From 5e0eddcea7a49c4d1e251e41b51a8641633b0329 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 10 Jan 2024 13:46:36 +0100
Subject: [PATCH] mmcif writer: Set user defined mmCIF entities
---
modules/io/pymod/export_mmcif_io.cc | 20 ++++++++++++++------
modules/io/src/mol/mmcif_writer.cc | 9 ++++++---
modules/io/src/mol/mmcif_writer.hh | 22 ++++++++++++++++++++--
3 files changed, 40 insertions(+), 11 deletions(-)
diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index f9a575b5f..411750b91 100644
--- a/modules/io/pymod/export_mmcif_io.cc
+++ b/modules/io/pymod/export_mmcif_io.cc
@@ -84,14 +84,16 @@ void WrapStarWriterWrite(StarWriter& writer, const String& data_name,
void WrapSetStructureHandle(MMCifWriter& writer,
const ost::mol::EntityHandle& ent,
- bool mmcif_conform) {
- writer.SetStructure(ent, mmcif_conform);
+ bool mmcif_conform,
+ const std::vector<MMCifWriterEntity>& entity_info) {
+ writer.SetStructure(ent, mmcif_conform, entity_info);
}
void WrapSetStructureView(MMCifWriter& writer,
const ost::mol::EntityView& ent,
- bool mmcif_conform) {
- writer.SetStructure(ent, mmcif_conform);
+ bool mmcif_conform,
+ const std::vector<MMCifWriterEntity>& entity_info) {
+ writer.SetStructure(ent, mmcif_conform, entity_info);
}
void export_mmcif_io()
@@ -159,9 +161,15 @@ void export_mmcif_io()
.add_property("asym_ids", &MMCifWriterEntity::asym_ids)
;
+ class_<std::vector<MMCifWriterEntity> >("MMCifWriterEntityList", init<>())
+ .def(vector_indexing_suite<std::vector<MMCifWriterEntity> >())
+ ;
+
class_<MMCifWriter, bases<StarWriter> >("MMCifWriter", init<>())
- .def("SetStructure", &WrapSetStructureHandle, (arg("ent"), arg("mmcif_conform")=true))
- .def("SetStructure", &WrapSetStructureView, (arg("ent"), arg("mmcif_conform")=true))
+ .def("SetStructure", &WrapSetStructureHandle, (arg("ent"), arg("mmcif_conform")=true,
+ arg("entity_info")=std::vector<MMCifWriterEntity>()))
+ .def("SetStructure", &WrapSetStructureView, (arg("ent"), arg("mmcif_conform")=true,
+ arg("entity_info")=std::vector<MMCifWriterEntity>()))
;
enum_<MMCifInfoCitation::MMCifInfoCType>("MMCifInfoCType")
diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index 16cf083f6..a2b3ba02e 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -1461,18 +1461,21 @@ int MMCifWriterEntity::GetAsymIdx(const String& asym_id) const {
}
void MMCifWriter::SetStructure(const ost::mol::EntityHandle& ent,
- bool mmcif_conform) {
-
+ bool mmcif_conform,
+ const std::vector<MMCifWriterEntity>& entity_info) {
this->Setup();
+ entity_info_ = entity_info;
ProcessEnt(ent, mmcif_conform, comp_info_, entity_info_, atom_site_,
pdbx_poly_seq_scheme_);
this->Finalize();
}
void MMCifWriter::SetStructure(const ost::mol::EntityView& ent,
- bool mmcif_conform) {
+ bool mmcif_conform,
+ const std::vector<MMCifWriterEntity>& entity_info) {
this->Setup();
+ entity_info_ = entity_info;
ProcessEnt(ent, mmcif_conform, comp_info_, entity_info_, atom_site_,
pdbx_poly_seq_scheme_);
this->Finalize();
diff --git a/modules/io/src/mol/mmcif_writer.hh b/modules/io/src/mol/mmcif_writer.hh
index 98c62c4be..85b3f9a2a 100644
--- a/modules/io/src/mol/mmcif_writer.hh
+++ b/modules/io/src/mol/mmcif_writer.hh
@@ -41,6 +41,22 @@ struct MMCifWriterEntity {
int GetAsymIdx(const String& asym_id) const;
+ bool operator==(const MMCifWriterEntity& rhs) const {
+ return (type == rhs.type)
+ && (poly_type == rhs.poly_type)
+ && (branch_type == rhs.branch_type)
+ && (asym_ids == rhs.asym_ids)
+ && (is_poly == rhs.is_poly)
+ && (mon_ids == rhs.mon_ids)
+ && (seq_olcs == rhs.seq_olcs)
+ && (seq_can_olcs == rhs.seq_can_olcs)
+ && (asym_alns == rhs.asym_alns);
+ }
+
+ bool operator!=(const MMCifWriterEntity& rhs) const {
+ return !(*this == rhs);
+ }
+
// _entity.type
String type;
@@ -88,9 +104,11 @@ public:
virtual ~MMCifWriter() { }
- void SetStructure(const ost::mol::EntityHandle& ent, bool mmcif_conform=true);
+ void SetStructure(const ost::mol::EntityHandle& ent, bool mmcif_conform=true,
+ const std::vector<MMCifWriterEntity>& entity_info=std::vector<MMCifWriterEntity>());
- void SetStructure(const ost::mol::EntityView& ent, bool mmcif_conform=true);
+ void SetStructure(const ost::mol::EntityView& ent, bool mmcif_conform=true,
+ const std::vector<MMCifWriterEntity>& entity_info=std::vector<MMCifWriterEntity>());
private:
--
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