#include <haatgroup.h>
Inheritance diagram for HaResidue:
Public Member Functions | |
| HaResidue (const HaResidue &ref_res) | |
| HaResidue (HaChain *new_phost_ch) | |
| bool | SetParamFrom (const HaResidue &res_ref) |
| Copy residue parameters from another residue. | |
| bool | operator== (const HaResidue &rhs) const |
| bool | operator< (const HaResidue &rhs) const |
| HaAtom * | AddNewAtom () |
| Add new atom to the residue. | |
| HaAtom * | GetAtomByName (const char *atname) |
| Get Atom of the residue by its name. | |
| const HaAtom * | GetAtomByName (const char *atname) const |
| Get Atom of the residue by its name (const version). | |
| HaChain * | GetHostChain () |
| Get the chain of the residue belongs to. | |
| bool | SetHostChain (HaChain *new_phost) |
| Set the chain of the residue belongs to. | |
| HaMolecule * | GetHostMol () |
| Get the molecule the residue belongs to. | |
| const HaMolecule * | GetHostMol () const |
| Get const pointer to the molecule the residue belongs to. | |
| HaResidue * | GetNextResInChain () |
| Get Next Residue in Chain. | |
| HaResidue * | GetPrevResInChain () |
| Get Previous Residue in Chain. | |
| bool | IsBonded (HaResidue *res2) |
| Check if this residue bonded to another residue. | |
| int | HasBackBHBond (HaResidue *res2) |
| Check if amino acid residue has a backbone H-bond to another aminoacid. | |
| const char * | GetName () const |
| Get the basic name of the residue. | |
| int | SetName (const char *ptr, int max_len=0) |
| Set Residue Name. | |
| void | SetNameModifier (const char *new_name_mod) |
| const char * | GetNameModifier () |
| Get Residue Name Modifier. | |
| HaString | GetFullName () const |
| Get Name of the residue with the modifier. | |
| HaString | GetRef () const |
| Get the text reference of the residue. | |
| virtual bool | FillRef (char *buf, int mode=0) const |
| Write the text reference of the residue to the buffer. | |
| int | Selected () |
| Check if some of the atoms of the residue are selected. | |
| bool | SetUniqueAtomNames () |
| Give unique names to atoms of the residue. | |
| HaString | GetUniqueAtomName (int elem_no) |
| Get unique atom name for element elem_no. | |
| bool | SplitResidue () |
| int | SetStdPK () |
| Set standard pK value for a residue. | |
| int | SetStdPK_G1 () |
| Set standard pK value for most protonation active residues (HIS,HEM,terminal groups). | |
| bool | SetStdPKforAtName (const char *at_name, double std_pk_new) |
| Set standard pk value for the protonation involving atom at_name. | |
| void | PrintPK () const |
| Print to Std output current pK values for alternative protonation states. | |
| int | GetNumAltStates () const |
| Get the number of alternative residue states. | |
| AltChemState * | GetAltChemState (int alt_state_idx) |
| Get alternate residue state by index. | |
| AltChemState * | GetAltChemStateByAtName (const char *at_name) |
| Get alternate residue state by protonated atom name. | |
| int | SetStdCharges () |
| Set atomic charges corresponding to the template of the residue. | |
| int | SetAltCharges (AltChemState *alt_res_st, double weight=1.0) |
| Set atomic charges corresponding to the particular alt residue state. | |
| int | InterpolResParams (const char *res_name_1, const char *res_name_2, double weight_1) |
| Make the residue parameters intermediate between two templates. | |
| HaResidue * | GetTemplate () |
| Get template corresponding to a current residue full name. | |
| int | CheckStruct () |
| Check if the structure of the residue correspond to a template. | |
| bool | SetChargesForPH (double pH_val) |
| Set Atomic Charges corresponding to a given pH value and current pK. | |
| int | GetSerNo () const |
| Get a serial number if the residue in the chain. | |
| bool | IsAmino () const |
| Check if the residue is an aminoacid. | |
| bool | IsAminoNucleo () const |
| bool | IsNucleo () const |
| bool | IsProtein () const |
| bool | IsDNA () const |
| bool | IsSolvent () const |
| bool | IsWater () const |
| bool | IsIon () const |
| bool | IsPyrimidine () const |
| bool | IsPurine () const |
| bool | IsRNA () const |
| bool | IsProline () const |
| bool | IsHistidine () const |
| bool | IsCysteine () const |
| bool | IsAdenine () const |
| bool | IsCytosine () const |
| bool | IsGuanine () const |
| bool | IsThymine () const |
| bool | IsCoenzyme () const |
| bool | IsTerm () const |
| int | CalcStdCrdSys (int fit_std_geom=FALSE) |
| Calculate standard coordinate system. | |
Static Public Member Functions | |
| HaString | GetResNameFromFullName (const char *res_full_name) |
| Extract Short Residue name from the full residue name (with modifier). | |
| const char * | GetResNameInTable (const int j) |
| Get residue name in the table of residue names ResNames by index. | |
| double | CalcPhiAngle (const HaResidue *prev, const HaResidue *curr) |
| double | CalcPsiAngle (const HaResidue *curr, const HaResidue *next) |
| int | InitStdResNames () |
| Initiate table of Residue Names with Standard Residue Names. | |
| int | InitResSynonym () |
| Initialize the table of Residue Name Synonyms. | |
Public Attributes | |
| HaChain * | phost_ch |
| chain the residue belongs to | |
| short | serno |
| Residue serial number. | |
| double | width |
| Ribbon Width. | |
| short | col1 |
| Ribbon Colour #1. | |
| short | col2 |
| Ribbon Colour #2. | |
| char | insert |
| PDB insertion code. | |
| int | refno |
| Residue Name index in ResNames table. | |
| Byte | struc |
| Secondary Structure. | |
| Byte | flag |
| Database flags. | |
| HaString | NameModifier |
| Modifier of the residue name. | |
| vector< AltChemState > | alt_res_states |
| Alternative Residue States (protonated, deprotonated etc). | |
| Vec3D_arr | std_crd_sys |
| Standard coordinate system. | |
Static Public Attributes | |
| StrVec | ResNames |
| table of Residue Names | |
| int | init_res_names_flag = FALSE |
| flag to indicate if residue names arrays were initiated | |
| StrStrMap | ResSynonym |
| the table of Residue Name Synonyms | |
Protected Member Functions | |
| void | ResetData () |
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Set atomic charges corresponding to the particular alt residue state. if weight = -1.0 set charges equal to the difference between standard and alternative charges |
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Make the residue parameters intermediate between two templates.
Set parameters of the residue intermidiate between template residues res_fname_1 and res_fname_2 Atom parameters(charges) the same in two templates are not modified (provision if they are altered from the standard for example if there are more than one alternative proteonation states for a residue) |
1.3.6