Bio::Structure::Entry - Bioperl structure Object, describes the whole entry #add synopsis here 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 choosen.

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://bio.perl.org/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email kris.boulez@algonomics.com 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 : Args :

chain()
Title : chain Usage : @chains = $structure->chain($chain); Function: Connects a (or a list of) Chain 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_chain()
Title : add_chain Usage : @chains = $structure->add_chain($add_chain); Function: Adds a (or a list of) Chain objects to a Bio::Structure::Entry. Returns : Args :

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 = $structure->add_residue($residue); Function: Adds 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

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

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 serial number for the source atom

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 : Description : This is a bit of a kludge, but it's the best for now. Conect info might need to go in a sepearte 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 : $structure->get_atom_by_serial($module, $serial); Function: get the Atom for a for get_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)

_remove_models()
Title : _remove_models Usage : Function: Removes the models attached to an Entry. Tells the models they don't 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 object's child(ren) Returns : a reference to an array of child(ren) if it 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