Rosetta 3.4
Classes | Public Types | Public Member Functions | Static Public Member Functions
core::pose::PDBInfo Class Reference

maintains pdb residue & atom information inside a Pose More...

#include <PDBInfo.hh>

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List of all members.

Classes

struct  AtomRecord
 internal struct for storing PDB atom related information
struct  ResidueRecord
 internal struct for storing PDB residue related information

Public Types

typedef
utility::pointer::ReferenceCount 
Super
typedef core::Size Size
typedef core::Real Real
typedef std::string String
typedef core::pose::Remarks Remarks

Public Member Functions

 PDBInfo ()
 default constructor, obsolete is *true*
 PDBInfo (Size const n)
 size constructor (ensure space for 'n' residue records), obsolete is *true*
 PDBInfo (Pose const &pose, bool init=true)
 Pose constructor (ensures space for residue and atom records relative to Pose)
 PDBInfo (PDBInfo const &info)
 copy constructor
virtual ~PDBInfo ()
 default destructor
PDBInfooperator= (PDBInfo const &info)
 copy assignment
core::conformation::Conformation
const * 
is_observing ()
 Returns the Conformation if this PDBInfo is currently observing a conformation, otherwise return NULL.
void attach_to (core::conformation::Conformation &conf)
 Attaches the Conformation <conf> and begins observation.
void detach_from ()
 Detaches the Conformation and stops observation.
void on_connection_change (core::conformation::signals::ConnectionEvent const &event)
 Updates when connection to Conformation is changed.
void on_identity_change (core::conformation::signals::IdentityEvent const &event)
 Updates atom records when residue identity changes in Conformation.
void on_length_change (core::conformation::signals::LengthEvent const &event)
 Updates residue and atom records when length changes in Conformation, obsoletes PDBInfo.
bool obsolete () const
 Returns true if PDBInfo is obsolete and needs updating.
void obsolete (bool flag)
 Sets the obsolete state to <flag>
Size nres () const
 Returns the number of residues represented in PDBInfo.
Size natoms (Size const res) const
 Returns the number of atoms represented for the residue <res>
void resize_residue_records (Size const n)
 Resizes for <n> residue records.
void resize_atom_records (Size const res, Size const n, bool const zero=true)
 Ensures <n> atom records for residue <res> are available.
void resize_atom_records (Size const n, bool const zero=true)
 Ensures <n> atom records for residue <res> are available.
void resize_atom_records (Pose const &pose)
 Updates the number of atom records with respect to atoms in <pose>
void tighten_memory ()
 Tightens memory usage.
String const & name () const
 Returns the pdb name.
void name (String const &s)
 Sets the pdb name.
String const & modeltag () const
 Returns the model tag for a multi-model pdb.
void modeltag (String const &tag)
 Sets the model tag for a multi-model pdb to <tag>
Remarks const & remarks () const
 Returns the pdb remarks (const)
Remarksremarks ()
 Returns the pdb remarks (mutable)
void remarks (Remarks const &in)
 Sets the pdb remarks to <in>
char const & chain (Size const res) const
 Returns the chain id for pose residue <res>
int const & number (Size const res) const
 Returns the pdb sequence number of pose residue <res>
char const & icode (Size const res) const
 Returns the pdb insertion code of residue <res>
Size pdb2pose (char const chain, int const res, char const icode= ' ') const
 Returns the pose numbering of the pdb residue with chain <chain>, pdb residue <res>, and insertion code <icode>
String pose2pdb (Size const res) const
 Returns the pdb numbering string of pose residue <res>
void chain (Size const res, char const chain_id)
 Sets the chain id of pose residue <res> to <chain_id>
void number (Size const res, int const pdb_res)
 Sets the pdb sequence residue number of pose residue <res> to <pdb_res>
void icode (Size const res, char const ins_code)
