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libcifpp
Commit 1f6b86d5 by Maarten L. Hekkelman
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Merge branch 'develop' of github.com:PDB-REDO/libcifpp into develop

parents 31499b97 7f39d401
Showing with 527 additions and 394 deletions
include/cif++/Cif++.hpp
...@@ -36,6 +36,7 @@ ...@@ -36,6 +36,7 @@
#include <regex> #include <regex>
#include <set> #include <set>
#include <sstream> #include <sstream>
#include <shared_mutex>
#include "cif++/CifUtils.hpp" #include "cif++/CifUtils.hpp"
...@@ -142,13 +143,13 @@ class Item ...@@ -142,13 +143,13 @@ class Item
Item() {} Item() {}
template <typename T, std::enable_if_t<std::is_arithmetic_v<T>, int> = 0> template <typename T, std::enable_if_t<std::is_arithmetic_v<T>, int> = 0>
Item(const std::string &name, const T &value) Item(const std::string_view name, const T &value)
: mName(name) : mName(name)
, mValue(std::to_string(value)) , mValue(std::to_string(value))
{ {
} }
Item(const std::string &name, const std::string &value) Item(const std::string_view name, const std::string_view value)
: mName(name) : mName(name)
, mValue(value) , mValue(value)
{ {
...@@ -221,7 +222,7 @@ class Datablock ...@@ -221,7 +222,7 @@ class Datablock
using iterator = CategoryList::iterator; using iterator = CategoryList::iterator;
using const_iterator = CategoryList::const_iterator; using const_iterator = CategoryList::const_iterator;
Datablock(const std::string &name); Datablock(const std::string_view name);
~Datablock(); ~Datablock();
Datablock(const Datablock &) = delete; Datablock(const Datablock &) = delete;
...@@ -230,8 +231,6 @@ class Datablock ...@@ -230,8 +231,6 @@ class Datablock
std::string getName() const { return mName; } std::string getName() const { return mName; }
void setName(const std::string &n) { mName = n; } void setName(const std::string &n) { mName = n; }
std::string firstItem(const std::string &tag) const;
iterator begin() { return mCategories.begin(); } iterator begin() { return mCategories.begin(); }
iterator end() { return mCategories.end(); } iterator end() { return mCategories.end(); }
...@@ -245,7 +244,7 @@ class Datablock ...@@ -245,7 +244,7 @@ class Datablock
bool isValid(); bool isValid();
void validateLinks() const; void validateLinks() const;
void setValidator(Validator *v); void setValidator(const Validator *v);
// this one only looks up a Category, returns nullptr if it does not exist // this one only looks up a Category, returns nullptr if it does not exist
const Category *get(std::string_view name) const; const Category *get(std::string_view name) const;
...@@ -256,7 +255,7 @@ class Datablock ...@@ -256,7 +255,7 @@ class Datablock
void write(std::ostream &os); void write(std::ostream &os);
// convenience function, add a line to the software category // convenience function, add a line to the software category
void add_software(const std::string &name, const std::string &classification, void add_software(const std::string_view name, const std::string &classification,
const std::string &versionNr, const std::string &versionDate); const std::string &versionNr, const std::string &versionDate);
friend bool operator==(const Datablock &lhs, const Datablock &rhs); friend bool operator==(const Datablock &lhs, const Datablock &rhs);
...@@ -264,9 +263,10 @@ class Datablock ...@@ -264,9 +263,10 @@ class Datablock
friend std::ostream& operator<<(std::ostream &os, const Datablock &data); friend std::ostream& operator<<(std::ostream &os, const Datablock &data);
private: private:
std::list<Category> mCategories; CategoryList mCategories; // LRU
mutable std::shared_mutex mLock;
std::string mName; std::string mName;
Validator *mValidator; const Validator *mValidator;
Datablock *mNext; Datablock *mNext;
}; };
...@@ -1816,12 +1816,12 @@ class Category ...@@ -1816,12 +1816,12 @@ class Category
friend class Row; friend class Row;
friend class detail::ItemReference; friend class detail::ItemReference;
Category(Datablock &db, const std::string &name, Validator *Validator); Category(Datablock &db, const std::string_view name, const Validator *Validator);
Category(const Category &) = delete; Category(const Category &) = delete;
Category &operator=(const Category &) = delete; Category &operator=(const Category &) = delete;
~Category(); ~Category();
const std::string name() const { return mName; } const std::string &name() const { return mName; }
using iterator = iterator_impl<Row>; using iterator = iterator_impl<Row>;
using const_iterator = iterator_impl<const Row>; using const_iterator = iterator_impl<const Row>;
...@@ -2064,7 +2064,7 @@ class Category ...@@ -2064,7 +2064,7 @@ class Category
Datablock &db() { return mDb; } Datablock &db() { return mDb; }
void setValidator(Validator *v); void setValidator(const Validator *v);
iset fields() const; iset fields() const;
iset mandatoryFields() const; iset mandatoryFields() const;
...@@ -2121,14 +2121,24 @@ class Category ...@@ -2121,14 +2121,24 @@ class Category
size_t addColumn(std::string_view name); size_t addColumn(std::string_view name);
struct Linked
{
Category *linked;
const ValidateLink *v;
};
void updateLinks();
Datablock &mDb; Datablock &mDb;
std::string mName; std::string mName;
Validator *mValidator; const Validator *mValidator;
const ValidateCategory *mCatValidator = nullptr; const ValidateCategory *mCatValidator = nullptr;
std::vector<ItemColumn> mColumns; std::vector<ItemColumn> mColumns;
ItemRow *mHead; ItemRow *mHead;
ItemRow *mTail; ItemRow *mTail;
class CatIndex *mIndex; class CatIndex *mIndex;
std::vector<Linked> mParentLinks, mChildLinks;
}; };
// -------------------------------------------------------------------- // --------------------------------------------------------------------
...@@ -2162,7 +2172,8 @@ class File ...@@ -2162,7 +2172,8 @@ class File
void loadDictionary(); // load the default dictionary, that is mmcifDdl in this case void loadDictionary(); // load the default dictionary, that is mmcifDdl in this case
void loadDictionary(const char *dict); // load one of the compiled in dictionaries void loadDictionary(const char *dict); // load one of the compiled in dictionaries
void loadDictionary(std::istream &is); // load dictionary from input stream
void setValidator(const Validator *v);
bool isValid(); bool isValid();
void validateLinks() const; void validateLinks() const;
...@@ -2226,10 +2237,8 @@ class File ...@@ -2226,10 +2237,8 @@ class File
void getTagOrder(std::vector<std::string> &tags) const; void getTagOrder(std::vector<std::string> &tags) const;
private: private:
void setValidator(Validator *v);
Datablock *mHead; Datablock *mHead;
Validator *mValidator; const Validator *mValidator;
}; };
// -------------------------------------------------------------------- // --------------------------------------------------------------------
......
include/cif++/CifParser.hpp
...@@ -28,8 +28,8 @@ ...@@ -28,8 +28,8 @@
#include "cif++/Cif++.hpp" #include "cif++/Cif++.hpp"
#include <stack>
#include <map> #include <map>
#include <stack>
namespace cif namespace cif
{ {
...@@ -39,7 +39,7 @@ namespace cif ...@@ -39,7 +39,7 @@ namespace cif
class CifParserError : public std::runtime_error class CifParserError : public std::runtime_error
{ {
public: public:
CifParserError(uint32_t lineNr, const std::string& message); CifParserError(uint32_t lineNr, const std::string &message);
}; };
// -------------------------------------------------------------------- // --------------------------------------------------------------------
...@@ -48,7 +48,8 @@ extern const uint32_t kMaxLineLength; ...@@ -48,7 +48,8 @@ extern const uint32_t kMaxLineLength;
extern const uint8_t kCharTraitsTable[128]; extern const uint8_t kCharTraitsTable[128];
enum CharTraitsMask: uint8_t { enum CharTraitsMask : uint8_t
{
kOrdinaryMask = 1 << 0, kOrdinaryMask = 1 << 0,
kNonBlankMask = 1 << 1, kNonBlankMask = 1 << 1,
kTextLeadMask = 1 << 2, kTextLeadMask = 1 << 2,
...@@ -81,7 +82,7 @@ inline bool isAnyPrint(int ch) ...@@ -81,7 +82,7 @@ inline bool isAnyPrint(int ch)
(ch >= 0x20 and ch <= 0x7f and (kCharTraitsTable[ch - 0x20] & kAnyPrintMask) != 0); (ch >= 0x20 and ch <= 0x7f and (kCharTraitsTable[ch - 0x20] & kAnyPrintMask) != 0);
} }
inline bool isUnquotedString(const char* s) inline bool isUnquotedString(const char *s)
{ {
bool result = isOrdinary(*s++); bool result = isOrdinary(*s++);
while (result and *s != 0) while (result and *s != 0)
...@@ -94,7 +95,7 @@ inline bool isUnquotedString(const char* s) ...@@ -94,7 +95,7 @@ inline bool isUnquotedString(const char* s)
// -------------------------------------------------------------------- // --------------------------------------------------------------------
using DatablockIndex = std::map<std::string,std::size_t>; using DatablockIndex = std::map<std::string, std::size_t>;
// -------------------------------------------------------------------- // --------------------------------------------------------------------
// sac Parser, analogous to SAX Parser (simple api for xml) // sac Parser, analogous to SAX Parser (simple api for xml)
...@@ -102,7 +103,7 @@ using DatablockIndex = std::map<std::string,std::size_t>; ...@@ -102,7 +103,7 @@ using DatablockIndex = std::map<std::string,std::size_t>;
class SacParser class SacParser
{ {
public: public:
