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libcifpp
Commit 9c4170d9 by Maarten L. Hekkelman
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- Added more const members 

- change PDB writing interface
parent 4a82a8d5
Showing with 93 additions and 67 deletions
CMakeLists.txt
......@@ -25,7 +25,7 @@
cmake_minimum_required(VERSION 3.16)
# set the project name
project(cifpp VERSION 4.0.0 LANGUAGES CXX)
project(cifpp VERSION 4.0.1 LANGUAGES CXX)
list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
......
changelog
Version 4.0.1
- Added a bunch of const methods to Datablock and Category.
- Changed PDB writing interface to accept Datablock instead of File.
Version 4.0.0
- getResidue in mmcif::Structure now requires both a
sequence ID and an auth sequence ID. As a result the code was cleaned
......
include/cif++/Cif++.hpp
......@@ -254,8 +254,15 @@ class Datablock
const_iterator begin() const { return mCategories.begin(); }
const_iterator end() const { return mCategories.end(); }
/// \brief Access to the category with name \a name, will create it if it doesn't exist.
Category &operator[](std::string_view name);
// /// \brief Access to the category with name \a name, will throw if it doesn't exist.
// const Category &operator[](std::string_view name) const;
/// \brief Access to the category with name \a name, will return an empty category if is doesn't exist.
const Category &operator[](std::string_view name) const;
std::tuple<iterator, bool> emplace(std::string_view name);
bool isValid();
......@@ -285,6 +292,9 @@ class Datablock
std::string mName;
const Validator *mValidator;
Datablock *mNext;
// for returning empty categories in the const operator[]
mutable std::unique_ptr<Category> mNullCategory;
};
// --------------------------------------------------------------------
......@@ -1863,6 +1873,9 @@ class Category
Row front() { return Row(mHead); }
Row back() { return Row(mTail); }
const Row front() const { return Row(mHead); }
const Row back() const { return Row(mTail); }
Row operator[](Condition &&cond);
const Row operator[](Condition &&cond) const;
......
include/cif++/Cif2PDB.hpp
......@@ -28,12 +28,12 @@
#include "cif++/Cif++.hpp"
void WritePDBFile(std::ostream& pdbFile, cif::File& cifFile);
void WritePDBFile(std::ostream &os, const cif::Datablock &data);
/// \brief Just the HEADER, COMPND, SOURCE and AUTHOR lines
void WritePDBHeaderLines(std::ostream& os, cif::File& cifFile);
void WritePDBHeaderLines(std::ostream &os, const cif::Datablock &data);
std::string GetPDBHEADERLine(cif::File& cifFile, std::string::size_type truncate_at = 127);
std::string GetPDBCOMPNDLine(cif::File& cifFile, std::string::size_type truncate_at = 127);
std::string GetPDBSOURCELine(cif::File& cifFile, std::string::size_type truncate_at = 127);
std::string GetPDBAUTHORLine(cif::File& cifFile, std::string::size_type truncate_at = 127);
std::string GetPDBHEADERLine(const cif::Datablock &data, std::string::size_type truncate_at = 127);
std::string GetPDBCOMPNDLine(const cif::Datablock &data, std::string::size_type truncate_at = 127);
std::string GetPDBSOURCELine(const cif::Datablock &data, std::string::size_type truncate_at = 127);
std::string GetPDBAUTHORLine(const cif::Datablock &data, std::string::size_type truncate_at = 127);
src/Cif++.cpp
......@@ -409,6 +409,22 @@ Category &Datablock::operator[](std::string_view name)
return *i;
}
const Category &Datablock::operator[](std::string_view name) const
{
using namespace std::literals;
auto result = get(name);
if (result == nullptr)
// throw std::out_of_range("The category with name " + std::string(name) + " does not exist");
{
std::unique_lock lock(mLock);
if (not mNullCategory)
mNullCategory.reset(new Category(const_cast<Datablock&>(*this), "<null>", nullptr));
result = mNullCategory.get();
}
return *result;
}
Category *Datablock::get(std::string_view name)
{
std::shared_lock lock(mLock);
......@@ -1525,6 +1541,11 @@ void Category::drop(const std::string &field)
}
}
const Row Category::operator[](Condition &&cond) const
{
return const_cast<Category*>(this)->operator[](std::forward<Condition>(cond));
}
Row Category::operator[](Condition &&cond)
{
Row result;
......