 Sets the insertion code of pose residue <res> to <ins_code>
void set_resinfo (Size const res, char const chain_id, int const pdb_res, char const ins_code= ' ')
 Sets the chain id, pdb sequence residue numbering, and insertion code for pose residue <res> to <chain_id> , <pdb_res> , and <ins_code> respectfully.
bool const & is_het (Size const res, Size const atom_index) const
 Returns true if the <atom_index> atom of pose residue <res> is a heteratom.
char const & alt_loc (Size const res, Size const atom_index) const
 Returns the alternate location for the <atom_index> atom of pose residue <res>
Real const & occupancy (Size const res, Size const atom_index) const
 Returns the occupancy for the <atom_index> atom of pose residue <res>
Real const & temperature (Size const res, Size const atom_index) const
 Returns the temperature for the <atom_index> atom of pose residue <res>
void is_het (Size const res, Size const atom_index, bool const flag)
 Sets the heteroatom flag of the <atom_index> atom of pose residue <res> to <flag>
void alt_loc (Size const res, Size const atom_index, char const loc)
 Sets the alternate location of the <atom_index> atom of pose residue <res> to <loc>
void occupancy (Size const res, Size const atom_index, Real const occ)
 Sets the occupancy of the <atom_index> atom of pose residue <res> to <occ>
void temperature (Size const res, Size const atom_index, Real const t)
 Sets the temperature of the <atom_index> atom of pose residue <res> to <t>
PDBPoseMap const & pdb2pose () const
 Returns the internally maintained PDBPoseMap.
void show (std::ostream &out) const
 Displays segments of PDB information, segments may or may not be entire chains.
void set_chains (char const id)
 Sets all residue chain ids to the character <id>
template<typename CharIterator >
void set_chains (CharIterator const &begin, CharIterator const &end)
 Sets the residue chain ids from some char container, iterator version.
template<typename CharContainer >
void set_chains (CharContainer const &c)
 Sets the residue chain ids from some char container, e.g. utility::vector1.
template<typename IntIterator >
void set_numbering (IntIterator const &begin, IntIterator const &end)
 Sets the pdb sequence residue numbering from some int container, iterator version.
template<typename IntContainer >
void set_numbering (IntContainer const &c)
 Sets the pdb sequence residue numbering from some int container, e.g. utility::vector1.
template<typename CharIterator >
void set_icodes (CharIterator const &begin, CharIterator const &end)
 Sets the insertion codes from some char container, iterator version.
template<typename CharContainer >
void set_icodes (CharContainer const &c)
 Sets the insertion codes from some char container, e.g. utility::vector1.
void copy (PDBInfo const &input_info, Size const copy_from, Size const copy_to, Size const start_from)
 Copyies a section from PDBInfo <input_info>
void append_res (Size const res, Size const natoms, Size const n=1)
 Appends residue records given a pose residue number <res>
void prepend_res (Size const res, Size const natoms, Size const n=1)
 Prepends residue records before given pose residue number <res>
void replace_res (Size const res, Size const natoms)
 "Replaces" residue record for pose residue <res>
void delete_res (Size const res, Size const n=1)
 Deletes <n> residue records starting from pose residue <res>
utility::vector1
< UnrecognizedAtomRecord >
const & 
get_unrecognized_atoms () const
 remembers info about atoms not read into the pose
core::Size const & get_num_unrecognized_atoms () const
core::Size const & get_num_unrecognized_res () const
std::string const & get_unrecognized_res_name (core::Size const &i) const
core::Size const & get_unrecognized_res_size (core::Size const &i) const
void add_unrecognized_atom (Size resnum, std::string resname, std::string atomname, numeric::xyzVector< Real > coords, Real temp)
 remembers info about atoms not read into the pose
void rebuild_pdb2pose ()
 rebuilds PDBPoseMap from scratch