SacParser(std::istream& is, bool init = true); SacParser(std::istream &is, bool init = true);
virtual ~SacParser() {} virtual ~SacParser() {}
enum CIFToken enum CIFToken
...@@ -120,7 +121,7 @@ class SacParser ...@@ -120,7 +121,7 @@ class SacParser
eCIFTokenValue, eCIFTokenValue,
}; };
static const char* kTokenName[]; static const char *kTokenName[];
enum CIFValueType enum CIFValueType
{ {
...@@ -133,7 +134,7 @@ class SacParser ...@@ -133,7 +134,7 @@ class SacParser
eCIFValueUnknown eCIFValueUnknown
}; };
static const char* kValueName[]; static const char *kValueName[];
int getNextChar(); int getNextChar();
...@@ -143,10 +144,10 @@ class SacParser ...@@ -143,10 +144,10 @@ class SacParser
CIFToken getNextToken(); CIFToken getNextToken();
void match(CIFToken token); void match(CIFToken token);
bool parseSingleDatablock(const std::string& datablock); bool parseSingleDatablock(const std::string &datablock);
DatablockIndex indexDatablocks(); DatablockIndex indexDatablocks();
bool parseSingleDatablock(const std::string& datablock, const DatablockIndex &index); bool parseSingleDatablock(const std::string &datablock, const DatablockIndex &index);
void parseFile(); void parseFile();
void parseGlobal(); void parseGlobal();
...@@ -156,17 +157,16 @@ class SacParser ...@@ -156,17 +157,16 @@ class SacParser
void parseDictionary(); void parseDictionary();
void error(const std::string& msg); void error(const std::string &msg);
// production methods, these are pure virtual here // production methods, these are pure virtual here
virtual void produceDatablock(const std::string& name) = 0; virtual void produceDatablock(const std::string &name) = 0;
virtual void produceCategory(const std::string& name) = 0; virtual void produceCategory(const std::string &name) = 0;
virtual void produceRow() = 0; virtual void produceRow() = 0;
virtual void produceItem(const std::string& category, const std::string& item, const std::string& value) = 0; virtual void produceItem(const std::string &category, const std::string &item, const std::string &value) = 0;
protected: protected:
enum State enum State
{ {
eStateStart, eStateStart,
...@@ -181,11 +181,11 @@ class SacParser ...@@ -181,11 +181,11 @@ class SacParser
eStateTextField, eStateTextField,
eStateFloat = 100, eStateFloat = 100,
eStateInt = 110, eStateInt = 110,
// eStateNumericSuffix = 200, // eStateNumericSuffix = 200,
eStateValue = 300 eStateValue = 300
}; };
std::istream& mData; std::istream &mData;
// Parser state // Parser state
bool mValidate; bool mValidate;
...@@ -203,16 +203,16 @@ class SacParser ...@@ -203,16 +203,16 @@ class SacParser
class Parser : public SacParser class Parser : public SacParser
{ {
public: public:
Parser(std::istream& is, File& f, bool init = true); Parser(std::istream &is, File &f, bool init = true);
virtual void produceDatablock(const std::string& name); virtual void produceDatablock(const std::string &name);
virtual void produceCategory(const std::string& name); virtual void produceCategory(const std::string &name);
virtual void produceRow(); virtual void produceRow();
virtual void produceItem(const std::string& category, const std::string& item, const std::string& value); virtual void produceItem(const std::string &category, const std::string &item, const std::string &value);
protected: protected:
File& mFile; File &mFile;
Datablock* mDataBlock; Datablock *mDataBlock;
Datablock::iterator mCat; Datablock::iterator mCat;
Row mRow; Row mRow;
}; };
...@@ -222,23 +222,21 @@ class Parser : public SacParser ...@@ -222,23 +222,21 @@ class Parser : public SacParser
class DictParser : public Parser class DictParser : public Parser
{ {
public: public:
DictParser(Validator &validator, std::istream &is);
DictParser(Validator& validator, std::istream& is);
~DictParser(); ~DictParser();
void loadDictionary(); void loadDictionary();
private: private:
virtual void parseSaveFrame(); virtual void parseSaveFrame();
bool collectItemTypes(); bool collectItemTypes();
void linkItems(); void linkItems();
Validator& mValidator; Validator &mValidator;
File mFile; File mFile;
struct DictParserDataImpl* mImpl; struct DictParserDataImpl *mImpl;
bool mCollectedItemTypes = false; bool mCollectedItemTypes = false;
}; };
} } // namespace cif
include/cif++/CifUtils.hpp
...@@ -67,9 +67,7 @@ std::string get_version_nr(); ...@@ -67,9 +67,7 @@ std::string get_version_nr();
// some basic utilities: Since we're using ASCII input only, we define for optimisation // some basic utilities: Since we're using ASCII input only, we define for optimisation
// our own case conversion routines. // our own case conversion routines.
// bool iequals(const std::string &a, const std::string &b);
bool iequals(std::string_view a, std::string_view b); bool iequals(std::string_view a, std::string_view b);
// int icompare(const std::string &a, const std::string &b);
int icompare(std::string_view a, std::string_view b); int icompare(std::string_view a, std::string_view b);
bool iequals(const char *a, const char *b); bool iequals(const char *a, const char *b);
......
include/cif++/CifValidator.hpp
...@@ -38,6 +38,7 @@ namespace cif ...@@ -38,6 +38,7 @@ namespace cif
{ {
struct ValidateCategory; struct ValidateCategory;
class ValidatorFactory;
// -------------------------------------------------------------------- // --------------------------------------------------------------------
...@@ -154,9 +155,8 @@ struct ValidateLink ...@@ -154,9 +155,8 @@ struct ValidateLink
class Validator class Validator
{ {
public: public:
friend class DictParser;
Validator(); Validator(std::string_view name, std::istream &is);
~Validator(); ~Validator();
Validator(const Validator &rhs) = delete; Validator(const Validator &rhs) = delete;
...@@ -165,6 +165,9 @@ class Validator ...@@ -165,6 +165,9 @@ class Validator
Validator(Validator &&rhs); Validator(Validator &&rhs);
Validator &operator=(Validator &&rhs); Validator &operator=(Validator &&rhs);
friend class DictParser;
friend class ValidatorFactory;
void addTypeValidator(ValidateType &&v); void addTypeValidator(ValidateType &&v);
const ValidateType *getValidatorForType(std::string_view typeCode) const; const ValidateType *getValidatorForType(std::string_view typeCode) const;
...@@ -175,7 +178,7 @@ class Validator ...@@ -175,7 +178,7 @@ class Validator
std::vector<const ValidateLink *> getLinksForParent(std::string_view category) const; std::vector<const ValidateLink *> getLinksForParent(std::string_view category) const;
std::vector<const ValidateLink *> getLinksForChild(std::string_view category) const; std::vector<const ValidateLink *> getLinksForChild(std::string_view category) const;
void reportError(const std::string &msg, bool fatal); void reportError(const std::string &msg, bool fatal) const;
std::string dictName() const { return mName; } std::string dictName() const { return mName; }
void dictName(const std::string &name) { mName = name; } void dictName(const std::string &name) { mName = name; }
...@@ -184,6 +187,7 @@ class Validator ...@@ -184,6 +187,7 @@ class Validator
void dictVersion(const std::string &version) { mVersion = version; } void dictVersion(const std::string &version) { mVersion = version; }
private: private:
// name is fully qualified here: // name is fully qualified here:
ValidateItem *getValidatorForItem(std::string_view name) const; ValidateItem *getValidatorForItem(std::string_view name) const;
...@@ -196,4 +200,27 @@ class Validator ...@@ -196,4 +200,27 @@ class Validator
std::vector<ValidateLink> mLinkValidators; std::vector<ValidateLink> mLinkValidators;
}; };
// --------------------------------------------------------------------
class ValidatorFactory
{
public:
static ValidatorFactory &instance()
{
return sInstance;
}
const Validator &operator[](std::string_view dictionary);
private:
static ValidatorFactory sInstance;
ValidatorFactory();
std::mutex mMutex;
std::list<Validator> mValidators;
};
} // namespace cif } // namespace cif
include/cif++/Structure.hpp
...@@ -109,12 +109,12 @@ class Atom ...@@ -109,12 +109,12 @@ class Atom
float occupancy() const; float occupancy() const;
template <typename T> template <typename T>
T property(const std::string &name) const; T property(const std::string_view name) const;
void property(const std::string &name, const std::string &value); void property(const std::string_view name, const std::string &value);
template <typename T, std::enable_if_t<std::is_arithmetic_v<T>, int> = 0> template <typename T, std::enable_if_t<std::is_arithmetic_v<T>, int> = 0>
void property(const std::string &name, const T &value) void property(const std::string_view name, const T &value)
{ {
property(name, std::to_string(value)); property(name, std::to_string(value));
} }
...@@ -404,7 +404,7 @@ class File : public std::enable_shared_from_this<File> ...@@ -404,7 +404,7 @@ class File : public std::enable_shared_from_this<File>
File(const File &) = delete; File(const File &) = delete;
File &operator=(const File &) = delete; File &operator=(const File &) = delete;
cif::Datablock& createDatablock(const std::string &name); cif::Datablock& createDatablock(const std::string_view name);
void load(const std::filesystem::path &path); void load(const std::filesystem::path &path);
void save(const std::filesystem::path &path); void save(const std::filesystem::path &path);
......
