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Michal Malý
Molstar
Commits
d13ee0a2
Commit
d13ee0a2
authored
5 years ago
by
JonStargaryen
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ui integration
parent
82612767
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2
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2 changed files
src/extensions/membrane-orientation/behavior.ts
+87
-11
87 additions, 11 deletions
src/extensions/membrane-orientation/behavior.ts
src/extensions/membrane-orientation/representation.ts
+4
-0
4 additions, 0 deletions
src/extensions/membrane-orientation/representation.ts
with
91 additions
and
11 deletions
src/extensions/membrane-orientation/behavior.ts
+
87
−
11
View file @
d13ee0a2
...
...
@@ -8,11 +8,13 @@
import
{
ParamDefinition
as
PD
}
from
'
../../mol-util/param-definition
'
;
import
{
StructureRepresentationPresetProvider
,
PresetStructureRepresentations
}
from
'
../../mol-plugin-state/builder/structure/representation-preset
'
;
import
{
MembraneOrientationProvider
,
MembraneOrientation
}
from
'
./membrane-orientation
'
;
import
{
StateObjectRef
}
from
'
../../mol-state
'
;
import
{
StateObjectRef
,
StateAction
,
StateTransformer
,
StateTransform
}
from
'
../../mol-state
'
;
import
{
Task
}
from
'
../../mol-task
'
;
import
{
PluginBehavior
}
from
'
../../mol-plugin/behavior
'
;
import
{
MembraneOrientationRepresentationProvider
}
from
'
./representation
'
;
import
{
MembraneOrientationRepresentationProvider
,
MembraneOrientationParams
,
MembraneOrientationRepresentation
}
from
'
./representation
'
;
import
{
HydrophobicityColorThemeProvider
}
from
'
../../mol-theme/color/hydrophobicity
'
;
import
{
PluginStateObject
,
PluginStateTransform
}
from
'
../../mol-plugin-state/objects
'
;
import
{
PluginContext
}
from
'
../../mol-plugin/context
'
;
export
const
MembraneOrientationData
=
PluginBehavior
.
create
<
{
autoAttach
:
boolean
}
>
({
name
:
'
membrane-orientation-prop
'
,
...
...
@@ -25,10 +27,10 @@ export const MembraneOrientationData = PluginBehavior.create<{ autoAttach: boole
private
provider
=
MembraneOrientationProvider
register
():
void
{
console
.
log
(
'
beh @ register
'
);
this
.
ctx
.
state
.
data
.
actions
.
add
(
InitMembraneOrientation3D
);
this
.
ctx
.
customStructureProperties
.
register
(
this
.
provider
,
this
.
params
.
autoAttach
);
this
.
ctx
.
representation
.
structure
.
themes
.
colorThemeRegistry
.
add
(
HydrophobicityColorThemeProvider
);
this
.
ctx
.
representation
.
structure
.
registry
.
add
(
MembraneOrientationRepresentationProvider
);
this
.
ctx
.
query
.
structure
.
registry
.
add
(
MembraneOrientation
.
isTransmembrane
);
...
...
@@ -43,10 +45,9 @@ export const MembraneOrientationData = PluginBehavior.create<{ autoAttach: boole
}
unregister
()
{
this
.
ctx
.
state
.
data
.
actions
.
remove
(
InitMembraneOrientation3D
);
this
.
ctx
.
customStructureProperties
.
unregister
(
this
.
provider
.
descriptor
.
name
);
this
.
ctx
.
representation
.
structure
.
themes
.
colorThemeRegistry
.
remove
(
HydrophobicityColorThemeProvider
);
this
.
ctx
.
representation
.
structure
.
registry
.
remove
(
MembraneOrientationRepresentationProvider
);
this
.
ctx
.
query
.
structure
.
registry
.
remove
(
MembraneOrientation
.
isTransmembrane
);
...
...
@@ -58,13 +59,75 @@ export const MembraneOrientationData = PluginBehavior.create<{ autoAttach: boole
})
});
export
const
InitMembraneOrientation3D
=
StateAction
.
build
({
display
:
{
name
:
'
Membrane Orientation
'
,
description
:
'
Initialize Membrane Orientation planes and rims. Data calculated with ANVIL algorithm.
'
},
from
:
PluginStateObject
.
Molecule
.
