Commit a4cb71cb authored by Alessia Vignolo's avatar Alessia Vignolo
Browse files

added example_workshop

parent b75a0a0b
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###############################################################################
###################### NanoShaper 0.3.1 Configuration file ###################
###############################################################################
Compute_Vertex_Normals = true
Save_Mesh_MSMS_Format = true
Load_Balancing = true
Print_Available_Surfaces = false
Example_Surface_Parameter = 2.0
# NOTE
# for big molecules consider reducing to 1.5 for limiting memory usage.
# if still memory usage is too high, remove accurate triangulation
# and enable status map
################################ Grid params ##################################
# Grid scale
Grid_scale = 2.0
# Percentage that the surface occupies with respect to the total grid volume
# default value is 90.0; in the case of very small molecules (e.g. fullerene) keep more margin
# (e.g. lower the value to 50%)
Grid_perfil = 90.0
# Input atoms xyzr file name
XYZR_FileName = 1vsz.xyzr
#XYZR_FileName = 1crn.xyzr
############################## Internal maps ##################################
# Enable/Disable build of epsilon (dielectric) map
Build_epsilon_maps = false
# Enable/Disable build of map for cavity detection and for a non analytical
# triangulation
Build_status_map = true
########################## Surface Type params ################################
# Possible values: skin,blobby,mesh,ses,example
Surface = skin
# Apply final surface smoothing
Smooth_Mesh = false
# Number of total threads
Number_thread = 16
# Skin surface parameter [0.05,0.95]
# the extrema are possibly not numerically stable,
# the suggested range is [0.15,0.95]
# default value is 0.45
Skin_Surface_Parameter = 0.45
# Blobbyness value for the blobby surface [-0.5,-5.0]
# default value is -2.5
Blobbyness = -2.5
# Name of the input surface file used if mesh Surface is enabled or msms.
# In case of msms remove any extension, .face and .vert file will be
# automatically loaded.
# In case of mesh, .off and .ply files are supported
Surface_File_Name = triangulatedSurf.vert
######################## Surface Processing params ############################
# Enable or disable cavity detection together with the volume conditional
# filling of voids and cavities
Cavity_Detection_Filling = false
# It is the value of the minimal volume of a cavity to get filled if
# cavity detection is enabled.
# The default value is an approximation of the volume of the water molecule
# default value is 11.4, this is the approximate volume of a water molecule
# in Angstrom
Conditional_Volume_Filling_Value = 11.4
# If this flag is true, cavities where a sphere of Probe_Radius cannot fit,
# are removed.
# Use this feature when cavity detection is enabled to filter out bad shaped
# cavities whose
# volume is higher than Conditional_Volume_Filling_Value.
Keep_Water_Shaped_Cavities = false
# The radius of the sphere that represents a water molecule in Angstrom
# default value is 1.4 Angstrom
Probe_Radius = 1.4
# Enable accurate triangulation: if accurate triangulation is enable all points
# are sampled from the original surface. If disabled the points are not
# analytically sampled and an high memory saving can be obtained
# together with a 3x speed-up on ray casting if both epsmap is disabled
# MC phase will be slower because vertices are calculated on the fly
Accurate_Triangulation = true
# Perform triangulation using a single ray-casting process. Vertex data is
# inferred.
Triangulation = true
# Check duplicated vertices when reading
Check_duplicated_vertices = false
# If true save the status map. Enable this for cavity detection and
# visualization of the coloured FD grid
Save_Status_map = false
# Save Skin/SES in a PovRay file for ray-tracing.
# This is a purely graphics representation because the surface is not in
# a left handed system as it should in Pov-Ray
Save_PovRay = false
####################### Acceleration Data Structures ##########################
# Mesh Projection(3D)/Ray Casting (3D) acceleration grid
# Increase *_size to increase performance and memory usage.
# Increase *_cell if requested by NanoShaper
# default 100
Max_mesh_auxiliary_grid_size = 100
# default 250
Max_mesh_patches_per_auxiliary_grid_cell = 250;
# default 100
Max_mesh_auxiliary_grid_2d_size = 100
# default 250
Max_mesh_patches_per_auxiliary_grid_2d_cell = 250
# SES Projection(3D)/Ray Casting (3D) acceleration grid
# default 100
Max_ses_patches_auxiliary_grid_size = 100
# default 400
Max_ses_patches_per_auxiliary_grid_cell = 400
# defualt 40
Max_ses_patches_auxiliary_grid_2d_size = 40
# default 400
Max_ses_patches_per_auxiliary_grid_2d_cell = 400
# Skin Projection(3D)/Ray Casting (3D) acceleration grid
# default 100
Max_skin_patches_auxiliary_grid_size = 100
# default 400
Max_skin_patches_per_auxiliary_grid_cell = 400
# default 50
Max_skin_patches_auxiliary_grid_2d_size = 50
# default 400
Max_skin_patches_per_auxiliary_grid_2d_cell = 600
###############################################################################
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