From ac4ffe27ded452078fdf29cd09b8bc3de5c8f618 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 5 Jan 2024 14:57:02 +0100
Subject: [PATCH] mmcif writer: enable ost::mol::EntityHandle in MMCifWriter
---
modules/io/pymod/export_mmcif_io.cc | 15 +-
modules/io/src/mol/mmcif_writer.cc | 244 +++++++++++++++++-----------
modules/io/src/mol/mmcif_writer.hh | 13 ++
3 files changed, 172 insertions(+), 100 deletions(-)
diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index de498d382..15c0beebe 100644
--- a/modules/io/pymod/export_mmcif_io.cc
+++ b/modules/io/pymod/export_mmcif_io.cc
@@ -70,6 +70,18 @@ void WrapStarWriterWrite(StarWriter& writer, const String& data_name,
writer.Write(data_name, filename);
}
+void WrapSetStructureHandle(MMCifWriter& writer,
+ const ost::mol::EntityHandle& ent,
+ bool mmcif_conform) {
+ writer.SetStructure(ent, mmcif_conform);
+}
+
+void WrapSetStructureView(MMCifWriter& writer,
+ const ost::mol::EntityView& ent,
+ bool mmcif_conform) {
+ writer.SetStructure(ent, mmcif_conform);
+}
+
void export_mmcif_io()
{
class_<MMCifReader, boost::noncopyable>("MMCifReader", init<const String&, EntityHandle&, const IOProfile&>())
@@ -124,7 +136,8 @@ void export_mmcif_io()
;
class_<MMCifWriter, bases<StarWriter> >("MMCifWriter", init<>())
- .def("SetStructure", &MMCifWriter::SetStructure, (arg("ent"), arg("mmcif_conform")=true))
+ .def("SetStructure", &WrapSetStructureHandle, (arg("ent"), arg("mmcif_conform")=true))
+ .def("SetStructure", &WrapSetStructureView, (arg("ent"), arg("mmcif_conform")=true))
;
enum_<MMCifInfoCitation::MMCifInfoCType>("MMCifInfoCType")
diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index 35dd15c6b..2c5490ea4 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -68,7 +68,9 @@ namespace {
std::vector<int> indices;
};
- String GuessEntityPolyType(const ost::mol::ResidueHandleList& res_list) {
+ // template to allow ost::mol::ResidueHandleList and ost::mol::ResidueViewList
+ template<class T>
+ String GuessEntityPolyType(const T& res_list) {
// guesses _entity_poly.type based on residue chem classes
@@ -152,7 +154,9 @@ namespace {
return "other";
}
- String GuessEntityType(const ost::mol::ResidueHandleList& res_list) {
+ // template to allow ost::mol::ResidueHandleList and ost::mol::ResidueViewList
+ template<class T>
+ String GuessEntityType(const T& res_list) {
// guesses _entity.type based on residue chem classes
@@ -188,11 +192,6 @@ namespace {
return "polymer";
}
- // internal object with all info to fill chem_comp_ category
- struct CompInfo {
- String type;
- };
-
inline String ChemClassToChemCompType(char chem_class) {
String type = "";
switch(chem_class) {
@@ -435,8 +434,10 @@ namespace {
return "(" + mon_id + ")";
}
- void SetupChemComp(const ost::mol::ResidueHandleList& res_list,
- std::map<String, CompInfo>& comp_infos) {
+ // template to allow ost::mol::ResidueHandleList and ost::mol::ResidueViewList
+ template<class T>
+ void SetupChemComp(const T& res_list,
+ std::map<String, ost::io::MMCifWriterComp>& comp_infos) {
for(auto res: res_list) {
String res_name = res.GetName();
String type = ChemClassToChemCompType(res.GetChemClass());
@@ -450,7 +451,7 @@ namespace {
if(type == "OTHER") {
continue;
} else if (it->second.type == "OTHER") {
- CompInfo info;
+ ost::io::MMCifWriterComp info;
info.type = type;
comp_infos[res_name] = info;
} else {
@@ -463,14 +464,16 @@ namespace {
}
}
} else {
- CompInfo info;
+ ost::io::MMCifWriterComp info;
info.type = type;
comp_infos[res_name] = info;
}
}
}
- bool MatchEntity(const ost::mol::ResidueHandleList& res_list,
+ // template to allow ost::mol::ResidueHandleList and ost::mol::ResidueViewList
