From 80aedec84cbadf7d218926e086b3d18fdf084e29 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 18 Dec 2023 18:45:37 +0100
Subject: [PATCH] mmcif writer: Make entity info a property of mmcif writer
Previously, information on entities was constructed on the fly and
written to file. Now, entity infos are a property of the writer.
The idea is that this can be set in advance, i.e. to set SEQRES.
---
modules/io/src/mol/mmcif_writer.cc | 98 +++++++++++++-----------------
modules/io/src/mol/mmcif_writer.hh | 37 +++++++++++
2 files changed, 79 insertions(+), 56 deletions(-)
diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index 553692418..b5e6bb56f 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -546,38 +546,8 @@ namespace {
}
}
- // internal object with all info to fill entity_, struct_asym_,
- // entity_poly_seq_ categories
- struct EntityInfo {
-
- int GetAsymIdx(const String& asym_id) const {
- for(size_t i = 0; i < asym_ids.size(); ++i) {
- if(asym_ids[i] == asym_id) {
- return i;
- }
- }
- throw "asdf";
- }
-
- String type; // relevant for _entity
- String poly_type; // relevant for _entity_poly
- bool is_poly; // in principle type == "polymer"
- std::vector<String> asym_ids; // relevant for _struct_asym.id
- std::vector<String> mon_ids; // relevant for _entity_poly_seq.mon_id
- std::vector<String> seq_olcs; // relevant for pdbx_seq_one_letter_code
- std::vector<String> seq_can_olcs; // relevant for pdbx_seq_one_letter_code_can
- std::vector<std::vector<String> > asym_alns; // one alignment to mon_ids for
- // each element in asym_ids.
- // relevant for label_seq_id
- // contains "-" for residues
- // that are missing in ATOMSEQ.
- // in theory that would only be
- // necessary for polymers but
- // here we add everything...
- };
-
bool Match_entity_resnum(const ost::mol::ResidueHandleList& res_list,
- const EntityInfo& info,
+ const ost::io::MMCifWriterEntity& info,
Real beyond_frac = 0.05) {
// Checks if res_list matches SEQRES given in info.mon_ids
// It may be that res_list defines residues beyond this SEQRES or
@@ -614,7 +584,7 @@ namespace {
}
bool Match_entity(const ost::mol::ResidueHandleList& res_list,
- const EntityInfo& info) {
+ const ost::io::MMCifWriterEntity& info) {
// checks if the residue names in res_list are an exact match
// with mon_ids in info
std::vector<String> mon_ids;
@@ -625,7 +595,7 @@ namespace {
}
void Add_asym(const String& asym_chain_name,
- EntityInfo& info) {
+ ost::io::MMCifWriterEntity& info) {
// adds asym_chain_name to info under the assumption that mon_ids
// exactly match => just add a copy of mon_ids to asym_alns
info.asym_ids.push_back(asym_chain_name);
@@ -634,7 +604,7 @@ namespace {
void Add_asym_resnum(const String& asym_chain_name,
const ost::mol::ResidueHandleList& res_list,
- EntityInfo& info) {
+ ost::io::MMCifWriterEntity& info) {
if(!info.is_poly) {
// no need for SEQRES alignment vodoo
@@ -698,7 +668,7 @@ namespace {
const String& poly_type,
const ost::mol::ResidueHandleList& res_list,
bool resnum_alignment,
- std::vector<EntityInfo>& entity_infos) {
+ std::vector<ost::io::MMCifWriterEntity>& entity_infos) {
bool is_poly = type == "polymer";
@@ -775,7 +745,7 @@ namespace {
int entity_idx = entity_infos.size();
- entity_infos.push_back(EntityInfo());
+ entity_infos.push_back(ost::io::MMCifWriterEntity());
entity_infos.back().type = type;
entity_infos.back().poly_type = poly_type;
