Teague Sterling 2014
Dependencies:
- Python 2.7.x
- Numpy 1.6
- Scipy
- MSRoll
Preprocessing: msroll -m PDBID.pdb -t PDBID.vet
Execution with default parameters: python surface_mapper.py PDBID.vet PDBID.sphmap [OPTIONS]
Command Help (python surface_mapper.py --help): usage: surface_mapper.py [-h] [--voxel-resolution VOXEL_RESOLUTION] [--voxel-padding VOXEL_PADDING] [--contour-faces CONTOUR_FACES] [--contour-scale CONTOUR_SCALE] [--normalize-contour-distance NORMALIZE_CONTOUR_DISTANCE] [--timestep TIMESTEP] [--cvf-scale CVF_SCALE] [--gvf-scale GVF_SCALE] [--push-scale PUSH_SCALE] [--snap-scale SNAP_SCALE] [--internal-scale INTERNAL_SCALE] [--internal-tension INTERNAL_TENSION] [--internal-stiffness INTERNAL_STIFFNESS] [--gvf-smoothness GVF_SMOOTHNESS] [--gvf-timestep GVF_TIMESTEP] [--gvf-max-steps GVF_MAX_STEPS] [--gvf-normalize-distance GVF_NORMALIZE_DISTANCE] [--cvf-normalize-distance CVF_NORMALIZE_DISTANCE] [--convergence-threshold CONVERGENCE_THRESHOLD] [--converge-on-snapping CONVERGE_ON_SNAPPING] [--max-iterations MAX_ITERATIONS] [--visualize {convergence,mapping,none}] [--visualize-file VISUALIZE_FILE] [--visualize-every VISUALIZE_EVERY] [--show-accuracy SHOW_ACCURACY] [surface_file] [mapping_file]
positional arguments:
surface\_file Vet (MSRoll) file to map [Default: -]
mapping\_file Destination to write sphere mapping [Default: -]
optional arguments:
-h, --help show this help message and exit
--voxel-resolution VOXEL\_RESOLUTION
Resolution at which to voxelize surface (in Angstroms)
[Default: 0.75]
--voxel-padding VOXEL\_PADDING
Padding to add to voxelized image [Default: 5.0]
--contour-faces CONTOUR\_FACES
Number of faces to generate in contour [Default: >=
source mesh]
--contour-scale CONTOUR\_SCALE
Scale factor for contour [Default: 1.0]
--normalize-contour-distance NORMALIZE\_CONTOUR\_DISTANCE
Normalize contour distance to protein surface
[Default: False] (Warning: May require signifigant
padding!)
--timestep TIMESTEP Global system timestep [Default: 0.15]
--cvf-scale CVF\_SCALE
Curvature Vector Flow scale factor [Default: 0.75]
--gvf-scale GVF\_SCALE
Gradient Vector Flow scale factor [Default: 0.5]
--push-scale PUSH\_SCALE
Boundary push scale factor [Default: 1]
--snap-scale SNAP\_SCALE
Surface snapping scale factor [Default: 1]
--internal-scale INTERNAL\_SCALE
Global internal energy scale factor [Default: 1]
--internal-tension INTERNAL\_TENSION
Internal tension (elasticity) energy [Default: 0.5]
--internal-stiffness INTERNAL\_STIFFNESS
Internal stiffness (rigidity) energy [Default: 0.35]
--gvf-smoothness GVF\_SMOOTHNESS
Gradient vector flow smoothness parameter [Default:
0.1]
--gvf-timestep GVF\_TIMESTEP
Gradient vector flow generation timestep [Default:
0.15]
--gvf-max-steps GVF\_MAX\_STEPS
Gradient vector flow iterations [Default: Guessed]
--gvf-normalize-distance GVF\_NORMALIZE\_DISTANCE
Normalize GVF after Euclidian distance from surface
term [Default: 10]
--cvf-normalize-distance CVF\_NORMALIZE\_DISTANCE
Normalize CVF after Euclidian distance from surface
term [Default: 15]
--convergence-threshold CONVERGENCE\_THRESHOLD
Average movement threshold for termination [Default:
0.015]
--converge-on-snapping CONVERGE\_ON\_SNAPPING
Only consider snapping in convergence [Default: False]
--max-iterations MAX\_ITERATIONS
Maxiumum number of iterations to run before forced
termination [Default: 100]
--visualize {convergence,mapping,none}
Display visualization (Requires MayaVI) [Default:
none]
--visualize-file VISUALIZE\_FILE
Display visualization (Requires MayaVI) [Default:
none]
--visualize-every VISUALIZE\_EVERY
Interrupt iterations to visualize every N steps
[Default: None]
--show-accuracy SHOW\_ACCURACY
Compute and display mapping quality information
[Default: True]