def _cgoArrowhead(viewer,
tail,
head,
radius,
color,
label,
headFrac=0.3,
nSteps=10,
aspect=.5):
global _globalArrowCGO
delta = head - tail
normal = _getVectNormal(delta)
delta.Normalize()
dv = head - tail
dv.Normalize()
dv *= headFrac
startP = head
normal *= headFrac * aspect
cgo = [
BEGIN, TRIANGLE_FAN, COLOR, color[0], color[1], color[2], NORMAL, dv.x,
dv.y, dv.z, VERTEX, head.x + dv.x, head.y + dv.y, head.z + dv.z
]
base = [
BEGIN, TRIANGLE_FAN, COLOR, color[0], color[1], color[2], NORMAL,
-dv.x, -dv.y, -dv.z, VERTEX, head.x, head.y, head.z
]
v = startP + normal
cgo.extend([NORMAL, normal.x, normal.y, normal.z])
cgo.extend([VERTEX, v.x, v.y, v.z])
base.extend([VERTEX, v.x, v.y, v.z])
for i in range(1, nSteps):
v = FeatDirUtils.ArbAxisRotation(360. / nSteps * i, delta, normal)
cgo.extend([NORMAL, v.x, v.y, v.z])
v += startP
cgo.extend([VERTEX, v.x, v.y, v.z])
base.extend([VERTEX, v.x, v.y, v.z])
cgo.extend([NORMAL, normal.x, normal.y, normal.z])
cgo.extend([
VERTEX, startP.x + normal.x, startP.y + normal.y, startP.z + normal.z
])
base.extend([
VERTEX, startP.x + normal.x, startP.y + normal.y, startP.z + normal.z
])
cgo.append(END)
base.append(END)
cgo.extend(base)
#viewer.server.renderCGO(cgo,label)
_globalArrowCGO.extend(cgo)
def ShowMolFeats(mol,
factory,
viewer,
radius=0.5,
confId=-1,
showOnly=True,
name='',
transparency=0.0,
colors=None,
excludeTypes=[],
useFeatDirs=True,
featLabel=None,
dirLabel=None,
includeArrowheads=True,
writeFeats=False,
showMol=True,
featMapFile=False):
global _globalSphereCGO
if not name:
if mol.HasProp('_Name'):
name = mol.GetProp('_Name')
else:
name = 'molecule'
if not colors:
colors = _featColors
if showMol:
viewer.ShowMol(mol, name=name, showOnly=showOnly, confId=confId)
molFeats = factory.GetFeaturesForMol(mol)
if not featLabel:
featLabel = f'{name}-feats'
viewer.server.resetCGO(featLabel)
if not dirLabel:
dirLabel = featLabel + "-dirs"
viewer.server.resetCGO(dirLabel)
for feat in molFeats:
family = feat.GetFamily()
if family in excludeTypes:
continue
pos = feat.GetPos(confId)
color = colors.get(family, (.5, .5, .5))
if transparency:
_globalSphereCGO.extend([ALPHA, 1 - transparency])
else:
_globalSphereCGO.extend([ALPHA, 1])
_globalSphereCGO.extend([
COLOR, color[0], color[1], color[2], SPHERE, pos.x, pos.y, pos.z,
radius
])
if writeFeats:
aidText = ' '.join([str(x + 1) for x in feat.GetAtomIds()])
print(
f'{family}\t{pos.x:.3f}\t{pos.y:.3f}\t{pos.z:.3f}\t1.0\t# {aidText}'
)
if featMapFile:
print(
f" family={family} pos=({pos.x:.3f}, {pos.y:.3f}, {pos.z:.3f}) weight=1.0",
end='',
file=featMapFile)
if useFeatDirs:
ps = []
if family == 'Aromatic':
ps, _ = FeatDirUtils.GetAromaticFeatVects(
mol.GetConformer(confId),
feat.GetAtomIds(),
pos,
scale=1.0)
elif family == 'Donor':
aids = feat.GetAtomIds()
if len(aids) == 1:
FeatVectsDictMethod = {
1: FeatDirUtils.GetDonor1FeatVects,
2: FeatDirUtils.GetDonor2FeatVects,
3: FeatDirUtils.GetDonor3FeatVects,
}
featAtom = mol.GetAtomWithIdx(aids[0])
numHvyNbrs = len([
1 for x in featAtom.GetNeighbors()
if x.GetAtomicNum() > 1
])
ps, _ = FeatVectsDictMethod[numHvyNbrs](
mol.GetConformer(confId), aids, scale=1.0)
elif family == 'Acceptor':
aids = feat.GetAtomIds()
if len(aids) == 1:
FeatVectsDictMethod = {
1: FeatDirUtils.GetDonor1FeatVects,
2: FeatDirUtils.GetDonor2FeatVects,
3: FeatDirUtils.GetDonor3FeatVects,
}
featAtom = mol.GetAtomWithIdx(aids[0])
numHvyNbrs = len([
x for x in featAtom.GetNeighbors()