Static Public Member Functions

static char empty_record ()
 Returns the chain id character specifying "empty record", currently '^'.

Detailed Description

maintains pdb residue & atom information inside a Pose

Upon creation of new residue records, e.g. when calling the constructors without 'init' or appending/prepending residues, the chain id for the new records will be set to a character, currently '^', denoting "empty record". This character may be looked up by calling the static method PDBInfo::empty_record().

Remarks:
Class implementation is biased towards simplicity and fast lookup. Residue/atom information are kept in vectors. An internally maintained PDBPoseMap provides mapping from pdb -> pose residue numbering. This causes residue mutators to be a bit more expensive due to map updates, but this is ok because they are typically called sparingly. Accessors and mutators have overloaded method convention, while special mutators use .set_* convention.

Member Typedef Documentation

typedef std::string core::pose::PDBInfo::String

Constructor & Destructor Documentation

core::pose::PDBInfo::PDBInfo ( )

default constructor, obsolete is *true*

core::pose::PDBInfo::PDBInfo ( Size const  n)

size constructor (ensure space for 'n' residue records), obsolete is *true*

core::pose::PDBInfo::PDBInfo ( Pose const &  pose,
bool  init = true 
)

Pose constructor (ensures space for residue and atom records relative to Pose)

Parameters:
[in]posePose
[in]initif true (default), then residue records are initialized and obsolete set to false, otherwise obsolete is true using Pose residue numbering and chains of the Residues in the Conformation

References core::conformation::Residue::chain(), core::pose::chr_chains(), rebuild_pdb2pose(), core::pose::Pose::residue(), resize_atom_records(), and core::pose::Pose::total_residue().

core::pose::PDBInfo::PDBInfo ( PDBInfo const &  info)

copy constructor

core::pose::PDBInfo::~PDBInfo ( ) [virtual]

default destructor

References detach_from().


Member Function Documentation

void core::pose::PDBInfo::add_unrecognized_atom ( Size  resnum,
std::string  resname,
std::string  atomname,
numeric::xyzVector< Real coords,
Real  temp 
)

remembers info about atoms not read into the pose

void core::pose::PDBInfo::alt_loc ( Size const  res,
Size const  atom_index,
char const  loc 
) [inline]

Sets the alternate location of the <atom_index> atom of pose residue <res> to <loc>

Note:
: <loc> is an alternate location character
char const& core::pose::PDBInfo::alt_loc ( Size const  res,
Size const  atom_index 
) const [inline]

Returns the alternate location for the <atom_index> atom of pose residue <res>

example(s): pose.pdb_info().alt_loc(1,1) See also: Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

void core::pose::PDBInfo::append_res ( Size const  res,
Size const  natoms,
Size const  n = 1 
)

Appends residue records given a pose residue number <res>

append residue records after given residue number

Parameters:
[in]resresidue to append after (in internal/pose numbering)
[in]natomsnumber of atoms in type of appended residue
[in]nnumber of residue records to append

References core::pose::PDBPoseMap::insert().

Referenced by on_length_change().

void core::pose::PDBInfo::attach_to ( core::conformation::Conformation conf)
char const& core::pose::PDBInfo::chain ( Size const  res) const [inline]
void core::pose::PDBInfo::chain ( Size const  res,
char const  chain_id 
)

Sets the chain id of pose residue <res> to <chain_id>

set chain id for residue

Remarks:
chain id should not be the empty record character, currently '^' Returns the pdb insertion code of residue <res>

example(s): pose.pdb_info().chain(3,"R") See also: Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

Remarks:
chain id should not be the empty record character, currently '^'

References core::pose::PDBPoseMap::conditional_erase(), core::pose::PDBPoseMap::insert(), and nres().

void core::pose::PDBInfo::copy ( PDBInfo const &  input_info,
Size const  copy_from,
Size const  copy_to,
Size const  start_from 
)

Copyies a section from PDBInfo <input_info>

copy a section from another PDBInfo

Parameters:
[in]input_infothe PDBInfo to copy from
[in]copy_fromthe first residue position in input_info to copy
[in]copy_tothe final residue position in input_info to copy
[in]start_fromthe first residue position in this PDBInfo to copy into

References make_table_of_pilot_apps::begin, core::sequence::end, core::pose::PDBPoseMap::erase(), and core::pose::PDBPoseMap::insert().

void core::pose::PDBInfo::delete_res ( Size const  res,
Size const  n = 1 
)

Deletes <n> residue records starting from pose residue <res>

delete 'n' residue records starting from given residue

Parameters:
[in]resresidue to start deleting from (in internal/pose numbering)
[in]nnumber of residue records to delete

References core::pose::PDBPoseMap::erase(), and core::pose::PDBPoseMap::insert().

Referenced by on_length_change().

void core::pose::PDBInfo::detach_from ( )

Detaches the Conformation and stops observation.

detach from Conformation and stop observation

Remarks:
takes no arguments because PDBInfo can only observe one Conformation at a time

example(s): pose.pdb_info().detach_from() See also: Pose PDBInfo

Remarks:
takes no arguments because PDBInfo can only observe one Conformation at a time

References core::conformation::Conformation::detach_connection_obs(), core::conformation::Conformation::detach_identity_obs(), core::conformation::Conformation::detach_length_obs(), on_connection_change(), on_identity_change(), and on_length_change().

