def test_07SurfaceAreaCalculations():
print("____________________________")
print("test_07SurfaceAreaCalculations")
print("____________________________")
from mslib import MSMS, msms
m = MSMS(filename='Data/1crn.xyzrn')
m.compute()
m.compute_ses_area()
print(m.sesr.fst.a_reent_area)
print(m.sesr.fst.a_toric_area)
print(m.sesr.fst.a_contact_area)
print(m.sesr.fst.a_ses_area)
print(m.sesr.fst.a_sas_area)
#m.write_ses_area(filename='testAllComp.area', component=None)
#m.write_ses_area(filename='testAllComp.area', component=0)
m.compute_numeric_area_vol()
m.compute_numeric_area_vol(component=0)
m.compute_numeric_area_vol(component=0, mode=msms.MS_NUMERICAL)
print(m.sesr.fst.n_ses_volume)
m.compute_numeric_area_vol(component=0, mode=msms.MS_SEMI_ANALYTICAL)
print(m.sesr.fst.n_ses_volume)
print(m.sesr.fst.n_sas_volume)
print(m.sesr.fst.n_ses_area)
print(m.sesr.fst.n_sas_area)
print(m.detailed_info())
print(m.info())
vfloat, vint, tri = m.getTriangles()
print("triangles", len(vfloat), len(vint), len(tri))
def test_07SurfaceAreaCalculations() :
print("____________________________")
print("test_07SurfaceAreaCalculations")
print("____________________________")
from mslib import MSMS, msms
m = MSMS(filename='Data/1crn.xyzrn')
m.compute()
m.compute_ses_area()
print(m.sesr.fst.a_reent_area)
print(m.sesr.fst.a_toric_area)
print(m.sesr.fst.a_contact_area)
print(m.sesr.fst.a_ses_area)
print(m.sesr.fst.a_sas_area)
#m.write_ses_area(filename='testAllComp.area', component=None)
#m.write_ses_area(filename='testAllComp.area', component=0)
m.compute_numeric_area_vol()
m.compute_numeric_area_vol(component=0)
m.compute_numeric_area_vol(component=0, mode=msms.MS_NUMERICAL)
print(m.sesr.fst.n_ses_volume)
m.compute_numeric_area_vol(component=0, mode=msms.MS_SEMI_ANALYTICAL)
print(m.sesr.fst.n_ses_volume)
print(m.sesr.fst.n_sas_volume)
print(m.sesr.fst.n_ses_area)
print(m.sesr.fst.n_sas_area)
print(m.detailed_info())
print(m.info())
vfloat, vint, tri = m.getTriangles()
print("triangles", len(vfloat), len(vint), len(tri))
def test_08BuriedSurfaceCalculations():
print("______________________________")
print("test_08BuriedSurfaceCalculations")
print("______________________________")
from mslib import MSMS, readxyzr, msms
output1 = readxyzr('Data/1tpa_e.xyzr')
coords_e = output1[0]
names = output1[1]
#coords_e, names = readxyzr('Data/1tpa_e.xyzr')
output2 = readxyzr('Data/1tpa_i.xyzr')
coords_i = output2[0]
names = output2[1]
#coords_i, names = readxyzr('Data/1tpa_i.xyzr')
coords = coords_e[:, :3]
rad = coords_e[:, 3]
m = MSMS(coords=coords, radii=rad)
m.compute()
m.buriedVertices(coords_i)
vfloat, vint, tri = m.getTriangles()
indBuried = Numeric.nonzero(vint[:, 2])
print(len(indBuried), " vertices buried")
m.resetBuriedVertexArea()
m.compute_numeric_area_vol(component=0, mode=msms.MS_SEMI_ANALYTICAL)
print(m.sesr.fst.n_ses_volume)
print(m.sesr.fst.n_ses_area)
m.buriedSurfaceArea()
print(m.sesr.fst.n_buried_ses_area)
print(m.sesr.fst.n_buried_sas_area)
vfloat, vint, tri = m.getBuriedSurfaceTriangles(selnum=1)
print(
"getBuriedSurfaceTriangles(selnum=1): len(vfloat): %d, len(vint): %d, len(tri): %d"
% (len(vfloat), len(vint), len(tri)))
vfloat, vint, tri = m.getBuriedSurfaceTriangles(selnum=2)
print(
"getBuriedSurfaceTriangles(selnum=2): len(vfloat): %d, len(vint): %d, len(tri): %d"
% (len(vfloat), len(vint), len(tri)))
vfloat, vint, tri = m.getBuriedSurfaceTriangles(selnum=3)
print(
"getBuriedSurfaceTriangles(selnum=3): len(vfloat): %d, len(vint): %d, len(tri): %d"
% (len(vfloat), len(vint), len(tri)))
def test_08BuriedSurfaceCalculations():
print("______________________________")
print("test_08BuriedSurfaceCalculations")
print("______________________________")
from mslib import MSMS, readxyzr, msms
output1 = readxyzr('Data/1tpa_e.xyzr')
coords_e=output1[0]
names = output1[1]
#coords_e, names = readxyzr('Data/1tpa_e.xyzr')
output2 = readxyzr('Data/1tpa_i.xyzr')
coords_i=output2[0]
names = output2[1]
#coords_i, names = readxyzr('Data/1tpa_i.xyzr')
coords = coords_e[:,:3]
rad = coords_e[:,3]
m = MSMS(coords=coords, radii = rad)
m.compute()
m.buriedVertices(coords_i)
vfloat, vint, tri = m.getTriangles()
indBuried = Numeric.nonzero(vint[:,2])
print(len(indBuried)," vertices buried")
m.resetBuriedVertexArea()
m.compute_numeric_area_vol(component=0, mode=msms.MS_SEMI_ANALYTICAL)
print(m.sesr.fst.n_ses_volume)
print(m.sesr.fst.n_ses_area)
m.buriedSurfaceArea()
print(m.sesr.fst.n_buried_ses_area)
print(m.sesr.fst.n_buried_sas_area)
vfloat, vint, tri = m.getBuriedSurfaceTriangles(selnum=1)
print("getBuriedSurfaceTriangles(selnum=1): len(vfloat): %d, len(vint): %d, len(tri): %d" % (len(vfloat), len(vint), len(tri)))
vfloat, vint, tri = m.getBuriedSurfaceTriangles(selnum=2)
print("getBuriedSurfaceTriangles(selnum=2): len(vfloat): %d, len(vint): %d, len(tri): %d" % (len(vfloat), len(vint), len(tri)))
vfloat, vint, tri = m.getBuriedSurfaceTriangles(selnum=3)
print("getBuriedSurfaceTriangles(selnum=3): len(vfloat): %d, len(vint): %d, len(tri): %d" % (len(vfloat), len(vint), len(tri)))