include/cif++/Symmetry.hpp
...@@ -37,6 +37,11 @@ namespace mmcif ...@@ -37,6 +37,11 @@ namespace mmcif
// -------------------------------------------------------------------- // --------------------------------------------------------------------
enum class SpacegroupName
{
full, xHM, Hall
};
struct Spacegroup struct Spacegroup
{ {
const char* name; const char* name;
...@@ -133,6 +138,7 @@ CIFPP_EXPORT extern const std::size_t kSymopNrTableSize; ...@@ -133,6 +138,7 @@ CIFPP_EXPORT extern const std::size_t kSymopNrTableSize;
// -------------------------------------------------------------------- // --------------------------------------------------------------------
int GetSpacegroupNumber(std::string spacegroup); // alternative for clipper's parsing code int GetSpacegroupNumber(std::string spacegroup); // alternative for clipper's parsing code, using SpacegroupName::full
int GetSpacegroupNumber(std::string spacegroup, SpacegroupName type); // alternative for clipper's parsing code
} }
src/Cif++.cpp
...@@ -33,6 +33,7 @@ ...@@ -33,6 +33,7 @@
#include <stack> #include <stack>
#include <tuple> #include <tuple>
#include <unordered_map> #include <unordered_map>
#include <shared_mutex>
#include <filesystem> #include <filesystem>
...@@ -351,7 +352,7 @@ namespace detail ...@@ -351,7 +352,7 @@ namespace detail
// -------------------------------------------------------------------- // --------------------------------------------------------------------
// Datablock implementation // Datablock implementation
Datablock::Datablock(const std::string &name) Datablock::Datablock(const std::string_view name)
: mName(name) : mName(name)
, mValidator(nullptr) , mValidator(nullptr)
, mNext(nullptr) , mNext(nullptr)
...@@ -363,43 +364,42 @@ Datablock::~Datablock() ...@@ -363,43 +364,42 @@ Datablock::~Datablock()
delete mNext; delete mNext;
} }
std::string Datablock::firstItem(const std::string &tag) const auto Datablock::emplace(std::string_view name) -> std::tuple<iterator, bool>
{ {
std::string result; // LRU code
std::string catName, itemName; std::shared_lock lock(mLock);
std::tie(catName, itemName) = splitTagName(tag);
for (auto &cat : mCategories) bool isNew = true;
auto i = begin();
while (i != end())
{ {
if (iequals(cat.name(), catName)) if (iequals(name, i->name()))
{ {
for (auto row : cat) isNew = false;
if (i != begin())
{ {
result = row[itemName].as<std::string>(); auto n = std::next(i);
break; mCategories.splice(begin(), mCategories, i, n);
} }
break; break;
} }
}
return result; ++i;
} }
auto Datablock::emplace(std::string_view name) -> std::tuple<iterator, bool>
{
bool isNew = false;
iterator i = find_if(begin(), end(), [name](const Category &cat) -> bool
{ return iequals(cat.name(), name); });
if (i == end()) if (isNew)
{ {
isNew = true; mCategories.emplace(begin(), *this, std::string(name), mValidator);
i = mCategories.emplace(end(), *this, std::string(name), mValidator);
for (auto &cat : mCategories)
cat.updateLinks();
} }
return std::make_tuple(i, isNew); return std::make_tuple(begin(), isNew);
} }
Category &Datablock::operator[](std::string_view name) Category &Datablock::operator[](std::string_view name)
...@@ -411,22 +411,34 @@ Category &Datablock::operator[](std::string_view name) ...@@ -411,22 +411,34 @@ Category &Datablock::operator[](std::string_view name)
Category *Datablock::get(std::string_view name) Category *Datablock::get(std::string_view name)
{ {
auto i = find_if(begin(), end(), [name](const Category &cat) -> bool std::shared_lock lock(mLock);
{ return iequals(cat.name(), name); });
for (auto &cat : mCategories)
{
if (iequals(cat.name(), name))
return &cat;
}
return i == end() ? nullptr : &*i; return nullptr;
} }
const Category *Datablock::get(std::string_view name) const const Category *Datablock::get(std::string_view name) const
{ {
auto i = find_if(begin(), end(), [name](const Category &cat) -> bool std::shared_lock lock(mLock);
{ return iequals(cat.name(), name); });
return i == end() ? nullptr : &*i; for (auto &cat : mCategories)
{
if (iequals(cat.name(), name))
return &cat;
}
return nullptr;
} }
bool Datablock::isValid() bool Datablock::isValid()
{ {
std::shared_lock lock(mLock);
if (mValidator == nullptr) if (mValidator == nullptr)
throw std::runtime_error("Validator not specified"); throw std::runtime_error("Validator not specified");
...@@ -438,20 +450,26 @@ bool Datablock::isValid() ...@@ -438,20 +450,26 @@ bool Datablock::isValid()
void Datablock::validateLinks() const void Datablock::validateLinks() const
{ {
std::shared_lock lock(mLock);
for (auto &cat : *this) for (auto &cat : *this)
cat.validateLinks(); cat.validateLinks();
} }
void Datablock::setValidator(Validator *v) void Datablock::setValidator(const Validator *v)
{ {
std::shared_lock lock(mLock);
mValidator = v; mValidator = v;
for (auto &cat : *this) for (auto &cat : *this)
cat.setValidator(v); cat.setValidator(v);
} }
void Datablock::add_software(const std::string &name, const std::string &classification, const std::string &versionNr, const std::string &versionDate) void Datablock::add_software(const std::string_view name, const std::string &classification, const std::string &versionNr, const std::string &versionDate)
{ {
std::shared_lock lock(mLock);
Category &cat = operator[]("software"); Category &cat = operator[]("software");
auto ordNr = cat.size() + 1; auto ordNr = cat.size() + 1;
// TODO: should we check this ordinal number??? // TODO: should we check this ordinal number???
...@@ -465,12 +483,16 @@ void Datablock::add_software(const std::string &name, const std::string &classif ...@@ -465,12 +483,16 @@ void Datablock::add_software(const std::string &name, const std::string &classif
void Datablock::getTagOrder(std::vector<std::string> &tags) const void Datablock::getTagOrder(std::vector<std::string> &tags) const
{ {
std::shared_lock lock(mLock);
for (auto &cat : *this) for (auto &cat : *this)
cat.getTagOrder(tags); cat.getTagOrder(tags);
} }
void Datablock::write(std::ostream &os) void Datablock::write(std::ostream &os)
{ {
std::shared_lock lock(mLock);
os << "data_" << mName << std::endl os << "data_" << mName << std::endl
<< "# " << std::endl; << "# " << std::endl;
...@@ -505,6 +527,8 @@ void Datablock::write(std::ostream &os) ...@@ -505,6 +527,8 @@ void Datablock::write(std::ostream &os)
void Datablock::write(std::ostream &os, const std::vector<std::string> &order) void Datablock::write(std::ostream &os, const std::vector<std::string> &order)
{ {
std::shared_lock lock(mLock);
os << "data_" << mName << std::endl os << "data_" << mName << std::endl
<< "# " << std::endl; << "# " << std::endl;
...@@ -580,6 +604,9 @@ void Datablock::write(std::ostream &os, const std::vector<std::string> &order) ...@@ -580,6 +604,9 @@ void Datablock::write(std::ostream &os, const std::vector<std::string> &order)
bool operator==(const cif::Datablock &dbA, const cif::Datablock &dbB) bool operator==(const cif::Datablock &dbA, const cif::Datablock &dbB)
{ {
std::shared_lock lockA(dbA.mLock);
std::shared_lock lockB(dbB.mLock);
std::vector<std::string> catA, catB; std::vector<std::string> catA, catB;
for (auto &cat : dbA) for (auto &cat : dbA)
...@@ -1311,7 +1338,7 @@ RowSet &RowSet::orderBy(std::initializer_list<std::string> items) ...@@ -1311,7 +1338,7 @@ RowSet &RowSet::orderBy(std::initializer_list<std::string> items)
// -------------------------------------------------------------------- // --------------------------------------------------------------------
Category::Category(Datablock &db, const std::string &name, Validator *Validator) Category::Category(Datablock &db, const std::string_view name, const Validator *Validator)
: mDb(db) : mDb(db)
, mName(name) , mName(name)
, mValidator(Validator) , mValidator(Validator)
...@@ -1346,7 +1373,7 @@ Category::~Category() ...@@ -1346,7 +1373,7 @@ Category::~Category()
delete mIndex; delete mIndex;
} }
void Category::setValidator(Validator *v) void Category::setValidator(const Validator *v)
{ {
mValidator = v; mValidator = v;
...@@ -1371,6 +1398,33 @@ void Category::setValidator(Validator *v) ...@@ -1371,6 +1398,33 @@ void Category::setValidator(Validator *v)
} }
else else
mCatValidator = nullptr; mCatValidator = nullptr;
updateLinks();
}
void Category::updateLinks()
{
mChildLinks.clear();
mParentLinks.clear();
if (mValidator != nullptr)
{
for (auto link : mValidator->getLinksForParent(mName))
{
auto childCat = mDb.get(link->mChildCategory);
if (childCat == nullptr)
continue;
mChildLinks.push_back({ childCat, link });
}
for (auto link : mValidator->getLinksForChild(mName))
{
auto parentCat = mDb.get(link->mParentCategory);
if (parentCat == nullptr)
continue;
mParentLinks.push_back({ parentCat, link });
}
}
} }
bool Category::hasColumn(std::string_view name) const bool Category::hasColumn(std::string_view name) const
...@@ -1816,12 +1870,8 @@ auto Category::erase(iterator pos) -> iterator ...@@ -1816,12 +1870,8 @@ auto Category::erase(iterator pos) -> iterator
if (mValidator != nullptr) if (mValidator != nullptr)
{ {
for (auto &link : mValidator->getLinksForParent(mName)) for (auto &&[childCat, link] : mChildLinks)
{ {
auto childCat = mDb.get(link->mChildCategory);
if (childCat == nullptr)
continue;
Condition cond; Condition cond;
for (size_t ix = 0; ix < link->mParentKeys.size(); ++ix) for (size_t ix = 0; ix < link->mParentKeys.size(); ++ix)
...@@ -1959,12 +2009,8 @@ bool Category::isOrphan(Row r) ...@@ -1959,12 +2009,8 @@ bool Category::isOrphan(Row r)
return false; return false;
bool isOrphan = true; bool isOrphan = true;
for (auto &link : mValidator->getLinksForChild(mName)) for (auto &&[parentCat, link] : mParentLinks)
{ {
auto parentCat = mDb.get(link->mParentCategory);
if (parentCat == nullptr)
continue;
Condition cond; Condition cond;
for (size_t ix = 0; ix < link->mChildKeys.size(); ++ix) for (size_t ix = 0; ix < link->mChildKeys.size(); ++ix)
{ {
...@@ -1995,12 +2041,8 @@ bool Category::hasChildren(Row r) const ...@@ -1995,12 +2041,8 @@ bool Category::hasChildren(Row r) const
bool result = false; bool result = false;
for (auto &link : mValidator->getLinksForParent(mName)) for (auto &&[childCat, link] : mChildLinks)
{ {
auto childCat = mDb.get(link->mChildCategory);
if (childCat == nullptr)
continue;
Condition cond; Condition cond;
for (size_t ix = 0; ix < link->mParentKeys.size(); ++ix) for (size_t ix = 0; ix < link->mParentKeys.size(); ++ix)
...@@ -2026,12 +2068,8 @@ bool Category::hasParents(Row r) const ...@@ -2026,12 +2068,8 @@ bool Category::hasParents(Row r) const
bool result = false; bool result = false;
for (auto &link : mValidator->getLinksForChild(mName)) for (auto &&[parentCat, link] : mParentLinks)
{ {
auto parentCat = mDb.get(link->mParentCategory);
if (parentCat == nullptr)
continue;
Condition cond; Condition cond;
for (size_t ix = 0; ix < link->mChildKeys.size(); ++ix) for (size_t ix = 0; ix < link->mChildKeys.size(); ++ix)
...@@ -2240,23 +2278,17 @@ bool Category::isValid() ...@@ -2240,23 +2278,17 @@ bool Category::isValid()
void Category::validateLinks() const void Category::validateLinks() const
{ {
