Bio::Structure::Entry(3pm)

NAME

Bio::Structure::Entry - Bioperl structure Object, describes the whole entry

SYNOPSIS

  #add synopsis here

DESCRIPTION

This object stores a whole Bio::Structure entry. It can consist of one or more models (Bio::Structure::Model), which in turn consist of one or more chains (Bio::Structure::Chain). A chain is composed of residues (Bio::Structure::Residue) and a residue consists of atoms (Bio::Structure::Atom). If no specific model or chain is chosen, the first one is chosen.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Kris Boulez

Email [email protected]

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new()

 Title   : new()
 Usage   : $struc = Bio::Structure::Entry->new( 
                                           -id  => 'structure_id',
                                           );
 Function: Returns a new Bio::Structure::Entry object from basic 
                constructors. Probably most called from Bio::Structure::IO.
 Returns : a new Bio::Structure::Model object

model()

 Title   : model
 Function: Connects a (or a list of) Model objects to a Bio::Structure::Entry.
                To add a Model (and keep the existing ones) use add_model()
                It returns a list of Model objects.
 Returns : List of Bio::Structure::Model objects
 Args    : One Model or a reference to an array of Model objects

add_model()

 Title   : add_model
 Usage   : $structure->add_model($model);
 Function: Adds a (or a list of) Model objects to a Bio::Structure::Entry.
 Returns : 
 Args    : One Model or a reference to an array of Model objects

get_models()

 Title   : get_models
 Usage   : $structure->get_models($structure);
 Function: general get method for models attached to an Entry
 Returns : a list of models attached to this entry
 Args    : an Entry

id()

 Title   : id
 Usage   : $entry->id("identity");
 Function: Gets/sets the ID 
 Returns : The ID
 Args    :

chain()

 Title   : chain
 Usage   : @chains  = $structure->chain($chain);
 Function: Connects a Chain or a list of Chain objects to a Bio::Structure::Entry.
 Returns : List of Bio::Structure::Chain objects
 Args    : A Chain or a reference to an array of Chain objects

add_chain()

 Title   : add_chain
 Usage   : @chains  = $structure->add_chain($model,$chain);
 Function: Adds one or more Chain objects to a Bio::Structure::Entry.
 Returns : List of Chain objects associated with the Model
 Args    : A Model object and a Chain object or a reference to an array of 
           of Chain objects

get_chains()

 Title   : get_chains
 Usage   : $entry->get_chains($model);
 Function: General get method for Chains attached to a Model
 Returns : A list of Chains attached to this model
 Args    : A Model

residue()

 Title   : residue
 Usage   : @residues  = $structure->residue($residue);
 Function: Connects a (or a list of) Residue objects to a Bio::Structure::Entry.
 Returns : List of Bio::Structure::Residue objects
 Args    : One Residue or a reference to an array of Residue objects

add_residue()

 Title   : add_residue
 Usage   : @residues  = $structure->add_residue($chain,$residue);
 Function: Adds one or more Residue objects to a Bio::Structure::Entry.
 Returns : List of Bio::Structure::Residue objects
 Args    : A Chain object and a Residue object or a reference to an array of 
           Residue objects

get_residues()

 Title   : get_residues
 Usage   : $structure->get_residues($chain);
 Function: General get method for Residues attached to a Chain
 Returns : A list of residues attached to this Chain
 Args    : A Chain

add_atom()

 Title   : add_atom
 Usage   : @atoms  = $structure->add_atom($residue,$atom);
 Function: Adds a (or a list of) Atom objects to a Bio::Structure::Residue.
 Returns : List of Bio::Structure::Atom objects
 Args    : A Residue and an Atom

get_atoms()

 Title   : get_atoms
 Usage   : $structure->get_atoms($residue);
 Function: General get method for Atoms attached to a Residue
 Returns : A list of Atoms attached to this Residue
 Args    : A Residue

parent()

