#include <hamolecule.h>
Inheritance diagram for HaMolecule:
Public Types | |
| typedef BondIteratorMolecule | BondIterator |
| Bond iterator type for the molecule. | |
| typedef ResidueIteratorMolecule | ResidueIterator |
| Residue iterator type for the molecule. | |
Public Member Functions | |
| HaMolecule (HaMolSet *new_phost_mset, HaString new_name="HARLEMMOL") | |
| HaMolecule (const HaMolecule &Mol_ref) | |
| HaMolSet * | GetHostMolSet () |
| const HaMolSet * | GetHostMolSet () const |
| bool | AddMolCopy (const HaMolecule &Mol_ref, bool create_new_chain=true, map< HaAtom *, HaAtom *, less< HaAtom * > > *ptr_atom_map=NULL) |
| int | CombineMolecules (HaMolecule *frag_mol, HaAtom *catom_host, HaAtom *catom_frag) |
| HaString | GetRef () const |
| get a text reference for a molecule | |
| bool | FillRef (char *buf, int mode=0) const |
| Fill string with a molecule text reference. | |
| virtual bool | SetObjName (const char *new_name) |
| virtual function from Object3D | |
| virtual int | RotateObj (const HaMat_double &rot_mat, const Vec3D &cnt) |
| Rotate object around the center. | |
| virtual int | Translate (const Vec3D &tr_vec) |
| Translate the molecule by (dx,dy,dz). | |
| int | GetStdPosition (HaMat_double &rot_std, Vec3D &trans_std) |
| Determine std rot matric and translation for a given molecule. | |
| int | SetPosition (const HaMat_double &rot_new, const Vec3D &trans_new) |
| Set molecular orientations corresponding to a given std rotation and translation. | |
| int | SetPosEulerTrans (double phi, double cos_theta, double psi, const Vec3D &trans) |
| Set the molecule position using Euler angles and translation vectors. | |
| void | GetPosEulerTrans (double &phi, double &cos_theta, double &psi, Vec3D &trans) |
| get std translational and rotational (Euler angles) coordinates for a given molecule position | |
| int | SetIntCoordFromStr (const char *int_crd_str) |
| int | SetAtomScreenCoord (HaMolView *pview) |
| Display Related functions:. | |
| bool | SetUniqueAtomNames () |
| bool | InitAtomsGRWF () |
| load atom coordinates from Gaussian rwf file | |
| bool | InitAtoms (GauFile &gfile) |
| load atom coordinates from Gaussian rwf file | |
| HaAtom * | AddAtomFromTempl (HaAtom *aptr2, HaAtom *aptr3, HaAtom *aptr4, const HaAtom *aptr_templ, const HaAtom *aptr_templ_2, const HaAtom *aptr_templ_3, const HaAtom *aptr_templ_4) |
| add atom from a template | |
| int | GetSeqNumOfAtom (const HaAtom *aptr) const |
| get the postion of the atom in the atomic sequence of the molecule | |
| HaAtom * | GetAtomBySeqNum (const int index) |
| get a pointer to an atom by its sequence number | |
| const HaAtom * | GetAtomBySeqNum (const int index) const |
| get a pointer to an atom by its sequence number const version | |
| HaAtom * | GetAtomByRef (const char *at_ref) |
| Get an atom of the molecule by its text reference. | |
| virtual int | GetNAtoms () const |
| return the number of atoms in molecule | |
| virtual int | IsMember (const HaAtom *aptr) const |
| Check if the Atom belongs to the Molecule. | |
| virtual AtomIterator * | GetAtomIterator () |
| Create AtomIterator for the molecule. | |
| int | GetNBonds () const |
| Get the number of bonds in the molecule. | |
| int | GetNHBonds () const |
| Get the number of H-bonds in the molecule. | |
| int | GetNSSBonds () const |
| Get the number of SS-bonds in the molecule. | |
| int | AreHBonded (HaAtom *src, HaAtom *dst) const |
| check if there is an H-bond between two(heavy) atoms of the molecule | |
| void | CalcHydrogenBonds () |
| Find hydrogen bonds in the molecule. | |
| bool | AreHBondsFound () const |
| Check if hydrogen bonds have been found for the molecule. | |
| bool | AreSSBondsFound () const |
| Check if SS-bonds have been found for the molecule. | |
| void | CreateMoleculeBonds () |
| HaBond * | AddBond (HaAtom *src, HaAtom *dst, int flag) |
| Create a covalent bond. | |
| HaHBond * | AddHBond (HaAtom *src, HaAtom *dst) |
| Create a hydrogen bond. | |
| HaHBond * | AddSSBond (HaAtom *src, HaAtom *dst) |
| Create SS-bond. | |
| bool | DeleteBond (HaAtom *src, HaAtom *dst) |
| int | AddAllMissingAtoms (ADD_ATOM_TYPE atom_type) |
| Add all Missing Atoms in the molecule. | |
| int | AddMissingAtoms (HaResidue *pres, ADD_ATOM_TYPE atom_type) |
| Add atoms missing in the residue using residue template. | |
| int | AddWaterHydrogens (HaResidue *pres) |
| Add Hydrogens to water molecule residue. | |
| void | BondIfClose (HaAtom *sptr, HaAtom *dptr) |
| Function to make a bond between two atoms if they close enough. | |
| void | CreateHydrogenBond (HaAtom *src, HaAtom *dst, int energy, int offset) |
| void | CalcNucleicHBonds (HaChain *chn1) |
| void | CalcProteinHBonds (HaChain *chn1) |
| int | CalculateBondEnergy (HaResidue *group) |
