19 #ifndef OST_CONOP_PROCESSOR_HH
20 #define OST_CONOP_PROCESSOR_HH
26 namespace ost {
namespace conop {
58 bool strict_hydrogens)
const;
60 bool fix_element)
const;
70 check_bond_feasibility_(bf), assign_torsions_(at), connect_(cn),
71 connect_aa_(aa), connect_hetatm_(ch), zero_occ_treatment_(zo) {}
73 assign_torsions_(true), connect_(true), connect_aa_(true),
74 connect_hetatm_(true), zero_occ_treatment_(
CONOP_SILENT) {}
84 assign_torsions_ = flag;
87 return assign_torsions_;
98 return connect_hetatm_;
105 return check_bond_feasibility_;
109 check_bond_feasibility_ = flag;
113 return zero_occ_treatment_;
116 zero_occ_treatment_ =
action;
119 virtual String ToString()
const = 0;
121 String OptionsToString()
const;
123 bool check_bond_feasibility_;
124 bool assign_torsions_;
127 bool connect_hetatm_;
158 bool strict_hydrogens=
false);
Processor(bool bf, bool at, bool cn, bool aa, bool ch, ConopAction zo)
void SetCheckBondFeasibility(bool flag)
void SetConnectAminoAcids(bool c)
bool GetConnectHetatm() const
virtual bool BeginProcessing(DiagnosticsPtr diags, mol::EntityHandle ent) const
#define DLLEXPORT_OST_CONOP
boost::shared_ptr< Processor > ProcessorPtr
bool GetAssignTorsions() const
bool GetCheckBondFeasibility() const
boost::shared_ptr< Diagnostics > DiagnosticsPtr
void SetAssignTorsions(bool flag)
std::vector< ResidueHandle > ResidueHandleList
void DLLIMPORT AssignBackboneTorsions(mol::ChainHandle chain)
assigns phi/psi/omega to all residues marked peptide-linking of the chain
virtual bool EndProcessing(DiagnosticsPtr diags, mol::EntityHandle ent) const
String DLLIMPORT StringFromConopAction(ConopAction action)
void SetZeroOccTreatment(ConopAction action)
mol::AtomHandleList DLLIMPORT GetUnknownAtomsOfResidue(mol::ResidueHandle residue, CompoundPtr compound, bool strict_hydrogens=false)
boost::shared_ptr< Compound > CompoundPtr
void SetConnect(bool connect)
ConopAction GetZeroOccTreatment() const
bool GetConnectAminoAcids() const
void SetConnectHetatm(bool c)
ConopAction DLLIMPORT ConopActionFromString(const String &name)
bool DLLIMPORT IsBondFeasible(const mol::AtomHandle &, const mol::AtomHandle &)
std::vector< AtomHandle > AtomHandleList
mol::ChemClass DLLIMPORT GuessChemClass(mol::ResidueHandle res)
guess chemclass based on atoms of residue
String DLLIMPORT GuessAtomElement(const String &atom_name, bool hetatm, int atom_count)
guess element of atom based on name and hetatm flag