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Michal Malý
Molstar
Commits
320144b3
Commit
320144b3
authored
6 years ago
by
Alexander Rose
Browse files
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Plain Diff
swissmodel download option, label improvements
parent
91a79e3a
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Changes
2
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2 changed files
src/mol-plugin/state/actions/structure.ts
+17
-3
17 additions, 3 deletions
src/mol-plugin/state/actions/structure.ts
src/mol-plugin/state/transforms/model.ts
+2
-2
2 additions, 2 deletions
src/mol-plugin/state/transforms/model.ts
with
19 additions
and
5 deletions
src/mol-plugin/state/actions/structure.ts
+
17
−
3
View file @
320144b3
...
@@ -69,6 +69,8 @@ export const GroProvider: DataFormatProvider<any> = {
...
@@ -69,6 +69,8 @@ export const GroProvider: DataFormatProvider<any> = {
}
}
}
}
type
StructureFormat
=
'
pdb
'
|
'
cif
'
|
'
gro
'
//
//
const
DownloadStructurePdbIdSourceOptions
=
PD
.
Group
({
const
DownloadStructurePdbIdSourceOptions
=
PD
.
Group
({
...
@@ -99,6 +101,10 @@ const DownloadStructure = StateAction.build({
...
@@ -99,6 +101,10 @@ const DownloadStructure = StateAction.build({
id
:
PD
.
Text
(
'
1tqn
'
,
{
label
:
'
Id
'
}),
id
:
PD
.
Text
(
'
1tqn
'
,
{
label
:
'
Id
'
}),
options
:
DownloadStructurePdbIdSourceOptions
options
:
DownloadStructurePdbIdSourceOptions
},
{
isFlat
:
true
}),
},
{
isFlat
:
true
}),
'
swissmodel
'
:
PD
.
Group
({
id
:
PD
.
Text
(
'
Q9Y2I8
'
,
{
label
:
'
UniProtKB AC
'
}),
options
:
DownloadStructurePdbIdSourceOptions
},
{
isFlat
:
true
,
description
:
'
Loads the best homology model or experimental structure
'
}),
'
url
'
:
PD
.
Group
({
'
url
'
:
PD
.
Group
({
url
:
PD
.
Text
(
''
),
url
:
PD
.
Text
(
''
),
format
:
PD
.
Select
(
'
cif
'
,
[[
'
cif
'
,
'
CIF
'
],
[
'
pdb
'
,
'
PDB
'
]]),
format
:
PD
.
Select
(
'
cif
'
,
[[
'
cif
'
,
'
CIF
'
],
[
'
pdb
'
,
'
PDB
'
]]),
...
@@ -113,6 +119,7 @@ const DownloadStructure = StateAction.build({
...
@@ -113,6 +119,7 @@ const DownloadStructure = StateAction.build({
[
'
rcsb
'
,
'
RCSB
'
],
[
'
rcsb
'
,
'
RCSB
'
],
[
'
pdb-dev
'
,
'
PDBDEV
'
],
[
'
pdb-dev
'
,
'
PDBDEV
'
],
[
'
bcif-static
'
,
'
BinaryCIF (static PDBe Updated)
'
],
[
'
bcif-static
'
,
'
BinaryCIF (static PDBe Updated)
'
],
[
'
swissmodel
'
,
'
SWISS-MODEL
'
],
[
'
url
'
,
'
URL
'
]
[
'
url
'
,
'
URL
'
]
]
]
})
})
...
@@ -121,12 +128,13 @@ const DownloadStructure = StateAction.build({
...
@@ -121,12 +128,13 @@ const DownloadStructure = StateAction.build({
const
b
=
state
.
build
();
const
b
=
state
.
build
();
const
src
=
params
.
source
;
const
src
=
params
.
source
;
let
downloadParams
:
StateTransformer
.
Params
<
Download
>
[];
let
downloadParams
:
StateTransformer
.