| void | TestDisulphideBridge (HaResidue *group1, HaResidue *group2, HaAtom *cys1) |
| int | SetTermResNames () |
| Set proper terminal residue name modfiers (N & C terminal for proteins) (3' and 5' for Nucleic Acids). | |
| int | SetCysBridgeNames () |
| Set proper residue name for cys involved in disulfide bridges. | |
| bool | Print_info (ostream &sout, const int level) const |
| Print information about the molecule. | |
| HaResidue * | CreateMolResidue () |
| Create first chain and first 'MOL' residue. | |
| int | GetNRes () const |
| get the number of residues in the molecule | |
| HaResidue * | GetResByRef (const HaString &res_str) |
| Get a residue of the molecule by its text reference. | |
| int | GetNChains () |
| Get the number of chains in the molecule. | |
| HaChain * | AddChain (char ident) |
| Add Blank Chain to the list. | |
| HaChain * | GetFirstChain () |
| get a pointer to the first Chain of Molecule | |
| HaChain * | GetNextChain () |
| get a pointer to the next Chain of the molecule | |
| HaChain * | GetChain (const char chain_id) |
| Get a chain by id. | |
| virtual PointIterator * | GetPointIterator () |
| create Point Interator and return pointer (should be deleted when done) | |
| virtual int | GetPtNum () |
| Get total of number of points in the collection. | |
| bool | FixChainsIdent () |
| set unique chain ident on the molecule | |
| void | DescribeMolecule () |
| void | DetermineStructure (int flag) |
| Compute sceondary structure of the molecule. | |
| void | FindDisulphideBridges () |
| FInd Disulphide bridges. | |
| void | Renumber (int start) |
| void | DescribeSequence () |
| FeatEntry * | AddFeature () |
| int | GetNumFeatures (const int itype) const |
| void | UpdateFeature (FeatEntry *ptr, int mask) |
| void | ProcessFeatures () |
| bool | IsSecStructFound () |
| bool | GetMinMaxCrd (double &MinX_v, double &MinY_v, double &MinZ_v, double &MaxX_v, double &MaxY_v, double &MaxZ_v) |
| Get Min and Max coordinates of the molecule. | |
| bool | GetAverageCoord (double &avx, double &avy, double &avz) |
| Get average coordinates of the molecule:. | |
| bool | GetStdRotMat (HaMat_double &rot_mat) |
| Get Standard Rotation matrix for a given molecule's orientation:. | |
Static Public Member Functions | |
| int | AttachFragment (HaAtom *catom_host, HaAtom *catom_frag) |
| bool | SetCoordSubstH (const HaAtom *aptr1, const HaAtom *aptr2, HaAtom *haptr) |
| generate coordinates of the hydrogen connected to aptr1 in the direction of aptr2 | |
Public Attributes | |
| bool | sec_struct_found |
| flag to indicate that secondary structure is found | |
| int | structsource |
| indicate wheter sceondary structure were loaded from PDB or computed | |
| list< FeatEntry > | Features |
| list< HaChain > | Chains |
| List of Chains. | |
| set< HaHBond, less< HaHBond > > | HBonds |
| Hydrogen Bonds of the molecule. | |
| set< HaHBond, less< HaHBond > > | SSBonds |
| SS bridges of the molecule. | |
| set< HaBond, less< HaBond > > | Bonds |
| Valence bonds of the molecule. | |
| list< HaAtom > | Atoms |
| Atoms of the molecule. | |
| bool | SSBonds_found |
| bool | HBonds_found |
| flag to show if H-bonds have been created | |
| HaString | classification |
| HaString | identcode |
| HaResidue * | CurResidue |
| Pointer to the last added Residue (from Rasmol). | |
| HaChain * | CurChain |
| Pointer to the last added chain. | |
Static Public Attributes | |
| int | SeqFormat = 0 |
| Format Sequence in DesribeSequence() function. | |
Protected Member Functions | |
| int | AddMissingAtoms_2 (HaResidue *pres, HaResidue *prtempl, ADD_ATOM_TYPE atom_type) |
| void | FindAlphaHelix (int pitch, int flag) |
| void | FindTurnStructure () |
| void | FindBetaTurns () |
| void | FindBetaSheets () |
| void | TestLadder (list< HaChain >::iterator chain_ref, HaResidue *prevri, HaResidue *curri, HaResidue *nexti) |
Protected Attributes | |
| HaMolSet * | phost_mset |
| vector< AtomNode > | nodes |
| list< HaChain >::iterator | CurChainItr |
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Determine std rot matric and translation for a given molecule. Determine standard rotation matrix and standard translation vector for a given orientation of the molecule |
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Set molecular orientations corresponding to a given std rotation and translation. Rotate and translate the molecule according standardtized rotation matrix rot_new and translation vector trans_new |
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Set the molecule position using Euler angles and translation vectors. Rotate and translate the molecule according standardtized rotation matrix determined by euler angles, translation vector transx, transy, transz |
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in seq x,y,z, phi,cost,psi |
1.3.6