Main Page | Namespace List | Alphabetical List | Class List | Directories | File List | Namespace Members | Class Members | Examples

dsrpdb Namespace Reference

Detailed Description

All exposed classes are put in this namespace.


Classes

class  Atom
 A class repesenting an atom. More...
struct  Atom_coordinates
 Take an atom label, atom pair and return the coordinates. More...
struct  Atom_index
class  Projection_iterator
 Take an iterator which returns atoms and return their coordinates instead. More...
class  Filter_iterator
 Filters the iterator output. More...
struct  Yes
 Functor that returns true. More...
struct  Is_backbone
 Return true if an atom is a backbone atoms. More...
struct  Is_CA
 Returns true if an atom is a CA atom. More...
struct  label
struct  labeled_index
class  Model
 A class representing a single model from a PDB file. More...
class  PDB
 A class for representing a whole PDB file with possibly several models. More...
class  PDB_index
 A class for representing indices in a pdb. More...
class  Point
 A class representing a geometric point. More...
struct  Squared_distance
 A functor that computes the squared distance between two points. More...
class  Protein
 A class representing a single chain of a protein. More...
class  Residue
 The class representing a residue. More...
class  small_map
struct  Transform
 This class provides a simple rigid transformation matrix. More...

Namespaces

namespace  Residue_data

Typedefs

typedef Projection_iterator<
Filter_iterator< Protein::Const_atoms_iterator,
Is_backbone >, Atom_coordinates > 		Protein_backbone_coordinates_iterator
typedef Projection_iterator<
Filter_iterator< Protein::Const_atoms_iterator,
Is_CA >, Atom_coordinates > 		Ca_backbone_coordinates_iterator
typedef Projection_iterator<
Filter_iterator< Protein::Const_atoms_iterator,
Yes >, Atom_coordinates > 		All_coordinates_iterator
typedef Projection_iterator<
Filter_iterator< Protein::Const_atoms_iterator,
Is_backbone >, Atom_index > 		Protein_backbone_indices_iterator
typedef TNT::Array2D< double > Matrix
typedef Point Vector

Functions

double no_align_cRMS (const Protein &a, const Protein &b)
double no_align_ca_cRMS (const Protein &a, const Protein &b)
double cRMS (const Protein &a, const Protein &b)
double ca_cRMS (const Protein &a, const Protein &b)
double dRMS (const Protein &a, const Protein &b)
double ca_dRMS (const Protein &a, const Protein &b)
Matrix distance_matrix (const Protein &a)
Matrix ca_distance_matrix (const Protein &a)
Matrix distance_matrix (const Model &a)
Matrix ca_distance_matrix (const Model &a)
template<class Ait, class Voit>
void coordinates (Ait ab, Ait ae, Voit out)
template<class Ait, class Voit>
void backbone_coordinates (Ait ab, Ait ae, Voit out)
template<class Ait, class Voit>
void ca_coordinates (Ait ab, Ait ae, Voit out)
template<class Voit, class Boit>
void coordinates_and_bonds (const Protein &p, Voit out, Boit bout)
template<class Voit, class Boit>
void backbone_coordinates_and_bonds (const Protein &p, Voit out, Boit bout)
template<class Voit, class Boit>
void ca_coordinates_and_bonds (const Protein &p, Voit out, Boit bout)
template<class Voit, class Boit>
int simplified_coordinates_and_bonds (const Protein &p, Voit out, Boit bout)
template<class It, class Proj>
Projection_iterator< It, Proj > projection_iterator (It a, Proj proj)
template<class It, class F>
Filter_iterator< It, F > filter_iterator (It b, It e, F f)
Protein_backbone_coordinates_iterator backbone_coordinates_begin (const Protein &p)
Protein_backbone_coordinates_iterator backbone_coordinates_end (const Protein &p)
Ca_backbone_coordinates_iterator ca_coordinates_begin (const Protein &p)
Ca_backbone_coordinates_iterator ca_coordinates_end (const Protein &p)
All_coordinates_iterator all_coordinates_begin (const Protein &p)
All_coordinates_iterator all_coordinates_end (const Protein &p)
Protein_backbone_indices_iterator protein_backbone_indices_begin (const Protein &p)
Protein_backbone_indices_iterator protein_backbone_indices_end (const Protein &p)
template<class T>
std::ostream & operator<< (std::ostream &o, PDB_index< T > i)
std::ostream & operator<< (std::ostream &o, const Point &p)
std::istream & operator>> (std::istream &i, Point &p)
std::ostream & operator<< (std::ostream &out, const Transform &t)