src/Cif2PDB.cpp
......@@ -146,7 +146,7 @@ std::string cif2pdbSymmetry(std::string s)
return s;
}
std::string cif2pdbAtomName(std::string name, std::string resName, Datablock& db)
std::string cif2pdbAtomName(std::string name, std::string resName, const Datablock& db)
{
if (name.length() < 4)
{
......@@ -166,7 +166,7 @@ std::string cif2pdbAtomName(std::string name, std::string resName, Datablock& db
enum SoftwareType { eRefinement, eDataScaling, eDataExtraction, eDataReduction, ePhasing };
std::string cifSoftware(Datablock& db, SoftwareType sw)
std::string cifSoftware(const Datablock& db, SoftwareType sw)
{
std::string result = "NULL";
......@@ -210,7 +210,7 @@ std::string cifSoftware(Datablock& db, SoftwareType sw)
}
// Map asym ID's back to PDB Chain ID's
std::vector<std::string> MapAsymIDs2ChainIDs(const std::vector<std::string>& asymIDs, Datablock& db)
std::vector<std::string> MapAsymIDs2ChainIDs(const std::vector<std::string>& asymIDs, const Datablock& db)
{
std::set<std::string> result;
......@@ -275,7 +275,7 @@ size_t WriteOneContinuedLine(std::ostream& pdbFile, std::string header, int cLen
return WriteContinuedLine(pdbFile, header, count, cLen, line, lStart);
}
size_t WriteCitation(std::ostream& pdbFile, Datablock& db, Row r, int reference)
size_t WriteCitation(std::ostream& pdbFile, const Datablock& db, Row r, int reference)
{
size_t result = 0;
......@@ -361,7 +361,7 @@ size_t WriteCitation(std::ostream& pdbFile, Datablock& db, Row r, int reference)
return result;
}
void WriteHeaderLines(std::ostream& pdbFile, Datablock& db)
void WriteHeaderLines(std::ostream& pdbFile, const Datablock& db)
{
// 0 1 2 3 4 5 6 7 8
// HEADER xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxDDDDDDDDD IIII
......@@ -592,7 +592,7 @@ void WriteHeaderLines(std::ostream& pdbFile, Datablock& db)
WriteOneContinuedLine(pdbFile, "AUTHOR ", 2, ba::join(authors, ","));
}
void WriteTitle(std::ostream& pdbFile, Datablock& db)
void WriteTitle(std::ostream& pdbFile, const Datablock& db)
{
WriteHeaderLines(pdbFile, db);
......@@ -644,7 +644,7 @@ void WriteTitle(std::ostream& pdbFile, Datablock& db)
}
}
void WriteRemark1(std::ostream& pdbFile, Datablock& db)
void WriteRemark1(std::ostream& pdbFile, const Datablock& db)
{
int reference = 0;
......@@ -662,7 +662,7 @@ void WriteRemark1(std::ostream& pdbFile, Datablock& db)
}
}
void WriteRemark2(std::ostream& pdbFile, Datablock& db)
void WriteRemark2(std::ostream& pdbFile, const Datablock& db)
{
auto& refine = db["refine"];
if (refine.empty())
......@@ -698,7 +698,7 @@ class FBase
protected:
FBase(Row r, const char* f)
: mRow(r), mField(f) {}
FBase(Category& cat, cif::Condition&& cond, const char* f)
FBase(const Category& cat, cif::Condition&& cond, const char* f)
: mField(f)
{
auto r = cat.find(std::move(cond));
......@@ -714,7 +714,7 @@ class Fi : public FBase
{
public:
Fi(Row r, const char* f) : FBase(r, f) {}
Fi(Category& cat, cif::Condition&& cond, const char* f) : FBase(cat, std::move(cond), f) {}
Fi(const Category& cat, cif::Condition&& cond, const char* f) : FBase(cat, std::move(cond), f) {}
virtual void out(std::ostream& os)
{
......@@ -734,7 +734,7 @@ class Ff : public FBase
{
public:
