_, comp_info_);
- Feed_atom_type(atom_type_, atom_site_);
+ Feed_atom_type(atom_type_, atom_site_);
+ Feed_pdbx_entity_branch(pdbx_entity_branch_, entity_info_);
// finalize
this->Push(chem_comp_);
@@ -1443,6 +1490,7 @@ void MMCifWriter::Finalize() {
this->Push(entity_poly_seq_);
this->Push(pdbx_poly_seq_scheme_);
this->Push(atom_type_);
+ this->Push(pdbx_entity_branch_);
this->Push(atom_site_);
structure_set_ = true;
diff --git a/modules/io/src/mol/mmcif_writer.hh b/modules/io/src/mol/mmcif_writer.hh
index c176ac74f..e0ce06eaa 100644
--- a/modules/io/src/mol/mmcif_writer.hh
+++ b/modules/io/src/mol/mmcif_writer.hh
@@ -40,6 +40,9 @@ struct MMCifWriterEntity {
// _entity_poly.type
String poly_type;
+ // __pdbx_entity_branch.type
+ String branch_type;
+
// Names of chains in AU that are assigned to this entity
std::vector<String> asym_ids;
@@ -98,6 +101,7 @@ private:
StarWriterLoopPtr entity_poly_;
StarWriterLoopPtr entity_poly_seq_;
StarWriterLoopPtr chem_comp_;
+ StarWriterLoopPtr pdbx_entity_branch_;
bool structure_set_;
};
--
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