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Commit 42af2a3f authored by Claudia Canevari's avatar Claudia Canevari
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lightweighten regression tests

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tests/1VSZ_protonated_EDT/1VSZ_protonated_EDT_conf.prm deleted 100644 → 0
View file @ 69aee126
###############################################################################
###################### NanoShaper 0.3.1 Configuration file ###################
###############################################################################
Compute_Vertex_Normals = false
Save_Mesh_MSMS_Format = false
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 = 1.0
# 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
#XYZR_FileName = sphere.xyzr
XYZR_FileName = 1VSZ_protonated_EDT.xyzr
# Input atoms xyzr file name
#XYZR_FileName = barstar.xyzr
#XYZR_FileName = 1crn.xyzr
#XYZR_FileName = ArgArg.xyzr
# if you enable fullerene (or a small molecule) use Grid_perfil = 70.0 or lower
#XYZR_FileName = fullerene.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 = ses
# Apply final surface smoothing
Smooth_Mesh = false
# Number of total threads
Number_thread = 1
# 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 = 400
###############################################################################
\ No newline at end of file
tests/1VSZ_protonated_EDT/output/triangleAreas.txt deleted 100644 → 0
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tests/1VSZ_protonated_EDT/output/triangulatedSurf.off deleted 100644 → 0
View file @ 69aee126
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tests/1VSZ_protonated_EDT_skin/1VSZ_protonated_EDT_skin_conf.prm deleted 100644 → 0
View file @ 69aee126
###############################################################################
###################### NanoShaper 0.3.1 Configuration file ###################
###############################################################################
Compute_Vertex_Normals = false
Save_Mesh_MSMS_Format = false
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 = 1.0
# 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
#XYZR_FileName = sphere.xyzr
XYZR_FileName = 1VSZ_protonated_EDT.xyzr
# Input atoms xyzr file name
#XYZR_FileName = barstar.xyzr
#XYZR_FileName = 1crn.xyzr
#XYZR_FileName = ArgArg.xyzr
# if you enable fullerene (or a small molecule) use Grid_perfil = 70.0 or lower
#XYZR_FileName = fullerene.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 = 1
# 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 = 800
###############################################################################
\ No newline at end of file
tests/1VSZ_protonated_EDT_skin/output/triangleAreas.txt deleted 100644 → 0
View file @ 69aee126
This diff is collapsed.
tests/1VSZ_protonated_EDT_skin_norm/1VSZ_protonated_EDT_skin_norm_conf.prm → tests/1crn_ses/1crn_ses_conf.prm
View file @ 42af2a3f
......@@ -17,21 +17,16 @@ Example_Surface_Parameter = 2.0
################################ Grid params ##################################
# Grid scale
Grid_scale = 1.0
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
#XYZR_FileName = sphere.xyzr
XYZR_FileName = 1VSZ_protonated_EDT.xyzr
# Input atoms xyzr file name
#XYZR_FileName = barstar.xyzr
#XYZR_FileName = 1crn.xyzr
#XYZR_FileName = ArgArg.xyzr
# if you enable fullerene (or a small molecule) use Grid_perfil = 70.0 or lower
#XYZR_FileName = fullerene.xyzr
XYZR_FileName = 1crn.xyzr
############################## Internal maps ##################################
# Enable/Disable build of epsilon (dielectric) map
......@@ -44,12 +39,14 @@ Build_status_map = true
########################## Surface Type params ################################
# Possible values: skin,blobby,mesh,ses,example
Surface = skin
Skip_Mem_CleanUp = false
Surface = ses
# 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]
......@@ -145,6 +142,6 @@ 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 = 800
Max_skin_patches_per_auxiliary_grid_2d_cell = 600
###############################################################################
tests/1crn_skin/1crn.xyzr 0 → 100644
View file @ 42af2a3f
17.047 14.099 3.625 1.70
16.967 12.784 4.338 2.00
15.685 12.755 5.133 1.74
15.268 13.825 5.594 1.40
18.170 12.703 5.337 2.00
19.334 12.829 4.463 1.60
18.150 11.546 6.304 2.00
15.115 11.555 5.265 1.70
13.856 11.469 6.066 2.00
14.164 10.785 7.379 1.74
14.993 9.862 7.443 1.40
12.732 10.711 5.261 2.00
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12.484 11.442 3.895 2.00
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13.660 10.707 9.787 2.00
12.269 10.431 10.323 1.74
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14.368 11.748 10.691 2.00
15.885 12.426 10.016 1.80
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11.659 8.296 13.491 1.40
10.057 7.752 10.682 2.00
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9.561 9.108 13.563 1.70
9.448 9.034 15.012 2.00
9.288 7.670 15.606 1.74
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8.875 6.686 14.796 1.70
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8.881 3.075 14.358 1.70
8.912 2.083 13.258 2.00
7.581 2.090 12.506 1.74
7.670 2.031 11.245 1.40
9.207 .677 13.924 2.00
10.714 .702 14.312 2.00
8.811 -.477 12.969 2.00
11.185 -.516 15.142 2.00
6.458 2.162 13.159 1.70
5.145 2.209 12.453 2.00
5.115 3.379 11.461 1.74
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2.716 2.891 12.869 2.00
3.758 1.032 14.208 2.00
5.606 4.546 11.941 1.70
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6.022 6.977 11.891 2.00
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10.752 3.607 8.149 2.00
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7.186 2.582 8.445 1.70
6.500 1.584 7.565 2.00
5.382 2.313 6.773 1.74
5.213 2.016 5.557 1.40
5.908 .462 8.400 2.00
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4.648 3.182 7.446 1.70
3.545 3.935 6.751 2.00
4.107 4.851 5.691 1.74
3.536 5.001 4.617 1.40
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6.900 4.390 3.989 1.70
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6.240 3.144 .684 1.40
8.145 2.404 3.240 2.00
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10.013 3.895 3.323 1.40
10.120 1.956 4.539 1.80
4.993 2.927 2.571 1.70
3.782 2.599 1.742 2.00
3.296 3.871 1.004 1.74
2.947 3.817 -.189 1.40
2.698 1.953 2.608 2.00
1.384 1.826 1.806 2.00
3.174 .533 3.005 2.00
3.321 4.987 1.720 1.70
2.890 6.285 1.126 2.00
3.687 6.597 -.111 1.74
3.200 7.147 -1.103 1.40
3.039 7.369 2.240 2.00
2.559 9.014 1.649 1.80
4.997 6.227 -.100 1.70
5.895 6.489 -1.213 2.00
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6.228 5.901 -3.507 1.40
7.370 6.507 -.731 2.00
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4.196 2.184 -2.863 2.00
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3.907 .097 -1.634 2.00
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2.792 5.376 -5.797 2.00
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20.138 15.023 5.878 1.40
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