Ff(Row r, const char* f) : FBase(r, f) {}
Ff(Category& cat, cif::Condition&& cond, const char* f) : FBase(cat, std::move(cond), f) {}
Ff(const Category& cat, cif::Condition&& cond, const char* f) : FBase(cat, std::move(cond), f) {}
virtual void out(std::ostream& os)
{
......@@ -765,7 +765,7 @@ class Fs : public FBase
{
public:
Fs(Row r, const char* f, int remarkNr = 3) : FBase(r, f), mNr(remarkNr) {}
Fs(Category& cat, cif::Condition&& cond, const char* f, int remarkNr = 3) : FBase(cat, std::move(cond), f), mNr(remarkNr) {}
Fs(const Category& cat, cif::Condition&& cond, const char* f, int remarkNr = 3) : FBase(cat, std::move(cond), f), mNr(remarkNr) {}
virtual void out(std::ostream& os)
{
......@@ -831,7 +831,7 @@ std::ostream& operator<<(std::ostream& os, SEP&& sep)
// --------------------------------------------------------------------
void WriteRemark3BusterTNT(std::ostream& pdbFile, Datablock& db)
void WriteRemark3BusterTNT(std::ostream& pdbFile, const Datablock& db)
{
auto refine = db["refine"].front();
auto ls_shell = db["refine_ls_shell"].front();
......@@ -1009,7 +1009,7 @@ void WriteRemark3BusterTNT(std::ostream& pdbFile, Datablock& db)
// --------------------------------------------------------------------
void WriteRemark3CNS(std::ostream& pdbFile, Datablock& db)
void WriteRemark3CNS(std::ostream& pdbFile, const Datablock& db)
{
auto refine = db["refine"].front();
auto ls_shell = db["refine_ls_shell"].front();
......@@ -1149,7 +1149,7 @@ void WriteRemark3CNS(std::ostream& pdbFile, Datablock& db)
// --------------------------------------------------------------------
void WriteRemark3Refmac(std::ostream& pdbFile, Datablock& db)
void WriteRemark3Refmac(std::ostream& pdbFile, const Datablock& db)
{
auto refine = db["refine"].front();
auto ls_shell = db["refine_ls_shell"].front();
......@@ -1476,7 +1476,7 @@ void WriteRemark3Refmac(std::ostream& pdbFile, Datablock& db)
<< RM3("") << std::endl;
}
void WriteRemark3Shelxl(std::ostream& pdbFile, Datablock& db)
void WriteRemark3Shelxl(std::ostream& pdbFile, const Datablock& db)
{
auto refine = db["refine"].front();
// auto ls_shell = db["refine_ls_shell"].front();
......@@ -1555,7 +1555,7 @@ void WriteRemark3Shelxl(std::ostream& pdbFile, Datablock& db)
<< RM3("") << std::endl;
}
void WriteRemark3Phenix(std::ostream& pdbFile, Datablock& db)
void WriteRemark3Phenix(std::ostream& pdbFile, const Datablock& db)
{
auto refine = db["refine"].front();
// auto ls_shell = db["refine_ls_shell"].front();
......@@ -1782,7 +1782,7 @@ void WriteRemark3Phenix(std::ostream& pdbFile, Datablock& db)
pdbFile << RM3("") << std::endl;
}
void WriteRemark3XPlor(std::ostream& pdbFile, Datablock& db)
void WriteRemark3XPlor(std::ostream& pdbFile, const Datablock& db)
{
auto refine = db["refine"].front();
auto ls_shell = db["refine_ls_shell"].front();
......@@ -1897,7 +1897,7 @@ void WriteRemark3XPlor(std::ostream& pdbFile, Datablock& db)
<< RM3("") << std::endl;
}
void WriteRemark3NuclSQ(std::ostream& pdbFile, Datablock& db)
void WriteRemark3NuclSQ(std::ostream& pdbFile, const Datablock& db)
{
auto refine = db["refine"].front();
auto pdbx_refine = db["pdbx_refine"].front();