Referenced by attach_to(), on_connection_change(), on_identity_change(), on_length_change(), and ~PDBInfo().

static char core::pose::PDBInfo::empty_record ( ) [inline, static]
core::Size const& core::pose::PDBInfo::get_num_unrecognized_atoms ( ) const [inline]
core::Size const& core::pose::PDBInfo::get_num_unrecognized_res ( ) const [inline]
utility::vector1< UnrecognizedAtomRecord > const& core::pose::PDBInfo::get_unrecognized_atoms ( ) const [inline]

remembers info about atoms not read into the pose

std::string const& core::pose::PDBInfo::get_unrecognized_res_name ( core::Size const &  i) const [inline]
core::Size const& core::pose::PDBInfo::get_unrecognized_res_size ( core::Size const &  i) const [inline]
void core::pose::PDBInfo::icode ( Size const  res,
char const  ins_code 
)

Sets the insertion code of pose residue <res> to <ins_code>

set insertion code for residue

Returns the pdb insertion code of residue <res>

example(s):

See also: Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

References core::pose::PDBPoseMap::conditional_erase(), and core::pose::PDBPoseMap::insert().

char const& core::pose::PDBInfo::icode ( Size const  res) const [inline]

Returns the pdb insertion code of residue <res>

example(s): pose.pdb_info().icode(3) See also: Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

Referenced by core::pose::PDBPoseMap::fill(), pdb2pose(), core::pose::renumber_pdbinfo_based_on_conf_chains(), and show().

bool const& core::pose::PDBInfo::is_het ( Size const  res,
Size const  atom_index 
) const [inline]

Returns true if the <atom_index> atom of pose residue <res> is a heteratom.

Note:
: atom index within instance of core::conformation::Residue, currently Rosetta's pdb file output treats the value of .is_het() as an override -- if this is set to true, the record will be hetatm, otherwise it will decide by Residue type (the usual default)
void core::pose::PDBInfo::is_het ( Size const  res,
Size const  atom_index,
bool const  flag 
) [inline]

Sets the heteroatom flag of the <atom_index> atom of pose residue <res> to <flag>

Note:
currently Rosetta's pdb file output treats the value of .is_het() as an override -- if this is set to true, the record will be hetatm, otherwise it will decide by Residue type (the usual default)
core::conformation::Conformation const * core::pose::PDBInfo::is_observing ( )

Returns the Conformation if this PDBInfo is currently observing a conformation, otherwise return NULL.

is this PDBInfo currently observing a conformation?

example(s): pose.pdb_info().is_observing() See also: Pose PDBInfo

Returns:
the Conformation being observed, otherwise NULL
String const& core::pose::PDBInfo::modeltag ( ) const [inline]

Returns the model tag for a multi-model pdb.

example(s): pose.pdb_info().modeltag() See also: Pose PDBInfo

void core::pose::PDBInfo::modeltag ( String const &  tag) [inline]

Sets the model tag for a multi-model pdb to <tag>

example(s): pose.pdb_info().modeltag('Number1') See also: Pose PDBInfo

void core::pose::PDBInfo::name ( String const &  s) [inline]

Sets the pdb name.

example(s): pose.pdb_info().name('MyPDB') See also: Pose PDBInfo

String const& core::pose::PDBInfo::name ( ) const [inline]

Returns the pdb name.

example(s): pose.pdb_info().name() See also: Pose PDBInfo

Referenced by show().

Size core::pose::PDBInfo::natoms ( Size const  res) const [inline]

Returns the number of atoms represented for the residue <res>

Note:
: residue <res> must be in pose numbering

example(s): pose.pdb_info().natoms(3) See also: Pose PDBInfo

Referenced by show().

