PointArray defines a double array of points with values in a 3D space. More...

#include <pdbreader.h>

Public Types
enum	Density2PointsArrayAlgorithm { PEAKS_SUB , PEAKS_DIV , KMEANS }

Public Member Functions
	PDBReader ()

	PDBReader (int nn)

	~PDBReader ()

void	zero ()

PDBReader *	copy ()

PDBReader &	operator= (PDBReader &pa)

size_t	get_number_points () const

void	set_number_points (size_t nn)

bool	read_from_pdb (const char *file)
	Reads and parses all information from file. More...

void	save_to_pdb (const char *file) const
	Saves all atom information into a pdb in the official format. More...

double *	get_points_array ()
	Returns the double array of points. More...

void	set_points_array (double *p)
	Allows the user to set the double array of points. More...

vector< float >	get_points ()
	Returns all x,y,z triplets packed into a vector<float> More...

void	right_transform (const Transform &transform)
	Does Transformv as opposed to vTransform (as in the transform function) More...

PointArray *	makePointArray (const PDBReader &p)

vector< float >	get_x ()

vector< float >	get_y ()

vector< float >	get_z ()

vector< string >	get_atomName ()

vector< string >	get_resName ()

vector< int >	get_resNum ()

Private Attributes
double *	points

vector< int >	pointInfo

vector< string >	pWords

vector< string >	atomName

vector< string >	residueName

vector< string >	chainId

vector< string >	elementSym

vector< string >	tail

vector< string >	head

vector< string >	lines

size_t	n

int	ter_stop

int	count_stop

vector< float >	x

vector< float >	y

vector< float >	z

vector< int >	resNum

Detailed Description

PointArray defines a double array of points with values in a 3D space.

Definition at line 54 of file pdbreader.h.

Member Enumeration Documentation

◆ Density2PointsArrayAlgorithm

enum EMAN::PDBReader::Density2PointsArrayAlgorithm

Enumerator
PEAKS_SUB
PEAKS_DIV
KMEANS

Definition at line 57 of file pdbreader.h.

                {
                        PEAKS_SUB, PEAKS_DIV, KMEANS
                };

Constructor & Destructor Documentation

◆ PDBReader() [1/2]

PDBReader::PDBReader ( )

Definition at line 42 of file pdbreader.cpp.

{
        points = 0;
        n = 0;
}

References n, and points.

Referenced by copy().

◆ PDBReader() [2/2]

PDBReader::PDBReader ( int nn )

explicit

Definition at line 48 of file pdbreader.cpp.

{
        n = nn;
        points = (double *) calloc(4 * n, sizeof(double));
        ter_stop = 0;
}

References n, points, and ter_stop.

◆ ~PDBReader()

PDBReader::~PDBReader ( )

Definition at line 55 of file pdbreader.cpp.

{
        if( points )
        {
                free(points);
                points = 0;
        }
}

References points.

Member Function Documentation

◆ copy()

PDBReader * PDBReader::copy ( )

Definition at line 71 of file pdbreader.cpp.

{
        PDBReader *pa2 = new PDBReader();
        pa2->set_number_points(get_number_points());
        double *pa2data = pa2->get_points_array();
        memcpy(pa2data, get_points_array(), sizeof(double) * 4 * get_number_points());
        pa2->pWords = pWords;
        pa2->atomName = atomName;
        pa2->residueName = residueName;
        pa2->chainId = chainId;
        pa2->elementSym = elementSym;
        pa2->tail = tail;
        pa2->head = head;
        pa2->pointInfo = pointInfo;
        pa2->lines = lines;
        return pa2;
}

References atomName, chainId, elementSym, get_number_points(), get_points_array(), head, lines, PDBReader(), pointInfo, pWords, residueName, set_number_points(), and tail.

◆ get_atomName()

vector< string > PDBReader::get_atomName ( )

Definition at line 149 of file pdbreader.cpp.

                                       {
        return atomName;
}

References atomName.

◆ get_number_points()

size_t PDBReader::get_number_points ( ) const

Definition at line 99 of file pdbreader.cpp.

{
        return n;
}

References n.

Referenced by copy(), operator=(), and read_from_pdb().