......@@ -2001,7 +2001,7 @@ void WriteRemark3NuclSQ(std::ostream& pdbFile, Datablock& db)
<< RM3("") << std::endl;
}
void WriteRemark3ProlSQ(std::ostream& pdbFile, Datablock& db)
void WriteRemark3ProlSQ(std::ostream& pdbFile, const Datablock& db)
{
auto refine = db["refine"].front();
auto pdbx_refine = db["pdbx_refine"].front();
......@@ -2120,7 +2120,7 @@ void WriteRemark3ProlSQ(std::ostream& pdbFile, Datablock& db)
<< RM3("") << std::endl;
}
void WriteRemark3(std::ostream& pdbFile, Datablock& db)
void WriteRemark3(std::ostream& pdbFile, const Datablock& db)
{
std::string program, authors;
......@@ -2200,7 +2200,7 @@ void WriteRemark3(std::ostream& pdbFile, Datablock& db)
}
}
void WriteRemark200(std::ostream& pdbFile, Datablock& db)
void WriteRemark200(std::ostream& pdbFile, const Datablock& db)
{
typedef RM<200> RM;
......@@ -2335,7 +2335,7 @@ void WriteRemark200(std::ostream& pdbFile, Datablock& db)
}
}
void WriteRemark280(std::ostream& pdbFile, Datablock& db)
void WriteRemark280(std::ostream& pdbFile, const Datablock& db)
{
typedef RM<280> RM;
......@@ -2397,7 +2397,7 @@ void WriteRemark280(std::ostream& pdbFile, Datablock& db)
}
}
void WriteRemark350(std::ostream& pdbFile, Datablock& db)
void WriteRemark350(std::ostream& pdbFile, const Datablock& db)
{
auto& c1 = db["pdbx_struct_assembly"];
if (c1.empty())
......@@ -2517,7 +2517,7 @@ void WriteRemark350(std::ostream& pdbFile, Datablock& db)
}
}
void WriteRemark400(std::ostream& pdbFile, Datablock& db)
void WriteRemark400(std::ostream& pdbFile, const Datablock& db)
{
for (auto& r: db["pdbx_entry_details"])
{
......@@ -2527,7 +2527,7 @@ void WriteRemark400(std::ostream& pdbFile, Datablock& db)
}
}
void WriteRemark450(std::ostream& pdbFile, Datablock& db)
void WriteRemark450(std::ostream& pdbFile, const Datablock& db)
{
for (auto& r: db["pdbx_entry_details"])
{
......@@ -2538,7 +2538,7 @@ void WriteRemark450(std::ostream& pdbFile, Datablock& db)
}
}
void WriteRemark465(std::ostream& pdbFile, Datablock& db)
void WriteRemark465(std::ostream& pdbFile, const Datablock& db)
{
bool first = true;
typedef RM<465> RM;
......@@ -2587,7 +2587,7 @@ void WriteRemark465(std::ostream& pdbFile, Datablock& db)
}
}
void WriteRemark470(std::ostream& pdbFile, Datablock& db)
void WriteRemark470(std::ostream& pdbFile, const Datablock& db)
{
typedef RM<470> RM;
boost::format fmt("REMARK 470 %3.3s %3.3s %1.1s%4.4d%1.1s ");
......@@ -2646,12 +2646,12 @@ void WriteRemark470(std::ostream& pdbFile, Datablock& db)
}
}
void WriteRemark610(std::ostream& pdbFile, Datablock& db)
void WriteRemark610(std::ostream& pdbFile, const Datablock& db)
{
// #warning("unimplemented!");
}
void WriteRemark800(std::ostream& pdbFile, Datablock& db)
void WriteRemark800(std::ostream& pdbFile, const Datablock& db)
{
int nr = 0;
for (auto r: db["struct_site"])
......@@ -2676,7 +2676,7 @@ void WriteRemark800(std::ostream& pdbFile, Datablock& db)
}
}
void WriteRemark999(std::ostream& pdbFile, Datablock& db)
void WriteRemark999(std::ostream& pdbFile, const Datablock& db)
{
for (auto& r: db["pdbx_entry_details"])
{
......@@ -2687,7 +2687,7 @@ void WriteRemark999(std::ostream& pdbFile, Datablock& db)
}
}
void WriteRemarks(std::ostream& pdbFile, Datablock& db)
