Topology enh - more pubic methods from cpptraj

pytraj/topology/topology.pxd

@@ -10,31 +10,43 @@ from ..trajectory.frame cimport _Frame, Frame
 from libcpp.string cimport string
 from ..core.c_core cimport _FileName, FileName, _ArgList, ArgList
 
+cdef extern from "Range.h":
+    cdef cppclass _Range "Range" nogil:
+        _Range()
+        _Range(int)
+        bint Empty() const
+        unsigned int Size() const
+        int Back() const
+        int Front() const
+        void Clear()
+        int SetRange(int, int)
+        void AddToRange(int)
+
 
 ctypedef cppvector[_Atom].const_iterator atom_iterator
 ctypedef cppvector[_Residue].const_iterator res_iterator
 ctypedef cppvector[_Molecule].const_iterator mol_iterator
 ctypedef cppvector[int].const_iterator bond_iterator
 
-cdef extern from "CoordinateInfo.h": 
+cdef extern from "CoordinateInfo.h":
     cdef cppclass _CoordinateInfo "CoordinateInfo" nogil:
-        _CoordinateInfo() 
+        _CoordinateInfo()
         _CoordinateInfo(const _Box& b, bint v, bint t, bint m)
-        bint HasBox() const 
-        const _Box& TrajBox() const 
-        bint HasVel() const 
-        bint HasTemp() const 
-        bint HasTime() const 
-        bint HasForce() const 
-        bint HasReplicaDims() const 
+        bint HasBox() const
+        const _Box& TrajBox() const
+        bint HasVel() const
+        bint HasTemp() const
+        bint HasTime() const
+        bint HasForce() const
+        bint HasReplicaDims() const
         void SetTime(bint m)
         void SetTemperature(bint t)
         void SetVelocity(bint v)
         void SetBox(const _Box& b)
 