+ template<class T>
+ bool MatchEntity(const T& res_list,
const ost::io::MMCifWriterEntity& info) {
// checks if the residue names in res_list are an exact match
// with mon_ids in info
@@ -489,7 +492,9 @@ namespace {
info.asym_alns.push_back(info.mon_ids);
}
- bool MatchEntityResnum(const ost::mol::ResidueHandleList& res_list,
+ // template to allow ost::mol::ResidueHandleList and ost::mol::ResidueViewList
+ template<class T>
+ bool MatchEntityResnum(const T& res_list,
const ost::io::MMCifWriterEntity& info,
Real beyond_frac = 0.05) {
// Checks if res_list matches SEQRES given in info.mon_ids
@@ -540,8 +545,10 @@ namespace {
}
}
+ // template to allow ost::mol::ResidueHandleList and ost::mol::ResidueViewList
+ template<class T>
void AddAsymResnum(const String& asym_chain_name,
- const ost::mol::ResidueHandleList& res_list,
+ const T& res_list,
ost::io::MMCifWriterEntity& info) {
if(!info.is_poly) {
@@ -584,10 +591,9 @@ namespace {
for(size_t i = 0; i < resnums.size(); ++i) {
if(info.mon_ids[resnums[i]-1] == "-") {
info.mon_ids[resnums[i]-1] = mon_ids[i];
- const ost::mol::ResidueHandle& res = res_list[i];
- info.seq_olcs[resnums[i]-1] = MonIDToOLC(res.GetChemClass(),
+ info.seq_olcs[resnums[i]-1] = MonIDToOLC(res_list[i].GetChemClass(),
mon_ids[i]);
- char olc = res.GetOneLetterCode();
+ char olc = res_list[i].GetOneLetterCode();
if(olc < 'A' || olc > 'Z') {
info.seq_can_olcs[resnums[i]-1] = "X";
} else {
@@ -601,10 +607,12 @@ namespace {
info.asym_alns.push_back(aln_mon_ids);
}
+ // template to allow ost::mol::ResidueHandleList and ost::mol::ResidueViewList
+ template<class T>
int SetupEntity(const String& asym_chain_name,
const String& type,
const String& poly_type,
- const ost::mol::ResidueHandleList& res_list,
+ const T& res_list,
bool resnum_alignment,
std::vector<ost::io::MMCifWriterEntity>& entity_infos) {
@@ -678,10 +686,9 @@ namespace {
seq_can.assign(max_resnum, "-");
for(size_t i = 0; i < res_mon_ids.size(); ++i) {
mon_ids[resnums[i]-1] = res_mon_ids[i];
- const ost::mol::ResidueHandle& res = res_list[i];
- seq[resnums[i]-1] = MonIDToOLC(res.GetChemClass(),
+ seq[resnums[i]-1] = MonIDToOLC(res_list[i].GetChemClass(),
mon_ids[resnums[i]-1]);
- char olc = res.GetOneLetterCode();
+ char olc = res_list[i].GetOneLetterCode();
if(olc < 'A' || olc > 'Z') {
seq_can[resnums[i]-1] = "X";
} else {
@@ -725,8 +732,10 @@ namespace {
return entity_idx;
}
+ // template to allow ost::mol::ResidueHandleList and ost::mol::ResidueViewList
+ template<class T>
int SetupEntity(const String& asym_chain_name,
- const ost::mol::ResidueHandleList& res_list,
+ const T& res_list,
bool resnum_alignment,
std::vector<ost::io::MMCifWriterEntity>& entity_infos) {
// use chem types in res_list to determine _entity.type and
@@ -741,9 +750,11 @@ namespace {
resnum_alignment, entity_infos);
}
+ // template to allow ost::mol::ResidueHandleList and ost::mol::ResidueViewList
+ template<class T>
int SetupEntity(const String& asym_chain_name,
ost::mol::ChainType chain_type,
- const ost::mol::ResidueHandleList& res_list,
+ const T& res_list,
bool resnum_alignment,
std::vector<ost::io::MMCifWriterEntity>& entity_infos) {
// use chain_type info attached to chain to determine
@@ -864,11 +875,13 @@ namespace {
}
}
+ // template to allow ost::mol::ResidueHandleList and ost::mol::ResidueViewList
+ template<class T>
void Feed_pdbx_poly_seq_scheme(ost::io::StarWriterLoopPtr pdbx_poly_seq_scheme_ptr,
const String& label_asym_id,
int label_entity_id,
ost::io::MMCifWriterEntity& entity_info,
- const ost::mol::ResidueHandleList& res_list) {
+ const T& res_list) {
std::vector<ost::io::StarWriterValue> data;
data.push_back(ost::io::StarWriterValue::FromString(label_asym_id));
@@ -916,7 +929,7 @@ namespace {
if(ins_code == '\0') {
data[6] = ost::io::StarWriterValue::FromString("");
} else {
- data[6] = ost::io::StarWriterValue::FromString(String(1, ' '));
+ data[6] = ost::io::StarWriterValue::FromString(String(1, ins_code));
}
}
pdbx_poly_seq_scheme_ptr->AddData(data);
@@ -924,11 +937,13 @@ namespace {
}
}
+ // template to allow ost::mol::ResidueHandleList and ost::mol::ResidueViewList
+ template<class T>
void Feed_atom_site(ost::io::StarWriterLoopPtr atom_site_ptr,
const String& label_asym_id,
int label_entity_id,
const ost::io::MMCifWriterEntity& entity_info,
- const ost::mol::ResidueHandleList& res_list) {
+ const T& res_list) {
int asym_idx = entity_info.GetAsymIdx(label_asym_id);
const std::vector<String>& aln = entity_info.asym_alns[asym_idx];
@@ -937,7 +952,7 @@ namespace {
for(auto res: res_list) {
String comp_id = res.GetName();
- ost::mol::AtomHandleList at_list = res.GetAtomList();
+ auto at_list = res.GetAtomList();
String auth_asym_id = res.GetChain().GetName();
if(res.HasProp("pdb_auth_chain_name")) {
auth_asym_id = res.GetStringProp("pdb_auth_chain_name");
@@ -1086,7 +1101,7 @@ namespace {
}
void Feed_chem_comp(ost::io::StarWriterLoopPtr chem_comp_ptr,
- const std::map<String, CompInfo>& comp_infos) {
+ const std::map<String, ost::io::MMCifWriterComp>& comp_infos) {
std::vector<ost::io::StarWriterValue> comp_data;
comp_data.push_back(ost::io::StarWriterValue::FromString("ALA"));
comp_data.push_back(ost::io::StarWriterValue::FromString("L-PEPTIDE LINKING"));
@@ -1097,54 +1112,27 @@ namespace {
}
}
- void ProcessEnt(const ost::mol::EntityHandle& ent,
- std::map<String, CompInfo>& comp_infos,
- std::vector<ost::io::MMCifWriterEntity>& entity_info,
- ost::io::StarWriterLoopPtr atom_site,
- ost::io::StarWriterLoopPtr pdbx_poly_seq_scheme) {
- ost::mol::ChainHandleList chain_list = ent.GetChainList();
- for(auto ch: chain_list) {
-
- ost::mol::ResidueHandleList res_list = ch.GetResidueList();
-
- SetupChemComp(res_list, comp_infos);
- String chain_name = ch.GetName();
- int entity_id = SetupEntity(chain_name,
- ch.GetType(),
- res_list,
- true,
- entity_info);
- Feed_atom_site(atom_site, chain_name, entity_id, entity_info[entity_id],
- res_list);
- if(entity_info[entity_id].is_poly) {
- Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, chain_name,
- entity_id, entity_info[entity_id], res_list);
- }
- }
- }
-
- void ProcessEntmmCIFify(const ost::mol::EntityHandle& ent,
- std::map<String, CompInfo>& comp_infos,
+ // template to allow ost::mol::ResidueHandleList and ost::mol::ResidueViewList
+ template<class T>
+ void ProcessEntmmCIFify(const std::vector<T>& res_lists,
+ std::map<String, ost::io::MMCifWriterComp>& comp_infos,
std::vector<ost::io::MMCifWriterEntity>& entity_info,
ost::io::StarWriterLoopPtr atom_site,
ost::io::StarWriterLoopPtr pdbx_poly_seq_scheme) {
ChainNameGenerator chain_name_gen;
- ost::mol::ChainHandleList chain_list = ent.GetChainList();
- for(auto ch: chain_list) {
-
- ost::mol::ResidueHandleList res_list = ch.GetResidueList();
+ for(auto res_list: res_lists) {
SetupChemComp(res_list, comp_infos);
- std::vector<ost::mol::ResidueHandle> L_chain;
- std::vector<ost::mol::ResidueHandle> D_chain;
- std::vector<ost::mol::ResidueHandle> P_chain;
- std::vector<ost::mol::ResidueHandle> R_chain;
- std::vector<ost::mol::ResidueHandle> S_chain;
- std::vector<ost::mol::ResidueHandle> Z_chain;
- std::vector<ost::mol::ResidueHandle> W_chain;
+ T L_chain;
+ T D_chain;
+ T P_chain;
+ T R_chain;
+ T S_chain;
+ T Z_chain;
+ T W_chain;
// first scan only concerning peptides...