void WriteRemarks(std::ostream& pdbFile, const Datablock& db)
{
WriteRemark1(pdbFile, db);
WriteRemark2(pdbFile, db);
......@@ -2709,7 +2709,7 @@ void WriteRemarks(std::ostream& pdbFile, Datablock& db)
WriteRemark999(pdbFile, db);
}
int WritePrimaryStructure(std::ostream& pdbFile, Datablock& db)
int WritePrimaryStructure(std::ostream& pdbFile, const Datablock& db)
{
int numSeq = 0;
......@@ -2863,7 +2863,7 @@ int WritePrimaryStructure(std::ostream& pdbFile, Datablock& db)
return numSeq;
}
int WriteHeterogen(std::ostream& pdbFile, Datablock& db)
int WriteHeterogen(std::ostream& pdbFile, const Datablock& db)
{
int numHet = 0;
......@@ -3132,7 +3132,7 @@ int WriteHeterogen(std::ostream& pdbFile, Datablock& db)
return numHet;
}
std::tuple<int,int> WriteSecondaryStructure(std::ostream& pdbFile, Datablock& db)
std::tuple<int,int> WriteSecondaryStructure(std::ostream& pdbFile, const Datablock& db)
{
int numHelix = 0, numSheet = 0;
......@@ -3290,7 +3290,7 @@ std::tuple<int,int> WriteSecondaryStructure(std::ostream& pdbFile, Datablock& db
return std::make_tuple(numHelix, numSheet);
}
void WriteConnectivity(std::ostream& pdbFile, cif::Datablock& db)
void WriteConnectivity(std::ostream& pdbFile, const cif::Datablock& db)
{
// SSBOND
// have to filter out alts
......@@ -3406,7 +3406,7 @@ void WriteConnectivity(std::ostream& pdbFile, cif::Datablock& db)
}
}
int WriteMiscellaneousFeatures(std::ostream& pdbFile, Datablock& db)
int WriteMiscellaneousFeatures(std::ostream& pdbFile, const Datablock& db)
{
int numSite = 0;
......@@ -3459,7 +3459,7 @@ int WriteMiscellaneousFeatures(std::ostream& pdbFile, Datablock& db)
return numSite;
}
void WriteCrystallographic(std::ostream& pdbFile, Datablock& db)
void WriteCrystallographic(std::ostream& pdbFile, const Datablock& db)
{
auto r = db["symmetry"][cif::Key("entry_id") == db.getName()];
std::string symmetry = r["space_group_name_H-M"].as<std::string>();
......@@ -3479,7 +3479,7 @@ void WriteCrystallographic(std::ostream& pdbFile, Datablock& db)
% r["Z_PDB"].as<double>()) << std::endl;
}
int WriteCoordinateTransformation(std::ostream& pdbFile, Datablock& db)
int WriteCoordinateTransformation(std::ostream& pdbFile, const Datablock& db)
{
int result = 0;
......@@ -3520,7 +3520,7 @@ int WriteCoordinateTransformation(std::ostream& pdbFile, Datablock& db)
return result;
}
std::tuple<int,int> WriteCoordinatesForModel(std::ostream& pdbFile, Datablock& db,
std::tuple<int,int> WriteCoordinatesForModel(std::ostream& pdbFile, const Datablock& db,
const std::map<std::string,std::tuple<std::string,int,std::string>>& last_resseq_for_chain_map,
std::set<std::string>& TERminatedChains, int model_nr)
{
......@@ -3658,7 +3658,7 @@ std::tuple<int,int> WriteCoordinatesForModel(std::ostream& pdbFile, Datablock& d
return std::make_tuple(numCoord, numTer);
}
std::tuple<int,int> WriteCoordinate(std::ostream& pdbFile, Datablock& db)
std::tuple<int,int> WriteCoordinate(std::ostream& pdbFile, const Datablock& db)
{
// residues known from seqres
// map<tuple<std::string,int,std::string>,std::string> res2chain_map;
......@@ -3718,7 +3718,7 @@ std::tuple<int,int> WriteCoordinate(std::ostream& pdbFile, Datablock& db)
return result;
}
