Class ModelSystem

This is where all information regarding the model system are stored.
A few things to note:
   1. All CTs in an object of this class have corresponding entries in the project table.
   2. All structures are wrapped in an object of a `CtObj' class -- see below.
   3. PT stands for project table.

Here are the attributes:
   task_mode       = task_mode     # - Should be initialized to be one of the values: 0 = Mini; 1 = FEP; 2 = DDG; 3 = LRM.
   basename        = None          # - Will point to a `StringVar' object from `_SysSpec'.
   
   # Toggles:
   sys_type        = None          # - Valid values: COMPLEX, LIG_ONLY, PROT_ONLY, and ZMATRIX
                                   # - Will point to an `IntVar' object that stores and controls the system type toggle on
                                   #   `_SysSpec'. See `_SysSpec's `initialize' method.
   has_movie       = False         # - Will be `True' if we have the ligand-perturbation movie.
   use_charge      = None          # - Will point to an `IntVar' object from `_Import', indicating whether we use the
                                   #   charges from the structure file (1) or not (0).
   use_prot_zmat   = None          # - Will point to an `IntVar' object from `_Import', indicating whether we use an
                                   #   existing zmatrix for the protien (1) or not (0).
   use_reflig      = None          # - Will point to an `IntVar' object from `_Import', indicating whether we use a
                                   #   reference ligand (1) or not (0).
   is_flex_lig     = None          # - Will point to an `IntVar' object from `Flex', indicating whether the ligand is
                                   #   fully flexible (1) or not (0).
   is_flex_cof     = None          # - Will point to an `IntVar' object from `Flex', indicating whether the cofactor is
                                   #   fully flexible (1) or not (0).
   is_cartesian    = 0             # - 0 = cartesian; 1 = internal coordinate minimization
   is_prepared     = False         # - True if the final system was created on Maestro, false otherwise.
   prot_constr     = None          # - Will point to a `StringVar' object from `Flex', indicating whether the protein is
                                   #   fully flexible ('0') or fully rigid ('1') or partially rigid ('2').

   # Structures (`CtObj' objects):
   lig             = [None, None, None,]
                                   # - Ligand structures: lig[0] = reference, lig[1] = original, lig[2] = perturbed
   prot            = None          # - Raw/untreated protein
   chop            = None          # - Chopped protein
   neut            = None          # - Neutralized protein
   prot_final      = None          # - Final protein
   lig_final       = None          # - Final ligand
   prot_zmat_fname = None          # - Name of the existing protein zmatrix file
   sys_zmat        = None          # - Existing zmatrix structure
   movie_ct        = None          # - A series of structures simulating the perturbation from `lig[1]' to `lig[2]'
   
   # Misc.
   ffield          = None          # - Will point to a `StringVar' object from `Flex', storing the force field type.
   r_chop          = None          # - Will point to a `StringVar' object from `ChopCap', storing the chop radius.
   r_flex          = None          # - Will point to a `StringVar' object from `Flex', storing the flexible-region radius.
   neut_target     = None          # - Will point to an `EntryField object from `Neut', storing the target charge.
   neut_to_target  = None          # - Will point to a `StringVar' object from `Neut', indicating if alternative target charge is to be used
   gen_success     = None          # - Will be a function to send out signal saying the final model system is ready.
   rtr_success     = None          # - Will be a function to send out signal saying the final model system is not ready.
   tol_bond        = None          # - Will point to a `EntryField' object from `Flex', storing the bond tolernace.
   tol_angle       = None          # - Will point to a `EntryField' object from `Flex', storing the angle tolernace.
   tol_dih         = None          # - Will point to a `EntryField' object from `Flex', storing the dihedral tolernace.