class Prot

class representing the protein

Public Methods

Prot()

Prot(long i_id)

~Prot()

int read_input(const char* i_pdbfile, const TProt& i_tprot)

void write_output(int i_num_res, TProt &i_tprot, FILE* outfile)

bool swap_at(Atom* i_at1, Atom* i_at2)

methods that act on the atoms,tors,res'

bool swap_tor(Tor* i_tor1, Tor* i_tor2)

bool swap_res(Res* i_res1, Res* i_res2)

bool disable_at(Atom* i_at)

bool disable_tor(Tor* i_tor)

bool disable_res(Res* i_res)

bool enable_at(Atom* i_at)

bool enable_tor(Tor* i_tor)

bool enable_res(Res* i_res)

bool delete_at(Atom* i_at)

bool delete_tor(Tor* i_tor)

bool delete_res(Res* i_res)

long add_at(Atom* i_at)

long add_tor(Tor* i_tor)

int add_res(Res* i_res)

int get_num_res() const

long get_num_at() const

long get_num_tor() const

Tor* get_tor(long i_id)

position in vector is the id of tor

Atom* get_at(long i_id)

position in vector is the id of at

Res* get_res(long i_id)

position in vector is the id of res

const Tor* get_const_tor(long i_id) const

const Atom* get_const_at(long i_id) const

const Res* get_const_res(long i_id) const

bool sync_atoms(Res* i_prev_res, Res* i_res, vector<Atom*>& i_ats, const TProt& i_tprot)

assign all the associated and bonded atoms to each atom in the given residue

Private Fields

long id

vector<Atom*> * at_list

vector<Tor*> * tor_list

vector<Res*> * res_list

int cur_res_id

long cur_at_id

long cur_tor_id

Private Methods

bool check_rel(Res* i_res, vector<Atom*>& i_ats, vector<Tor*>& i_tors, const TProt& i_tprot)

check if all the entities involved in the relationship have been provided in the input

Documentation

class representing the protein

Prot()

Prot(long i_id)

~Prot()

int read_input(const char* i_pdbfile, const TProt& i_tprot)

void write_output(int i_num_res, TProt &i_tprot, FILE* outfile)

bool swap_at(Atom* i_at1, Atom* i_at2)

methods that act on the atoms,tors,res'

bool swap_tor(Tor* i_tor1, Tor* i_tor2)

bool swap_res(Res* i_res1, Res* i_res2)

bool disable_at(Atom* i_at)

bool disable_tor(Tor* i_tor)

bool disable_res(Res* i_res)

bool enable_at(Atom* i_at)

bool enable_tor(Tor* i_tor)

bool enable_res(Res* i_res)

bool delete_at(Atom* i_at)

bool delete_tor(Tor* i_tor)

bool delete_res(Res* i_res)

long add_at(Atom* i_at)

long add_tor(Tor* i_tor)

int add_res(Res* i_res)

int get_num_res() const

long get_num_at() const

long get_num_tor() const

Tor* get_tor(long i_id)

position in vector is the id of tor

Atom* get_at(long i_id)

position in vector is the id of at

Res* get_res(long i_id)

position in vector is the id of res

const Tor* get_const_tor(long i_id) const

const Atom* get_const_at(long i_id) const

const Res* get_const_res(long i_id) const

bool sync_atoms(Res* i_prev_res, Res* i_res, vector<Atom*>& i_ats, const TProt& i_tprot)

assign all the associated and bonded atoms to each atom in the given residue

bool check_rel(Res* i_res, vector<Atom*>& i_ats, vector<Tor*>& i_tors, const TProt& i_tprot)

check if all the entities involved in the relationship have been provided in the input

long id

vector<Atom*> * at_list

vector<Tor*> * tor_list

vector<Res*> * res_list

int cur_res_id

long cur_at_id

long cur_tor_id

This class has no child classes.

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