entity_infos.back().mon_ids = mon_ids;
@@ -795,7 +765,7 @@ namespace {
int Setup_entity_(const String& asym_chain_name,
const ost::mol::ResidueHandleList& res_list,
bool resnum_alignment,
- std::vector<EntityInfo>& entity_infos) {
+ std::vector<ost::io::MMCifWriterEntity>& entity_infos) {
String type = GuessEntityType(res_list);
bool is_poly = type == "polymer";
@@ -811,7 +781,7 @@ namespace {
ost::mol::ChainType chain_type,
const ost::mol::ResidueHandleList& res_list,
bool resnum_alignment,
- std::vector<EntityInfo>& entity_infos) {
+ std::vector<ost::io::MMCifWriterEntity>& entity_infos) {
// use chain_type info attached to chain to determine
// _entity.type and _entity_poly.type
String type = GuessEntityType(chain_type);
@@ -952,7 +922,7 @@ namespace {
void Feed_pdbx_poly_seq_scheme(ost::io::StarLoop* pdbx_poly_seq_scheme_ptr,
const String& label_asym_id,
int label_entity_id,
- EntityInfo& entity_info,
+ ost::io::MMCifWriterEntity& entity_info,
const ost::mol::ResidueHandleList& res_list) {
std::vector<ost::io::StarLoopDataItemDO> data;
@@ -1017,7 +987,7 @@ namespace {
void Feed_atom_site_(ost::io::StarLoop* atom_site_ptr,
const String& label_asym_id,
int label_entity_id,
- const EntityInfo& entity_info,
+ const ost::io::MMCifWriterEntity& entity_info,
const ost::mol::ResidueHandleList& res_list) {
int asym_idx = entity_info.GetAsymIdx(label_asym_id);
@@ -1103,7 +1073,7 @@ namespace {
}
void Feed_entity_(ost::io::StarLoop* entity_ptr,
- const std::vector<EntityInfo>& entity_info) {
+ const std::vector<ost::io::MMCifWriterEntity>& entity_info) {
for(size_t entity_idx = 0; entity_idx < entity_info.size(); ++entity_idx) {
std::vector<ost::io::StarLoopDataItemDO> ent_data;
ent_data.push_back(ost::io::StarLoopDataItemDO(entity_idx));
@@ -1113,7 +1083,7 @@ namespace {
}
void Feed_struct_asym_(ost::io::StarLoop* struct_asym_ptr,
- const std::vector<EntityInfo>& entity_info) {
+ const std::vector<ost::io::MMCifWriterEntity>& 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;
@@ -1125,7 +1095,7 @@ namespace {
}
void Feed_entity_poly_seq_(ost::io::StarLoop* entity_poly_seq_ptr,
- const std::vector<EntityInfo>& entity_info) {
+ const std::vector<ost::io::MMCifWriterEntity>& entity_info) {
// reuse data vector for efficiency
std::vector<ost::io::StarLoopDataItemDO> entity_poly_seq_data;
entity_poly_seq_data.push_back(ost::io::StarLoopDataItemDO(0));
@@ -1146,7 +1116,7 @@ namespace {
}
void Feed_entity_poly_(ost::io::StarLoop* entity_poly_ptr,
- const std::vector<EntityInfo>& entity_info) {
+ const std::vector<ost::io::MMCifWriterEntity>& entity_info) {
// reuse data vector for efficiency
std::vector<ost::io::StarLoopDataItemDO> entity_poly_data;
entity_poly_data.push_back(ost::io::StarLoopDataItemDO(0));
@@ -1194,7 +1164,7 @@ namespace {
void SetStructure_(const ost::mol::EntityHandle& ent,
std::map<String, CompInfo>& comp_infos,
- std::vector<EntityInfo>& entity_info,
+ std::vector<ost::io::MMCifWriterEntity>& entity_info,
ost::io::StarLoop* atom_site,
ost::io::StarLoop* pdbx_poly_seq_scheme) {
ost::mol::ChainHandleList chain_list = ent.GetChainList();
@@ -1220,7 +1190,7 @@ namespace {
void SetStructuremmCIFify_(const ost::mol::EntityHandle& ent,
std::map<String, CompInfo>& comp_infos,
- std::vector<EntityInfo>& entity_info,
+ std::vector<ost::io::MMCifWriterEntity>& entity_info,
ost::io::StarLoop* atom_site,
ost::io::StarLoop* pdbx_poly_seq_scheme) {