// Avoid mix of both in same chain: L-peptide linking, D-peptide linking
@@ -1193,7 +1181,7 @@ namespace {
} else if(res.GetChemClass() == ost::mol::ChemClass::NON_POLYMER ||
res.GetChemClass() == ost::mol::ChemClass::UNKNOWN) {
// already process non-poly and unknown
- ost::mol::ResidueHandleList tmp;
+ T tmp;
tmp.push_back(res);
String chain_name = chain_name_gen.Get();
int entity_id = SetupEntity(chain_name,
@@ -1212,11 +1200,7 @@ namespace {
}
// process poly chains
- std::vector<ost::mol::ResidueHandle>* poly_chains[5] = {&L_chain,
- &D_chain,
- &P_chain,
- &R_chain,
- &S_chain};
+ T* poly_chains[5] = {&L_chain, &D_chain, &P_chain, &R_chain, &S_chain};
for(int i = 0; i < 5; ++i) {
if(!poly_chains[i]->empty()) {
String chain_name = chain_name_gen.Get();
@@ -1259,8 +1243,70 @@ namespace {
}
}
+ void ProcessEntmmCIFify(const ost::mol::EntityHandle& ent,
+ std::map<String, ost::io::MMCifWriterComp>& comp_infos,
+ std::vector<ost::io::MMCifWriterEntity>& entity_info,
+ ost::io::StarWriterLoopPtr atom_site,
+ ost::io::StarWriterLoopPtr pdbx_poly_seq_scheme) {
+ std::vector<ost::mol::ResidueHandleList> res_lists;
+ ost::mol::ChainHandleList chain_list = ent.GetChainList();
+ for(auto ch: chain_list) {
+ res_lists.push_back(ch.GetResidueList());
+ }
+ ProcessEntmmCIFify(res_lists, comp_infos, entity_info,
+ atom_site, pdbx_poly_seq_scheme);
+ }
+
+ void ProcessEntmmCIFify(const ost::mol::EntityView& ent,
+ std::map<String, ost::io::MMCifWriterComp>& comp_infos,
+ std::vector<ost::io::MMCifWriterEntity>& entity_info,
+ ost::io::StarWriterLoopPtr atom_site,
+ ost::io::StarWriterLoopPtr pdbx_poly_seq_scheme) {
+ std::vector<ost::mol::ResidueViewList> res_lists;
+ ost::mol::ChainViewList chain_list = ent.GetChainList();
+ for(auto ch: chain_list) {
+ res_lists.push_back(ch.GetResidueList());
+ }
+ ProcessEntmmCIFify(res_lists, comp_infos, entity_info,
+ atom_site, pdbx_poly_seq_scheme);
+ }
+
+ // template to allow ost::mol::EntityHandle and ost::mol::EntityView
+ template<class T>
+ void ProcessEnt(const T& ent,
+ bool mmcif_conform,
+ std::map<String, ost::io::MMCifWriterComp>& comp_infos,
+ std::vector<ost::io::MMCifWriterEntity>& entity_info,
+ ost::io::StarWriterLoopPtr atom_site,
+ ost::io::StarWriterLoopPtr pdbx_poly_seq_scheme) {
+
+ if(mmcif_conform) {
+ auto chain_list = ent.GetChainList();
+ for(auto ch: chain_list) {
+ auto res_list = ch.GetResidueList();
+ SetupChemComp(res_list, comp_infos);
+ String chain_name = ch.GetName();
+ int entity_id = SetupEntity(chain_name,
+ ch.GetType(),
+ res_list,
+ true,
+ entity_info);
+ Feed_atom_site(atom_site, chain_name, entity_id, entity_info[entity_id],
+ res_list);
+ if(entity_info[entity_id].is_poly) {
+ Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, chain_name,
+ entity_id, entity_info[entity_id], res_list);
+ }
+ }
+ } else {
+ // delegate to more complex ProcessEntmmCIFify
+ ProcessEntmmCIFify(ent, comp_infos, entity_info, atom_site,
+ pdbx_poly_seq_scheme);
+ }
+ }
+
void ProcessUnknowns(std::vector<ost::io::MMCifWriterEntity>& entity_infos,
- std::map<String, CompInfo>& comp_infos) {
+ std::map<String, ost::io::MMCifWriterComp>& comp_infos) {
for(size_t entity_idx = 0; entity_idx < entity_infos.size(); ++entity_idx) {
if(entity_infos[entity_idx].is_poly) {
@@ -1278,7 +1324,7 @@ namespace {
entity_infos[entity_idx].seq_olcs[mon_id_idx] = "(UNK)";
entity_infos[entity_idx].seq_can_olcs[mon_id_idx] = "X";
if(comp_infos.find("UNK") == comp_infos.end()) {
