Bio::Structure::Entry(3pm) | User Contributed Perl Documentation | Bio::Structure::Entry(3pm) |
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 chosen.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
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
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
Title : id Usage : $entry->id("identity"); Function: Gets/sets the ID Returns : The ID Args :
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
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
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
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
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
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
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
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
Title : parent Usage : $structure->parent($residue); Function: Returns the parent of the argument Returns : The parent of the argument Args : A Bio::Structure object
Title : connect Usage : Function: Alias to conect() Returns : Args :
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
Title : get_all_connect_source Usage : Function: Alias to get_all_conect_source() Returns : Args :
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
Title : master Usage : $structure->master($source); Function: Get/set method for master Returns : The master line Args : The master line for this entry
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
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)
Title : annotation Usage : $obj->annotation($seq_obj) Function: Example : Returns : value of annotation Args : newvalue (optional)
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 :
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 :
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 :
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 :
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 :
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
2018-10-27 | perl v5.26.2 |