auto &validator = getValidator(); for (auto &&[parentCat, link] : mParentLinks)
for (auto linkValidator : validator.getLinksForChild(mName))
{ {
auto parent = mDb.get(linkValidator->mParentCategory);
if (parent == nullptr)
continue;
size_t missing = 0; size_t missing = 0;
for (auto r : *this) for (auto r : *this)
if (not hasParent(r, *parent, *linkValidator)) if (not hasParent(r, *parentCat, *link))
++missing; ++missing;
if (missing) if (missing)
{ {
std::cerr << "Links for " << linkValidator->mLinkGroupLabel << " are incomplete" << std::endl std::cerr << "Links for " << link->mLinkGroupLabel << " are incomplete" << std::endl
<< " There are " << missing << " items in " << mName << " that don't have matching parent items in " << parent->mName << std::endl; << " There are " << missing << " items in " << mName << " that don't have matching parent items in " << parentCat->mName << std::endl;
} }
} }
} }
...@@ -2697,17 +2729,10 @@ void Category::update_value(RowSet &&rows, const std::string &tag, const std::st ...@@ -2697,17 +2729,10 @@ void Category::update_value(RowSet &&rows, const std::string &tag, const std::st
row.assign(colIx, value, true); row.assign(colIx, value, true);
// see if we need to update any child categories that depend on this value // see if we need to update any child categories that depend on this value
auto &validator = getValidator();
auto &db = mDb;
for (auto parent : rows) for (auto parent : rows)
{ {
for (auto linked : validator.getLinksForParent(mName)) for (auto &&[childCat, linked] : mChildLinks)
{ {
auto childCat = db.get(linked->mChildCategory);
if (childCat == nullptr)
continue;
if (std::find(linked->mParentKeys.begin(), linked->mParentKeys.end(), tag) == linked->mParentKeys.end()) if (std::find(linked->mParentKeys.begin(), linked->mParentKeys.end(), tag) == linked->mParentKeys.end())
continue; continue;
...@@ -2864,18 +2889,8 @@ void Row::assign(const std::vector<Item> &values) ...@@ -2864,18 +2889,8 @@ void Row::assign(const std::vector<Item> &values)
// auto iv = col.mValidator; // auto iv = col.mValidator;
if (mCascade) if (mCascade)
{ {
auto &validator = cat->getValidator(); for (auto &&[childCat, linked] : cat->mChildLinks)
auto &db = cat->db();
for (auto linked : validator.getLinksForParent(cat->mName))
{ {
auto childCat = db.get(linked->mChildCategory);
if (childCat == nullptr)
continue;
// if (find(linked->mParentKeys.begin(), linked->mParentKeys.end(), iv->mTag) == linked->mParentKeys.end())
// continue;
Condition cond; Condition cond;
std::string childTag; std::string childTag;
...@@ -3016,15 +3031,8 @@ void Row::assign(size_t column, const std::string &value, bool skipUpdateLinked) ...@@ -3016,15 +3031,8 @@ void Row::assign(size_t column, const std::string &value, bool skipUpdateLinked)
auto iv = col.mValidator; auto iv = col.mValidator;
if (not skipUpdateLinked and iv != nullptr and mCascade) if (not skipUpdateLinked and iv != nullptr and mCascade)
{ {
auto &validator = cat->getValidator(); for (auto &&[childCat, linked] : cat->mChildLinks)
auto &db = cat->db();
for (auto linked : validator.getLinksForParent(cat->mName))
{ {
auto childCat = db.get(linked->mChildCategory);
if (childCat == nullptr)
continue;
if (find(linked->mParentKeys.begin(), linked->mParentKeys.end(), iv->mTag) == linked->mParentKeys.end()) if (find(linked->mParentKeys.begin(), linked->mParentKeys.end(), iv->mTag) == linked->mParentKeys.end())
continue; continue;
...@@ -3203,18 +3211,13 @@ void Row::swap(size_t cix, ItemRow *a, ItemRow *b) ...@@ -3203,18 +3211,13 @@ void Row::swap(size_t cix, ItemRow *a, ItemRow *b)
auto parentColName = cat->getColumnName(cix); auto parentColName = cat->getColumnName(cix);
// see if we need to update any child categories that depend on these values // see if we need to update any child categories that depend on these values
auto &validator = cat->getValidator();
auto parentCatValidator = cat->getCatValidator(); auto parentCatValidator = cat->getCatValidator();
for (auto &link : validator.getLinksForParent(cat->mName)) for (auto &&[childCat, link] : cat->mChildLinks)
{ {
if (find(link->mParentKeys.begin(), link->mParentKeys.end(), parentColName) == link->mParentKeys.end()) if (find(link->mParentKeys.begin(), link->mParentKeys.end(), parentColName) == link->mParentKeys.end())
continue; continue;
auto childCat = cat->db().get(link->mChildCategory);
if (childCat == nullptr or childCat->empty())
continue;
auto childCatValidator = childCat->getCatValidator(); auto childCatValidator = childCat->getCatValidator();
if (childCatValidator == nullptr) if (childCatValidator == nullptr)
continue; continue;
...@@ -3426,7 +3429,6 @@ File::File(File &&rhs) ...@@ -3426,7 +3429,6 @@ File::File(File &&rhs)
File::~File() File::~File()
{ {
delete mHead; delete mHead;
delete mValidator;
} }
void File::append(Datablock *e) void File::append(Datablock *e)
...@@ -3503,7 +3505,7 @@ void File::save(const std::filesystem::path &p) ...@@ -3503,7 +3505,7 @@ void File::save(const std::filesystem::path &p)
void File::load(std::istream &is) void File::load(std::istream &is)
{ {
Validator *saved = mValidator; auto saved = mValidator;
setValidator(nullptr); setValidator(nullptr);
Parser p(is, *this); Parser p(is, *this);
...@@ -3518,7 +3520,7 @@ void File::load(std::istream &is) ...@@ -3518,7 +3520,7 @@ void File::load(std::istream &is)
void File::load(std::istream &is, const std::string &datablock) void File::load(std::istream &is, const std::string &datablock)
{ {
Validator *saved = mValidator; auto saved = mValidator;
setValidator(nullptr); setValidator(nullptr);
Parser p(is, *this); Parser p(is, *this);
...@@ -3607,67 +3609,10 @@ void File::loadDictionary() ...@@ -3607,67 +3609,10 @@ void File::loadDictionary()
void File::loadDictionary(const char *dict) void File::loadDictionary(const char *dict)
{ {
fs::path dict_name(dict); setValidator(&ValidatorFactory::instance()[dict]);
auto data = loadResource(dict);
if (not data and dict_name.extension().string() != ".dic")
data = loadResource(dict_name.parent_path() / (dict_name.filename().string() + ".dic"));
if (data)
loadDictionary(*data);
else
{
// might be a compressed dictionary on disk
fs::path p = dict;
if (p.extension() == ".dic")
p = p.parent_path() / (p.filename().string() + ".gz");
else
p = p.parent_path() / (p.filename().string() + ".dic.gz");
#if defined(CACHE_DIR) and defined(DATA_DIR)
if (not fs::exists(p))
{
for (const char *dir : {CACHE_DIR, DATA_DIR})
{
auto p2 = fs::path(dir) / p;
if (fs::exists(p2))
{
swap(p, p2);
break;
}
}
}
#endif
if (fs::exists(p))
{
std::ifstream file(p, std::ios::binary);
if (not file.is_open())
throw std::runtime_error("Could not open dictionary (" + p.string() + ")");
io::filtering_stream<io::input> in;
in.push(io::gzip_decompressor());
in.push(file);
loadDictionary(in);
}
else
throw std::runtime_error("Dictionary not found or defined (" + dict_name.string() + ")");
}
}
void File::loadDictionary(std::istream &is)
{
std::unique_ptr<Validator> v(new Validator());
DictParser p(*v, is);
p.loadDictionary();
setValidator(v.release());
} }
void File::setValidator(Validator *v) void File::setValidator(const Validator *v)
{ {
mValidator = v; mValidator = v;
......
src/CifParser.cpp
...@@ -42,7 +42,7 @@ namespace cif ...@@ -42,7 +42,7 @@ namespace cif
const uint32_t kMaxLineLength = 132; const uint32_t kMaxLineLength = 132;
const uint8_t kCharTraitsTable[128] = { const uint8_t kCharTraitsTable[128] = {
// 0 1 2 3 4 5 6 7 8 9 a b c d e f // 0 1 2 3 4 5 6 7 8 9 a b c d e f
14, 15, 14, 14, 14, 15, 15, 14, 15, 15, 15, 15, 15, 15, 15, 15, // 2 14, 15, 14, 14, 14, 15, 15, 14, 15, 15, 15, 15, 15, 15, 15, 15, // 2
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 15, 15, 15, 15, // 3 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 15, 15, 15, 15, // 3
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, // 4 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, // 4
...@@ -53,14 +53,14 @@ const uint8_t kCharTraitsTable[128] = { ...@@ -53,14 +53,14 @@ const uint8_t kCharTraitsTable[128] = {
// -------------------------------------------------------------------- // --------------------------------------------------------------------
CifParserError::CifParserError(uint32_t lineNr, const std::string& message) CifParserError::CifParserError(uint32_t lineNr, const std::string &message)
: std::runtime_error("parse error at line " + std::to_string(lineNr) + ": " + message) : std::runtime_error("parse error at line " + std::to_string(lineNr) + ": " + message)
{ {
} }
// -------------------------------------------------------------------- // --------------------------------------------------------------------
const char* SacParser::kTokenName[] = { const char *SacParser::kTokenName[] = {
"unknown", "unknown",
"EOF", "EOF",
"DATA", "DATA",
...@@ -69,22 +69,20 @@ const char* SacParser::kTokenName[] = { ...@@ -69,22 +69,20 @@ const char* SacParser::kTokenName[] = {
"SAVE", "SAVE",
"STOP", "STOP",
"Tag", "Tag",
"Value" "Value"};
};
const char* SacParser::kValueName[] = { const char *SacParser::kValueName[] = {
"Int", "Int",
"Float", "Float",
"Numeric", "Numeric",
"String", "String",
"TextField", "TextField",
"Inapplicable", "Inapplicable",
"Unknown" "Unknown"};
};
// -------------------------------------------------------------------- // --------------------------------------------------------------------
SacParser::SacParser(std::istream& is, bool init) SacParser::SacParser(std::istream &is, bool init)
: mData(is) : mData(is)
{ {
mValidate = true; mValidate = true;
...@@ -95,7 +93,7 @@ SacParser::SacParser(std::istream& is, bool init) ...@@ -95,7 +93,7 @@ SacParser::SacParser(std::istream& is, bool init)
mLookahead = getNextToken(); mLookahead = getNextToken();
} }
void SacParser::error(const std::string& msg) void SacParser::error(const std::string &msg)
{ {
throw CifParserError(mLineNr, msg); throw CifParserError(mLineNr, msg);
} }
...@@ -291,8 +289,8 @@ SacParser::CIFToken SacParser::getNextToken() ...@@ -291,8 +289,8 @@ SacParser::CIFToken SacParser::getNextToken()
else if (ch == kEOF) else if (ch == kEOF)
error("unterminated textfield"); error("unterminated textfield");
else if (not isAnyPrint(ch)) else if (not isAnyPrint(ch))
// error("invalid character in text field '" + string({ static_cast<char>(ch) }) + "' (" + to_string((int)ch) + ")"); // error("invalid character in text field '" + string({ static_cast<char>(ch) }) + "' (" + to_string((int)ch) + ")");
std::cerr << "invalid character in text field '" << std::string({ static_cast<char>(ch) }) << "' (" << ch << ") line: " << mLineNr << std::endl; std::cerr << "invalid character in text field '" << std::string({static_cast<char>(ch)}) << "' (" << ch << ") line: " << mLineNr << std::endl;
break; break;
case eStateTextField + 1: case eStateTextField + 1:
...@@ -360,9 +358,9 @@ SacParser::CIFToken SacParser::getNextToken() ...@@ -360,9 +358,9 @@ SacParser::CIFToken SacParser::getNextToken()
break; break;
case eStateFloat + 1: case eStateFloat + 1:
// if (ch == '(') // numeric??? // if (ch == '(') // numeric???