Typedef Documentation

typedef Projection_iterator<Filter_iterator<Protein::Const_atoms_iterator, Yes>, Atom_coordinates> dsrpdb::All_coordinates_iterator
 

An iterator for iterating through the coordinates of all atoms of a protein.

Definition at line 219 of file iterator.h.

typedef Projection_iterator<Filter_iterator<Protein::Const_atoms_iterator, Is_CA>, Atom_coordinates > dsrpdb::Ca_backbone_coordinates_iterator
 

An iterator for iterating through the coordinates of C_alpha atoms of a protein.

Definition at line 205 of file iterator.h.

typedef TNT::Array2D<double> dsrpdb::Matrix
 

Use TNT::Array2D<double> as a matrix.

Examples:
pdb_distance.cc.

Definition at line 8 of file Matrix.h.

typedef Projection_iterator<Filter_iterator<Protein::Const_atoms_iterator, Is_backbone>, Atom_coordinates> dsrpdb::Protein_backbone_coordinates_iterator
 

An iterator for iterating through the coordinates of backbone atoms of a protein.

Definition at line 188 of file iterator.h.

typedef Projection_iterator<Filter_iterator<Protein::Const_atoms_iterator, Is_backbone>, Atom_index> dsrpdb::Protein_backbone_indices_iterator
 

An iterator through the indices of the backbone atoms.

Definition at line 233 of file iterator.h.

Function Documentation

All_coordinates_iterator dsrpdb::all_coordinates_begin (  const Protein &  p  )  [inline]
 

a begin iterator for iterating through the coordinates of all the atoms of a protein

Definition at line 222 of file iterator.h.

References dsrpdb::Protein::atoms_begin(), dsrpdb::Protein::atoms_end(), filter_iterator(), and projection_iterator().

All_coordinates_iterator dsrpdb::all_coordinates_end (  const Protein &  p  )  [inline]
 

an end iterator for iterating through the coordinates of all the atoms of a protein

Definition at line 227 of file iterator.h.

References dsrpdb::Protein::atoms_end(), filter_iterator(), and projection_iterator().

template<class Ait, class Voit>
void dsrpdb::backbone_coordinates (  Ait  ab,
Ait  ae,
Voit  out
)  [inline]
 

Insert all the backbone atom coordinates from the list in to the output iterator.

See the file check_protein.cc for an example of usage. Either dsrpdb::Residue::Atoms_iterator or dsrpdb::Protein::Atoms_iterator are appropriate input.

Examples:
check_protein.cc, and pdb_align_points.cc.

Definition at line 47 of file geometry.h.

template<class Voit, class Boit>
void dsrpdb::backbone_coordinates_and_bonds (  const Protein &  p,
Voit  out,
Boit  bout
)  [inline]
 

Insert the backbone atom coordinates from the protein in to the output iterator and an edge corresponding to each bond in the second output iterator.

The bonds differ from those returned by the bonds returned by the protein in that they are renumbered to correspond to the sequence positions of the atom coordinates.

Definition at line 80 of file geometry.h.

Protein_backbone_coordinates_iterator dsrpdb::backbone_coordinates_begin (  const Protein &  p  )  [inline]
 

a begin iterator for iterating through the coordinates of backbone atoms of a protein

This is a good example of how to use the various iterator classes.

Definition at line 194 of file iterator.h.

References dsrpdb::Protein::atoms_begin(), dsrpdb::Protein::atoms_end(), filter_iterator(), and projection_iterator().