◆ get_points()

vector< float > PDBReader::get_points ( )

Returns all x,y,z triplets packed into a vector<float>

Returns: All points packed into a vector<float>

Definition at line 308 of file pdbreader.cpp.

                                    {
vector<float> ret;
for (unsigned int i=0; i<n; i++) {
        ret.push_back((float)points[i*4]);
        ret.push_back((float)points[i*4+1]);
        ret.push_back((float)points[i*4+2]);
}
 
return ret;
}

References n, and points.

◆ get_points_array()

double * PDBReader::get_points_array ( )

Returns the double array of points.

Returns: A double array of points

Definition at line 113 of file pdbreader.cpp.

{
        return points;
}

References points.

Referenced by copy(), and operator=().

◆ get_resName()

vector< string > PDBReader::get_resName ( )

Definition at line 153 of file pdbreader.cpp.

                                      {
        return residueName;
}

References residueName.

◆ get_resNum()

vector< int > PDBReader::get_resNum ( )

Definition at line 157 of file pdbreader.cpp.

                                  {
        return resNum;
}

References resNum.

◆ get_x()

vector< float > PDBReader::get_x ( )

Definition at line 126 of file pdbreader.cpp.

                               {
        if (count_stop == 0) {count_stop = atomName.size();}
        for (int i=0; i<count_stop; i++) {
                x.push_back((float)points[4*i]);
                y.push_back((float)points[4*i + 1]);
                z.push_back((float)points[4*i + 2]);
                resNum.push_back(pointInfo[2*i+1]);
        }
 
        return x;
}

References atomName, count_stop, pointInfo, points, resNum, x, y, and z.

◆ get_y()

vector< float > PDBReader::get_y ( )

Definition at line 139 of file pdbreader.cpp.

                               {
        //cout << y.size() << endl;
        return y;
}

References y.

◆ get_z()

vector< float > PDBReader::get_z ( )

Definition at line 145 of file pdbreader.cpp.

                               {
        return z;
}

References z.

◆ makePointArray()

PointArray * PDBReader::makePointArray ( const PDBReader & p )

Definition at line 331 of file pdbreader.cpp.

                                                         {
        PointArray* pArray  = new PointArray;
        p.save_to_pdb("thisFile3.txt");
        pArray->read_from_pdb("thisFile3.txt");
        remove("thisFile3.txt");
        
        return pArray;
}

References EMAN::PointArray::read_from_pdb(), and save_to_pdb().

◆ operator=()

PDBReader & PDBReader::operator= ( PDBReader & pa )

Definition at line 90 of file pdbreader.cpp.

{
        if (this != &pa) {
                set_number_points(pa.get_number_points());
                memcpy(get_points_array(), pa.get_points_array(), sizeof(double) * 4 * get_number_points());
        }
        return *this;
}

References get_number_points(), get_points_array(), and set_number_points().

◆ read_from_pdb()

bool PDBReader::read_from_pdb ( const char * file )

Reads and parses all information from file.

Parameters

The	.pdb file that you want to read from

Definition at line 163 of file pdbreader.cpp.

{
 
        pWords.clear();
        atomName.clear();
        residueName.clear();
        chainId.clear();
        elementSym.clear();
        tail.clear();
        head.clear();
        lines.clear();
        pointInfo.clear();
        ter_stop = 0;
        count_stop = 0;
 
        struct stat filestat;
        stat(file, &filestat);
        set_number_points(( int)(filestat.st_size / 80 + 1)); //80 bytes per line
#ifdef DEBUG
        printf("PDBReader::read_pdb(): try %4lu atoms first\n", get_number_points());
#endif
 
        FILE *fp = fopen(file, "r");
        if(!fp) {
                fprintf(stderr,"ERROR in PDBReader::read_pdb(): cannot open file %s\n",file);
                throw;
        }
        char s[200];
        size_t count = 0;
 
        while ((fgets(s, 200, fp) != NULL)) {
                lines.push_back(s);
                if ((strncmp(s, "ENDMDL", 6) == 0) && (ter_stop==0)){
                        ter_stop =1;
                        count_stop = count;
                }
                if (strncmp(s, "END", 6) == 0){
                        break;
                }
                //if ((strncmp(s, "TER", 3) == 0) && (ter_stop ==0)){
                        //if (count !=0) {ter_stop = 1;}
                        //count_stop = count;
                //}
                if (strncmp(s, "ATOM", 4) != 0) {
                        if (count == 0) {head.push_back(s);}
                        else {tail.push_back(s);}
                }
                else {
                        pWords.push_back(s);
                        atomName.push_back(pWords[count].substr(12,4));
                        residueName.push_back(pWords[count].substr(17,3));
                        chainId.push_back(pWords[count].substr(21,1));
                        if (pWords[count].size()>78)
                                elementSym.push_back(pWords[count].substr(76,2));
                        else
                                elementSym.push_back(string("Null"));
 
