Skip to content
Snippets Groups Projects
Select Git revision
  • cf2d6ad77649872d2d697564ef57713e88184203
  • master default protected
  • emoUS
  • add_default_vectorizer_and_pretrained_loading
  • clean_code
  • readme
  • issue127
  • generalized_action_dicts
  • ppo_num_dialogues
  • crossowoz_ddpt
  • issue_114
  • robust_masking_feature
  • scgpt_exp
  • e2e-soloist
  • convlab_exp
  • change_system_act_in_env
  • pre-training
  • nlg-scgpt
  • remapping_actions
  • soloist
20 results

evaluate.py

Blame
  • Code owners
    Assign users and groups as approvers for specific file changes. Learn more.
    optsol_blockedReact-class.Rd 5.01 KiB
    \name{optsol_blockedReact-class}
    
    \Rdversion{1.1}
    \docType{class}
    
    \alias{optsol_blockedReact-class}
    
    \alias{blocked,optsol_blockedReact-method}
    \alias{blocked<-,optsol_blockedReact-method}
    \alias{blocked}
    \alias{blocked<-}
    \alias{react,optsol_blockedReact-method}
    \alias{react<-,optsol_blockedReact-method}
    \alias{react<-}
    \alias{maxSol,optsol_blockedReact-method}
    \alias{minSol,optsol_blockedReact-method}
    \alias{maxSol}
    \alias{minSol}
    
    \title{Class \code{"optsol_blockedReact"}}
    
    \description{
      Structure of the class \code{"optsol_blockedReact"}. Objects of that class are
      returned by the function \code{\link{blockedReact}}.
    }
    
    \section{Objects from the Class}{
      Objects can be created by calls of the form
      \code{new("optsol_blockedReact", ...)}.
    }
    
    \section{Slots}{
      \describe{
        \item{\code{blocked}:}{Object of class \code{"logical"}
          indicating if a reaction is blocked, or not.
        }
        \item{\code{react}:}{Object of class \code{"reactId"}
          containing the reaction id's of checked reactions.
        }
        \item{\code{mod_id}:}{Object of class \code{"character"}
          containing the model id of the used model.
        }
        \item{\code{mod_key}:}{Object of class \code{"character"}
          containing the model key of the used model.
        }
        \item{\code{solver}:}{Object of class \code{"character"}
          indicating the used solver.
        }
        \item{\code{method}:}{Object of class \code{"character"}
          indicating the used method.
        }
        \item{\code{algorithm}:}{Object of class \code{"character"}
          containing the name of the algorithm used for optimizations.
        }
        \item{\code{num_of_prob}:}{Object of class \code{"integer"}
          indicating the number of optimization problems.
        }
        \item{\code{lp_num_cols}:}{Object of class \code{"integer"}
          indicating the number of columns.
        }
        \item{\code{lp_num_rows}:}{Object of class \code{"integer"}
          indicating the number of rows.
        }
        \item{\code{lp_obj}:}{Object of class \code{"numeric"}
          containing the optimal values of the objective function after
          optimization. If no flux distribution is available, slot \code{lp_obj}
          contains the cross-product of the objective coefficients in slot
          \code{obj_coef} and the part of the flux distribution in slot
          \code{fluxdist} containing the values representing fluxes in the entire
          metabolic network (slot \code{fldind}).
        }
        \item{\code{lp_ok}:}{Object of class \code{"integer"}
          containing the exit code of the optimization.
        }
        \item{\code{lp_stat}:}{Object of class \code{"integer"}
          containing the solution status of the optimization.
        }
        \item{\code{lp_dir}:}{Object of class \code{"character"}
          indicating the direction of optimization.
        }
        \item{\code{obj_coef}:}{Object of class \code{"numeric"}
          containing the objective coefficients of the used model (slot
          \code{obj_coef} of an object of class \code{\linkS4class{modelorg}}).
          These are not necessarily the objective coefficients of the used
          algorithm. 
        }
        \item{\code{obj_func}:}{Object of class \code{"character"}
          containing the objective function of the used model. Usually, it contains
          the return value of \code{\link{printObjFunc}}. 
        }
        \item{\code{fldind}:}{Object of class \code{"integer"}
          pointers to columns (variables) representing a flux (reaction) in the
          original network. The variable \code{fldind[i]} in the problem object
          represents reaction \code{i} in the original network. 
        }
        \item{\code{fluxdist}:}{Object of class \code{"fluxDistribution"}
          containing the solutions flux distributions.
        }
        \item{\code{alg_par}:}{Object of class \code{"list"}
          containing a named list containing algorithm specific parameters.
        }
      }
    }
    
    \section{Extends}{
      Class \code{"\linkS4class{optsol}"}, directly.
    }
    
    \section{Methods}{
      \describe{
        \item{\code{blocked}:}{
          \code{signature(object = "optsol_blockedReact")}: gets the \code{blocked} slot.
        }
        \item{\code{blocked<-}:}{
          \code{signature(object = "optsol_blockedReact")} sets the \code{blocked} slot.
        }
        \item{\code{react}:}{
          \code{signature(object = "optsol_blockedReact")}: gets the \code{react} slot.
        }
        \item{\code{react<-}:}{
          \code{signature(object = "optsol_blockedReact")} sets the \code{react} slot.
        }
        \item{\code{maxSol}:}{
          \code{signature(object = "optsol_blockedReact")}(\code{slot}): returns the
          values in the slot given in \code{slot} for optimizations in \dQuote{max}
          direction.
        }
        \item{\code{minSol}:}{
          \code{signature(object = "optsol_blockedReact")}(\code{slot}): returns the
          values in the slot given in \code{slot} for optimizations in \dQuote{min}
          direction.
        }
      }
    }
    
    \author{
      Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>
    
      Maintainer: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
    }
    
    
    \seealso{
      \code{\link{checkOptSol}} and \code{\linkS4class{optsol}}
    }
          
    \examples{
      showClass("optsol_blockedReact")
    }
    
    \keyword{classes}