if x.GetAtomicNum() > 1
])
ps, _ = FeatVectsDictMethod[numHvyNbrs](
mol.GetConformer(confId), aids, scale=1.0)
for tail, head in ps:
ShowArrow(viewer,
tail,
head,
radius,
color,
dirLabel,
transparency=transparency,
includeArrowhead=includeArrowheads)
if featMapFile:
vect = head - tail
print(f'dir=({vect.x:.3f}, {vect.y:.3f}, {vect.z:.3f})',
end='',
file=featMapFile)
if featMapFile:
aidText = ' '.join([str(x + 1) for x in feat.GetAtomIds()])
print(f'# {aidText}', file=featMapFile)
def ShowMolFeats(mol,
factory,
viewer,
radius=0.5,
confId=-1,
showOnly=True,
name='',
transparency=0.0,
colors=None,
excludeTypes=[],
useFeatDirs=True,
featLabel=None,
dirLabel=None,
includeArrowheads=True,
writeFeats=False,
showMol=True,
featMapFile=False):
global _globalSphereCGO
if not name:
if mol.HasProp('_Name'):
name = mol.GetProp('_Name')
else:
name = 'molecule'
if not colors:
colors = _featColors
if showMol:
viewer.ShowMol(mol, name=name, showOnly=showOnly, confId=confId)
molFeats = factory.GetFeaturesForMol(mol)
if not featLabel:
featLabel = '%s-feats' % name
viewer.server.resetCGO(featLabel)
if not dirLabel:
dirLabel = featLabel + "-dirs"
viewer.server.resetCGO(dirLabel)
for i, feat in enumerate(molFeats):
family = feat.GetFamily()
if family in excludeTypes:
continue
pos = feat.GetPos(confId)
color = colors.get(family, (.5, .5, .5))
nm = '%s(%d)' % (family, i + 1)
if transparency:
_globalSphereCGO.extend([ALPHA, 1 - transparency])
else:
_globalSphereCGO.extend([ALPHA, 1])
_globalSphereCGO.extend([
COLOR, color[0], color[1], color[2], SPHERE, pos.x, pos.y, pos.z,
radius
])
if writeFeats:
aidText = ' '.join([str(x + 1) for x in feat.GetAtomIds()])
print('%s\t%.3f\t%.3f\t%.3f\t1.0\t# %s' %
(family, pos.x, pos.y, pos.z, aidText))
if featMapFile:
print(" family=%s pos=(%.3f,%.3f,%.3f) weight=1.0" %
(family, pos.x, pos.y, pos.z),
end='',
file=featMapFile)
if useFeatDirs:
ps = []
if family == 'Aromatic':
ps, fType = FeatDirUtils.GetAromaticFeatVects(
mol.GetConformer(confId),
feat.GetAtomIds(),
pos,
scale=1.0)
elif family == 'Donor':
aids = feat.GetAtomIds()
if len(aids) == 1:
featAtom = mol.GetAtomWithIdx(aids[0])
hvyNbrs = [
x for x in featAtom.GetNeighbors()
if x.GetAtomicNum() != 1
]
if len(hvyNbrs) == 1:
ps, fType = FeatDirUtils.GetDonor1FeatVects(
mol.GetConformer(confId), aids, scale=1.0)
elif len(hvyNbrs) == 2:
ps, fType = FeatDirUtils.GetDonor2FeatVects(
mol.GetConformer(confId), aids, scale=1.0)
elif len(hvyNbrs) == 3:
ps, fType = FeatDirUtils.GetDonor3FeatVects(
mol.GetConformer(confId), aids, scale=1.0)
elif family == 'Acceptor':
aids = feat.GetAtomIds()
if len(aids) == 1:
featAtom = mol.GetAtomWithIdx(aids[0])
hvyNbrs = [
x for x in featAtom.GetNeighbors()
if x.GetAtomicNum() != 1
]
if len(hvyNbrs) == 1:
ps, fType = FeatDirUtils.GetAcceptor1FeatVects(
mol.GetConformer(confId), aids, scale=1.0)
elif len(hvyNbrs) == 2:
ps, fType = FeatDirUtils.GetAcceptor2FeatVects(
mol.GetConformer(confId), aids, scale=1.0)
elif len(hvyNbrs) == 3:
ps, fType = FeatDirUtils.GetAcceptor3FeatVects(
mol.GetConformer(confId), aids, scale=1.0)
for tail, head in ps:
ShowArrow(viewer,
tail,
head,
radius,
color,
dirLabel,
transparency=transparency,
includeArrowhead=includeArrowheads)
if featMapFile:
vect = head - tail
print('dir=(%.3f,%.3f,%.3f)' % (vect.x, vect.y, vect.z),
end='',
file=featMapFile)
if featMapFile:
aidText = ' '.join([str(x + 1) for x in feat.GetAtomIds()])
print('# %s' % (aidText), file=featMapFile)