cmf_view_mol_field_cofield_mopac: View molecule, co-field and field

In conmolfields: Continuous molecular fields

Description

View molecule, co-field and field

Arguments

mdb_fname	"ligands-train.mol2"
train_mopac_res_fname	"ligands-mopac-res-train.RData"
imol	1
ft	"q"
grid_fname	"ligands-grid-krr.RData"
alpha_from_model	FALSE
model_fname	"ligands-model.RData"
alpha	0.3
rlevel	0.5
alpha_g	0.7
draw_field	TRUE
draw_cofield	TRUE
draw_overlap	FALSE

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
cmf_view_mol_field_cofield_mopac <- function
(
  mdb_fname = "ligands-train.mol2",                        # File name for molecular database 
  train_mopac_res_fname = "ligands-mopac-res-train.RData", # File with MOPAC results for the training set
  imol = 1,                                                # Molecule to visualize
  ft = "q",                                                # Field type to visualize
  grid_fname = "ligands-grid-krr.RData",                   # File name for grid with co-fields
  alpha_from_model = FALSE,                                # Take alpha from model? (TRUE/FALSE, 1/0)
  model_fname = "ligands-model.RData",                     # Model file name
  alpha = 0.3,                                             # Alpha value (if not taken from model)
  rlevel = 0.5,                                            # Isosurface level
  alpha_g = 0.7,                                           # Alpha (non-transperancy) level
  draw_field = TRUE,                                       # Whether to draw field
  draw_cofield = TRUE,                                     # Whether to draw co-field
  draw_overlap = FALSE,                                    # Whether to draw overlap between fields and co-fields
  ...
)

conmolfields documentation built on May 2, 2019, 4:18 p.m.