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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.

   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

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

bioperl-l@bioperl.org

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:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Kris Boulez

Email kris.boulez@algonomics.com

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 choosen
  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