Structure
,
isApplicable
:
(
a
)
=>
MembraneOrientationProvider
.
isApplicable
(
a
.
data
)
})(({
a
,
ref
,
state
},
plugin
:
PluginContext
)
=>
Task
.
create
(
'
Init Membrane Orientation
'
,
async
ctx
=>
{
try
{
const
propCtx
=
{
runtime
:
ctx
,
assetManager
:
plugin
.
managers
.
asset
};
await
MembraneOrientationProvider
.
attach
(
propCtx
,
a
.
data
);
}
catch
(
e
)
{
plugin
.
log
.
error
(
`Membrane Orientation:
${
e
}
`
);
return
;
}
const
tree
=
state
.
build
().
to
(
ref
)
.
applyOrUpdateTagged
(
'
membrane-orientation-3d
'
,
MembraneOrientation3D
);
await
state
.
updateTree
(
tree
).
runInContext
(
ctx
);
}));
export
{
MembraneOrientation3D
};
type
MembraneOrientation3D
=
typeof
MembraneOrientation3D
const
MembraneOrientation3D
=
PluginStateTransform
.
BuiltIn
({
name
:
'
membrane-orientation-3d
'
,
display
:
{
name
:
'
Membrane Orientation
'
,
description
:
'
Membrane Orientation planes and rims. Data calculated with ANVIL algorithm.
'
},
from
:
PluginStateObject
.
Molecule
.
Structure
,
to
:
PluginStateObject
.
Shape
.
Representation3D
,
params
:
(
a
)
=>
{
return
{
...
MembraneOrientationParams
,
};
}
})({
canAutoUpdate
({
oldParams
,
newParams
})
{
return
true
;
},
apply
({
a
,
params
},
plugin
:
PluginContext
)
{
return
Task
.
create
(
'
Membrane Orientation
'
,
async
ctx
=>
{
await
MembraneOrientationProvider
.
attach
({
runtime
:
ctx
,
assetManager
:
plugin
.
managers
.
asset
},
a
.
data
);
const
repr
=
MembraneOrientationRepresentation
({
webgl
:
plugin
.
canvas3d
?.
webgl
,
...
plugin
.
representation
.
structure
.
themes
},
()
=>
MembraneOrientationParams
);
await
repr
.
createOrUpdate
(
params
,
a
.
data
).
runInContext
(
ctx
);
return
new
PluginStateObject
.
Shape
.
Representation3D
({
repr
,
source
:
a
});
});
},
update
({
a
,
b
,
newParams
},
plugin
:
PluginContext
)
{
return
Task
.
create
(
'
Membrane Orientation
'
,
async
ctx
=>
{
await
MembraneOrientationProvider
.
attach
({
runtime
:
ctx
,
assetManager
:
plugin
.
managers
.
asset
},
a
.
data
);
const
props
=
{
...
b
.
data
.
repr
.
props
,
...
newParams
};
await
b
.
data
.
repr
.
createOrUpdate
(
props
,
a
.
data
).
runInContext
(
ctx
);
return
StateTransformer
.
UpdateResult
.
Updated
;
});
},
isApplicable
(
a
)
{
return
MembraneOrientationProvider
.
isApplicable
(
a
.
data
);
}
});
export
const
MembraneOrientationPreset
=
StructureRepresentationPresetProvider
({
id
:
'
preset-membrane-orientation
'
,
display
:
{
name
:
'
Membrane Orientation
'
,
group
:
'
Annotation
'
,
description
:
'
Initialize
orientation of membrane layers. Data calculated with ANVIL algorithm.
'
// TODO add ' or obtained via RCSB PDB'
description
:
'
Shows
orientation of membrane layers. Data calculated with ANVIL algorithm.
'
// TODO add ' or obtained via RCSB PDB'
},
isApplicable
(
a
)
{
console
.
log
(
`present applicable:
${
MembraneOrientationProvider
.
isApplicable
(
a
.
data
)}
`
);
return
MembraneOrientationProvider
.
isApplicable
(
a
.
data
);
},
params
:
()
=>
StructureRepresentationPresetProvider
.
CommonParams
,
...
...
@@ -73,11 +136,24 @@ export const MembraneOrientationPreset = StructureRepresentationPresetProvider({
const
structure
=
structureCell
?.
obj
?.
data
;
if
(
!
structureCell
||
!
structure
)
return
{};
if
(
!