// mState = eStateNumericSuffix; // mState = eStateNumericSuffix;
// else // else
if (ch == '.') if (ch == '.')
mState = eStateFloat + 2; mState = eStateFloat + 2;
else if (tolower(ch) == 'e') else if (tolower(ch) == 'e')
...@@ -379,9 +377,9 @@ SacParser::CIFToken SacParser::getNextToken() ...@@ -379,9 +377,9 @@ SacParser::CIFToken SacParser::getNextToken()
// parsed '.' // parsed '.'
case eStateFloat + 2: case eStateFloat + 2:
// if (ch == '(') // numeric??? // if (ch == '(') // numeric???
// mState = eStateNumericSuffix; // mState = eStateNumericSuffix;
// else // else
if (tolower(ch) == 'e') if (tolower(ch) == 'e')
mState = eStateFloat + 3; mState = eStateFloat + 3;
else if (isWhite(ch) or ch == kEOF) else if (isWhite(ch) or ch == kEOF)
...@@ -412,9 +410,9 @@ SacParser::CIFToken SacParser::getNextToken() ...@@ -412,9 +410,9 @@ SacParser::CIFToken SacParser::getNextToken()
break; break;
case eStateFloat + 5: case eStateFloat + 5:
// if (ch == '(') // if (ch == '(')
// mState = eStateNumericSuffix; // mState = eStateNumericSuffix;
// else // else
if (isWhite(ch) or ch == kEOF) if (isWhite(ch) or ch == kEOF)
{ {
retract(); retract();
...@@ -443,22 +441,22 @@ SacParser::CIFToken SacParser::getNextToken() ...@@ -443,22 +441,22 @@ SacParser::CIFToken SacParser::getNextToken()
restart(); restart();
break; break;
// case eStateNumericSuffix: // case eStateNumericSuffix:
// if (isdigit(ch)) // if (isdigit(ch))
// mState = eStateNumericSuffix + 1; // mState = eStateNumericSuffix + 1;
// else // else
// restart(); // restart();
// break; // break;
// //
// case eStateNumericSuffix + 1: // case eStateNumericSuffix + 1:
// if (ch == ')') // if (ch == ')')
// { // {
// result = eCIFTokenValue; // result = eCIFTokenValue;
// mTokenType = eCIFValueNumeric; // mTokenType = eCIFValueNumeric;
// } // }
// else if (not isdigit(ch)) // else if (not isdigit(ch))
// restart(); // restart();
// break; // break;
case eStateValue: case eStateValue:
if (isNonBlank(ch)) if (isNonBlank(ch))
...@@ -530,8 +528,15 @@ DatablockIndex SacParser::indexDatablocks() ...@@ -530,8 +528,15 @@ DatablockIndex SacParser::indexDatablocks()
// first locate the start, as fast as we can // first locate the start, as fast as we can
auto &sb = *mData.rdbuf(); auto &sb = *mData.rdbuf();
enum { enum
start, comment, string, string_quote, qstring, data, data_name {
start,
comment,
string,
string_quote,
qstring,
data,
data_name
} state = start; } state = start;
int quote = 0; int quote = 0;
...@@ -590,7 +595,7 @@ DatablockIndex SacParser::indexDatablocks() ...@@ -590,7 +595,7 @@ DatablockIndex SacParser::indexDatablocks()
case data: case data:
if (dblk[si] == 0 and isNonBlank(ch)) if (dblk[si] == 0 and isNonBlank(ch))
{ {
datablock = { static_cast<char>(ch) }; datablock = {static_cast<char>(ch)};
state = data_name; state = data_name;
} }
else if (dblk[si++] != ch) else if (dblk[si++] != ch)
...@@ -618,13 +623,19 @@ DatablockIndex SacParser::indexDatablocks() ...@@ -618,13 +623,19 @@ DatablockIndex SacParser::indexDatablocks()
return index; return index;
} }
bool SacParser::parseSingleDatablock(const std::string& datablock) bool SacParser::parseSingleDatablock(const std::string &datablock)
{ {
// first locate the start, as fast as we can // first locate the start, as fast as we can
auto &sb = *mData.rdbuf(); auto &sb = *mData.rdbuf();
enum { enum
start, comment, string, string_quote, qstring, data {
start,
comment,
string,
string_quote,
qstring,
data
} state = start; } state = start;
int quote = 0; int quote = 0;
...@@ -701,7 +712,7 @@ bool SacParser::parseSingleDatablock(const std::string& datablock) ...@@ -701,7 +712,7 @@ bool SacParser::parseSingleDatablock(const std::string& datablock)
return found; return found;
} }
bool SacParser::parseSingleDatablock(const std::string& datablock, const DatablockIndex &index) bool SacParser::parseSingleDatablock(const std::string &datablock, const DatablockIndex &index)
{ {
bool result = false; bool result = false;
...@@ -792,7 +803,7 @@ void SacParser::parseDataBlock() ...@@ -792,7 +803,7 @@ void SacParser::parseDataBlock()
{ {
produceRow(); produceRow();
for (auto tag: tags) for (auto tag : tags)
{ {
produceItem(cat, tag, mTokenValue); produceItem(cat, tag, mTokenValue);
match(eCIFTokenValue); match(eCIFTokenValue);
...@@ -841,18 +852,20 @@ void SacParser::parseSaveFrame() ...@@ -841,18 +852,20 @@ void SacParser::parseSaveFrame()
// -------------------------------------------------------------------- // --------------------------------------------------------------------
Parser::Parser(std::istream& is, File& f, bool init) Parser::Parser(std::istream &is, File &f, bool init)
: SacParser(is, init), mFile(f), mDataBlock(nullptr) : SacParser(is, init)
, mFile(f)
, mDataBlock(nullptr)
{ {
} }
void Parser::produceDatablock(const std::string& name) void Parser::produceDatablock(const std::string &name)
{ {
mDataBlock = new Datablock(name); mDataBlock = new Datablock(name);
mFile.append(mDataBlock); mFile.append(mDataBlock);
} }
void Parser::produceCategory(const std::string& name) void Parser::produceCategory(const std::string &name)
{ {
if (VERBOSE >= 4) if (VERBOSE >= 4)
std::cerr << "producing category " << name << std::endl; std::cerr << "producing category " << name << std::endl;
...@@ -870,7 +883,7 @@ void Parser::produceRow() ...@@ -870,7 +883,7 @@ void Parser::produceRow()
mRow.lineNr(mLineNr); mRow.lineNr(mLineNr);
} }
void Parser::produceItem(const std::string& category, const std::string& item, const std::string& value) void Parser::produceItem(const std::string &category, const std::string &item, const std::string &value)
{ {
if (VERBOSE >= 4) if (VERBOSE >= 4)
std::cerr << "producing _" << category << '.' << item << " -> " << value << std::endl; std::cerr << "producing _" << category << '.' << item << " -> " << value << std::endl;
...@@ -887,12 +900,14 @@ struct DictParserDataImpl ...@@ -887,12 +900,14 @@ struct DictParserDataImpl
{ {
// temporary values for constructing dictionaries // temporary values for constructing dictionaries
std::vector<ValidateCategory> mCategoryValidators; std::vector<ValidateCategory> mCategoryValidators;
std::map<std::string,std::vector<ValidateItem>> mItemValidators; std::map<std::string, std::vector<ValidateItem>> mItemValidators;
std::set<std::tuple<std::string,std::string>> mLinkedItems; std::set<std::tuple<std::string, std::string>> mLinkedItems;
}; };
DictParser::DictParser(Validator& validator, std::istream& is) DictParser::DictParser(Validator &validator, std::istream &is)
: Parser(is, mFile), mValidator(validator), mImpl(new DictParserDataImpl) : Parser(is, mFile)
, mValidator(validator)
, mImpl(new DictParserDataImpl)
{ {
} }
...@@ -945,7 +960,7 @@ void DictParser::parseSaveFrame() ...@@ -945,7 +960,7 @@ void DictParser::parseSaveFrame()
cat->emplace({}); cat->emplace({});
auto row = cat->back(); auto row = cat->back();
for (auto tag: tags) for (auto tag : tags)
{ {
row[tag] = mTokenValue; row[tag] = mTokenValue;
match(eCIFTokenValue); match(eCIFTokenValue);
...@@ -976,14 +991,15 @@ void DictParser::parseSaveFrame() ...@@ -976,14 +991,15 @@ void DictParser::parseSaveFrame()
if (isCategorySaveFrame) if (isCategorySaveFrame)
{ {
std::string category = dict.firstItem("_category.id"); std::string category;
cif::tie(category) = dict["category"].front().get("id");
std::vector<std::string> keys; std::vector<std::string> keys;
for (auto k: dict["category_key"]) for (auto k : dict["category_key"])
keys.push_back(std::get<1>(splitTagName(k["name"].as<std::string>()))); keys.push_back(std::get<1>(splitTagName(k["name"].as<std::string>())));
iset groups; iset groups;
for (auto g: dict["category_group"]) for (auto g : dict["category_group"])
groups.insert(g["id"].as<std::string>()); groups.insert(g["id"].as<std::string>());
mImpl->mCategoryValidators.push_back(ValidateCategory{category, keys, groups}); mImpl->mCategoryValidators.push_back(ValidateCategory{category, keys, groups});
...@@ -991,21 +1007,23 @@ void DictParser::parseSaveFrame() ...@@ -991,21 +1007,23 @@ void DictParser::parseSaveFrame()
else else
{ {
// if the type code is missing, this must be a pointer, just skip it // if the type code is missing, this must be a pointer, just skip it
std::string typeCode = dict.firstItem("_item_type.code"); std::string typeCode;
cif::tie(typeCode) = dict["item_type"].front().get("code");
const ValidateType* tv = nullptr; const ValidateType *tv = nullptr;
if (not (typeCode.empty() or typeCode == "?")) if (not(typeCode.empty() or typeCode == "?"))
