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mrdna
Commits
13f6cbb3
Commit
13f6cbb3
authored
Feb 10, 2021
by
cmaffeo2
Browse files
Added support for ARBD group sites
parent
f03f6d8a
Changes
1
Hide whitespace changes
Inline
Side-by-side
mrdna/arbdmodel/__init__.py
View file @
13f6cbb3
...
...
@@ -730,6 +730,22 @@ class PdbModel(Transformable, Parent):
class
ArbdModel
(
PdbModel
):
class
_GroupSite
():
""" Class to represent a collection of particles that can be used by bond potentials """
def
__init__
(
self
,
particles
,
weights
=
None
):
if
weights
is
not
None
:
raise
NotImplementedError
self
.
particles
=
particles
self
.
idx
=
None
def
get_center
(
self
):
c
=
np
.
array
((
0
,
0
,
0
))
for
p
in
self
.
particles
:
c
=
c
+
p
.
collapsedPosition
()
c
=
c
/
len
(
self
.
particles
)
return
c
def
__init__
(
self
,
children
,
origin
=
None
,
dimensions
=
(
1000
,
1000
,
1000
),
temperature
=
291
,
timestep
=
50e-6
,
particle_integrator
=
'Brown'
,
cutoff
=
50
,
decomp_period
=
1000
,
pairlist_distance
=
None
,
nonbonded_resolution
=
0.1
,
...
...
@@ -764,6 +780,13 @@ class ArbdModel(PdbModel):
self
.
cacheUpToDate
=
False
self
.
group_sites
=
[]
def
add_group_site
(
self
,
particles
,
weights
=
None
):
g
=
ArbdModel
.
_GroupSite
(
particles
,
weights
)
self
.
group_sites
.
append
(
g
)
return
g
def
clear_all
(
self
,
keep_children
=
False
):
Parent
.
clear_all
(
self
,
keep_children
=
keep_children
)
self
.
particles
=
[]
...
...
@@ -771,6 +794,7 @@ class ArbdModel(PdbModel):
self
.
type_counts
=
None
self
.
_nbParamFiles
=
[]
self
.
_written_bond_files
=
dict
()
self
.
group_sites
=
[]
def
_getNbScheme
(
self
,
typeA
,
typeB
):
scheme
=
None
...
...
@@ -804,8 +828,12 @@ class ArbdModel(PdbModel):
# self.particles = sorted(particles, key=lambda p: (p.type_, p.idx))
## Update particle indices
for
p
,
i
in
zip
(
self
.
particles
,
range
(
len
(
self
.
particles
)
))
:
for
i
,
p
in
enumerate
(
self
.
particles
):
p
.
idx
=
i
## TODO recurse through childrens' group_sites
for
i
,
g
in
enumerate
(
self
.
group_sites
):
g
.
idx
=
len
(
self
.
particles
)
+
i
# self.initialCoords = np.array([p.initialPosition for p in self.particles])
...
...
@@ -916,6 +944,7 @@ class ArbdModel(PdbModel):
self
.
_exclusion_filename
=
"%s/%s.exculsions.txt"
%
(
d
,
prefix
)
self
.
_bond_angle_filename
=
"%s/%s.bondangles.txt"
%
(
d
,
prefix
)
self
.
_product_potential_filename
=
"%s/%s.prodpot.txt"
%
(
d
,
prefix
)
self
.
_group_sites_filename
=
"%s/%s.groups.txt"
%
(
d
,
prefix
)
# self._writeArbdCoordFile( prefix + ".coord.txt" )
self
.
_writeArbdParticleFile
(
prefix
+
".particles.txt"
)
...
...
@@ -926,6 +955,7 @@ class ArbdModel(PdbModel):
self
.
_writeArbdExclusionFile
()
self
.
_writeArbdBondAngleFile
()
self
.
_writeArbdProductPotentialFile
()
self
.
_writeArbdGroupSitesFile
()
self
.
_writeArbdPotentialFiles
(
prefix
,
directory
=
d
)
self
.
_writeArbdConf
(
prefix
,
numSteps
=
numSteps
,
outputPeriod
=
outputPeriod
,
restart_file
=
restart_file
)
...
...
@@ -1123,6 +1153,9 @@ tabulatedPotential 1
exclusions
=
self
.
get_exclusions
()
bond_angles
=
self
.
get_bond_angles
()
prod_pots
=
self
.
get_product_potentials
()
# group_sites = self.get_group_sites()
group_sites
=
self
.
group_sites
if
len
(
bonds
)
>
0
:
for
b
in
self
.
_get_bond_potentials
():
fh
.
write
(
"tabulatedBondFile %s
\n
"
%
b
)
...
...
@@ -1149,6 +1182,8 @@ tabulatedPotential 1
fh
.
write
(
"inputBondAngles %s
\n
"
%
self
.
_bond_angle_filename
)
if
len
(
prod_pots
)
>
0
:
fh
.
write
(
"inputProductPotentials %s
\n
"
%
self
.
_product_potential_filename
)
if
len
(
group_sites
)
>
0
:
fh
.
write
(
"inputGroups %s
\n
"
%
self
.
_group_sites_filename
)
write_null_dx
=
False
for
pt
,
num
in
self
.
getParticleTypesAndCounts
():
...
...
@@ -1290,6 +1325,13 @@ component "data" value 3
line
=
line
+
" "
.
join
([
str
(
x
)
for
x
in
[
type_
,
b
]
if
x
!=
""
])
+
" "
fh
.
write
(
line
)
def
_writeArbdGroupSitesFile
(
self
):
if
len
(
self
.
group_sites
)
>
0
:
with
open
(
self
.
_group_sites_filename
,
'w'
)
as
fh
:
for
i
,
g
in
enumerate
(
self
.
group_sites
):
assert
(
i
+
len
(
self
.
particles
)
==
g
.
idx
)
ids
=
" "
.
join
([
str
(
int
(
p
.
idx
))
for
p
in
g
.
particles
])
fh
.
write
(
"GROUP %s
\n
"
%
ids
)
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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