Model-class              package:rsbml              R Documentation

_S_B_M_L _t_y_p_e "_M_o_d_e_l"

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

     The central SBML element. Contains the 'Species', 'Reaction's,
     'Compartment's and other components of the model. See the SBML
     specification, at the reference, for further details.

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

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

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


     '_i_d': Object of class '"character"' uniquely identifying this
          component. 

     '_n_a_m_e': Object of class '"character"' naming this component. 

     '_f_u_n_c_t_i_o_n_D_e_f_i_n_i_t_i_o_n_s': Object of class '"list"' containing
          'FunctionDefinition's.

     '_u_n_i_t_D_e_f_i_n_i_t_i_o_n_s': Object of class '"list"' containing
          'UnitDefinition's. 

     '_c_o_m_p_a_r_t_m_e_n_t_s': Object of class '"list"' containing
          'Compartment's. 

     '_s_p_e_c_i_e_s': Object of class '"list"' containing 'Species's. 

     '_p_a_r_a_m_e_t_e_r_s': Object of class '"list"' containing 'Parameter's. 

     '_r_u_l_e_s': Object of class '"list"' containing 'Rule's. 

     '_r_e_a_c_t_i_o_n_s': Object of class '"list"' containing 'Reaction's. 

     '_e_v_e_n_t_s': Object of class '"list"' containing 'Event's. 

     '_l_a_y_o_u_t_s': Object of class '"list"' containing 'Layout's. 

     '_s_p_e_c_i_e_s_T_y_p_e_s': Object of class '"list"' containing
          'SpeciesType's.

     '_c_o_m_p_a_r_t_m_e_n_t_T_y_p_e_s': Object of class '"list"' containing
          'CompartmentType's.

     '_c_o_n_s_t_r_a_i_n_t_s': Object of class '"list"' containing 'Constraint's.

     '_i_n_i_t_i_a_l_A_s_s_i_g_n_m_e_n_t_s': Object of class '"list"' containing
          'InitialAssignment's.

     '_m_o_d_e_l_H_i_s_t_o_r_y': Object of class 'ModelHistory' recording the
          history of the model.

     '_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.

     '_c_v_T_e_r_m_s': Object of class '"list"' containing instances of
          'CVTerm' associated with this element.

     '_s_b_o_T_e_r_m': Object of class '"integer"' identifying a term in the
          Systems Biology Ontology (SBO).

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

     Class '"SBase"', directly.

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


     _i_d 'signature(object = "Model")': gets the 'id' slot 

     _i_d<- 'signature(object = "Model")': sets the 'id' slot 

     _n_a_m_e 'signature(object = "Model")': gets the 'name' slot 

     _n_a_m_e<- 'signature(object = "Model")': sets the 'name' slot 

     _c_o_m_p_a_r_t_m_e_n_t_s 'signature(object = "Model")': gets the
          'compartments' slot 

     _c_o_m_p_a_r_t_m_e_n_t_s<- 'signature(object = "Model")': sets the
          'compartments' slot 

     _e_v_e_n_t_s 'signature(object = "Model")': gets the 'events' slot 

     _e_v_e_n_t_s<- 'signature(object = "Model")': sets the 'events' slot 

     _f_u_n_c_t_i_o_n_D_e_f_i_n_i_t_i_o_n_s 'signature(object = "Model")': gets the
          'functionDefinitions' slot 

     _f_u_n_c_t_i_o_n_D_e_f_i_n_i_t_i_o_n_s<- 'signature(object = "Model")': sets the
          'functionDefinitions' slot 

     _l_a_y_o_u_t_s 'signature(object = "Model")': gets the 'layouts' slot 

     _l_a_y_o_u_t_s<- 'signature(object = "Model")': sets the 'layouts' slot 

     _p_a_r_a_m_e_t_e_r_s 'signature(object = "Model")': gets the 'parameters'
          slot 

     _p_a_r_a_m_e_t_e_r_s<- 'signature(object = "Model")': sets the 'parameters'
          slot 

     _s_p_e_c_i_e_s 'signature(object = "Model")': gets the 'species' slot 

     _s_p_e_c_i_e_s<- 'signature(object = "Model")': sets the 'species' slot 

     _r_e_a_c_t_i_o_n_s 'signature(object = "Model")': gets the 'reactions' slot 

     _r_e_a_c_t_i_o_n_s<- 'signature(object = "Model")': sets the 'reactions'
          slot 

     _r_u_l_e_s 'signature(object = "Model")': gets the 'rules' slot 

     _r_u_l_e_s<- 'signature(object = "Model")': sets the 'rules' slot 

     _u_n_i_t_D_e_f_i_n_i_t_i_o_n_s 'signature(object = "Model")': gets the
          'unitDefinitions' slot 

     _u_n_i_t_D_e_f_i_n_i_t_i_o_n_s<- 'signature(object = "Model")': sets the
          'unitDefinitions' slot 

     _c_o_m_p_a_r_t_m_e_n_t_T_y_p_e_s 'signature(object = "Model")': gets the
          'compartmentTypes' slot 

     _c_o_m_p_a_r_t_m_e_n_t_T_y_p_e_s<- 'signature(object = "Model")': sets the
          'compartmentTypes' slot 

     _c_o_n_s_t_r_a_i_n_t_s 'signature(object = "Model")': gets the 'constraints'
          slot 

     _c_o_n_s_t_r_a_i_n_t_s<- 'signature(object = "Model")': sets the
          'constraints' slot 

     _i_n_i_t_i_a_l_A_s_s_i_g_n_m_e_n_t_s 'signature(object = "Model")': gets the
          'initialAssignments' slot 

     _i_n_i_t_i_a_l_A_s_s_i_g_n_m_e_n_t_s<- 'signature(object = "Model")': sets the
          'initialAssignments' slot 

     _s_p_e_c_i_e_s_T_y_p_e_s 'signature(object = "Model")': gets the
          'speciesTypes' slot 

     _s_p_e_c_i_e_s_T_y_p_e_s<- 'signature(object = "Model")': sets the
          'speciesTypes'slot 

     _m_o_d_e_l_H_i_s_t_o_r_y 'signature(object = "Model")': gets the
          'modelHistory' slot 

     _m_o_d_e_l_H_i_s_t_o_r_y<- 'signature(object = "Model")': sets the
          'modelHistory' 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/>