Protein_backbone_coordinates_iterator dsrpdb::backbone_coordinates_end (  const Protein &  p  )  [inline]
 

an end iterator for iterating through the coordinates of backbone atoms of a protein

Definition at line 199 of file iterator.h.

References dsrpdb::Protein::atoms_end(), filter_iterator(), and projection_iterator().

template<class Ait, class Voit>
void dsrpdb::ca_coordinates (  Ait  ab,
Ait  ae,
Voit  out
)  [inline]
 

Insert all the c_alpha coordinates from the list in to the output iterator.

See the file check_protein.cc for an example of usage. Either dsrpdb::Residue::Atoms_iterator or dsrpdb::Protein::Atoms_iterator are appropriate input.

Examples:
pdb_align_points.cc, and pdb_distance.cc.

Definition at line 57 of file geometry.h.

template<class Voit, class Boit>
void dsrpdb::ca_coordinates_and_bonds (  const Protein &  p,
Voit  out,
Boit  bout
)  [inline]
 

Insert the ca atom coordinates from the protein in to the output iterator and an edge corresponding to each bond in the second output iterator.

The bonds differ from those returned by the bonds returned by the protein in that they are renumbered to correspond to the sequence positions of the atom coordinates.

Definition at line 91 of file geometry.h.

Ca_backbone_coordinates_iterator dsrpdb::ca_coordinates_begin (  const Protein &  p  )  [inline]
 

a begin iterator for iterating through the coordinates of C_alpha atoms of a protein

Definition at line 208 of file iterator.h.

References dsrpdb::Protein::atoms_begin(), dsrpdb::Protein::atoms_end(), filter_iterator(), and projection_iterator().

Ca_backbone_coordinates_iterator dsrpdb::ca_coordinates_end (  const Protein &  p  )  [inline]
 

an end iterator for iterating through the coordinates of C_alpha atoms of a protein

Definition at line 213 of file iterator.h.

References dsrpdb::Protein::atoms_end(), filter_iterator(), and projection_iterator().

double dsrpdb::ca_cRMS (  const Protein &  a,
const Protein &  b
) 
 

Compute the C_alpha cRMS between two proteins.

Precondition:
{a and b must have the same number of atoms. This is checked.}

Matrix dsrpdb::ca_distance_matrix (  const Model &  a  ) 
 

Return the C_alpha distance matrix of a protein.

Matrix dsrpdb::ca_distance_matrix (  const Protein &  a  ) 
 

Return the C_alpha distance matrix of a protein.

Examples:
pdb_distance.cc.

double dsrpdb::ca_dRMS (  const Protein &  a,
const Protein &  b
) 
 

Compute the C_alpha cRMS between two proteins.

Precondition:
{a and b must have the same number of atoms. This is checked.}
See pdb_distance.cc for an example.
Examples:
pdb_distance.cc.

template<class Ait, class Voit>
void dsrpdb::coordinates (  Ait  ab,
Ait  ae,
Voit  out
)  [inline]
 

Insert all the atom coordinates from the list in to the output iterator.

See the file check_protein.cc for an example of usage. Either dsrpdb::Residue::Atoms_iterator or dsrpdb::Protein::Atoms_iterator are appropriate input.

Examples:
check_protein.cc, pdb_align_points.cc, and pdb_distance.cc.

Definition at line 37 of file geometry.h.

template<class Voit, class Boit>
void dsrpdb::coordinates_and_bonds (  const Protein &  p,
Voit  out,
Boit  bout
)  [inline]
 

Insert all the atom coordinates from the protein in to the output iterator and an edge corresponding to each bond in the second output iterator.

The bonds differ from those returned by the bonds returned by the protein in that they are renumbered to correspond to the sequence positions of the atom coordinates.

Examples:
check_protein.cc.

Definition at line 70 of file geometry.h.

double dsrpdb::cRMS (  const Protein &  a,
const Protein &  b
) 
 

Compute the all-atom cRMS between two proteins.

