Skip to content

Fix index issue in make_whole #1986

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
jbarnoud wants to merge 1 commit into from
Closed

Fix index issue in make_whole #1986

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
11 changes: 6 additions & 5 deletions package/MDAnalysis/lib/_cutil.pyx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -166,7 +166,7 @@ def make_whole(atomgroup, reference_atom=None):
.. versionadded:: 0.11.0
"""
cdef intset agset, refpoints, todo, done
cdef int i, nloops, ref, atom, other
cdef int i, nloops, ref, atom, other, first
cdef intmap bonding
cdef int[:, :] bonds
cdef float[:, :] oldpos, newpos
Expand All @@ -176,8 +176,9 @@ def make_whole(atomgroup, reference_atom=None):
cdef float inverse_box[3]
cdef double vec[3]

first = atomgroup[0].index
if reference_atom is None:
ref = atomgroup[0].index
ref = first
else:
# Sanity check
if not reference_atom in atomgroup:
Expand Down Expand Up @@ -228,7 +229,7 @@ def make_whole(atomgroup, reference_atom=None):
# initially we have one starting atom whose position we trust
refpoints.insert(ref)
for i in range(3):
newpos[ref, i] = oldpos[ref, i]
newpos[ref - first, i] = oldpos[ref - first, i]

nloops = 0
while refpoints.size() < agset.size() and nloops < agset.size():
Expand All @@ -244,15 +245,15 @@ def make_whole(atomgroup, reference_atom=None):
continue
# Draw vector from atom to other
for i in range(3):
vec[i] = oldpos[other, i] - oldpos[atom, i]
vec[i] = oldpos[other - first, i] - oldpos[atom - first, i]
# Apply periodic boundary conditions to this vector
if ortho:
minimum_image(&vec[0], &box[0], &inverse_box[0])
else:
minimum_image_triclinic(&vec[0], <coordinate*>&tri_box[0])
# Then define position of other based on this vector
for i in range(3):
newpos[other, i] = newpos[atom, i] + vec[i]
newpos[other - first, i] = newpos[atom - first, i] + vec[i]

# This other atom can now be used as a reference point
refpoints.insert(other)
Expand Down