def computeMSMSvolume(atmCoords, atmRadii, pRadius, dens ):
srf = MSMS(coords=atmCoords, radii=atmRadii)
srf.compute(probe_radius=pRadius, density=dens)
vf, vi, f = srf.getTriangles()
vertices=vf[:,:3]
normals=vf[:,3:6]
triangles=f[:,:3]
return meshVolume(vertices, normals, triangles)
def computeMSMSvolume(atmCoords, atmRadii, pRadius, dens):
srf = MSMS(coords=atmCoords, radii=atmRadii)
srf.compute(probe_radius=pRadius, density=dens)
vf, vi, f = srf.getTriangles()
vertices = vf[:, :3]
normals = vf[:, 3:6]
triangles = f[:, :3]
return meshVolume(vertices, normals, triangles)
def test_03SurfaceFromFile():
print("___________________")
print("test_03SurfacefroFile")
print("___________________")
from mslib import MSMS
#print "current dir:", os.getcwd()
m = MSMS(filename='Data/1crn.xyzrn')
#!/usr/bin/env python
from mslib import MSMS
from forcebalance.nifty import lp_load, lp_dump
import numpy as np
import os
# Designed to be called from GenerateQMData.py
# I wrote this because MSMS seems to have a memory leak
xyz, radii, density = lp_load(open('msms_input.p'))
MS = MSMS(coords = list(xyz), radii = radii)
MS.compute(density=density)
vfloat, vint, tri = MS.getTriangles()
with open(os.path.join('msms_output.p'), 'w') as f: lp_dump(vfloat, f)
def test_04RScalculations():
print("___________________")
print("test_04RScalculations")
print("___________________")
from mslib import MSMS, readxyzr, msms
# compute all components with default probe radius 1.5
global coords, rad
m1 = MSMS(coords=coords, radii=rad)
m1.compute_rs()
ar = m1.rsr.fst.far0
print("printing -n, -ct...")
print(ar._n())
print(ar._ct())
print(ar._cp())
print(ar._cc())
print(ar._rcc())
print(ar._ps())
print(ar._s())
# recompute reduced surface with probe sphere radius = 2.0
m1.compute_rs(probe_radius=2.0)
# Multiple components
output = readxyzr('Data/1crn.xyzr')
new_coords = output[0]
names = output[1]
#new_coords, names = readxyzr('Data/1crn.xyzr')
coords = new_coords[:, :3]
rad = new_coords[:, 3]
m2 = MSMS(coords=coords, radii=rad)
# "***** COMPUTE EXTERNAL COMPONENT"
m2.compute_rs()
print("Info1:")
print(m2.info())
# " ADD OTHER COMPONENTS"
m2.compute_rs(allComponents=1)
print("Info2:")
print(m2.info())
# " CLEAR RSR"
# " COMPUTE ONE CAVITY"
msms.MS_reset_RSR(m2.this)
m2.compute_rs(atoms=(11, -1, -1))
print("Info3:")
print(m2.info())
msms.MS_reset_RSR(m2.this)
m2.compute_rs(atoms=(13, -1, -1))
print("Info4:")
print(m2.info())
msms.MS_reset_RSR(m2.this)
m2.compute_rs(atoms=(93, -1, -1))
print("Info5:")
print(m2.info())
msms.MS_reset_RSR(m2.this)
m2.compute_rs(atoms=(11, 13, -1))
print("Info6:")
print(m2.info())
msms.MS_reset_RSR(m2.this)
m2.compute_rs(atoms=(13, 11, -1))
print("Info7:")
print(m2.info())
msms.MS_reset_RSR(m2.this)
m2.compute_rs(atoms=(13, 93, -1))
print("Info8:")
print(m2.info())
msms.MS_reset_RSR(m2.this)
m2.compute_rs(atoms=(13, 93, 11))
print("Info9:")
print(m2.info())
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_02SurfaceCoordsRadii():
print("___________________")
print("test_02SurfaceCoordsRadii")
print("___________________")
from mslib import MSMS
m = MSMS(coords=coords, radii=rad)
def test_06Triangulation():