void WritePDBFile(std::ostream& pdbFile, cif::File& cifFile)
void WritePDBFile(std::ostream& pdbFile, const Datablock &db)
{
io::filtering_ostream out;
out.push(FillOutLineFilter());
......@@ -3727,8 +3727,6 @@ void WritePDBFile(std::ostream& pdbFile, cif::File& cifFile)
auto filter = out.component<FillOutLineFilter>(0);
assert(filter);
auto& db = cifFile.firstDatablock();
int numRemark = 0, numHet = 0, numHelix = 0, numSheet = 0, numTurn = 0, numSite = 0, numXform = 0, numCoord = 0, numTer = 0, numConect = 0, numSeq = 0;
WriteTitle(out, db);
......@@ -3753,7 +3751,7 @@ void WritePDBFile(std::ostream& pdbFile, cif::File& cifFile)
<< "END" << std::endl;
}
void WritePDBHeaderLines(std::ostream& os, cif::File& cifFile)
void WritePDBHeaderLines(std::ostream& os, const Datablock &db)
{
// io::filtering_ostream out;
// out.push(FillOutLineFilter());
......@@ -3762,8 +3760,6 @@ void WritePDBHeaderLines(std::ostream& os, cif::File& cifFile)
// auto filter = out.component<FillOutLineFilter>(0);
// assert(filter);
auto& db = cifFile.firstDatablock();
WriteHeaderLines(os, db);
}
......@@ -3779,10 +3775,8 @@ std::string FixStringLength(const std::string& s, std::string::size_type l)
return result;
}
std::string GetPDBHEADERLine(cif::File& cifFile, std::string::size_type truncate_at)
std::string GetPDBHEADERLine(const Datablock &db, std::string::size_type truncate_at)
{
auto& db = cifFile.firstDatablock();
// 0 1 2 3 4 5 6 7 8
// HEADER xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxDDDDDDDDD IIII
const char kHeader[] =
......@@ -3825,10 +3819,8 @@ std::string GetPDBHEADERLine(cif::File& cifFile, std::string::size_type truncate
return FixStringLength((boost::format(kHeader) % keywords % date % db.getName()).str(), truncate_at);
}
std::string GetPDBCOMPNDLine(cif::File& cifFile, std::string::size_type truncate_at)
std::string GetPDBCOMPNDLine(const Datablock &db, std::string::size_type truncate_at)
{
auto& db = cifFile.firstDatablock();
// COMPND
using namespace std::placeholders;
......@@ -3886,10 +3878,8 @@ std::string GetPDBCOMPNDLine(cif::File& cifFile, std::string::size_type truncate
return FixStringLength("COMPND " + ba::join(cmpnd, "; "), truncate_at);
}
std::string GetPDBSOURCELine(cif::File& cifFile, std::string::size_type truncate_at)
std::string GetPDBSOURCELine(const Datablock &db, std::string::size_type truncate_at)
{
auto& db = cifFile.firstDatablock();
// SOURCE
int molID = 0;
......@@ -3971,10 +3961,8 @@ std::string GetPDBSOURCELine(cif::File& cifFile, std::string::size_type truncate
return FixStringLength("SOURCE " + ba::join(source, "; "), truncate_at);
}
std::string GetPDBAUTHORLine(cif::File& cifFile, std::string::size_type truncate_at)
std::string GetPDBAUTHORLine(const Datablock &db, std::string::size_type truncate_at)
{
auto& db = cifFile.firstDatablock();
// AUTHOR
std::vector<std::string> author;
for (auto r: db["audit_author"])
......
src/Structure.cpp
......@@ -1380,7 +1380,7 @@ void File::save(const std::filesystem::path &path)
out.push(outFile);
if (file.extension() == ".pdb")
WritePDBFile(out, *this);
WritePDBFile(out, data());
else
cif::File::save(out);
}
......
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