def create_esp_surfaces(Molecule):
Rads = [VdW99[i] for i in Molecule.elem]
#xyz = Molecule.xyzs[0]
na = Molecule.na
printxyz=True
np.set_printoptions(precision=10, linewidth=120)
# Pass 1: This will determine the number of ESP points.
num_esp = []
for i, xyz in enumerate(Molecule.xyzs):
print("Generating grid points for snapshot %i\r" % i)
num_esp_shell = []
for j in [1.4, 1.6, 1.8, 2.0]:
Radii = list(np.array(Rads)*j)
vfloat = drive_msms(xyz, Radii, 20.0/j)
if len(vfloat) < na:
warn_press_key("I generated less ESP points than atoms!")
num_esp_shell.append(len(vfloat))
num_esp.append(num_esp_shell)
num_esp = np.array(num_esp)
num_pts = np.amin(num_esp,axis=0) / 100
print("Number of points: ", num_pts)
input()
# We do not store.
# Pass 2: This will actually print out the ESP grids.
Mol_ESP = []
for i, xyz in enumerate(Molecule.xyzs):
esp_pts = []
for sh, j in enumerate([1.4, 1.6, 1.8, 2.0]):
Radii = list(np.array(Rads)*j)
vfloat = drive_msms(xyz, Radii, 20.0/j)
# print "Calling MSMS"
# MS = MSMS(coords = list(xyz), radii = Radii)
# print "Computing"
# MS.compute(density=20.0/j)
# print "Getting triangles"
# vfloat, vint, tri = MS.getTriangles()
# #vfloat = vfloat_shell[sh]
a = list(range(len(vfloat)))
random.shuffle(a)
# We'll be careful and generate lots of ESP points, mm.
# But we can't have a different number of points per snapshots, mm.
for idx in a[:num_pts[sh]]:
esp_pts.append(vfloat[idx][:3])
if printxyz:
Out = []
Out.append("%i" % (len(xyz) + len(esp_pts)))
Out.append("Molecule plus ESP points (heliums)")
for j, x in enumerate(xyz):
Out.append(format_xyz_coord(Molecule.elem[j], x))
for esp_pt in esp_pts:
Out.append(format_xyz_coord('He',esp_pt))
fout = open('molecule_esp.xyz','w' if i == 0 else 'a')
for line in Out:
print(line, file=fout)
fout.close()
Mol_ESP.append(esp_pts)
return Mol_ESP
def create_esp_surfaces(Molecule):
from forcebalance.mslib import MSMS
Rads = [VdW99[i] for i in Molecule.elem]
#xyz = Molecule.xyzs[0]
na = Molecule.na
Mol_ESP = []
printxyz=0
for i, xyz in enumerate(Molecule.xyzs):
print "Generating grid points for snapshot %i\r" % i
esp_pts = []
for j in [1.4, 1.6, 1.8, 2.0]:
MS = MSMS(coords = list(xyz), radii = list(np.array(Rads)*j))
MS.compute(density=0.5)
vfloat, vint, tri = MS.getTriangles()
a = range(len(vfloat))
random.shuffle(a)
if len(vfloat) < na:
warn_press_key("I generated less ESP points than atoms!")
for idx in a[:na]:
esp_pts.append(vfloat[idx][:3])
if printxyz:
Out = []
Out.append("%i" % (len(xyz) + len(esp_pts)))
Out.append("Molecule plus ESP points")
for j, x in enumerate(xyz):
Out.append(format_xyz_coord(Molecule.elem[j], x))
for esp_pt in esp_pts:
Out.append(format_xyz_coord('chg',esp_pt))
fout = open('Mao.xyz','w')
for line in Out:
print >> fout, line
fout.close()
sys.exit(1)
Mol_ESP.append(esp_pts)
return Mol_ESP