Size core::pose::PDBInfo::nres ( ) const [inline]

Returns the number of residues represented in PDBInfo.

example(s): pose.pdb_info().nres() See also: Pose PDBInfo

Referenced by chain(), core::pose::PDBPoseMap::fill(), and show().

int const& core::pose::PDBInfo::number ( Size const  res) const [inline]
void core::pose::PDBInfo::number ( Size const  res,
int const  pdb_res 
)

Sets the pdb sequence residue number of pose residue <res> to <pdb_res>

set pdb residue sequence number

Returns the pdb insertion code of residue <res>

example(s): pose.pdb_info().number(3,81) See also: Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

References core::pose::PDBPoseMap::conditional_erase(), and core::pose::PDBPoseMap::insert().

bool core::pose::PDBInfo::obsolete ( ) const [inline]

Returns true if PDBInfo is obsolete and needs updating.

This flag is currently not used within the class and is provided for user convenience. Setting this will forcibly turn off pdb numbering when dumping pdbs.

example(s): pose.pdb_info().obsolete() See also: Pose PDBInfo

Referenced by on_connection_change(), on_identity_change(), and on_length_change().

void core::pose::PDBInfo::obsolete ( bool  flag) [inline]

Sets the obsolete state to <flag>

this flag is currently not used within the class and is provided for user convenience. Setting this will forcibly turn off pdb numbering when dumping pdbs.

Real const& core::pose::PDBInfo::occupancy ( Size const  res,
Size const  atom_index 
) const [inline]

Returns the occupancy for the <atom_index> atom of pose residue <res>

example(s): pose.pdb_info().occupancy(1,1) See also: Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

void core::pose::PDBInfo::occupancy ( Size const  res,
Size const  atom_index,
Real const  occ 
) [inline]

Sets the occupancy of the <atom_index> atom of pose residue <res> to <occ>

void core::pose::PDBInfo::on_connection_change ( core::conformation::signals::ConnectionEvent const &  event)

Updates when connection to Conformation is changed.

update when connection to Conformation is changed

References detach_from(), obsolete(), and core::conformation::signals::ConnectionEvent::tag.

Referenced by attach_to(), and detach_from().

void core::pose::PDBInfo::on_identity_change ( core::conformation::signals::IdentityEvent const &  event)

Updates atom records when residue identity changes in Conformation.

update atom records when residue identity changes in Conformation

References detach_from(), obsolete(), core::conformation::signals::IdentityEvent::position, replace_res(), core::conformation::signals::IdentityEvent::residue, and core::conformation::signals::IdentityEvent::tag.

Referenced by attach_to(), and detach_from().

void core::pose::PDBInfo::on_length_change ( core::conformation::signals::LengthEvent const &  event)

Updates residue and atom records when length changes in Conformation, obsoletes PDBInfo.

update residue and atom records when length changes in Conformation, obsoletes PDBInfo

Residue and atoms records in PDBInfo will be automatically resized and the obsolete flag will be set to true, causing PDBInfo to not be used on pdb output. Existing data inside the PDBInfo is not touched. After filling in the data for the newly updated residues, setting PDBInfo::obsolete( false ) will re-enable usage of PDBInfo on pdb output. If PDBInfo receives a LengthEvent::INVALIDATE, it will obsolete and then detach itself for safety.

References append_res(), delete_res(), detach_from(), core::conformation::signals::LengthEvent::length_change, obsolete(), core::conformation::signals::LengthEvent::position, prepend_res(), core::conformation::signals::LengthEvent::residue, and core::conformation::signals::LengthEvent::tag.

Referenced by attach_to(), and detach_from().

PDBInfo & core::pose::PDBInfo::operator= ( PDBInfo const &  info)

copy assignment

any Conformation already being observed stays constant, there is no re-assignment

PDBPoseMap const& core::pose::PDBInfo::pdb2pose ( ) const [inline]

Returns the internally maintained PDBPoseMap.

example(s):

See also: Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

Size core::pose::PDBInfo::pdb2pose ( char const  chain,
int const  res,
char const  icode = ' ' 
) const [inline]

Returns the pose numbering of the pdb residue with chain <chain>, pdb residue <res>, and insertion code <icode>

Note:
: <icode> is not required, returns 0 if not found, pose numbering is sequential ie. starts at 1 and goes up pdb numbering can be anything

example(s): pose.pdb_info().pdb2pose("B",5) See also: Pose PDBInfo PDBInfo.pose2pdb

References core::pose::PDBPoseMap::find(), and icode().

