From 252bfa6549ecc17231b8d927f5f26bba65694cef Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 18 Dec 2023 16:09:57 +0100
Subject: [PATCH] mmcif writer: rename SetEntity to SetStructure
Avoids confusion with mmCIF entities
---
modules/io/pymod/export_mmcif_io.cc | 2 +-
modules/io/src/mol/mmcif_writer.cc | 36 ++++++++++++++---------------
modules/io/src/mol/mmcif_writer.hh | 2 +-
3 files changed, 20 insertions(+), 20 deletions(-)
diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index 59265e130..2cdee1b9b 100644
--- a/modules/io/pymod/export_mmcif_io.cc
+++ b/modules/io/pymod/export_mmcif_io.cc
@@ -77,7 +77,7 @@ void export_mmcif_io()
;
class_<MMCifWriter, boost::noncopyable>("MMCifWriter", init<const String&, const IOProfile&>())
- .def("SetEntity", &MMCifWriter::SetEntity, (arg("ent"), arg("mmcif_conform")=true))
+ .def("SetStructure", &MMCifWriter::SetStructure, (arg("ent"), arg("mmcif_conform")=true))
.def("Write", &MMCifWriter::Write)
;
diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index 9c0b8ce4d..553692418 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -1192,11 +1192,11 @@ namespace {
}
}
- void SetEntity_(const ost::mol::EntityHandle& ent,
- std::map<String, CompInfo>& comp_infos,
- std::vector<EntityInfo>& entity_info,
- ost::io::StarLoop* atom_site,
- ost::io::StarLoop* pdbx_poly_seq_scheme) {
+ void SetStructure_(const ost::mol::EntityHandle& ent,
+ std::map<String, CompInfo>& comp_infos,
+ std::vector<EntityInfo>& entity_info,
+ ost::io::StarLoop* atom_site,
+ ost::io::StarLoop* pdbx_poly_seq_scheme) {
ost::mol::ChainHandleList chain_list = ent.GetChainList();
for(auto ch: chain_list) {
@@ -1218,11 +1218,11 @@ namespace {
}
}
- void SetEntitymmCIFify_(const ost::mol::EntityHandle& ent,
- std::map<String, CompInfo>& comp_infos,
- std::vector<EntityInfo>& entity_info,
- ost::io::StarLoop* atom_site,
- ost::io::StarLoop* pdbx_poly_seq_scheme) {
+ void SetStructuremmCIFify_(const ost::mol::EntityHandle& ent,
+ std::map<String, CompInfo>& comp_infos,
+ std::vector<EntityInfo>& entity_info,
+ ost::io::StarLoop* atom_site,
+ ost::io::StarLoop* pdbx_poly_seq_scheme) {
std::vector<std::vector<ost::mol::ResidueHandle> > L_chains; // L_PEPTIDE_LINKING
std::vector<std::vector<ost::mol::ResidueHandle> > D_chains; // D_PEPTIDE_LINKING
@@ -1532,8 +1532,8 @@ MMCifWriter::~MMCifWriter() {
}
}
-void MMCifWriter::SetEntity(const ost::mol::EntityHandle& ent,
- bool mmcif_conform) {
+void MMCifWriter::SetStructure(const ost::mol::EntityHandle& ent,
+ bool mmcif_conform) {
// tabula rasa
if(atom_type_ != NULL) {
@@ -1573,7 +1573,7 @@ void MMCifWriter::SetEntity(const ost::mol::EntityHandle& ent,
std::map<String, CompInfo> comp_infos;
std::vector<EntityInfo> entity_info;
- // The SetEntity functions fill CompInfo and EntityInfo, i.e. gather info on
+ // The SetStructure functions fill CompInfo and EntityInfo, i.e. gather info on
// all unique compounds and entities observed in ent and relate the entities
// with asym chain names that are directly written to
// atom_site_/pdbx_poly_seq_scheme_.
@@ -1583,13 +1583,13 @@ void MMCifWriter::SetEntity(const ost::mol::EntityHandle& ent,
// chain type property set to the chains in ent. If any of the residues in
// the respective chains is incompatible with the set chain type, an error
// is thrown.
- SetEntity_(ent, comp_infos, entity_info,
- atom_site_, pdbx_poly_seq_scheme_);
+ SetStructure_(ent, comp_infos, entity_info,
+ atom_site_, pdbx_poly_seq_scheme_);
} else {
// rule based splitting of chains into mmCIF conform chains
- SetEntitymmCIFify_(ent, comp_infos, entity_info,
- atom_site_, pdbx_poly_seq_scheme_);
- }
+ SetStructuremmCIFify_(ent, comp_infos, entity_info,
+ atom_site_, pdbx_poly_seq_scheme_);
+ }
Feed_entity_(entity_, entity_info);
Feed_struct_asym_(struct_asym_, entity_info);
Feed_entity_poly_(entity_poly_, entity_info);
diff --git a/modules/io/src/mol/mmcif_writer.hh b/modules/io/src/mol/mmcif_writer.hh
index 0258242e6..262c516be 100644
--- a/modules/io/src/mol/mmcif_writer.hh
+++ b/modules/io/src/mol/mmcif_writer.hh
@@ -36,7 +36,7 @@ public:
virtual ~MMCifWriter();
- void SetEntity(const ost::mol::EntityHandle& ent, bool mmcif_conform=true);
+ void SetStructure(const ost::mol::EntityHandle& ent, bool mmcif_conform=true);
private:
IOProfile profile_;
--
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