def SetDomainZLines(self):
# Large buffer for intersections
for f in range(100):
self.FIntersect.append(linegrids.TLineSegment())
self.FIntersectHigh = -1
# Clear grid and set to nil to distinguish lines where core was processed
self.FDomainGrid.Shape.Grid = []
for f in range(self.FDomainGrid.Block.DomainEndX + 1):
self.FDomainGrid.Shape.Grid.append([])
for g in range(self.FDomainGrid.Block.DomainEndY + 1):
self.FDomainGrid.Shape.Grid[f].append([])
# Set lines with surface contacts
self.FOverlapIxs = basetypes.FilledInts(
2 * self.FDomainGrid.Block.ProbeEndZ +
self.FDomainGrid.Block.TargetEndZ, 0)
# FOverlapIxs used with accumulator, must span all range of surface, not actual domain
for x in range(len(self.FDomainGrid.Shape.NonEmpty)):
for y in range(len(self.FDomainGrid.Shape.NonEmpty[x])):
for yy in range(self.FDomainGrid.Shape.NonEmpty[x][y][0],
self.FDomainGrid.Shape.NonEmpty[x][y][1] + 1):
self.SetZExtremes(x, yy)
# Set lines with core overlaps
if self.RemoveCores:
self.FOverlapIxs = basetypes.FilledInts(
self.FDomainGrid.Block.DomainEndZ + 1, 0)
for x in range(len(self.FCoreContacts)):
if self.FCoreContacts[x] is not None:
for y in range(len(self.FCoreContacts[x])):
for yy in range(self.FCoreContacts[x][y][0],
self.FCoreContacts[x][y][1] + 1):
if self.FDomainGrid.Shape.Grid[x][yy] is not None and \
len(self.FDomainGrid.Shape.Grid[x][yy]) != 0:
self.RemoveZCores(x, yy)
def SelectAxesByMaxmin(self, MinDist, MaxAxes):
self.FSelectedAxes = basetypes.FilledInts(1, len(self.FAxes))
# This selects the last axis as te first point. The last axis is the Z axis
rows = basetypes.FilledInts(
1, 0
) # This is just a 0...N index to avoid using the FAxialDistances matrix
distances = [self.AxisDistances(self.FSelectedAxes[0])]
for f in range(1, MaxAxes):
distances.append([])
maxd = MinDist + 1
while (maxd > MinDist) and (len(self.FSelectedAxes) < MaxAxes):
mins = self.MinDistances(distances, rows)
maxd, maxix = basetypes.MaxValIx(mins)
self.FSelectedAxes.append(maxix)
rows.append(len(self.FSelectedAxes) - 1)
distances[len(self.FSelectedAxes) - 1] = self.AxisDistances(maxix)
self.FAxialDistance = maxd
def GroupsInContact(Groups1, Groups2, Dist):
hulls1 = CalcHulls(Groups1, Dist)
hulls2 = CalcHulls(Groups2, Dist)
interfixs1 = basetypes.FilledInts(len(hulls1), 0)
interfixs2 = basetypes.FilledInts(len(hulls2), 0)
for ix1 in range(len(hulls1)):
for ix2 in range(len(hulls2)):
if (basetypes.InContact(hulls1[ix1], hulls2[ix2])) and \
(AtomsInContact(Groups1[ix1].GroupAtoms, Groups2[ix2].GroupAtoms, Dist)):
interfixs1[ix1] = 1
interfixs2[ix2] = 1
Interface1 = []
for f in range(len(interfixs1)):
if interfixs1[f] > 0:
Interface1.append(f)
Interface2 = []
for f in range(len(interfixs2)):
if interfixs2[f] > 0:
Interface2.append(f)
# In Python return TIntegers, TIntegers
return Interface1, Interface2
def PlaneConstraint(self, Point, Normal, Margin):
# Scaling factors for the shapes
tres = 1 / self.FTargetResolution
pres = 1 / self.FProbeResolution
# Plane and line variables
planepoint = geomutils.Subtract(
geomutils.Add(Point, geomutils.Multiply(self.FTargetTransVec,
tres)),
geomutils.Multiply(self.FProbeTransVec, pres))
planepoint = geomutils.Subtract(
planepoint,
basetypes.TCoord(self.FDomainBlock.XOffset,
self.FDomainBlock.YOffset,
self.FDomainBlock.ZOffset))
xflags = basetypes.FilledInts(self.FDomainBlock.DomainEndX + 1, -1)
yflags = basetypes.FilledInts(self.FDomainBlock.DomainEndY + 1, -1)
zflags = basetypes.FilledInts(self.FDomainBlock.DomainEndZ + 1, -1)
for x in range(len(self.FXDomain)):
for xx in range(self.FXDomain[x][0], self.FXDomain[x][1] + 1):
self.SetYDomain(xx, yflags, zflags, planepoint, Normal, Margin)
if self.FYDomainAtX[xx] is not None and (len(
self.FYDomainAtX[xx]) != 0):
xflags[xx] = 1
self.FXDomain = linegrids.IntegersToLine(xflags)
def ComputeShapeStats(Shape):
Shape.ZMax = 0
Shape.TotalCount = 0
for x in range(len(Shape.Grid)):
tmpline = basetypes.FilledInts(len(Shape.Grid[0]), 0)
Shape.CellCounts.append([])
for y in range(len(Shape.Grid[0])):
Shape.CellCounts[x].append([])
if Shape.Grid[x][y] is not None and len(Shape.Grid[x][y]) != 0:
tmpline[y] = 1
if Shape.ZMax < Shape.Grid[x][y][len(Shape.Grid[x][y]) - 1][1]:
Shape.ZMax = Shape.Grid[x][y][len(Shape.Grid[x][y]) - 1][1]
Shape.CellCounts[x][y] = CountCells(Shape.Grid[x][y])
Shape.TotalCount = Shape.TotalCount + Shape.CellCounts[x][y]
Shape.NonEmpty.append(IntegersToLine(tmpline, 0))
def MagicFit(Probe,
Target,
SubMat,
TargetExclusion=None,
MinSequenceMatch=0.7,
MinAlfaCarbons=20):
Result = TFitResult()
Result.Rmsd = -1
alignments = BuildAlignmentMatrix(Probe, Target, SubMat, TargetExclusion)
# Target ix for each probe chain
map = basetypes.FilledInts(Probe.GroupCount, -1)
FindBestMap(0, Result, Probe, Target, map, alignments, MinSequenceMatch,
MinAlfaCarbons)
# Return TFitResult
return Result
def Score(self):
if self.FAddModel is not None:
# Large buffer for intersections
for f in range(basetypes.Max(len(self.FIntersect) - 1, 0), 100):
self.FIntersect.append(linegrids.TLineSegment())
for f in range(len(self.FIntersect) - 1, 99, -1):
del self.FIntersect[f]
self.FIntersectHigh = -1
self.FScores = basetypes.FilledInts(
self.FDomainGrid.Block.DomainEndZ + 1, 0)
for x in range(len(self.FDomainGrid.Shape.NonEmpty)):
for y in range(len(self.FDomainGrid.Shape.NonEmpty[x])):
for yy in range(
self.FDomainGrid.Shape.NonEmpty[x][y][0],
self.FDomainGrid.Shape.NonEmpty[x][y][1] + 1):
if self.FDomainGrid.Shape.Grid[x][yy] is not None and \
len(self.FDomainGrid.Shape.Grid[x][yy]) != 0:
self.ScoreOverlap(x, yy)
def FilledIntsTest():
ia = basetypes.FilledInts(5, 2)
for f in range(len(ia)):
print(str(ia[f]))