Precondition:
{a and b must have the same number of atoms. This is checked.}

Matrix dsrpdb::distance_matrix (  const Model &  a  ) 
 

Return the distance matrix of a protein.

Matrix dsrpdb::distance_matrix (  const Protein &  a  ) 
 

Return the distance matrix of a protein.

See pdb_distance_matrix.cc for an example.

Examples:
pdb_distance.cc.

double dsrpdb::dRMS (  const Protein &  a,
const Protein &  b
) 
 

Compute the all-atom dRMS between two proteins.

Precondition:
{a and b must have the same number of atoms. This is checked.}
See pdb_distance.cc for an example.
Examples:
pdb_align.cc, and pdb_distance.cc.

template<class It, class F>
Filter_iterator<It, F> dsrpdb::filter_iterator (  It  b,
It  e,
F  f
) 
 

Create a filter iterator by passing the functor and the iterator.

See Yes, Is_backbone and Is_CA for example filters.

Definition at line 160 of file iterator.h.

Referenced by all_coordinates_begin(), all_coordinates_end(), backbone_coordinates_begin(), backbone_coordinates_end(), ca_coordinates_begin(), ca_coordinates_end(), protein_backbone_indices_begin(), and protein_backbone_indices_end().

double dsrpdb::no_align_ca_cRMS (  const Protein &  a,
const Protein &  b
) 
 

Compute the calpha cRMS without aligning the proteins.

Precondition:
{a and b must have the same number of atoms. This is checked.}
See pdb_distance.cc for an example.
Examples:
pdb_distance.cc.

double dsrpdb::no_align_cRMS (  const Protein &  a,
const Protein &  b
) 
 

Compute the all-atom cRMS with no alignment.

This function assumes that a, and b have already been rigidly aligned externally.

Precondition:
{a and b must have the same number of atoms. This is checked.}
See pdb_distance.cc for an example.
Examples:
pdb_align.cc, and pdb_distance.cc.

std::ostream& dsrpdb::operator<< (  std::ostream &  out,
const Transform &  t
)  [inline]
 

Write the transformation matrix to a stream.

The output format is r r r t r r r t r r r t 0 0 0 1

Definition at line 96 of file Transform.h.

References dsrpdb::Transform::write().

template<class It, class Proj>
Projection_iterator<It, Proj> dsrpdb::projection_iterator (  It  a,
Proj  proj
) 
 

Create an atom coordinates iterator.

Definition at line 100 of file iterator.h.

Referenced by all_coordinates_begin(), all_coordinates_end(), backbone_coordinates_begin(), backbone_coordinates_end(), ca_coordinates_begin(), ca_coordinates_end(), protein_backbone_indices_begin(), and protein_backbone_indices_end().

Protein_backbone_indices_iterator dsrpdb::protein_backbone_indices_begin (  const Protein &  p  )  [inline]
 

Begin iterating through the indices of backbone atoms.

Definition at line 236 of file iterator.h.

References dsrpdb::Protein::atoms_begin(), dsrpdb::Protein::atoms_end(), filter_iterator(), and projection_iterator().

Protein_backbone_indices_iterator dsrpdb::protein_backbone_indices_end (  const Protein &  p  )  [inline]
 

an end iterator for iterating through the indices of all the backbone atoms of a protein

Definition at line 241 of file iterator.h.

References dsrpdb::Protein::atoms_end(), filter_iterator(), and projection_iterator().

template<class Voit, class Boit>
int dsrpdb::simplified_coordinates_and_bonds (  const Protein &  p,
Voit  out,
Boit  bout
)  [inline]
 

Inserts the backbone atoms and the sidechain centroids and appropriate bonds into the iterators.

Note that this now returns all the backbone atoms and puts all the sidechains after allthe backbone atoms. The number of backbone atoms is returned.

Examples:
check_protein.cc.

Definition at line 102 of file geometry.h.

References dsrpdb::Protein::residues_begin(), and dsrpdb::Protein::residues_end().