@@ -1493,6 +1463,23 @@ namespace {
namespace ost { namespace io {
+int MMCifWriterEntity::GetAsymIdx(const String& asym_id) const {
+ for(size_t i = 0; i < asym_ids.size(); ++i) {
+ if(asym_ids[i] == asym_id) {
+ return i;
+ }
+ }
+ std::stringstream ss;
+ ss << "Tried to find asym id " << asym_id << "in entity that has only ";
+ ss << "the following asym ids: ";
+ for(auto i: asym_ids) {
+ ss << i << ", ";
+ }
+ String err = ss.str();
+ err = err.substr(0, err.size()-2); // remove last ", "
+ throw ost::io::IOException(err);
+}
+
MMCifWriter::MMCifWriter(const String& filename, const IOProfile& profile):
StarWriter(filename),
profile_(profile),
@@ -1571,11 +1558,10 @@ void MMCifWriter::SetStructure(const ost::mol::EntityHandle& ent,
chem_comp_ = Setup_chem_comp_ptr();
std::map<String, CompInfo> comp_infos;
- std::vector<EntityInfo> entity_info;
- // 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
+ // The SetStructure functions fill comp_info and entity_info_, 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_.
if(mmcif_conform) {
// chains are assumed to be mmCIF conform - that means water in separate
@@ -1583,17 +1569,17 @@ void MMCifWriter::SetStructure(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.
- SetStructure_(ent, comp_infos, entity_info,
+ SetStructure_(ent, comp_infos, entity_info_,
atom_site_, pdbx_poly_seq_scheme_);
} else {
// rule based splitting of chains into mmCIF conform chains
- SetStructuremmCIFify_(ent, comp_infos, entity_info,
+ 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);
- Feed_entity_poly_seq_(entity_poly_seq_, entity_info);
+ Feed_entity_(entity_, entity_info_);
+ Feed_struct_asym_(struct_asym_, entity_info_);
+ Feed_entity_poly_(entity_poly_, entity_info_);
+ Feed_entity_poly_seq_(entity_poly_seq_, entity_info_);
Feed_chem_comp_(chem_comp_, comp_infos);
Feed_atom_type_(atom_type_, atom_site_);
diff --git a/modules/io/src/mol/mmcif_writer.hh b/modules/io/src/mol/mmcif_writer.hh
index 262c516be..fd91f6749 100644
--- a/modules/io/src/mol/mmcif_writer.hh
+++ b/modules/io/src/mol/mmcif_writer.hh
@@ -29,6 +29,42 @@
namespace ost { namespace io {
+
+struct MMCifWriterEntity {
+
+ int GetAsymIdx(const String& asym_id) const;
+
+ // _entity.type
+ String type;
+
+ // _entity_poly.type
+ String poly_type;
+
+ // Names of chains in AU that are assigned to this entity
+ std::vector<String> asym_ids;
+
+ // in principle type == "polymer"
+ bool is_poly;
+
+ // SEQRES... kind of... internally we're not working on one letter codes
+ // etc. but on full compound names. Only one element if is_poly is false.
+ std::vector<String> mon_ids;
+
+ // The respective strings for pdbx_seq_one_letter_code
+ // Irrelevant if is_poly is false.
+ std::vector<String> seq_olcs;
+
+ // same for pdbx_seq_one_letter_code_can
+ // Irrelevant if is_poly is false.
+ std::vector<String> seq_can_olcs;
+
+ // One alignment to mon_ids for each element in asym_ids, i.e. SEQRES-ATOMSEQ
+ // alignment. Contains "-" for residues that are missing in ATOMSEQ.
+ // irrelevant if is_poly is false.
+ std::vector<std::vector<String> > asym_alns;
+};
+
+
class DLLEXPORT_OST_IO MMCifWriter : public StarWriter {
public:
@@ -40,6 +76,7 @@ public:
private:
IOProfile profile_;
+ std::vector<MMCifWriterEntity> entity_info_;
StarLoop* atom_type_;
StarLoop* atom_site_;
StarLoop* pdbx_poly_seq_scheme_;
--
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