MembraneOrientationProvider
.
get
(
structure
).
value
)
{
await
plugin
.
runTask
(
Task
.
create
(
'
Membrane Orientation
'
,
async
runtime
=>
{
console
.
log
(
'
present: attaching
'
);
await
MembraneOrientationProvider
.
attach
({
runtime
,
assetManager
:
plugin
.
managers
.
asset
},
structure
);
}));
}
const
membraneOrientation
=
await
tryCreateMembraneOrientation
(
plugin
,
structureCell
);
const
colorTheme
=
HydrophobicityColorThemeProvider
.
name
as
any
;
return
await
PresetStructureRepresentations
.
auto
.
apply
(
ref
,
{
...
params
,
theme
:
{
globalName
:
colorTheme
,
focus
:
{
name
:
colorTheme
}
}
},
plugin
);
const
preset
=
await
PresetStructureRepresentations
.
auto
.
apply
(
ref
,
{
...
params
,
theme
:
{
globalName
:
colorTheme
,
focus
:
{
name
:
colorTheme
}
}
},
plugin
);
return
{
components
:
preset
.
components
,
representations
:
{
...
preset
.
representations
,
membraneOrientation
}
};
}
});
export
function
tryCreateMembraneOrientation
(
plugin
:
PluginContext
,
structure
:
StateObjectRef
<
PluginStateObject
.
Molecule
.
Structure
>
,
params
?:
StateTransformer
.
Params
<
MembraneOrientation3D
>
,
initialState
?:
Partial
<
StateTransform
.
State
>
)
{
const
state
=
plugin
.
state
.
data
;
const
membraneOrientation
=
state
.
build
().
to
(
structure
)
.
applyOrUpdateTagged
(
'
membrane-orientation-3d
'
,
MembraneOrientation3D
,
params
,
{
state
:
initialState
});
return
membraneOrientation
.
commit
({
revertOnError
:
true
});
}
This diff is collapsed.
Click to expand it.
src/extensions/membrane-orientation/representation.ts
+
4
−
0
View file @
d13ee0a2
...
...
@@ -74,11 +74,13 @@ export type MembraneOrientationParams = typeof MembraneOrientationParams
export
type
MembraneOrientationProps
=
PD
.
Values
<
MembraneOrientationParams
>
export
function
getMembraneOrientationParams
(
ctx
:
ThemeRegistryContext
,
structure
:
Structure
)
{
console
.
log
(
'
rep @ getParams
'
);
return
PD
.
clone
(
MembraneOrientationParams
);
}
export
type
MembraneOrientationRepresentation
=
StructureRepresentation
<
MembraneOrientationParams
>
export
function
MembraneOrientationRepresentation
(
ctx
:
RepresentationContext
,
getParams
:
RepresentationParamsGetter
<
Structure
,
MembraneOrientationParams
>
):
MembraneOrientationRepresentation
{
console
.
log
(
'
rep @ create
'
);
return
Representation
.
createMulti
(
'
Membrane Orientation
'
,
ctx
,
getParams
,
StructureRepresentationStateBuilder
,
MembraneOrientationVisuals
as
unknown
as
Representation
.
Def
<
Structure
,
MembraneOrientationParams
>
);
}
...
...
@@ -95,6 +97,7 @@ export const MembraneOrientationRepresentationProvider = StructureRepresentation
});
function
getBilayerRims
(
ctx
:
RuntimeContext
,
data
:
Structure
,
props
:
BilayerRimsProps
):
Shape
<
Lines
>
{
console
.
log
(
'
rims
'
);
const
{
p1
,
p2
,
centroid
,
normal
,
radius
}
=
MembraneOrientationProvider
.
get
(
data
).
value
!
;
const
scaledRadius
=
props
.
radiusFactor
*
radius
;
const
builder
=
LinesBuilder
.
create
(
128
,
64
);
...
...
@@ -131,6 +134,7 @@ function getCircle(p: Vec3, centroid: Vec3, normal: Vec3, radius: number) {
}
function
getBilayerPlanes
(
ctx
:
RuntimeContext
,
data
:
Structure
,
props
:
BilayerPlanesProps
,
shape
?:
Shape
<
Mesh
>
):
Shape
<
Mesh
>
{
console
.
log
(
'
planes
'
);
const
{
p1
,
p2
,
centroid
,
normal
,
radius
}
=
MembraneOrientationProvider
.
get
(
data
).
value
!
;
const
state
=
MeshBuilder
.
createState
(
128
,
64
,
shape
&&
shape
.
geometry
);
const
scaledRadius
=
props
.
radiusFactor
*
radius
;
...
...
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