tv = mValidator.getValidatorForType(typeCode); tv = mValidator.getValidatorForType(typeCode);
iset ess; iset ess;
for (auto e: dict["item_enumeration"]) for (auto e : dict["item_enumeration"])
ess.insert(e["value"].as<std::string>()); ess.insert(e["value"].as<std::string>());
std::string defaultValue = dict.firstItem("_item_default.value"); std::string defaultValue;
cif::tie(defaultValue) = dict["item_default"].front().get("value");
bool defaultIsNull = false; bool defaultIsNull = false;
if (defaultValue.empty()) if (defaultValue.empty())
{ {
for (auto& r: dict["_item_default"]) for (auto &r : dict["_item_default"])
{ {
defaultIsNull = r["value"].is_null(); defaultIsNull = r["value"].is_null();
break; break;
...@@ -1013,7 +1031,7 @@ void DictParser::parseSaveFrame() ...@@ -1013,7 +1031,7 @@ void DictParser::parseSaveFrame()
} }
// collect the dict from our dataBlock and construct validators // collect the dict from our dataBlock and construct validators
for (auto i: dict["item"]) for (auto i : dict["item"])
{ {
std::string tagName, category, mandatory; std::string tagName, category, mandatory;
...@@ -1025,12 +1043,12 @@ void DictParser::parseSaveFrame() ...@@ -1025,12 +1043,12 @@ void DictParser::parseSaveFrame()
if (catName.empty() or itemName.empty()) if (catName.empty() or itemName.empty())
error("Invalid tag name in _item.name " + tagName); error("Invalid tag name in _item.name " + tagName);
if (not iequals(category, catName) and not (category.empty() or category == "?")) if (not iequals(category, catName) and not(category.empty() or category == "?"))
error("specified category id does match the implicit category name for tag '" + tagName + '\''); error("specified category id does match the implicit category name for tag '" + tagName + '\'');
else else
category = catName; category = catName;
auto& ivs = mImpl->mItemValidators[category]; auto &ivs = mImpl->mItemValidators[category];
auto vi = find(ivs.begin(), ivs.end(), ValidateItem{itemName}); auto vi = find(ivs.begin(), ivs.end(), ValidateItem{itemName});
if (vi == ivs.end()) if (vi == ivs.end())
...@@ -1060,7 +1078,7 @@ void DictParser::parseSaveFrame() ...@@ -1060,7 +1078,7 @@ void DictParser::parseSaveFrame()
std::cerr << "inconsistent type for " << tagName << " in dictionary" << std::endl; std::cerr << "inconsistent type for " << tagName << " in dictionary" << std::endl;
} }
// vi->mMandatory = (iequals(mandatory, "yes")); // vi->mMandatory = (iequals(mandatory, "yes"));
if (vi->mType == nullptr) if (vi->mType == nullptr)
vi->mType = tv; vi->mType = tv;
...@@ -1072,7 +1090,7 @@ void DictParser::parseSaveFrame() ...@@ -1072,7 +1090,7 @@ void DictParser::parseSaveFrame()
} }
// collect the dict from our dataBlock and construct validators // collect the dict from our dataBlock and construct validators
for (auto i: dict["item_linked"]) for (auto i : dict["item_linked"])
{ {
std::string childTagName, parentTagName; std::string childTagName, parentTagName;
...@@ -1088,20 +1106,20 @@ void DictParser::linkItems() ...@@ -1088,20 +1106,20 @@ void DictParser::linkItems()
if (not mDataBlock) if (not mDataBlock)
error("no datablock"); error("no datablock");
auto& dict = *mDataBlock; auto &dict = *mDataBlock;
// links are identified by a parent category, a child category and a group ID // links are identified by a parent category, a child category and a group ID
using key_type = std::tuple<std::string,std::string,int>; using key_type = std::tuple<std::string, std::string, int>;
std::map<key_type,size_t> linkIndex; std::map<key_type, size_t> linkIndex;
// Each link group consists of a set of keys // Each link group consists of a set of keys
std::vector<std::tuple<std::vector<std::string>,std::vector<std::string>>> linkKeys; std::vector<std::tuple<std::vector<std::string>, std::vector<std::string>>> linkKeys;
auto addLink = [&](size_t ix, const std::string& pk, const std::string& ck) auto addLink = [&](size_t ix, const std::string &pk, const std::string &ck)
{ {
auto&& [pkeys, ckeys] = linkKeys.at(ix); auto &&[pkeys, ckeys] = linkKeys.at(ix);
bool found = false; bool found = false;
for (size_t i = 0; i < pkeys.size(); ++i) for (size_t i = 0; i < pkeys.size(); ++i)
...@@ -1120,9 +1138,9 @@ void DictParser::linkItems() ...@@ -1120,9 +1138,9 @@ void DictParser::linkItems()
} }
}; };
auto& linkedGroupList = dict["pdbx_item_linked_group_list"]; auto &linkedGroupList = dict["pdbx_item_linked_group_list"];
for (auto gl: linkedGroupList) for (auto gl : linkedGroupList)
{ {
std::string child, parent; std::string child, parent;
int link_group_id; int link_group_id;
...@@ -1136,7 +1154,7 @@ void DictParser::linkItems() ...@@ -1136,7 +1154,7 @@ void DictParser::linkItems()
if (piv == nullptr) if (piv == nullptr)
error("in pdbx_item_linked_group_list, item '" + parent + "' is not specified"); error("in pdbx_item_linked_group_list, item '" + parent + "' is not specified");
key_type key{ piv->mCategory->mName, civ->mCategory->mName, link_group_id }; key_type key{piv->mCategory->mName, civ->mCategory->mName, link_group_id};
if (not linkIndex.count(key)) if (not linkIndex.count(key))
{ {
linkIndex[key] = linkKeys.size(); linkIndex[key] = linkKeys.size();
...@@ -1151,7 +1169,7 @@ void DictParser::linkItems() ...@@ -1151,7 +1169,7 @@ void DictParser::linkItems()
if (linkedGroupList.empty()) if (linkedGroupList.empty())
{ {
// for links recorded in categories but not in pdbx_item_linked_group_list // for links recorded in categories but not in pdbx_item_linked_group_list
for (auto li: mImpl->mLinkedItems) for (auto li : mImpl->mLinkedItems)
{ {
std::string child, parent; std::string child, parent;
std::tie(child, parent) = li; std::tie(child, parent) = li;
...@@ -1164,7 +1182,7 @@ void DictParser::linkItems() ...@@ -1164,7 +1182,7 @@ void DictParser::linkItems()
if (piv == nullptr) if (piv == nullptr)
error("in pdbx_item_linked_group_list, item '" + parent + "' is not specified"); error("in pdbx_item_linked_group_list, item '" + parent + "' is not specified");
key_type key{ piv->mCategory->mName, civ->mCategory->mName, 0 }; key_type key{piv->mCategory->mName, civ->mCategory->mName, 0};
if (not linkIndex.count(key)) if (not linkIndex.count(key))
{ {
linkIndex[key] = linkKeys.size(); linkIndex[key] = linkKeys.size();
...@@ -1176,10 +1194,10 @@ void DictParser::linkItems() ...@@ -1176,10 +1194,10 @@ void DictParser::linkItems()
} }
} }
auto& linkedGroup = dict["pdbx_item_linked_group"]; auto &linkedGroup = dict["pdbx_item_linked_group"];
// now store the links in the validator // now store the links in the validator
for (auto& kv: linkIndex) for (auto &kv : linkIndex)
{ {
ValidateLink link = {}; ValidateLink link = {};
std::tie(link.mParentCategory, link.mChildCategory, link.mLinkGroupID) = kv.first; std::tie(link.mParentCategory, link.mChildCategory, link.mLinkGroupID) = kv.first;
...@@ -1187,7 +1205,7 @@ void DictParser::linkItems() ...@@ -1187,7 +1205,7 @@ void DictParser::linkItems()
std::tie(link.mParentKeys, link.mChildKeys) = linkKeys[kv.second]; std::tie(link.mParentKeys, link.mChildKeys) = linkKeys[kv.second];
// look up the label // look up the label
for (auto r: linkedGroup.find(cif::Key("category_id") == link.mChildCategory and cif::Key("link_group_id") == link.mLinkGroupID)) for (auto r : linkedGroup.find(cif::Key("category_id") == link.mChildCategory and cif::Key("link_group_id") == link.mLinkGroupID))
{ {
link.mLinkGroupLabel = r["label"].as<std::string>(); link.mLinkGroupLabel = r["label"].as<std::string>();
break; break;
...@@ -1198,9 +1216,9 @@ void DictParser::linkItems() ...@@ -1198,9 +1216,9 @@ void DictParser::linkItems()
// now make sure the itemType is specified for all itemValidators // now make sure the itemType is specified for all itemValidators
for (auto& cv: mValidator.mCategoryValidators) for (auto &cv : mValidator.mCategoryValidators)
{ {
for (auto& iv: cv.mItemValidators) for (auto &iv : cv.mItemValidators)
{ {
if (iv.mType == nullptr) if (iv.mType == nullptr)
std::cerr << "Missing item_type for " << iv.mTag << std::endl; std::cerr << "Missing item_type for " << iv.mTag << std::endl;
...@@ -1211,7 +1229,7 @@ void DictParser::linkItems() ...@@ -1211,7 +1229,7 @@ void DictParser::linkItems()
void DictParser::loadDictionary() void DictParser::loadDictionary()
{ {
std::unique_ptr<Datablock> dict; std::unique_ptr<Datablock> dict;
Datablock* savedDatablock = mDataBlock; Datablock *savedDatablock = mDataBlock;
try try
{ {
...@@ -1235,25 +1253,25 @@ void DictParser::loadDictionary() ...@@ -1235,25 +1253,25 @@ void DictParser::loadDictionary()
} }
} }
} }
catch (const std::exception&) catch (const std::exception &)
{ {
std::cerr << "Error parsing dictionary" << std::endl; std::cerr << "Error parsing dictionary" << std::endl;
throw; throw;
} }
// store all validators // store all validators
