Species-class             package:rsbml             R Documentation

_S_B_M_L _t_y_p_e "_S_p_e_c_i_e_s"

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

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

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

_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. 

     '_c_o_m_p_a_r_t_m_e_n_t': Object of class '"character"' identifying the
          compartment in which this species is located.

     '_i_n_i_t_i_a_l_A_m_o_u_n_t': Object of class '"numeric"' indicating the
          initial amount for this species (mutually exclusive with
          'initialConcentration').

     '_i_n_i_t_i_a_l_C_o_n_c_e_n_t_r_a_t_i_o_n': Object of class '"numeric"' indicating the
          initial concentration for this species (mutually exclusive
          with 'initialAmount').

     '_s_u_b_s_t_a_n_c_e_U_n_i_t_s': Object of class '"character"' identifying the
          units for the amount of this species or the numerator of the
          concentration.

     '_s_p_a_t_i_a_l_S_i_z_e_U_n_i_t_s': Object of class '"character"' identifying the
          units for the denominator of the species concentration.

     '_h_a_s_O_n_l_y_S_u_b_s_t_a_n_c_e_U_n_i_t_s': Object of class '"logical"' indicating 
          whether the quantity of this species is specified as an
          amount or a concentration.

     '_b_o_u_n_d_a_r_y_C_o_n_d_i_t_i_o_n': Object of class '"logical"'. If 'TRUE',
          indicates that the quantity of this species cannot be changed
          by a reaction.

     '_c_h_a_r_g_e': Object of class '"integer"' indicating the electrical
          charge of this species.

     '_c_o_n_s_t_a_n_t': Object of class '"logical"' indicating whether the
          quantity of this species can change.

     '_u_n_i_t_s': Object of class '"character"', deprecated. 

     '_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:

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

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

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

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

     _b_o_u_n_d_a_r_y_C_o_n_d_i_t_i_o_n 'signature(object = "Species")': gets the
          'boundaryCondition' slot 

     _b_o_u_n_d_a_r_y_C_o_n_d_i_t_i_o_n<- 'signature(object = "Species")': sets the
          'boundaryCondition' slot 

     _c_h_a_r_g_e 'signature(object = "Species")': gets the 'charge' slot 

     _c_h_a_r_g_e<- 'signature(object = "Species")': sets the 'charge' slot 

     _c_o_m_p_a_r_t_m_e_n_t 'signature(object = "Species")': gets the
          'compartment' slot 

     _c_o_m_p_a_r_t_m_e_n_t<- 'signature(object = "Species")': sets the
          'compartment' slot 

     _c_o_n_s_t_a_n_t 'signature(object = "Species")': gets the 'constant' slot 

     _c_o_n_s_t_a_n_t<- 'signature(object = "Species")': sets the 'constant'
          slot 

     _u_n_i_t_s 'signature(object = "Species")': gets the 'constant' slot 

     _u_n_i_t_s<- 'signature(object = "Species")': sets the 'constant' slot 

     _h_a_s_O_n_l_y_S_u_b_s_t_a_n_c_e_U_n_i_t_s 'signature(object = "Species")': gets the
          'hasOnlySubstanceUnits' slot 

     _h_a_s_O_n_l_y_S_u_b_s_t_a_n_c_e_U_n_i_t_s<- 'signature(object = "Species")': sets the
          'hasOnlySubstanceUnits' slot 

     _i_n_i_t_i_a_l_A_m_o_u_n_t 'signature(object = "Species")': gets the
          'initialAmount' slot 

     _i_n_i_t_i_a_l_A_m_o_u_n_t<- 'signature(object = "Species")': sets the
          'initialAmount' slot 

     _i_n_i_t_i_a_l_C_o_n_c_e_n_t_r_a_t_i_o_n 'signature(object = "Species")': gets the
          'initialConcentration' slot 

     _i_n_i_t_i_a_l_C_o_n_c_e_n_t_r_a_t_i_o_n<- 'signature(object = "Species")': sets the
          'initialConcentration' slot 

     _s_p_a_t_i_a_l_S_i_z_e_U_n_i_t_s 'signature(object = "Species")': gets the
          'spatialSizeUnits' slot 

     _s_p_a_t_i_a_l_S_i_z_e_U_n_i_t_s<- 'signature(object = "Species")': sets the
          'spatialSizeUnits' slot 

     _s_u_b_s_t_a_n_c_e_U_n_i_t_s 'signature(object = "Species")': gets the
          'substanceUnits' slot 

     _s_u_b_s_t_a_n_c_e_U_n_i_t_s<- 'signature(object = "Species")': sets the
          'substanceUnits' 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/>