                        float x, y, z, tf;
                        int an, sn;
                        sscanf(&s[6], "%d", &an);
                        sscanf(&s[23], "%d %f %f %f %*f %f", &sn, &x, &y, &z, &tf);
 
                        if (count + 1 > get_number_points()) {
                                set_number_points(2 * (count + 1)); 
                        }   //makes sure point array is big enough
 
                        points[4 * count] = x;
                        points[4 * count + 1] = y;
                        points[4 * count + 2] = z;
                        points[4 * count + 3] = tf;
                        pointInfo.push_back(an);
                        pointInfo.push_back(sn);
                        count++;
                }
        }
 
        fclose(fp);
        set_number_points(count);
        return true;
}

References atomName, chainId, count_stop, elementSym, get_number_points(), head, lines, pointInfo, points, pWords, residueName, set_number_points(), tail, ter_stop, x, y, and z.

◆ right_transform()

void PDBReader::right_transform ( const Transform & transform )

Does Transform*v as opposed to v*Transform (as in the transform function)

Parameters

transform an EMAN2 Transform object

Definition at line 320 of file pdbreader.cpp.

                                                          {
        for ( unsigned int i = 0; i < 4 * n; i += 4) {
                Transform s = transform.transpose();
                Vec3f v((float)points[i],(float)points[i+1],(float)points[i+2]);
                v= s*v;
                points[i]  =v[0];
                points[i+1]=v[1];
                points[i+2]=v[2];
        }
}

References n, points, and EMAN::Transform::transpose().

◆ save_to_pdb()

void PDBReader::save_to_pdb ( const char * file ) const

Saves all atom information into a pdb in the official format.

Parameters

The	file that you want the pdb info written to

Definition at line 280 of file pdbreader.cpp.

                                                  {
        FILE *fp = fopen(file, "w");
        int m = 0;
        for (size_t i =0; i< lines.size(); i++) {
                char liner [200];
                strcpy (liner, lines[i].c_str());
                if (strncmp(liner, "ATOM", 4) != 0) {
                        fprintf (fp, "%s", liner);
                }
                else {
                        string curr = pWords[m];
                        string mid, final;
                        mid = curr.substr(12, 10);
                        final = curr.substr(76,2);
                        char mid2 [12];
                        strcpy(mid2, mid.c_str());
                        char final2 [4];
                        strcpy(final2, final.c_str());
                        fprintf(fp, "ATOM  %5d %10s%4d    %8.3f%8.3f%8.3f  1.00%6.2f          %2s\n", pointInfo[2*m], mid2, pointInfo[2*m +1], points[4 * m], points[4 * m + 1], points[4 * m + 2], points[4*m + 3], final2);
                        m++;
                }
        }       
        fclose(fp);
 
}

References lines, pointInfo, points, and pWords.

Referenced by makePointArray().

◆ set_number_points()

void PDBReader::set_number_points ( size_t nn )

Definition at line 105 of file pdbreader.cpp.

{
        if (n != nn) {
                n = nn;
                points = (double *) realloc(points, 4 * n * sizeof(double));
        }
}

References n, and points.

Referenced by copy(), operator=(), and read_from_pdb().

◆ set_points_array()

void PDBReader::set_points_array ( double * p )

Allows the user to set the double array of points.

Parameters

A	double array of points

Definition at line 118 of file pdbreader.cpp.

{
        points = p;
}

References points.

◆ zero()

void PDBReader::zero ( )

Definition at line 64 of file pdbreader.cpp.

{
        memset((void *) points, 0, 4 * n * sizeof(double));
}

References n, and points.