-cdef extern from "Topology.h": 
+cdef extern from "Topology.h":
     cdef cppclass _Topology "Topology" nogil:
-        _Topology() 
+        _Topology()
         int DetermineMolecules()
         void SetOffset(double oIn)
         void SetDebug(int dIn)
@@ -48,20 +60,20 @@ cdef extern from "Topology.h":
         void SetParmName(const string&, const _FileName&)
         void SetDistMaskRef(_Frame)
         _Atom& GetAtomView "SetAtom" (int idx)
-        const string& Tag() const 
-        int Ipol() const 
-        int Pindex() const 
-        int Natom() const 
-        int Nres() const 
-        int Nmol() const 
-        int Nsolvent() const 
-        int Nframes() const 
-        int NextraPts() const 
-        bint HasVelInfo() const 
-        int NrepDims "NrepDim"() const 
-        const string& ParmName() const 
-        const _FileName& OriginalFilename() const 
-        const string& GBradiiSet() const 
+        const string& Tag() const
+        int Ipol() const
+        int Pindex() const
+        int Natom() const
+        int Nres() const
+        int Nmol() const
+        int Nsolvent() const
+        int Nframes() const
+        int NextraPts() const
+        bint HasVelInfo() const
+        int NrepDims "NrepDim"() const
+        const string& ParmName() const
+        const _FileName& OriginalFilename() const
+        const string& GBradiiSet() const
         bint NoRefCoords()
         int FinalSoluteRes()
         const char * c_str()
@@ -73,71 +85,97 @@ cdef extern from "Topology.h":
         inline res_iterator ResEnd()
         const _Residue& Res(int idx)
         _Residue& SetRes(int idx)
-        inline mol_iterator MolStart() const 
-        inline mol_iterator MolEnd() const 
-        const _Molecule& Mol(int idx) const 
-        void ClearMoleculeInfo() 
-        const BondArray& Bonds() const 
-        const BondArray& BondsH() const 
-        const BondParmArray& BondParm() const 
+        inline mol_iterator MolStart() const
+        inline mol_iterator MolEnd() const
+        const _Molecule& Mol(int idx) const
+        void ClearMoleculeInfo()
+        const BondArray& Bonds() const
+        const BondArray& BondsH() const
+        const BondParmArray& BondParm() const
         void AddBond(int, int)
         int SetBondInfo(const BondArray&, const BondArray&, const BondParmArray&)
-        const AngleArray& Angles() const 
-        const AngleArray& AnglesH() const 
-        const AngleParmArray& AngleParm() const 
+        const AngleArray& Angles() const
+        const AngleArray& AnglesH() const
+        const AngleParmArray& AngleParm() const
         int SetAngleInfo(const AngleArray&, const AngleArray&, const AngleParmArray&)
-        const DihedralArray& Dihedrals() const 
-        const DihedralArray& DihedralsH() const 
-        const DihedralParmArray& DihedralParm() const 
+        const DihedralArray& Dihedrals() const
+        const DihedralArray& DihedralsH() const
+        const DihedralParmArray& DihedralParm() const
         int SetDihedralInfo(const DihedralArray&, const DihedralArray&, const DihedralParmArray&)
-        const _NonbondParmType& Nonbond() const 
+        const _NonbondParmType& Nonbond() const
         int SetNonbondInfo(const _NonbondParmType&)
-        inline const _NonbondType& GetLJparam(int, int) const 
-        const _CapParmType& Cap() const 
+        inline const _NonbondType& GetLJparam(int, int) const
+        const _CapParmType& Cap() const
         void SetCap(const _CapParmType& c)
-        const _LES_ParmType& LES() const 
+        const _LES_ParmType& LES() const
         void SetLES(const _LES_ParmType& l)
-        const _ChamberParmType& Chamber() const 
+        const _ChamberParmType& Chamber() const
         void SetChamber(const _ChamberParmType& c)
-        inline const vector[double]& Solty() const 
-        inline const vector[_NameType]& Itree() const 
-        inline const vector[int]& Join() const 
-        inline const vector[int]& Irotat() const 
-        string TruncResAtomName(int) const 
-        string AtomMaskName(int atom) const 
-        string TruncResNameNum(int) const 
-        int FindAtomInResidue(int, const _NameType&) const 
-        #int FindResidueMaxNatom() const 
-        int SoluteAtoms() const 
+        inline const vector[double]& Solty() const
+        inline const vector[_NameType]& Itree() const
+        inline const vector[int]& Join() const
+        inline const vector[int]& Irotat() const
+        # String formatting methods
+        string TruncResAtomName(int) const
+        string TruncResNameAtomName(int) const
+        string TruncAtomNameNum(int) const
+        string TruncResNameOnumId(int) const
+        string ResNameNumAtomNameNum(int) const
+        string AtomMaskName(int atom) const
+        string TruncResNameNum(int) const
+
+        # Analysis and utility methods
+        unsigned int HeavyAtomCount() const
+        int NatomTypes() const
+        bint HasChargeInfo() const
+        double GetVDWsigma(int) const
+        double GetVDWdepth(int) const
+        bint MaskHasZeroMass(const _AtomMask&) const
+
+        # Residue and molecule operations
+        int NresInMol(int) const
+        _Range SoluteResidues() const
+        int MergeResidues(int, int)
+        int SetSingleMolecule()
+        int SplitResidue(const _AtomMask&, const _NameType&)
+
+        # Mask utilities
+        vector[int] ResnumsSelectedBy(const _AtomMask&) const
+        vector[int] MolnumsSelectedBy(const _AtomMask&) const
+
+        # Existing methods
+        int FindAtomInResidue(int, const _NameType&) const
+        #int FindResidueMaxNatom() const
+        int SoluteAtoms() const
         int SetSolvent(const string&)
-        void Summary() const 
-        void Brief(const char *) const 
-        void PrintAtomInfo(const string&) const 
-        void PrintBondInfo(const string&) const 
-        void PrintAngleInfo(const string&) const 
-        void PrintDihedralInfo(const string&) const 
-        void PrintMoleculeInfo(const string&) const 
-        void PrintResidueInfo(const string&) const 
-        int PrintChargeMassInfo(const string&, int) const 
+        void Summary() const
+        void Brief(const char *) const
+        void PrintAtomInfo(const string&) const
+        void PrintBondInfo(const string&) const
+        void PrintAngleInfo(const string&) const
+        void PrintDihedralInfo(const string&) const
+        void PrintMoleculeInfo(const string&) const
+        void PrintResidueInfo(const string&) const
+        int PrintChargeMassInfo(const string&, int) const
         void PrintBonds(const BondArray&, _AtomMask&, int&) const
         void PrintAngles(const AngleArray&, const _AtomMask&, int&) const
         void PrintDihedrals(const DihedralArray&, const _AtomMask&, int&) const
-        inline const _Box& ParmBox() const 
+        inline const _Box& ParmBox() const
         void SetParmBox(_Box& bIn)
         int AddTopAtom(_Atom&, _Residue&)
         void AddAngle(int, int, int)
         void AddDihedral(int, int, int, int)
-        void StartNewMol() 
+        void StartNewMol()
         int CommonSetup(bint)
         int SetAmberExtra(const vector[double]&, const vector[_NameType]&, const vector[int]&, const vector[int]&)
-        bint SetupIntegerMask(_AtomMask&) const 
-        bint SetupCharMask(_AtomMask&) const 
-        bint SetupIntegerMask(_AtomMask&, const _Frame&) const 
-        bint SetupCharMask(_AtomMask&, const _Frame&) const 
+        bint SetupIntegerMask(_AtomMask&) const
+        bint SetupCharMask(_AtomMask&) const
+        bint SetupIntegerMask(_AtomMask&, const _Frame&) const
+        bint SetupCharMask(_AtomMask&, const _Frame&) const
         void ScaleDihedralK(double)
-        _Topology* partialModifyStateByMask(const _AtomMask& m) const 
-        _Topology* modifyStateByMask(const _AtomMask& m) const 
-        _Topology* ModifyByMap(const vector[int]& m) const 
+        _Topology* partialModifyStateByMask(const _AtomMask& m) const
+        _Topology* modifyStateByMask(const _AtomMask& m) const
+        _Topology* ModifyByMap(const vector[int]& m) const
         int AppendTop(const _Topology &)
         # add more
         _CoordinateInfo& ParmCoordInfo() const
@@ -148,22 +186,22 @@ cdef class Topology:
     cdef public bint _own_memory
     cdef cppvector[int] _get_atom_bond_indices(self, _Atom)
 
-cdef extern from "ParmFile.h": 
+cdef extern from "ParmFile.h":
     ctypedef enum ParmFormatType "ParmFile::ParmFormatType":
         pass
         UNKNOWN_PARM "ParmFile::UNKNOWN_PARM"
     cdef cppclass _ParmFile "ParmFile" nogil:
         @staticmethod
-        void ReadOptions() 
+        void ReadOptions()
         @staticmethod
-        void WriteOptions() 
-        _ParmFile() 
+        void WriteOptions()
+        _ParmFile()
         int ReadTopology(_Topology&, const string&, const _ArgList&, int)
         int ReadTopology(_Topology& t, const string& n, int d)
         int WritePrefixTopology(const _Topology&, const string&, ParmFormatType, int)
         int WriteTopology(const _Topology&, const string&, const _ArgList&, ParmFormatType, int)
         int WriteTopology(const _Topology& t, const string& n, ParmFormatType f, int d)
-        const _FileName ParmFilename() 
+        const _FileName ParmFilename()
 
 
 cdef class ParmFile: