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tbgl
tools
mrdna
Commits
2161b99c
Commit
2161b99c
authored
Mar 27, 2018
by
cmaffeo2
Browse files
Fixed numerous issues; code seems to work
parent
daa829dd
Changes
3
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CanonicalNucleotideAtoms.py
View file @
2161b99c
...
...
@@ 21,17 +21,7 @@ def stringToIntTuples(string, tupleLen, offset):
return
ret
class
CanonicalNucleotide
(
Group
):
# DefaultOrientation = rotationAboutAxis([0,0,1], 68)
# DefaultOrientation = rotationAboutAxis([0,0,1], 68+180)
# DefaultOrientation = rotationAboutAxis([0,0,1], 68+18020)
DefaultOrientation
=
rotationAboutAxis
([
0
,
0
,
1
],
90
)
# DefaultOrientation = rotationAboutAxis([0,0,1], 90)
# DefaultOrientation = rotationAboutAxis([0,0,1], 60)
# DefaultOrientation = rotationAboutAxis([0,0,1], 90)
DefaultOrientation
=
rotationAboutAxis
([
0
,
0
,
1
],

30
)
DefaultOrientation
=
rotationAboutAxis
([
0
,
0
,
1
],

120
)
DefaultOrientation
=
rotationAboutAxis
([
0
,
0
,
1
],

150
)
DefaultOrientation
=
rotationAboutAxis
([
0
,
0
,
1
],
150
)
DefaultOrientation
=
rotationAboutAxis
([
0
,
0
,
1
],
80
)
def
__init__
(
self
,
prefix
,
seq
):
self
.
sequence
=
seq
# TODO: used?
self
.
resname
=
resnames
[
seq
]
...
...
arbdmodel.py
View file @
2161b99c
...
...
@@ 100,23 +100,23 @@ class Parent():
def
add_bond
(
self
,
i
,
j
,
bond
,
exclude
=
False
):
## TODO: how to handle duplicating and cloning bonds
beads
=
[
b
for
b
in
self
]
for
b
in
(
i
,
j
):
assert
(
b
in
beads
)
#
beads = [b for b in self]
#
for b in (i,j): assert(b in beads)
self
.
bonds
.
append
(
(
i
,
j
,
bond
,
exclude
)
)
def
add_angle
(
self
,
i
,
j
,
k
,
angle
):
beads
=
[
b
for
b
in
self
]
for
b
in
(
i
,
j
,
k
):
assert
(
b
in
beads
)
#
beads = [b for b in self]
#
for b in (i,j,k): assert(b in beads)
self
.
angles
.
append
(
(
i
,
j
,
k
,
angle
)
)
def
add_dihedral
(
self
,
i
,
j
,
k
,
l
,
dihedral
):
beads
=
[
b
for
b
in
self
]
for
b
in
(
i
,
j
,
k
,
l
):
assert
(
b
in
beads
)
#
beads = [b for b in self]
#
for b in (i,j,k,l): assert(b in beads)
self
.
dihedrals
.
append
(
(
i
,
j
,
k
,
l
,
dihedral
)
)
def
add_improper
(
self
,
i
,
j
,
k
,
l
,
dihedral
):
beads
=
[
b
for
b
in
self
]
for
b
in
(
i
,
j
,
k
,
l
):
assert
(
b
in
beads
)
#
beads = [b for b in self]
#
for b in (i,j,k,l): assert(b in beads)
self
.
impropers
.
append
(
(
i
,
j
,
k
,
l
,
dihedral
)
)
def
add_exclusion
(
self
,
i
,
j
):
...
...
segmentmodel.py
View file @
2161b99c
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