for (auto& ic: mImpl->mCategoryValidators) for (auto &ic : mImpl->mCategoryValidators)
mValidator.addCategoryValidator(std::move(ic)); mValidator.addCategoryValidator(std::move(ic));
mImpl->mCategoryValidators.clear(); mImpl->mCategoryValidators.clear();
for (auto& iv: mImpl->mItemValidators) for (auto &iv : mImpl->mItemValidators)
{ {
auto cv = mValidator.getValidatorForCategory(iv.first); auto cv = mValidator.getValidatorForCategory(iv.first);
if (cv == nullptr) if (cv == nullptr)
error("Undefined category '" + iv.first); error("Undefined category '" + iv.first);
for (auto& v: iv.second) for (auto &v : iv.second)
const_cast<ValidateCategory*>(cv)->addItemValidator(std::move(v)); const_cast<ValidateCategory *>(cv)->addItemValidator(std::move(v));
} }
// check all item validators for having a typeValidator // check all item validators for having a typeValidator
...@@ -1284,9 +1302,9 @@ bool DictParser::collectItemTypes() ...@@ -1284,9 +1302,9 @@ bool DictParser::collectItemTypes()
if (not mDataBlock) if (not mDataBlock)
error("no datablock"); error("no datablock");
auto& dict = *mDataBlock; auto &dict = *mDataBlock;
for (auto& t: dict["item_type_list"]) for (auto &t : dict["item_type_list"])
{ {
std::string code, primitiveCode, construct; std::string code, primitiveCode, construct;
cif::tie(code, primitiveCode, construct) = t.get("code", "primitive_code", "construct"); cif::tie(code, primitiveCode, construct) = t.get("code", "primitive_code", "construct");
...@@ -1298,20 +1316,19 @@ bool DictParser::collectItemTypes() ...@@ -1298,20 +1316,19 @@ bool DictParser::collectItemTypes()
try try
{ {
ValidateType v = { ValidateType v = {
code, mapToPrimitiveType(primitiveCode), boost::regex(construct, boost::regex::extended | boost::regex::optimize) code, mapToPrimitiveType(primitiveCode), boost::regex(construct, boost::regex::extended | boost::regex::optimize)};
};
mValidator.addTypeValidator(std::move(v)); mValidator.addTypeValidator(std::move(v));
} }
catch (const std::exception&) catch (const std::exception &)
{ {
throw_with_nested(CifParserError(t.lineNr(), "error in regular expression")); throw_with_nested(CifParserError(t.lineNr(), "error in regular expression"));
} }
// Do not replace an already defined type validator, this won't work with pdbx_v40 // Do not replace an already defined type validator, this won't work with pdbx_v40
// as it has a name that is too strict for its own names :-) // as it has a name that is too strict for its own names :-)
// if (mFileImpl.mTypeValidators.count(v)) // if (mFileImpl.mTypeValidators.count(v))
// mFileImpl.mTypeValidators.erase(v); // mFileImpl.mTypeValidators.erase(v);
if (VERBOSE >= 5) if (VERBOSE >= 5)
std::cerr << "Added type " << code << " (" << primitiveCode << ") => " << construct << std::endl; std::cerr << "Added type " << code << " (" << primitiveCode << ") => " << construct << std::endl;
...@@ -1322,5 +1339,4 @@ bool DictParser::collectItemTypes() ...@@ -1322,5 +1339,4 @@ bool DictParser::collectItemTypes()
return result; return result;
} }
} // namespace cif
}
src/CifUtils.cpp
...@@ -123,19 +123,12 @@ const uint8_t kCharToLowerMap[256] = ...@@ -123,19 +123,12 @@ const uint8_t kCharToLowerMap[256] =
// -------------------------------------------------------------------- // --------------------------------------------------------------------
bool iequals(const std::string &a, const std::string &b)
{
bool result = a.length() == b.length();
for (auto ai = a.begin(), bi = b.begin(); result and ai != a.end() and bi != b.end(); ++ai, ++bi)
result = tolower(*ai) == tolower(*bi);
return result;
}
bool iequals(std::string_view a, std::string_view b) bool iequals(std::string_view a, std::string_view b)
{ {
bool result = a.length() == b.length(); bool result = a.length() == b.length();
for (auto ai = a.begin(), bi = b.begin(); result and ai != a.end() and bi != b.end(); ++ai, ++bi) for (auto ai = a.begin(), bi = b.begin(); result and ai != a.end(); ++ai, ++bi)
result = tolower(*ai) == tolower(*bi); result = kCharToLowerMap[uint8_t(*ai)] == kCharToLowerMap[uint8_t(*bi)];
// result = tolower(*ai) == tolower(*bi);
return result; return result;
} }
...@@ -148,25 +141,6 @@ bool iequals(const char *a, const char *b) ...@@ -148,25 +141,6 @@ bool iequals(const char *a, const char *b)
return result and *a == *b; return result and *a == *b;
} }
int icompare(const std::string &a, const std::string &b)
{
int d = 0;
auto ai = a.begin(), bi = b.begin();
for (; d == 0 and ai != a.end() and bi != b.end(); ++ai, ++bi)
d = tolower(*ai) - tolower(*bi);
if (d == 0)
{
if (ai != a.end())
d = 1;
else if (bi != b.end())
d = -1;
}
return d;
}
int icompare(std::string_view a, std::string_view b) int icompare(std::string_view a, std::string_view b)
{ {
int d = 0; int d = 0;
......
src/CifValidator.cpp
...@@ -24,13 +24,20 @@ ...@@ -24,13 +24,20 @@
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/ */
#include <fstream>
#include <filesystem>
#include <boost/algorithm/string.hpp> #include <boost/algorithm/string.hpp>
#include <boost/iostreams/filtering_stream.hpp>
#include <boost/iostreams/filter/gzip.hpp>
#include "cif++/Cif++.hpp" #include "cif++/Cif++.hpp"
#include "cif++/CifParser.hpp" #include "cif++/CifParser.hpp"
#include "cif++/CifValidator.hpp" #include "cif++/CifValidator.hpp"
namespace ba = boost::algorithm; namespace ba = boost::algorithm;
namespace fs = std::filesystem;
namespace io = boost::iostreams;
extern int VERBOSE; extern int VERBOSE;
...@@ -219,8 +226,11 @@ const ValidateItem *ValidateCategory::getValidatorForItem(std::string_view tag) ...@@ -219,8 +226,11 @@ const ValidateItem *ValidateCategory::getValidatorForItem(std::string_view tag)
// -------------------------------------------------------------------- // --------------------------------------------------------------------
Validator::Validator() Validator::Validator(std::string_view name, std::istream &is)
: mName(name)
{ {
DictParser p(*this, is);
p.loadDictionary();
} }
Validator::~Validator() Validator::~Validator()
...@@ -340,7 +350,7 @@ std::vector<const ValidateLink *> Validator::getLinksForChild(std::string_view c ...@@ -340,7 +350,7 @@ std::vector<const ValidateLink *> Validator::getLinksForChild(std::string_view c
return result; return result;
} }
void Validator::reportError(const std::string &msg, bool fatal) void Validator::reportError(const std::string &msg, bool fatal) const
{ {
if (mStrict or fatal) if (mStrict or fatal)
throw ValidationError(msg); throw ValidationError(msg);
...@@ -348,4 +358,78 @@ void Validator::reportError(const std::string &msg, bool fatal) ...@@ -348,4 +358,78 @@ void Validator::reportError(const std::string &msg, bool fatal)
std::cerr << msg << std::endl; std::cerr << msg << std::endl;
} }
// --------------------------------------------------------------------
ValidatorFactory ValidatorFactory::sInstance;
ValidatorFactory::ValidatorFactory()
{
}
const Validator &ValidatorFactory::operator[](std::string_view dictionary)
{
std::lock_guard lock(mMutex);
for (auto &validator : mValidators)
{
if (iequals(validator.mName, dictionary))
return validator;
}
// not found, add it
fs::path dict_name(dictionary);
auto data = loadResource(dictionary);
if (not data and dict_name.extension().string() != ".dic")
data = loadResource(dict_name.parent_path() / (dict_name.filename().string() + ".dic"));
if (data)
mValidators.emplace_back(dictionary, *data);
else
{
// might be a compressed dictionary on disk
fs::path p = dictionary;
if (p.extension() == ".dic")
p = p.parent_path() / (p.filename().string() + ".gz");
else
p = p.parent_path() / (p.filename().string() + ".dic.gz");
#if defined(CACHE_DIR) and defined(DATA_DIR)
if (not fs::exists(p))
{
for (const char *dir : {CACHE_DIR, DATA_DIR})
{
auto p2 = fs::path(dir) / p;
if (fs::exists(p2))
{
swap(p, p2);
break;
}
}
}
#endif
if (fs::exists(p))
{
std::ifstream file(p, std::ios::binary);
if (not file.is_open())
throw std::runtime_error("Could not open dictionary (" + p.string() + ")");
io::filtering_stream<io::input> in;
in.push(io::gzip_decompressor());
in.push(file);
mValidators.emplace_back(dictionary, in);
}
else
throw std::runtime_error("Dictionary not found or defined (" + dict_name.string() + ")");
}
assert(iequals(mValidators.back().mName, dictionary));
return mValidators.back();
}
} // namespace cif } // namespace cif
src/Point.cpp
...@@ -468,14 +468,14 @@ Point CenterPoints(std::vector<Point>& Points) ...@@ -468,14 +468,14 @@ Point CenterPoints(std::vector<Point>& Points)
return t; return t;
} }
Point Centroid(std::vector<Point>& Points) Point Centroid(const std::vector<Point>& pts)
{ {
Point result; Point result;
for (Point& pt : Points) for (auto &pt : pts)
result += pt; result += pt;
result /= static_cast<float>(Points.size()); result /= static_cast<float>(pts.size());
return result; return result;
} }
......
