NanoShaper  0.7.2
NanoShaper is a tool able to triangulate and inspect an arbitray triangulated surface or several types of molecular surfaces
DelPhiShared Class Reference

This class is the DelPhi Shared variables environment which emulates the DelPhi environment. More...

#include <DelphiShared.h>

List of all members.

Public Member Functions

 DelPhiShared ()
void init ()
 DelPhiShared (double scale, double perfill, string fn, bool map, bool status, bool multi, bool atinfo=false)
void init (double scale, double perfill, string fn, bool eps_flag, bool stat_flag, bool multi, bool atinfo)
void DelPhiBinding (double xmin, double ymin, double zmin, double xmax, double ymax, double zmax, double c1, double c2, double c3, double rmax, double perf, int *local_i_epsmap, int igrid, double scale, double *local_i_scspos, double *local_i_scsnor, bool *local_i_idebmap, int *local_i_ibgp, int maxbgp, bool status, int *atsurf)
void finalizeBinding (int *ibnum)
void clear ()
void saveEpsMaps (char *fname)
void saveBGP (char *fname)
void saveStatus (char *fname)
void saveCavities (bool onlySaveNonFilled=false)
void saveCavities2 (bool onlySaveNonFilled, string sysName)
int cavitiesToAtoms (double rad)
void markPockets (short *status, vector< bool > &isPocket)
void clearCav2Atoms ()
void initCav2Atoms ()
void saveIdebMap (char *fname)
bool clearAndAllocEpsMaps ()
void clearEpsMaps ()
bool loadAtoms (string fn)
bool loadAtoms (int na, double *pos, double *r, double *q, int *d, char *atinf)
bool buildGrid (double scale, double perfill)
bool getDelphiBinding ()
void buildEpsmap (bool a)
void buildStatusmap (bool a)
bool getMultiDiel ()
int getNumAtoms ()

Static Public Member Functions

static void parseAtomInfo (char *atinfo, string mol, int na, double *xn1, double *rad)

Public Attributes

bool multi_diel
double scale
double perfill
bool delphiBinding
bool buildEpsMap
bool buildStatus
int * epsmap
int * ibgp
bool * idebmap
int maxbgp
double * scsnor
double * scsarea
double * scspos
bool isAvailableAtomInfo
int * atsurf
double A
double * x
double * y
double * z
int nbgp
double side
int nx
int ny
int nz
short * status
short * tempStatus
double rmaxdim
double xmin
double xmax
double ymin
double ymax
double zmin
double zmax
double baricenter [3]
Atom ** atoms
int numAtoms
char file [BUFLEN]
double hside
vector< vector< int * > * > * cavitiesVec
vector< double > cavitiesSize
vector< bool > cavitiesFlag
vector< set< int > * > cav2atoms

Detailed Description

This class is the DelPhi Shared variables environment which emulates the DelPhi environment.


Constructor & Destructor Documentation

DelPhiShared::DelPhiShared ( )

default constructor

DelPhiShared::DelPhiShared ( double  scale,
double  perfill,
string  fn,
bool  map,
bool  status,
bool  multi,
bool  atinfo = false 
)

constructor. map indicates epsmap and idebmap, status is status map and multi mean multidielectric


Member Function Documentation

bool DelPhiShared::buildGrid ( double  scale,
double  perfill 
)

Emulates DelPhi grid construction

int DelPhiShared::cavitiesToAtoms ( double  rad)

Convert grid cavity points in atoms files for NanoShaper. This function is usefull to triangulate by NanoShaper the envelope of the cavities

void DelPhiShared::clear ( )

deletion function

void DelPhiShared::clearCav2Atoms ( )

clear reference atoms for each cavity

void DelPhiShared::DelPhiBinding ( double  xmin,
double  ymin,
double  zmin,
double  xmax,
double  ymax,
double  zmax,
double  c1,
double  c2,
double  c3,
double  rmax,
double  perf,
int *  local_i_epsmap,
int  igrid,
double  scale,
double *  local_i_scspos,
double *  local_i_scsnor,
bool *  local_i_idebmap,
int *  local_i_ibgp,
int  maxbgp,
bool  status,
int *  atsurf 
)

Fortran DelPhi binding function. Allows to link DelPhi old code to the new surface framework

void DelPhiShared::finalizeBinding ( int *  ibnum)

If in DelPhi binding mode, call it before denstructor. It will be change the variables in a Fortran/DelPhi compatible mode and will avoid the denstruction of the variables passed to DelPhi. Always call this function ONLY just before the denstructor of the DelPhi shared environment

void DelPhiShared::init ( )

default init

void DelPhiShared::init ( double  scale,
double  perfill,
string  fn,
bool  eps_flag,
bool  stat_flag,
bool  multi,
bool  atinfo 
)

init function-constructor

void DelPhiShared::initCav2Atoms ( )

reinit cav2atoms vector to current number of cavities. If not empty it gets cleared

void DelPhiShared::markPockets ( short *  status,
vector< bool > &  isPocket 
)

given the status map of a 1.4 surf, mark for all the active cavites if they are pockets or cavities

void DelPhiShared::parseAtomInfo ( char *  atinfo,
string  mol,
int  na,
double *  xn1,
double *  rad 
) [static]

parse atinfo vector from DelPhi

void DelPhiShared::saveBGP ( char *  fname)

Save the boundary grid points in a format such that DelPhi can read them

void DelPhiShared::saveCavities ( bool  onlySaveNonFilled = false)

Save only cavities info

void DelPhiShared::saveCavities2 ( bool  onlySaveNonFilled,
string  sysName 
)

mimicks ProShape output

void DelPhiShared::saveEpsMaps ( char *  fname)

Save the epsmaps in a format such that DelPhi can read them

void DelPhiShared::saveIdebMap ( char *  fname)

Save idebmap

void DelPhiShared::saveStatus ( char *  fname)

Save internal status map for cavity detection


Member Data Documentation

vector< set<int>* > DelPhiShared::cav2atoms

dynamical vector whose index is the cavity and contains the set of atoms that produce that cavity

dynamical vector of cavities filling. true if cav is filled

vector< double> DelPhiShared::cavitiesSize

dynamical vector of cavities size

vector< vector <int* >* >* DelPhiShared::cavitiesVec

dynamical vector of cavities


The documentation for this class was generated from the following files: