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class FragmentDB
{
%TypeHeaderCode
#include <BALL/PYTHON/EXTENSIONS/pyUnaryProcessors.h>
#include <BALL/STRUCTURE/fragmentDB.h>
#include <BALL/STRUCTURE/reconstructFragmentProcessor.h>
using StringHashMapString = StringHashMap<String>;
%End
public:
enum FragmentTypes
{
TYPE__UNKNOWN = -1,
TYPE__FRAGMENT,
TYPE__RESIDUE,
TYPE__MOLECULE
};
typedef short Type;
FragmentDB();
FragmentDB(const String&);
FragmentDB(const FragmentDB&, bool deep = true);
~FragmentDB();
void destroy();
void init();
void setFilename(const String&);
const String& getFilename() const;
bool has(const String&) const;
FragmentDB::Type getFragmentType(const String&) const;
const Fragment* getFragment(const String&) const;
const Fragment* getReferenceFragment(const Fragment&) const;
const Residue* getResidue(const String&) const;
Fragment* getFragmentCopy(const String&) const;
Molecule* getMoleculeCopy(const String&) const;
Residue* getResidueCopy(const String&) const;
const StringHashMap<String>& getNamingStandard(const String&) const
throw(StringHashMapString::IllegalKey);
vector<String> getAvailableNamingStandards() const;
const String& getDefaultNamingStandard() const;
bool isValid() const;
NormalizeNamesProcessor normalize_names;
ReconstructFragmentProcessor add_hydrogens;
BuildBondsProcessor build_bonds;
ResourceEntry* tree;
};
class NormalizeNamesProcessor
: FragmentProcessor
{
%TypeHeaderCode
#include <BALL/PYTHON/EXTENSIONS/pyUnaryProcessors.h>
#include <BALL/STRUCTURE/fragmentDB.h>
using NormalizeNamesProcessor = FragmentDB::NormalizeNamesProcessor;
%End
public:
NormalizeNamesProcessor();
NormalizeNamesProcessor(FragmentDB&);
~NormalizeNamesProcessor();
void setFragmentDB(FragmentDB&);
void setNamingStandard(const String&);
const String& getNamingStandard();
virtual bool start();
virtual bool finish();
Processor::Result operator () (Fragment&);
%MethodCode
sipRes = sipCpp->operator () (*a0);
%End
};
class BuildBondsProcessor
: FragmentProcessor
{
%TypeHeaderCode
#include <BALL/PYTHON/EXTENSIONS/pyUnaryProcessors.h>
#include <BALL/STRUCTURE/fragmentDB.h>
using BuildBondsProcessor = FragmentDB::BuildBondsProcessor;
%End
public:
BuildBondsProcessor();
BuildBondsProcessor(const FragmentDB&);
~BuildBondsProcessor();
virtual bool finish();
virtual bool start();
Processor::Result operator () (Fragment&);
%MethodCode
sipRes = sipCpp->operator () (*a0);
%End
Size getNumberOfBondsBuilt();
void setFragmentDB(const FragmentDB&);
Size buildFragmentBonds(Fragment&) const;
Size buildInterFragmentBonds(Fragment&, Fragment&) const;
};
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