#include <nuclacidmod.h>
Inheritance diagram for NuclAcidMod:
Public Member Functions | |
| NuclAcidMod (HaMolSet *new_pmset=NULL) | |
| int | SetStdParams () |
| int | BuildNuclAcid () |
| Build Nucleic Acid from the sequence. | |
| int | UpdateXYZ () |
| Update Cartesian Coordinates for changed internal coordinates. | |
| int | MinEne () |
| Optimize Energy of the system. | |
| int | CalcEne () |
| Calculate Energy for the current conformation. | |
| int | CreateMolFromJumna () |
| Create Molecule from JUMNA structures. | |
| HaMolecule * | FindDNAMol () |
| Try to find DNA molecule in the current MolSet and assign it to the module. | |
| int | SaveAXEfile (const char *axe_file) |
| save internal variables to an axefile | |
| int | ReadAXEfile (const char *axe_file) |
| read internal variable from axefile | |
| int | SetSeq (const char *seq_str) |
| Set Nucleotide sequence of the DNA assuming the second strand is complimentary to the first. | |
| int | GenComplStrand () |
| Set sequence of the second strand complimentary to the first strand. | |
| int | SetFFtype (const char *new_ff_type) |
| Set Force Field Type. | |
| int | SetFFtypeIdx (const int i_ff_type) |
| Set Force Field Type. | |
| int | SetDielSlope (double slope_new) |
| Set slope of sigmoidal dielectric constant. | |
| int | SetPhosChrg (double phos_chrg_new) |
| Set Phosphate charge (FLEX Force-field). | |
| int | SetHelCoord (int i_strand, int i_res, int i_crd, double crd_val) |
| Set helicoidal internal coordinate of a nucleotide. | |
| int | LockHelCoord (int i_strand, int i_res, int i_crd, int do_lock) |
| Lock/unlock helicoidal internal coordinate of a nucleotide. | |
| int | IsHelCoordLocked (int ir, int i_crd) |
| Check if the helical coordinate i_crd(0-based) is locked for the residue ir(0-based). | |
| int | SetBBCoord (int i_strand, int i_res, int i_crd, double crd_val) |
| Set Backbone internal coordinate of a nucleotide. | |
| int | LockBBCoord (int i_strand, int i_res, int i_crd, int do_lock) |
| Lock/Unlock Backbone internal coordinate of a nucleotide. | |
| int | UpdateVarCoord () |
| Update the array of non-locked internal coordinates. | |
| int | SetCoordsFromJumna () |
| Set Coordinates from Jumna Structures. | |
| int | SetIntCoordsToJumna () |
| Set Internal Coordinates To Jumna Structures. | |
| int | SaveConfig () |
| Save current configuration (internal and cartesian coordinates). | |
| int | RestoreConfig () |
| Restore configuration saved by SaveConfig(). | |
| int | BBOffset (int ir) |
| offset of backbone cordinates of residue ir in sap | |
| int | IsRibRes (int ir) |
| Check is the residue a ribonucleotide. | |
| int | IsThymineRes (int ir) |
| Check if the residue is a thymine. | |
| int | NumIndBBVarRes (int ir) |
| The number of independent backbone variables of the residue. | |
| int | NumAllBBVarRes (int ir) |
| The number of all backbone variables (indep and dep) of the residue. | |
| int | Is3endRes (int ir) |
| Check is the residue at 3' DNA end. | |
| int | IsFstResInChain (int ir) |
| Check if the residue a first residue in chain. | |
| int | IdxResInChain (int ir) |
| Index of the residue in the chain (ir - is 0-based , and return value 0-based). | |
| int | ChainIdxOfRes (int ir) |
| Index of the chain (1-based) for the residue with index ir( 0-based). | |
| int | IsSupHlxConstr () |
| Check if Supehelical symmetry is assigned to the DNA. | |
| int | NumBBCoord () |
| Get a number of backbone internal coordinates. | |
| int | NumFreeBBCoord () |
| Get a number of non-locked backbone internal coordinates. | |
| int | IdxLastHelCoord () |
| Index (1-based) of the last helical variable in lock() and others arrays. | |
| int | IdxLastFreeHelCoord () |
| Index (1-based) of the last non-locked helical variable in var() array. | |
| int | SetShlxTwist (double shlx_tw) |
| Set twist of the first residue of a superhelix. | |
| double | GetAtomCrd (int at_num, int coord_num) |
