|
|
run_msms
|
run_msms (
xyzr,
probe_radius=None,
vertex_density=None,
all_components=None,
)
|
Exceptions
|
|
|
Surface_Calculation_Error, 'MSMS surface calculation failed, code %d' % status
Surface_Calculation_Error, 'No msms executable found'
|
|
|
|
read_msms_component_output
|
read_msms_component_output ( prefix, component )
|
|
|
read_binary_array
|
read_binary_array (
f,
d2,
type,
)
|
|
|
triangle_data
|
triangle_data ( srf )
|
|
|
write_binary_array
|
write_binary_array ( a, f )
|
|
|
read_msms_output
|
read_msms_output ( prefix, area_path )
|
|
|
doubles_from_pointer
|
doubles_from_pointer ( swig_double_p, n )
|
|
|
msms_geometry
|
msms_geometry (
atoms,
probe_radius=None,
vertex_density=None,
all_components=None,
separate_process=None,
)
|
|
|
run_mscalc
|
run_mscalc (
xyzr,
probe_radius=None,
vertex_density=None,
all_components=None,
fallback_to_single_component=None,
)
|
Exceptions
|
|
|
Surface_Calculation_Error, 'No mscalc executable found'
Surface_Calculation_Error, 'Starting mscalc failed.'
Surface_Calculation_Error, 'Surface calculation failed, mscalc returned code %d' % status
|
|
|
|
empty_surface
|
empty_surface ()
|
|
|
combine_triangle_data
|
combine_triangle_data ( tdata )
Combine triangulation data from all surface components.
vfloat elements (x,y,z,nx,ny,nz,sesA,sasA)
vint elements (type, closestAtomindex, buried)
tri elements (i, j, k, type, SESF_num)
|
|
|
parse_mscalc_output
|
parse_mscalc_output ( msouts )
|
|
|
run_shell_command
|
run_shell_command ( args, input )
|
|
|
read_atom_areas
|
read_atom_areas ( area_path )
|
|
|
xyzr_surface_geometry
|
xyzr_surface_geometry (
xyzr,
probe_radius=None,
vertex_density=None,
all_components=None,
separate_process=None,
)
|
|
|
atom_areas
|
atom_areas ( srf )
Get analytic per atom areas summed over all surface components and also
total areas for each surface component.
MSMS library doesn't wrap array of per-atom SES/SAS areas, just gives
C pointer so there is some ugly use of ctypes.
|
|
|
remove_msms_output
|
remove_msms_output ( prefix, area_path )
|
|