SBMLDocument-class           package:rsbml           R Documentation

"_S_B_M_L_D_o_c_u_m_e_n_t" _f_r_o_m _l_i_b_s_b_m_l

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

     Low-level libsbml document structure.

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

     A virtual Class: No objects may be created from it.

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

     Class '"oldClass"', directly.

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


     _r_s_b_m_l__c_h_e_c_k 'signature(object = "SBMLDocument")':
          'rsbml_check(object, quiet = FALSE, verbose = FALSE)':
          semantically validates the document. If 'quiet' is 'TRUE',
          emits warnings describing errors and fatal failures
          encountered when the document was parsed. If 'verbose' is
          also 'TRUE', reports less critical warnings about problems in
          the model, such as internal inconsistencies.

     _r_s_b_m_l__d_o_m 'signature(doc = "SBMLDocument")': Constructs an S4 
          object model from a libsbml document. 

     _r_s_b_m_l__g_r_a_p_h 'signature(doc = "SBMLDocument")': Converts a  libsbml
          document to a 'graph'. 

     _r_s_b_m_l__p_r_o_b_l_e_m_s 'signature(object = "SBMLDocument")':  reports
          problems encountered during parsing and/or validation.

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

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

     _s_i_m_u_l_a_t_e 'signature(object = "SBMLDocument")': 'simulate(object,
          nsim = 10, seed, ...)': a shortcut for simulating the model
          in this document using the SBML ODE Solver library. Arguments
          in '...' should match slots of 'SOSProtocol'. See 'simulate'
          for more details.

_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:

       # Read a document into an R DOM
       dom <- rsbml_read(system.file("sbml", "GlycolysisLayout.xml", package
     = "rsbml"))
       
       # Convert to a graph
       graph <- rsbml_graph(dom)
       
       # Write it out to a file
       ## Not run: rsbml_write(dom, "my.xml")
       
       # Or convert it to a string of XML
       rsbml_xml(dom)

       # Read into external libsbml data structure
       doc <- rsbml_read(system.file("sbml", "GlycolysisLayout.xml", package
     = "rsbml"), dom = FALSE)
       
       # Convert it explicitly to an S4 DOM
       dom <- rsbml_dom(doc)