PDBInfo::String core::pose::PDBInfo::pose2pdb ( Size const  res) const

Returns the pdb numbering string of pose residue <res>

translates the pose number to pdb numbering string for use in PyRosetta.

Note:
: pdb string contains the chainID and number pose numbering is sequential ie. starts at 1 and goes up pdb numbering can be anything

example(s): pose.pdb_info().pose2pdb(25) See also: Pose PDBInfo PDBInfo.pdb2pose

Parameters:
[in]respose residue number
Returns:
pdb string containing chainID and number
void core::pose::PDBInfo::prepend_res ( Size const  res,
Size const  natoms,
Size const  n = 1 
)

Prepends residue records before given pose residue number <res>

prepend residue records before given residue number

Parameters:
[in]resresidue to prepend before (in internal/pose numbering)
[in]natomsnumber of atoms in type of appended residue
[in]nnumber of residue records to prepend

References core::pose::PDBPoseMap::insert().

Referenced by on_length_change().

void core::pose::PDBInfo::rebuild_pdb2pose ( )
Remarks const& core::pose::PDBInfo::remarks ( ) const [inline]

Returns the pdb remarks (const)

example(s): pose.pdb_info().remarks() See also: Pose PDBInfo

Remarks& core::pose::PDBInfo::remarks ( ) [inline]

Returns the pdb remarks (mutable)

Note:
we allow direct access to the remarks vector because its state is independent of the rest of PDBInfo and it's much more convenient for the user

example(s): pose.pdb_info().remarks() See also: Pose PDBInfo

void core::pose::PDBInfo::remarks ( Remarks const &  in) [inline]

Sets the pdb remarks to <in>

example(s):

See also: Pose PDBInfo

void core::pose::PDBInfo::replace_res ( Size const  res,
Size const  natoms 
)

"Replaces" residue record for pose residue <res>

"replace" residue record for given residue number

Leaves information in residue record untouched, but resizes and zeroes atom records for the residue.

Parameters:
[in]resresidue to replace
[in]natomsnumber of atoms in type of residue

Referenced by on_identity_change().

void core::pose::PDBInfo::resize_atom_records ( Pose const &  pose)

Updates the number of atom records with respect to atoms in <pose>

update number of atom records with respect to atoms in Pose

Number of internally available atom records will be adjusted to match number of atoms within each residue in Pose. Only newly created records will be zeroed, any existing records are untouched.

References core::pose::Pose::n_residue(), core::conformation::Residue::natoms(), and core::pose::Pose::residue().

void core::pose::PDBInfo::resize_atom_records ( Size const  res,
Size const  n,
bool const  zero = true 
)

Ensures <n> atom records for residue <res> are available.

ensure 'n' available atom records for particular residue

Note:
: if <zero> is true, zero the atom records for this residue
Parameters:
[in]resresidue
[in]nnumber of atoms
[in]zeroif true, zero the atom records for this residue

Referenced by PDBInfo().

void core::pose::PDBInfo::resize_atom_records ( Size const  n,
bool const  zero = true 
)

Ensures <n> atom records for residue <res> are available.

ensure 'n' available atom records for every residue

Note:
: if <zero> is true, zero the atom records for this residue
Parameters:
[in]resresidue
[in]nnumber of atoms
[in]zeroif true, zero the atom records
void core::pose::PDBInfo::resize_residue_records ( Size const  n)

Resizes for <n> residue records.

resize for 'n' residue records

Leaves atom record state inconsistent. Atom records for remaining residues are untouched while new residues have no atom records, so make sure and call one of resize_atom_records() afterwards if necessary.

Warning:
Do not use this method for ins/del of residues, as it leaves the data state inconsistent. See append_res/prepend_res/delete_res for that type of functionality.

References rebuild_pdb2pose().

template<typename CharContainer >
void core::pose::PDBInfo::set_chains ( CharContainer const &  c) [inline]

Sets the residue chain ids from some char container, e.g. utility::vector1.

Container must have const .size(), .begin() and .end() iterator access methods.

Warning:
This function checks for size first and will cause failure if size of container does not match number of residues currently defined in object.

References set_chains().

void core::pose::PDBInfo::set_chains ( char const  id)

Sets all residue chain ids to the character <id>

set all residue chain IDs to a single character

References rebuild_pdb2pose().

