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tbgl
tools
mrdna
Commits
5d01a8a5
Commit
5d01a8a5
authored
Jun 25, 2020
by
cmaffeo2
Browse files
Updated bondAngle to be two angles, one bond
parent
9f55d328
Changes
1
Hide whitespace changes
Inline
Side-by-side
mrdna/arbdmodel/__init__.py
View file @
5d01a8a5
...
...
@@ -149,12 +149,12 @@ class Parent():
# for b in (i,j): assert(b in beads)
self
.
exclusions
.
append
(
(
i
,
j
)
)
def
add_bond_angle
(
self
,
i
,
j
,
k
,
bond_angle
,
exclude
=
False
):
assert
(
len
(
set
((
i
,
j
,
k
)))
==
3
)
def
add_bond_angle
(
self
,
i
,
j
,
k
,
l
,
bond_angle
,
exclude
=
False
):
assert
(
len
(
set
((
i
,
j
,
k
,
l
)))
==
4
)
## TODO: how to handle duplicating and cloning bonds
# beads = [b for b in self]
# for b in (i,j): assert(b in beads)
self
.
bond_angles
.
append
(
(
i
,
j
,
k
,
bond_angle
)
)
self
.
bond_angles
.
append
(
(
i
,
j
,
k
,
l
,
bond_angle
)
)
def
get_restraints
(
self
):
ret
=
[]
...
...
@@ -219,14 +219,14 @@ class Parent():
def
_get_bond_potentials
(
self
):
bonds
=
[
b
for
i
,
j
,
b
,
ex
in
self
.
get_bonds
()]
bondangles1
=
[
b
[
1
]
for
i
,
j
,
k
,
b
in
self
.
get_bond_angles
()]
bondangles2
=
[
b
[
2
]
for
i
,
j
,
k
,
b
in
self
.
get_bond_angles
()]
return
list
(
set
(
bonds
+
bondangles1
+
bondangles2
))
bondangles1
=
[
b
[
1
]
for
i
,
j
,
k
,
l
,
b
in
self
.
get_bond_angles
()]
return
list
(
set
(
bonds
+
bondangles1
))
def
_get_angle_potentials
(
self
):
angles
=
[
b
for
i
,
j
,
k
,
b
in
self
.
get_angles
()]
bondangles
=
[
b
[
0
]
for
i
,
j
,
k
,
b
in
self
.
get_bond_angles
()]
return
list
(
set
(
angles
+
bondangles
))
bondangles1
=
[
b
[
0
]
for
i
,
j
,
k
,
l
,
b
in
self
.
get_bond_angles
()]
bondangles2
=
[
b
[
2
]
for
i
,
j
,
k
,
l
,
b
in
self
.
get_bond_angles
()]
return
list
(
set
(
angles
+
bondangles1
+
bondangles2
))
## Removed because prohibitively slow
...
...
@@ -1240,7 +1240,7 @@ component "data" value 3
with
open
(
self
.
_bond_angle_filename
,
'w'
)
as
fh
:
for
b
in
self
.
get_bond_angles
():
item
=
tuple
([
p
.
idx
for
p
in
b
[:
-
1
]]
+
[
str
(
p
)
for
p
in
b
[
-
1
]])
fh
.
write
(
"BONDANGLE %d %d %d %s %s %s
\n
"
%
item
)
fh
.
write
(
"BONDANGLE %d %d %d
%d
%s %s %s
\n
"
%
item
)
def
dimensions_from_structure
(
self
,
padding_factor
=
1.5
,
isotropic
=
False
):
## TODO: cache coordinates using numpy arrays for quick min/max
...
...
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