Member Data Documentation

◆ atomName

vector<string> EMAN::PDBReader::atomName

private

Definition at line 120 of file pdbreader.h.

Referenced by copy(), get_atomName(), get_x(), and read_from_pdb().

◆ chainId

vector<string> EMAN::PDBReader::chainId

private

Definition at line 122 of file pdbreader.h.

Referenced by copy(), and read_from_pdb().

◆ count_stop

int EMAN::PDBReader::count_stop

private

Definition at line 129 of file pdbreader.h.

Referenced by get_x(), and read_from_pdb().

◆ elementSym

vector<string> EMAN::PDBReader::elementSym

private

Definition at line 123 of file pdbreader.h.

Referenced by copy(), and read_from_pdb().

◆ head

vector<string> EMAN::PDBReader::head

private

Definition at line 125 of file pdbreader.h.

Referenced by copy(), and read_from_pdb().

◆ lines

vector<string> EMAN::PDBReader::lines

private

Definition at line 126 of file pdbreader.h.

Referenced by copy(), read_from_pdb(), and save_to_pdb().

◆ n

size_t EMAN::PDBReader::n

private

Definition at line 127 of file pdbreader.h.

Referenced by get_number_points(), get_points(), PDBReader(), right_transform(), set_number_points(), and zero().

◆ pointInfo

vector<int> EMAN::PDBReader::pointInfo

private

Definition at line 118 of file pdbreader.h.

Referenced by copy(), get_x(), read_from_pdb(), and save_to_pdb().

◆ points

double* EMAN::PDBReader::points

private

Definition at line 117 of file pdbreader.h.

Referenced by get_points(), get_points_array(), get_x(), PDBReader(), read_from_pdb(), right_transform(), save_to_pdb(), set_number_points(), set_points_array(), zero(), and ~PDBReader().

◆ pWords

vector<string> EMAN::PDBReader::pWords

private

Definition at line 119 of file pdbreader.h.

Referenced by copy(), read_from_pdb(), and save_to_pdb().

◆ residueName

vector<string> EMAN::PDBReader::residueName

private

Definition at line 121 of file pdbreader.h.

Referenced by copy(), get_resName(), and read_from_pdb().

◆ resNum

vector<int> EMAN::PDBReader::resNum

private

Definition at line 134 of file pdbreader.h.

Referenced by get_resNum(), and get_x().

◆ tail

vector<string> EMAN::PDBReader::tail

private

Definition at line 124 of file pdbreader.h.

Referenced by copy(), and read_from_pdb().

◆ ter_stop

int EMAN::PDBReader::ter_stop

private

Definition at line 128 of file pdbreader.h.

Referenced by PDBReader(), and read_from_pdb().

◆ x

vector<float> EMAN::PDBReader::x

private

Definition at line 131 of file pdbreader.h.

Referenced by get_x(), and read_from_pdb().

◆ y

vector<float> EMAN::PDBReader::y

private

Definition at line 132 of file pdbreader.h.

Referenced by get_x(), get_y(), and read_from_pdb().

◆ z

vector<float> EMAN::PDBReader::z

private

Definition at line 133 of file pdbreader.h.

Referenced by get_x(), get_z(), and read_from_pdb().

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

Public Types

Public Member Functions

Private Attributes

Detailed Description

Member Enumeration Documentation

◆ Density2PointsArrayAlgorithm

Constructor & Destructor Documentation

◆ PDBReader() [1/2]

◆ PDBReader() [2/2]

◆ ~PDBReader()

Member Function Documentation

◆ copy()

◆ get_atomName()

◆ get_number_points()

◆ get_points()

◆ get_points_array()

◆ get_resName()

◆ get_resNum()

◆ get_x()

◆ get_y()

◆ get_z()

◆ makePointArray()

◆ operator=()

◆ read_from_pdb()

◆ right_transform()

◆ save_to_pdb()

◆ set_number_points()

◆ set_points_array()

◆ zero()

Member Data Documentation

◆ atomName

◆ chainId

◆ count_stop

◆ elementSym

◆ head

◆ lines

◆ n

◆ pointInfo

◆ points

◆ pWords

◆ residueName

◆ resNum

◆ tail

◆ ter_stop

◆ x

◆ y

◆ z