print("___________________")
print("test_06Triangulation")
print("___________________")
from mslib import MSMS, msms
# triangulate with default parameters, component = 0
m = MSMS(coords=coords, radii=rad)
m.compute_rs(allComponents=1)
m.compute_ses(0)
m.compute_ses(1)
print("trinagulate 1")
m.triangulate(component=0)
print(m.info())
# triangulate with default parameters, component = 1
print("trinagulate 2")
m.triangulate(component=1)
print(m.info())
# re-triangulate at density = 3.0
print("trinagulate 3")
m.triangulate(component=0, density=3.0)
print(m.info())
# triangulate all components
print("trinagulate 4")
m.triangulate(density=1.1)
# write triangulation
#m.write_triangulation('testAll')
#m.write_triangulation('testAllnoh', no_header=1)
#m.write_triangulation('testASES', component=1, format=msms.MS_ASES_ASCII)
#m.write_triangulation('testTAVS', component=0, format=msms.MS_TSES_ASCII_AVS)
#m.write_triangulation('testAAVS', component=0, format=msms.MS_ASES_ASCII_AVS)
vfloat, vint, tri = m.getTriangles()
print("getTriangles(): len(vfloat): %d, len(vint): %d, len(tri): %d" %
(len(vfloat), len(vint), len(tri)))
atomindices = [
131, 120, 143, 147, 128, 146, 142, 137, 139, 130, 135, 136, 134, 129,
145, 119, 133, 132, 141, 144, 138, 140
]
vfloat, vint, tri = m.getTriangles(atomIndices=atomindices)
print(
"getTriangles(atomIndices=atomindices): len(vfloat): %d, len(vint): %d, len(tri): %d"
% (len(vfloat), len(vint), len(tri)))
# reset all after triangulation
msms.MS_reset_RSR(m.this)
print(m.info())
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_04RScalculations():
print("___________________")
print("test_04RScalculations")
print("___________________")
from mslib import MSMS, readxyzr, msms
# compute all components with default probe radius 1.5
global coords, rad
m1 = MSMS(coords=coords, radii=rad)
m1.compute_rs()
ar = m1.rsr.fst.far0
print("printing -n, -ct...")
print(ar._n())
print(ar._ct())
print(ar._cp())
print(ar._cc())
print(ar._rcc())
print(ar._ps())
print(ar._s())
# recompute reduced surface with probe sphere radius = 2.0
m1.compute_rs(probe_radius=2.0)
# Multiple components
output = readxyzr('Data/1crn.xyzr')
new_coords = output[0]
names = output[1]
#new_coords, names = readxyzr('Data/1crn.xyzr')
coords = new_coords[:,:3]
rad = new_coords[:,3]
m2 = MSMS(coords=coords, radii = rad)
# "***** COMPUTE EXTERNAL COMPONENT"
m2.compute_rs()
print("Info1:")
print(m2.info())
# " ADD OTHER COMPONENTS"
m2.compute_rs( allComponents=1 )
print("Info2:")
print(m2.info())
# " CLEAR RSR"
# " COMPUTE ONE CAVITY"
msms.MS_reset_RSR(m2.this)
m2.compute_rs( atoms = (11, -1, -1) )
print("Info3:")
print(m2.info())
msms.MS_reset_RSR(m2.this)
m2.compute_rs( atoms = (13, -1, -1) )
print("Info4:")
print(m2.info())
msms.MS_reset_RSR(m2.this)
m2.compute_rs( atoms = (93, -1, -1) )
print("Info5:")
print(m2.info())
msms.MS_reset_RSR(m2.this)
m2.compute_rs( atoms = (11, 13, -1) )
print("Info6:")
print(m2.info())
msms.MS_reset_RSR(m2.this)
m2.compute_rs( atoms = (13, 11, -1) )
print("Info7:")
print(m2.info())
msms.MS_reset_RSR(m2.this)
m2.compute_rs( atoms = (13, 93, -1) )
print("Info8:")
print(m2.info())
msms.MS_reset_RSR(m2.this)
m2.compute_rs( atoms = (13, 93, 11) )
print("Info9:")
print(m2.info())
def test_05SEScalculations():
print("___________________")
print("test_05SEScalculations")
print("___________________")
from mslib import MSMS, msms
m = MSMS(coords=coords, radii=rad)
m.compute_rs(allComponents=1)
m.compute_ses()
print(m.info())
msms.MS_reset_RSR(m.this)
m.compute_rs(allComponents=1)
m.compute_ses(0)
m.compute_ses(1)
print(m.info())
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_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_06Triangulation():
print("___________________")
print("test_06Triangulation")
print("___________________")
from mslib import MSMS, msms
# triangulate with default parameters, component = 0
m = MSMS(coords=coords, radii = rad)
m.compute_rs(allComponents=1)
m.compute_ses(0 )
m.compute_ses(1)
print("trinagulate 1")
m.triangulate( component=0 )
print(m.info())
# triangulate with default parameters, component = 1
print("trinagulate 2")
m.triangulate( component=1 )
print(m.info())
# re-triangulate at density = 3.0
print("trinagulate 3")
m.triangulate( component=0, density=3.0 )
print(m.info())
# triangulate all components
print("trinagulate 4")
m.triangulate( density=1.1 )
# write triangulation
#m.write_triangulation('testAll')
#m.write_triangulation('testAllnoh', no_header=1)
#m.write_triangulation('testASES', component=1, format=msms.MS_ASES_ASCII)
#m.write_triangulation('testTAVS', component=0, format=msms.MS_TSES_ASCII_AVS)
#m.write_triangulation('testAAVS', component=0, format=msms.MS_ASES_ASCII_AVS)
vfloat, vint, tri = m.getTriangles()
print("getTriangles(): len(vfloat): %d, len(vint): %d, len(tri): %d" % (len(vfloat), len(vint), len(tri)))
atomindices = [131, 120, 143, 147, 128, 146, 142, 137, 139, 130, 135,
136, 134, 129, 145, 119, 133, 132, 141, 144, 138, 140]
vfloat, vint, tri = m.getTriangles(atomIndices=atomindices)
print("getTriangles(atomIndices=atomindices): len(vfloat): %d, len(vint): %d, len(tri): %d" % (len(vfloat), len(vint), len(tri)))
# reset all after triangulation
msms.MS_reset_RSR(m.this)
print(m.info())
def test_05SEScalculations():
print("___________________")
print("test_05SEScalculations")
print("___________________")
from mslib import MSMS, msms
m = MSMS(coords=coords, radii = rad)
m.compute_rs( allComponents=1 )
m.compute_ses()
print(m.info())
msms.MS_reset_RSR(m.this)
m.compute_rs( allComponents=1 )
m.compute_ses( 0 )
m.compute_ses( 1 )
print(m.info())
#if not os.path.exists(protsys+'_l_b.pqr'):
#raise ValueError, "File " + protsys+'_l_b.pqr not found'
#ligand = protsys+'_l_b.pqr'
# read molecule
from MolKit import Read
mols = Read(receptor)
# get coords and radii
coords = mols.allAtoms.coords
rads = mols.allAtoms.radius
print "Computing MSMS"
# compute MSMS
from mslib import MSMS
msms = MSMS(coords=coords, radii=rads)
stat = msms.compute(density=6.0)
print "error is: ", stat
print "Getting triangles"
# retrieve triangles
vf, vi, tri = msms.getTriangles()
print "Decimating mesh"
# decimate the mesh
verts = vf[:, :3]
faces = tri[:, :3]
normals = vf[:, 3:6]
# I think 2*nbAtoms triangles corresponds to nbAtoms vertices
targetTri = 2 * len(mols.allAtoms)