- CompInfo info;
+ ost::io::MMCifWriterComp info;
info.type = "L-PEPTIDE LINKING";
comp_infos["UNK"] = info;
}
@@ -1289,7 +1335,7 @@ namespace {
entity_infos[entity_idx].seq_olcs[mon_id_idx] = "(DN)";
entity_infos[entity_idx].seq_can_olcs[mon_id_idx] = "N";
if(comp_infos.find("DN") == comp_infos.end()) {
- CompInfo info;
+ ost::io::MMCifWriterComp info;
info.type = "DNA LINKING";
comp_infos["DN"] = info;
}
@@ -1301,7 +1347,7 @@ namespace {
entity_infos[entity_idx].seq_olcs[mon_id_idx] = "N";
entity_infos[entity_idx].seq_can_olcs[mon_id_idx] = "N";
if(comp_infos.find("N") == comp_infos.end()) {
- CompInfo info;
+ ost::io::MMCifWriterComp info;
info.type = "RNA LINKING";
comp_infos["N"] = info;
}
@@ -1343,6 +1389,22 @@ int MMCifWriterEntity::GetAsymIdx(const String& asym_id) const {
void MMCifWriter::SetStructure(const ost::mol::EntityHandle& ent,
bool mmcif_conform) {
+ this->Setup();
+ 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) {
+
+ this->Setup();
+ ProcessEnt(ent, mmcif_conform, comp_info_, entity_info_, atom_site_,
+ pdbx_poly_seq_scheme_);
+ this->Finalize();
+}
+
+void MMCifWriter::Setup() {
if(structure_set_) {
throw ost::io::IOException("SetStructure can be called only once on a "
"given MMCifWriter instance");
@@ -1356,37 +1418,21 @@ void MMCifWriter::SetStructure(const ost::mol::EntityHandle& ent,
entity_poly_ = Setup_entity_poly_ptr();
entity_poly_seq_ = Setup_entity_poly_seq_ptr();
chem_comp_ = Setup_chem_comp_ptr();
+}
- std::map<String, CompInfo> comp_infos;
-
- // The ProcessEnt 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
- // chains, ligands in separate chains etc. Chain types are inferred from
- // chain type property set to the chains in ent.
- ProcessEnt(ent, comp_infos, entity_info_,
- atom_site_, pdbx_poly_seq_scheme_);
- } else {
- // rule based splitting of chains into mmCIF conform chains
- ProcessEntmmCIFify(ent, comp_infos, entity_info_,
- atom_site_, pdbx_poly_seq_scheme_);
- }
-
- // depending on the strategy above, there might be gaps in the entities
- // mon_ids/ seq_olcs/ seq_can_olcs
+void MMCifWriter::Finalize() {
+ // depending on the strategy (mmcif_conform), there might be gaps in the
+ // entities mon_ids/ seq_olcs/ seq_can_olcs
// The following function adds valid stuff depending on chain type
// (e.g. UNK if we're having a peptide linking chain and then adds
// that UNK directly to comp_info)
- ProcessUnknowns(entity_info_, comp_infos);
+ ProcessUnknowns(entity_info_, comp_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_chem_comp(chem_comp_, comp_info_);
Feed_atom_type(atom_type_, atom_site_);
// finalize
diff --git a/modules/io/src/mol/mmcif_writer.hh b/modules/io/src/mol/mmcif_writer.hh
index cc44706df..c176ac74f 100644
--- a/modules/io/src/mol/mmcif_writer.hh
+++ b/modules/io/src/mol/mmcif_writer.hh
@@ -66,6 +66,11 @@ struct MMCifWriterEntity {
};
+struct MMCifWriterComp {
+ String type;
+};
+
+
class DLLEXPORT_OST_IO MMCifWriter : public StarWriter {
public:
@@ -75,8 +80,16 @@ public:
void SetStructure(const ost::mol::EntityHandle& ent, bool mmcif_conform=true);
+ void SetStructure(const ost::mol::EntityView& ent, bool mmcif_conform=true);
+
private:
+
+ void Setup();
+
+ void Finalize();
+
std::vector<MMCifWriterEntity> entity_info_;
+ std::map<String, MMCifWriterComp> comp_info_;
StarWriterLoopPtr atom_type_;
StarWriterLoopPtr atom_site_;
StarWriterLoopPtr pdbx_poly_seq_scheme_;
--
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