8 #ifndef PDBPREPARATION_PDBPROCESSOR_H
9 #define PDBPREPARATION_PDBPROCESSOR_H
24 namespace StructurePreparation {
25 class ProtonationHandler;
29 static constexpr
const char* model =
"PDB_Processor";
39 void prepare(
const std::string& structureFile,
const std::string& mode);
51 std::string
name()
const;
77 Utils::AtomCollection getAtomCollectionFromInput(
const std::string& structureFile,
bool includeH)
const;
81 void performInitialSetup(
const std::string& structureFile);
86 void processNonRegContainerSubstructure();
94 std::shared_ptr<Utils::Settings> settings_;
96 bool protonationDone_ =
false;
97 bool finalizationDone_ =
false;
103 #endif // PDBPREPARATION_PdbProcessor_H
void prepare(const std::string &structureFile, const std::string &mode)
Main function of this class. It prepares the protein input structure.
Definition: StructureProcessor.cpp:32
Utils::Settings & settings()
Accessor for the settings.
Definition: StructureProcessor.cpp:257
void analyzeStructure(const std::string &structureFile)
Analyzes the input structure.
Definition: StructureProcessor.cpp:70
This struct holds all objects used inside the MM parametrization algorithm.
Definition: StructurePreparationData.h:25
void protonate()
Protonates protein and nonRegContainer separately.
Definition: StructureProcessor.cpp:87
Definition: StructureProcessor.h:27
StructureProcessor()
Constructor.
Definition: StructureProcessor.cpp:27
void finalize()
This function merges protein and nonRegContainer, corrects the boundaries, adds optional solvation an...
Definition: StructureProcessor.cpp:106
std::string name() const
Getter for the name of the Parametrizer.
Definition: StructureProcessor.cpp:265
Definition: StructurePreparationData.h:90