SBML-class               package:rsbml               R Documentation

_S_B_M_L _t_y_p_e "_S_B_M_L"

_D_e_s_c_r_i_p_t_i_o_n:

     The root element of an SBML document. An actual SBML  'Model' may
     be retrieved from an instance of this class.

_I_n_s_t_a_n_t_i_a_t_i_o_n:

     Objects can be created by calls of the form 'new("SBML", ...)'.

_S_l_o_t_s:

     '_l_e_v_e_l': Object of class '"integer"' indicating the level of the
          SBML standard (currently at 2). 

     '_v_e_r': Object of class '"integer"' indicating the version of the
          level (currently at 2 for level 2). 

     '_m_o_d_e_l': Object of class '"Model"' the SBML model itself. 

     '_m_e_t_a_I_d': Object of class '"character"' that is an XML ID
          "described" by an RDF resource. This links an SBML element to
          an RDF resource. RDF may appear anywhere in an SBML element,
          but is usually placed inside the 'annotation' element.

     '_n_o_t_e_s': Object of class '"character"'  containing user-readable
          XHTML notes about an element. 

     '_a_n_n_o_t_a_t_i_o_n': Object of class '"character"' containing additional
          machine-readable information about an element, usually as
          RDF, such as BioPAX. This is where application-specific data
          belongs.

_E_x_t_e_n_d_s:

     Class '"SBase"', directly.

_M_e_t_h_o_d_s:

     _c_o_e_r_c_e 'signature(from = "SBMLDocument", to = "SBML")': 
          constructs the S4 object model from a low-level libsbml
          document.

     _c_o_e_r_c_e 'signature(from = "SBML", to = "SBMLDocument")':  converts
          the S4 object model to a low-level libsbml document. 

     _l_e_v_e_l 'signature(object = "SBML")': gets the 'level' slot 

     _l_e_v_e_l<- 'signature(object = "SBML")': sets the 'level' slot 

     _m_o_d_e_l 'signature(object = "SBML")': gets the 'model' slot 

     _m_o_d_e_l<- 'signature(object = "SBML")': sets the 'model' slot 

     _r_s_b_m_l__d_o_c 'signature(model = "SBML")': converts the S4 object
          model to a low-level libsbml document.

     _r_s_b_m_l__w_r_i_t_e 'signature(object = "SBML")': writes this document to
          a file as SBML.

     _r_s_b_m_l__x_m_l 'signature(object = "SBML")': converts this document to
          a string as SBML.

     _v_e_r 'signature(object = "SBML")': gets the 'ver' slot 

     _v_e_r<- 'signature(object = "SBML")': sets the 'ver' slot 

_A_u_t_h_o_r(_s):

     Michael Lawrence

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://sbml.org/documents/>

_E_x_a_m_p_l_e_s:

       # Get a DOM
       doc <- rsbml_read(system.file("sbml", "GlycolysisLayout.xml", package = "rsbml"))
       dom <- rsbml_dom(doc)
       
       # Get the species ID's
       sapply(species(model(dom)), id)
       
       # Convert DOM back to a low-level document for checking
       doc <- rsbml_doc(dom)
       rsbml_check(doc)
       
       # Write a DOM to a file
       ## Not run: rsbml_write(dom, "my.xml")