src/Structure.cpp
...@@ -216,9 +216,9 @@ struct AtomImpl ...@@ -216,9 +216,9 @@ struct AtomImpl
, mLocation(i.mLocation) , mLocation(i.mLocation)
, mRefcount(1) , mRefcount(1)
, mRow(i.mRow) , mRow(i.mRow)
, mCachedRefs(i.mCachedRefs)
, mCompound(i.mCompound) , mCompound(i.mCompound)
, mRadius(i.mRadius) , mRadius(i.mRadius)
, mCachedProperties(i.mCachedProperties)
, mSymmetryCopy(i.mSymmetryCopy) , mSymmetryCopy(i.mSymmetryCopy)
, mClone(true) , mClone(true)
// , mRTop(i.mRTop), mD(i.mD) // , mRTop(i.mRTop), mD(i.mD)
...@@ -270,9 +270,9 @@ struct AtomImpl ...@@ -270,9 +270,9 @@ struct AtomImpl
, mLocation(loc) , mLocation(loc)
, mRefcount(1) , mRefcount(1)
, mRow(impl.mRow) , mRow(impl.mRow)
, mCachedRefs(impl.mCachedRefs)
, mCompound(impl.mCompound) , mCompound(impl.mCompound)
, mRadius(impl.mRadius) , mRadius(impl.mRadius)
, mCachedProperties(impl.mCachedProperties)
, mSymmetryCopy(true) , mSymmetryCopy(true)
, mSymmetryOperator(sym_op) , mSymmetryOperator(sym_op)
{ {
...@@ -317,13 +317,15 @@ struct AtomImpl ...@@ -317,13 +317,15 @@ struct AtomImpl
auto cat = mDb.get("atom_site_anisotrop"); auto cat = mDb.get("atom_site_anisotrop");
if (cat) if (cat)
{ {
auto r = cat->find1(cif::Key("id") == mID); try
if (not r.empty())
{ {
result = true; auto r = cat->find1(cif::Key("id") == mID);
cif::tie(anisou[0], anisou[1], anisou[2], anisou[3], anisou[4], anisou[5]) = cif::tie(anisou[0], anisou[1], anisou[2], anisou[3], anisou[4], anisou[5]) =
r.get("U[1][1]", "U[1][2]", "U[1][3]", "U[2][2]", "U[2][3]", "U[3][3]"); r.get("U[1][1]", "U[1][2]", "U[1][3]", "U[2][2]", "U[2][3]", "U[3][3]");
result = true;
}
catch(const std::exception& e)
{
} }
} }
...@@ -338,9 +340,9 @@ struct AtomImpl ...@@ -338,9 +340,9 @@ struct AtomImpl
if (not mClone) if (not mClone)
{ {
mRow["Cartn_x"] = p.getX(); property("Cartn_x", std::to_string(p.getX()));
mRow["Cartn_y"] = p.getY(); property("Cartn_y", std::to_string(p.getY()));
mRow["Cartn_z"] = p.getZ(); property("Cartn_z", std::to_string(p.getZ()));
} }
// boost::format kPosFmt("%.3f"); // boost::format kPosFmt("%.3f");
...@@ -382,26 +384,31 @@ struct AtomImpl ...@@ -382,26 +384,31 @@ struct AtomImpl
return mRadius; return mRadius;
} }
const std::string &property(const std::string &name) const const std::string property(const std::string_view name) const
{ {
static std::string kEmptyString; for (auto &&[tag, ref] : mCachedRefs)
auto i = mCachedProperties.find(name);
if (i == mCachedProperties.end())
{ {
auto v = mRow[name]; if (tag == name)
if (v.empty()) return ref.as<std::string>();
return kEmptyString;
return mCachedProperties[name] = v.as<std::string>();
} }
else
return i->second; mCachedRefs.emplace_back(name, mRow[name]);
return std::get<1>(mCachedRefs.back()).as<std::string>();
} }
void property(const std::string &name, const std::string &value) void property(const std::string_view name, const std::string &value)
{
for (auto &&[tag, ref] : mCachedRefs)
{ {
mRow[name] = value; if (tag != name)
continue;
ref = value;
return;
}
mCachedRefs.emplace_back(name, mRow[name]);
std::get<1>(mCachedRefs.back()) = value;
} }
int compare(const AtomImpl &b) const int compare(const AtomImpl &b) const
...@@ -432,9 +439,11 @@ struct AtomImpl ...@@ -432,9 +439,11 @@ struct AtomImpl
Point mLocation; Point mLocation;
int mRefcount; int mRefcount;
cif::Row mRow; cif::Row mRow;
mutable std::vector<std::tuple<std::string,cif::detail::ItemReference>> mCachedRefs;
mutable const Compound *mCompound = nullptr; mutable const Compound *mCompound = nullptr;
float mRadius = std::nanf("4"); float mRadius = std::nanf("4");
mutable std::map<std::string, std::string> mCachedProperties;
bool mSymmetryCopy = false; bool mSymmetryCopy = false;
bool mClone = false; bool mClone = false;
...@@ -533,25 +542,25 @@ const cif::Row Atom::getRowAniso() const ...@@ -533,25 +542,25 @@ const cif::Row Atom::getRowAniso() const
} }
template <> template <>
std::string Atom::property<std::string>(const std::string &name) const std::string Atom::property<std::string>(const std::string_view name) const
{ {
return impl()->property(name); return impl()->property(name);
} }
template <> template <>
int Atom::property<int>(const std::string &name) const int Atom::property<int>(const std::string_view name) const
{ {
auto v = impl()->property(name); auto v = impl()->property(name);
return v.empty() ? 0 : stoi(v); return v.empty() ? 0 : stoi(v);
} }
template <> template <>
float Atom::property<float>(const std::string &name) const float Atom::property<float>(const std::string_view name) const
{ {
return stof(impl()->property(name)); return stof(impl()->property(name));
} }
void Atom::property(const std::string &name, const std::string &value) void Atom::property(const std::string_view name, const std::string &value)
{ {
impl()->property(name, value); impl()->property(name, value);
} }
...@@ -1736,7 +1745,7 @@ File::~File() ...@@ -1736,7 +1745,7 @@ File::~File()
delete mImpl; delete mImpl;
} }
cif::Datablock& File::createDatablock(const std::string &name) cif::Datablock& File::createDatablock(const std::string_view name)
{ {
auto db = new cif::Datablock(name); auto db = new cif::Datablock(name);
...@@ -1807,8 +1816,8 @@ Structure::Structure(File &f, size_t modelNr, StructureOpenOptions options) ...@@ -1807,8 +1816,8 @@ Structure::Structure(File &f, size_t modelNr, StructureOpenOptions options)
} }
if (mAtoms.empty()) if (mAtoms.empty())
throw std::runtime_error("No atoms loaded, refuse to continue"); std::cerr << "Warning: no atoms loaded" << std::endl;
else
loadData(); loadData();
} }
......
src/Symmetry.cpp
...@@ -90,4 +90,66 @@ int GetSpacegroupNumber(std::string spacegroup) ...@@ -90,4 +90,66 @@ int GetSpacegroupNumber(std::string spacegroup)
return result; return result;
} }
// --------------------------------------------------------------------
int GetSpacegroupNumber(std::string spacegroup, SpacegroupName type)
{
if (spacegroup == "P 21 21 2 A")
spacegroup = "P 21 21 2 (a)";
else if (spacegroup.empty())
throw std::runtime_error("No spacegroup, cannot continue");
int result = 0;
if (type == SpacegroupName::full)
{
const size_t N = kNrOfSpaceGroups;
int32_t L = 0, R = static_cast<int32_t>(N - 1);
while (L <= R)
{
int32_t i = (L + R) / 2;
int d = spacegroup.compare(kSpaceGroups[i].name);
if (d > 0)
L = i + 1;
else if (d < 0)
R = i - 1;
else
{
result = kSpaceGroups[i].nr;
break;
}
}
}
else if (type == SpacegroupName::xHM)
{
for (auto &sg : kSpaceGroups)
{
if (sg.xHM == spacegroup)
{
result = sg.nr;
break;
}
}
}
else
{
for (auto &sg : kSpaceGroups)
{
if (sg.Hall == spacegroup)
{
result = sg.nr;
break;
}
}
}
// not found, see if we can find a match based on xHM name
if (result == 0)
throw std::runtime_error("Spacegroup name " + spacegroup + " was not found in table");
return result;
}
} }
test/pdb2cif-test.cpp
...@@ -18,7 +18,6 @@ int main(int argc, char* argv[]) ...@@ -18,7 +18,6 @@ int main(int argc, char* argv[])
desc.add_options() desc.add_options()
("input,i", po::value<std::string>(), "Input file") ("input,i", po::value<std::string>(), "Input file")
("help,h", "Display help message") ("help,h", "Display help message")
("version", "Print version")
("verbose,v", "Verbose output") ("verbose,v", "Verbose output")
("debug,d", po::value<int>(), "Debug level (for even more verbose output)"); ("debug,d", po::value<int>(), "Debug level (for even more verbose output)");
...@@ -29,12 +28,6 @@ int main(int argc, char* argv[]) ...@@ -29,12 +28,6 @@ int main(int argc, char* argv[])
po::store(po::command_line_parser(argc, argv).options(desc).positional(p).run(), vm); po::store(po::command_line_parser(argc, argv).options(desc).positional(p).run(), vm);
po::notify(vm); po::notify(vm);
if (vm.count("version"))
{
std::cout << argv[0] << " version " PACKAGE_VERSION << std::endl;
exit(0);
}
if (vm.count("help") or vm.count("input") == 0) if (vm.count("help") or vm.count("input") == 0)
{ {
std::cerr << desc << std::endl; std::cerr << desc << std::endl;
......
test/unit-test.cpp
...@@ -33,6 +33,7 @@ ...@@ -33,6 +33,7 @@
// #include "cif++/DistanceMap.hpp" // #include "cif++/DistanceMap.hpp"
#include "cif++/Cif++.hpp" #include "cif++/Cif++.hpp"
#include "cif++/BondMap.hpp" #include "cif++/BondMap.hpp"
#include "cif++/CifValidator.hpp"
std::filesystem::path gTestDir = std::filesystem::current_path(); // filled in first test std::filesystem::path gTestDir = std::filesystem::current_path(); // filled in first test
...@@ -259,8 +260,10 @@ save__cat_2.desc ...@@ -259,8 +260,10 @@ save__cat_2.desc
std::istream is_dict(&buffer); std::istream is_dict(&buffer);
cif::Validator validator("test", is_dict);
cif::File f; cif::File f;
f.loadDictionary(is_dict); f.setValidator(&validator);
// -------------------------------------------------------------------- // --------------------------------------------------------------------
...@@ -387,8 +390,10 @@ save__cat_1.c ...@@ -387,8 +390,10 @@ save__cat_1.c
std::istream is_dict(&buffer); std::istream is_dict(&buffer);
cif::Validator validator("test", is_dict);
cif::File f; cif::File f;
f.loadDictionary(is_dict); f.setValidator(&validator);
// -------------------------------------------------------------------- // --------------------------------------------------------------------
...@@ -535,8 +540,10 @@ save__cat_2.desc ...@@ -535,8 +540,10 @@ save__cat_2.desc
std::istream is_dict(&buffer); std::istream is_dict(&buffer);
cif::Validator validator("test", is_dict);
cif::File f; cif::File f;
f.loadDictionary(is_dict); f.setValidator(&validator);
// -------------------------------------------------------------------- // --------------------------------------------------------------------
...@@ -741,8 +748,10 @@ save__cat_2.parent_id3 ...@@ -741,8 +748,10 @@ save__cat_2.parent_id3
std::istream is_dict(&buffer); std::istream is_dict(&buffer);
cif::Validator validator("test", is_dict);
cif::File f; cif::File f;
f.loadDictionary(is_dict); f.setValidator(&validator);
// -------------------------------------------------------------------- // --------------------------------------------------------------------
...@@ -963,8 +972,10 @@ cat_2 3 cat_2:cat_1:3 ...@@ -963,8 +972,10 @@ cat_2 3 cat_2:cat_1:3
std::istream is_dict(&buffer); std::istream is_dict(&buffer);
cif::Validator validator("test", is_dict);
cif::File f; cif::File f;
f.loadDictionary(is_dict); f.setValidator(&validator);
// -------------------------------------------------------------------- // --------------------------------------------------------------------
...@@ -1389,9 +1400,10 @@ cat_2 1 '_cat_2.num' '_cat_3.num' cat_3 ...@@ -1389,9 +1400,10 @@ cat_2 1 '_cat_2.num' '_cat_3.num' cat_3
} buffer(const_cast<char*>(dict), sizeof(dict) - 1); } buffer(const_cast<char*>(dict), sizeof(dict) - 1);
std::istream is_dict(&buffer); std::istream is_dict(&buffer);
cif::Validator validator("test", is_dict);
cif::File f; cif::File f;
f.loadDictionary(is_dict); f.setValidator(&validator);
// -------------------------------------------------------------------- // --------------------------------------------------------------------
......
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