 Title   : parent
 Usage   : $structure->parent($residue);
 Function: Returns the parent of the argument
 Returns : The parent of the argument
 Args    : A Bio::Structure object

connect

 Title   : connect
 Usage   : 
 Function: Alias to conect()
 Returns : 
 Args    :

conect()

 Title   : conect
 Usage   : $structure->conect($source);
 Function: Get/set method for conect
 Returns : A list of serial numbers for Atoms connected to source
                (together with $entry->get_atom_by_serial($model, $serial),
           this should be OK for now)
 Args    : The source, the serial number for the source Atom, and the type

get_all_connect_source

 Title   : get_all_connect_source
 Usage   : 
 Function: Alias to get_all_conect_source()
 Returns : 
 Args    :

get_all_conect_source()

 Title   : get_all_conect_source
 Usage   : @sources = $structure->get_all_conect_source;
 Function: Get all the sources for the conect records
 Returns : A list of serial numbers for atoms connected to source
                (together with $entry->get_atom_by_serial($model, $serial), 
           this should be OK for now)
 Args    : 
 Notes   : This is a bit of a kludge, but it is the best for now. Conect info might need
                to go in a separate object

master()

 Title   : master
 Usage   : $structure->master($source);
 Function: Get/set method for master
 Returns : The master line
 Args    : The master line for this entry

seqres()

 Title   : seqres
 Usage   : $seqobj = $structure->seqres("A");
 Function: Gets a sequence object containing the sequence from the SEQRES record.
                if a chain-ID is given, the sequence for this chain is given, if none
                is provided the first chain is chosen
 Returns : A Bio::PrimarySeq
 Args    : The chain-ID of the chain you want the sequence from

get_atom_by_serial()

 Title   : get_atom_by_serial
 Usage   : $structure->get_atom_by_serial($model,$serial);
 Function: Get the Atom by serial
 Returns : The Atom object with this serial number in the model
 Args    : Model on which to work, serial number for atom
                (if only a number is supplied, the first model is chosen)

annotation

 Title   : annotation
 Usage   : $obj->annotation($seq_obj)
 Function:
 Example :
 Returns : value of annotation
 Args    : newvalue (optional)

_remove_models()

 Title   : _remove_models
 Usage   : 
 Function: Removes the models attached to an Entry. Tells the models they
                do not belong to this Entry any more
 Returns : 
 Args    :

_create_default_model()

 Title   : _create_default_model
 Usage   : 
 Function: Creates a default Model for this Entry. Typical situation
                in an X-ray structure where there is only one model
 Returns : 
 Args    :

_create_default_chain()

 Title   : _create_default_chain
 Usage   : 
 Function: Creates a default Chain for this Model. Typical situation
                in an X-ray structure where there is only one chain
 Returns : 
 Args    :

_parent()

 Title   : _parent
 Usage   : This is an internal function only. It is used to have one 
                place that keeps track of which object has which other object 
                as parent. Thus allowing the underlying modules (Atom, Residue,...)
                to have no knowledge about all this (and thus removing the possibility
                of reference cycles).
                This method hides the details of manipulating references to an anonymous
                hash.
 Function: To get/set an objects parent 
 Returns : A reference to the parent if it exist, undef otherwise. In the 
                current implementation each node should have a parent (except Entry).
 Args    :

_child()

 Title   : _child
 Usage   : This is an internal function only. It is used to have one 
                place that keeps track of which object has which other object 
                as child. Thus allowing the underlying modules (Atom, Residue,...)
                to have no knowledge about all this (and thus removing the possibility
                to have no knowledge about all this (and thus removing the possibility
                of reference cycles).
                This method hides the details of manipulating references to an anonymous
                hash.
 Function: To get/set an the children of an object 
 Returns : A reference to an array of child(ren) if they exist, undef otherwise. 
 Args    :

_remove_from_graph()

 Title   : _remove_from_graph
 Usage   : This is an internal function only. It is used to remove from
                the parent/child graph. We only remove the links from object to
                his parent. Not the ones from object to its children.
 Function: To remove an object from the parent/child graph
 Returns : 
 Args    : The object to be orphaned