Referenced by set_chains().

template<typename CharIterator >
void core::pose::PDBInfo::set_chains ( CharIterator const &  begin,
CharIterator const &  end 
) [inline]

Sets the residue chain ids from some char container, iterator version.

Warning:
This function does not check if number of elements within span of iterators exceeds number of residues currently defined in object. User must ensure this independently.

References core::sequence::end, and rebuild_pdb2pose().

template<typename CharIterator >
void core::pose::PDBInfo::set_icodes ( CharIterator const &  begin,
CharIterator const &  end 
) [inline]

Sets the insertion codes from some char container, iterator version.

Warning:
This function does not check if number of elements within span of iterators exceeds number of residues currently defined in object. User must ensure this independently.

References core::sequence::end, and rebuild_pdb2pose().

Referenced by set_icodes().

template<typename CharContainer >
void core::pose::PDBInfo::set_icodes ( CharContainer const &  c) [inline]

Sets the insertion codes from some char container, e.g. utility::vector1.

Container must have const .size(), .begin() and .end() iterator access methods.

Warning:
This function checks for size first and will cause failure if size of container does not match number of residues currently defined in object.

References set_icodes().

template<typename IntContainer >
void core::pose::PDBInfo::set_numbering ( IntContainer const &  c) [inline]

Sets the pdb sequence residue numbering from some int container, e.g. utility::vector1.

Container must have const .size(), .begin() and .end() iterator access methods.

Warning:
This function checks for size first and will cause failure if size of container does not match number of residues currently defined in object.

References set_numbering().

template<typename IntIterator >
void core::pose::PDBInfo::set_numbering ( IntIterator const &  begin,
IntIterator const &  end 
) [inline]

Sets the pdb sequence residue numbering from some int container, iterator version.

Warning:
This function does not check if number of elements within span of iterators exceeds number of residues currently defined in object. User must ensure this independently.

References core::sequence::end, and rebuild_pdb2pose().

Referenced by set_numbering().

void core::pose::PDBInfo::set_resinfo ( Size const  res,
char const  chain_id,
int const  pdb_res,
char const  ins_code = ' ' 
)

Sets the chain id, pdb sequence residue numbering, and insertion code for pose residue <res> to <chain_id> , <pdb_res> , and <ins_code> respectfully.

set chain/pdb/insertion code for residue simultaneously

Note:
: convenience method; more efficient than doing each individually due to map updates Returns the pdb insertion code of residue <res>

example(s): pose.pdb_info().icode(3) See also: Pose PDBInfo PDBInfo.chain PDBInfo.icode PDBInfo.number PDBInfo.pdb2pose PDBInfo.pose2pdb

Note:
convenience method; more efficient than doing each individually due to map updates
Parameters:
[in]resresidue in pose numbering
[in]chain_idpdb chain id
[in]pdb_resresidue in pdb numbering
[in]ins_codepdb insertion code

References core::pose::PDBPoseMap::conditional_erase(), and core::pose::PDBPoseMap::insert().

Referenced by core::pose::renumber_pdbinfo_based_on_conf_chains().

void core::pose::PDBInfo::show ( std::ostream &  out) const

Displays segments of PDB information, segments may or may not be entire chains.

Displays the PDB info by expressing continuous chain segments.

example(s); pose.pdb_info().show()

See Also: PDBInfo PDBInfo.chain PDBInfo.icode PDBInfo.nres PDBInfo.number Pose Pose.pdb_info

References protocols::comparative_modeling::features::A, chain(), icode(), name(), natoms(), nres(), and number().

Referenced by core::pose::operator<<().

Real const& core::pose::PDBInfo::temperature ( Size const  res,
Size const  atom_index 
) const [inline]

Returns the temperature for the <atom_index> atom of pose residue <res>

example(s): pose.pdb_info().temperature(1,1) See also: Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

Referenced by protocols::match::BfactorMPM::get_ca_bfactors().

void core::pose::PDBInfo::temperature ( Size const  res,
Size const  atom_index,
Real const  t 
) [inline]

Sets the temperature of the <atom_index> atom of pose residue <res> to <t>

References core::scoring::hbonds::t().

void core::pose::PDBInfo::tighten_memory ( )

Tightens memory usage.

tighten memory usage


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