| Get cartesian coordinates of the atom. | |
| double | GetVarNum (int crd_num) |
| Get Unlocked variable by index(1-based) in var() array. | |
| int | CalcPdistToShlxCnt () |
| Print to the output distance of phosphorus atoms to the center of super-helix when superhelix constraints in place. | |
| int | CalcLocCrdSys () |
| Calculate local coordinate systems on bases. | |
| int | CalcLocHlxCrd (int for_bp=TRUE) |
| Calculate local helical coord of bases or base pairs. | |
| int | CalcAxis () |
| Calculate helical axis. | |
| int | CalcBend () |
| Calc Bending. | |
| int | CalcGlobHlxCrd () |
| Calc Global helical coordinates. | |
| int | CalcBBCrd () |
| Calculate Backbone internal coordinated. | |
| int | CalcAxisPar1 (HaMat_double &ax_hlxc, double &sum, HaVec_double &gra, HaVec_double &scp) |
| Calculate parameters characterizing helical axis. | |
| int | GetNRes () const |
| Get the number of residues in the DNA(RNA). | |
Public Attributes | |
| HaString | out_prefix |
| prefix for output file | |
| HaString | pdb_prefix |
| prefix for pdb file | |
| HaVec_int | nsym_unit |
| Symmetry unit sizes for the DNA sections. | |
| int | nbreak_1 |
| break 1 of the DNA chain to specify different symmetry (see param isym_partN) | |
| int | nbreak_2 |
| break 2 of the DNA chain to specify different symmetry (see param isym_partN) | |
| HaVec_int | homon_symm_flags |
| Flags to indicate Homonomous(interstrand) symmetry for DNA sections (JUMNA homo,homo2,homo3). | |
| HaVec_int | homon_symm_offs |
| residues offset to apply interstrand symmetry (mhomo,mhomo1,mhomo2). | |
| int | ene_per_unit_flag |
| Flag to compute energy per unit cell rather then total energy (JUMNA ecen). | |
| HaVec_int | dir_strand |
| Direction of the strand (positive means 5'->3' direction, negative 3'->5'). | |
| HaString | seq [4] |
| Nucleotide sequence of the strands. | |
| int | max_iter |
| max number of minimization iterations | |
| int | init_flag |
| flag to indicate that DNA(RNA) structure was created and data initialized | |
| double | sup_helix_rad |
| radius of superhelix (0.0 for no superhelical constraints DNA) | |
| double | sup_helix_pit |
| pitch of superhelix | |
| double | fst_twist |
| Twist of the first residue (when sup_helix_rad > 0.0). | |
| int | force_field |
| force field type | |
| double | diel_slope |
| Slope of the sigmoidal dielectric constant. | |
| double | phos_chrg |
| Phosphate charge (FLEX Force-field). | |
| HaVec_double | hel_crd |
| Vector of Helical internal Coordinates. | |
| HaVec_int | lock_hel |
| Lock flags of Helical coordinates. | |
| HaVec_double | bb_crd |
| Vector of Backbone Internal Coordinates. | |
| HaVec_int | lock_bb |
| Lock flags of Backbone Internal Coordinates. | |
| HaVec_int | bb_sidx |
| A vector of indexes of the starting positions of residue internal coordinates in int_coord. | |
| Vec3D_arr | u |
| Vec3D_arr | h |
| Vec3D_arr | o |
| helix axis parameters | |
| Vec3D_arr | uho |
| Vec3D_arr | hho |
| Vec3D_arr | ul |
| helix axis parameters | |
| HaVec_double | dif |
| inter nucleotide irregularity function | |
| HaMat_double | hel |
| HaMat_double | hold |
| HaMat_double | vold |
| HaMat_double | bend |
| HaMat_double | vkin |
| HaMat_double | tor |
| HaMat_double | sug |
| HaMat_double | bs_bs_pars |
| HaVec_int | ncrd_res |
| A number of internal coordinates per residue. | |
| HaVec_int | ncrd_ind_res |
| A number of independent internal coordinates per residue. | |
| int | update_var_flag |
| Flag to indicate that Var array needed to be updated due to lock changes or other. | |
| double | cur_energy |
| Current energy. | |
| HaMolecule * | p_dna_mol |
| the pointer to the DNA molecule | |
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Lock/unlock helicoidal internal coordinate of a nucleotide. i_strand - strand index (1-based) i_res - index of residue in the strand( 1-based) i_crd - helical coordinate index (1-based) |
1.3.6