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## Automatically adapted for numpy.oldnumeric Jul 23, 2007 by
import numpy.oldnumeric as Numeric
from bhtree import bhtreelib
#
# $Header: /opt/cvs/python/packages/share1.5/mglutil/bhtfunctions.py,v 1.9 2007/07/24 17:30:40 vareille Exp $
#
# $Id: bhtfunctions.py,v 1.9 2007/07/24 17:30:40 vareille Exp $
#
# ClosePointsDist2: result and dist are empty arrays large enough to contain
# all the points expected to be found. To be safe, they should be the same
# size as the list of coordinates. This function then puts in the results
# array the indices of the close points in the list (as supplied in the array
# ids): the dist array contains the corresponding distances.
def findNearestAtoms(mol,vertices, **kw):
"""None <- color(mol,vertices2,**kw)
mol: reference molecule
vertices: list of lists(coordinates): the first three items in each list
must be coordinates x,y,z of a point.
atomIndices is the index of the nearest atom to the vertex, such that
mol.allAtoms[atomIndices[x]] is the nearest atom to vertices[x]
vertexIndices is the list of nearest vertices to an atom, such that
vertexIndices[x] = [vertex1,vertex2,...] are the vertices associated with
mol.allAtoms[x]
"""
coords = mol.allAtoms.coords
if not hasattr(mol,'bhtree'):
print "Building bhtree for ",mol
ids = Numeric.arange(len(coords)).astype('i')
bhtree = bhtreelib.TBHTree(coords,ids,10,10,9999.0)
mol.bhtree = bhtree
vertexIndices={}
atomIndices={}
for x in range(len(coords)):
vertexIndices[x+1]=[]
cutoff=5.
for x in range(len(vertices)):
xyz = vertices[x]
result = Numeric.zeros( (len(vertices),) ).astype('i')
dist = Numeric.zeros( (len(vertices),) ).astype('f')
nb2 = mol.bhtree.ClosePointsDist2(tuple(xyz[:3]), cutoff, result, dist )
while nb2==0:
cutoff = cutoff+5.
nb2 = mol.bhtree.ClosePointsDist2(tuple(xyz[:3]), cutoff, result, dist )
result = result[:nb2]
dist = dist[:nb2]
idx = dist.tolist().index(min(dist))
atnum = result[idx]+1
atomIndices[x]=atnum
vertexIndices[atnum].append(x)
return atomIndices,vertexIndices
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