Params
<
Download
>
[];
let
supportProps
=
false
,
asTrajectory
=
false
;
let
supportProps
=
false
,
asTrajectory
=
false
,
format
:
StructureFormat
=
'
cif
'
;
switch
(
src
.
name
)
{
switch
(
src
.
name
)
{
case
'
url
'
:
case
'
url
'
:
downloadParams
=
[{
url
:
src
.
params
.
url
,
isBinary
:
src
.
params
.
isBinary
}];
downloadParams
=
[{
url
:
src
.
params
.
url
,
isBinary
:
src
.
params
.
isBinary
}];
supportProps
=
!!
src
.
params
.
options
.
supportProps
;
supportProps
=
!!
src
.
params
.
options
.
supportProps
;
format
=
src
.
params
.
format
break
;
break
;
case
'
pdbe-updated
'
:
case
'
pdbe-updated
'
:
downloadParams
=
getDownloadParams
(
src
.
params
.
id
,
id
=>
`https://www.ebi.ac.uk/pdbe/static/entry/
${
id
.
toLowerCase
()}
_updated.cif`
,
id
=>
`PDBe:
${
id
}
`
,
false
);
downloadParams
=
getDownloadParams
(
src
.
params
.
id
,
id
=>
`https://www.ebi.ac.uk/pdbe/static/entry/
${
id
.
toLowerCase
()}
_updated.cif`
,
id
=>
`PDBe:
${
id
}
`
,
false
);
...
@@ -155,6 +163,12 @@ const DownloadStructure = StateAction.build({
...
@@ -155,6 +163,12 @@ const DownloadStructure = StateAction.build({
supportProps
=
!!
src
.
params
.
options
.
supportProps
;
supportProps
=
!!
src
.
params
.
options
.
supportProps
;
asTrajectory
=
!!
src
.
params
.
options
.
asTrajectory
;
asTrajectory
=
!!
src
.
params
.
options
.
asTrajectory
;
break
;
break
;
case
'
swissmodel
'
:
downloadParams
=
getDownloadParams
(
src
.
params
.
id
,
id
=>
`https://swissmodel.expasy.org/repository/uniprot/
${
id
.
toUpperCase
()}
.pdb`
,
id
=>
`SWISS-MODEL:
${
id
}
`
,
false
);
supportProps
=
!!
src
.
params
.
options
.
supportProps
;
asTrajectory
=
!!
src
.
params
.
options
.
asTrajectory
;
format
=
'
pdb
'
break
;
default
:
throw
new
Error
(
`
${(
src
as
any
).
name
}
not supported.`
);
default
:
throw
new
Error
(
`
${(
src
as
any
).
name
}
not supported.`
);
}
}
...
@@ -164,7 +178,7 @@ const DownloadStructure = StateAction.build({
...
@@ -164,7 +178,7 @@ const DownloadStructure = StateAction.build({
}
else
{
}
else
{
for
(
const
download
of
downloadParams
)
{
for
(
const
download
of
downloadParams
)
{
const
data
=
b
.
toRoot
().
apply
(
StateTransforms
.
Data
.
Download
,
download
,
{
state
:
{
isGhost
:
true
}
});
const
data
=
b
.
toRoot
().
apply
(
StateTransforms
.
Data
.
Download
,
download
,
{
state
:
{
isGhost
:
true
}
});
const
traj
=
createModelTree
(
data
,
src
.
name
===
'
url
'
?
src
.
params
.
format
:
'
cif
'
);
const
traj
=
createModelTree
(
data
,
format
);
createStructureTree
(
ctx
,
traj
,
supportProps
)
createStructureTree
(
ctx
,
traj
,
supportProps
)
}
}
}
}
...
@@ -192,7 +206,7 @@ function createSingleTrajectoryModel(sources: StateTransformer.Params<Download>[
...
@@ -192,7 +206,7 @@ function createSingleTrajectoryModel(sources: StateTransformer.Params<Download>[
.
apply
(
StateTransforms
.
Model
.
ModelFromTrajectory
,
{
modelIndex
:
0
});
.
apply
(
StateTransforms
.
Model
.
ModelFromTrajectory
,
{
modelIndex
:
0
});
}
}
export
function
createModelTree
(
b
:
StateBuilder
.
To
<
PluginStateObject
.
Data
.
Binary
|
PluginStateObject
.
Data
.
String
>
,
format
:
'
pdb
'
|
'
cif
'
|
'
gro
'
=
'
cif
'
)
{
export
function
createModelTree
(
b
:
StateBuilder
.
To
<
PluginStateObject
.
Data
.
Binary
|
PluginStateObject
.
Data
.
String
>
,
format
:
StructureFormat
=
'
cif
'
)
{
let
parsed
:
StateBuilder
.
To
<
PluginStateObject
.
Molecule
.
Trajectory
>
let
parsed
:
StateBuilder
.
To
<
PluginStateObject
.
Molecule
.
Trajectory
>
switch
(
format
)
{
switch
(
format
)
{
case
'
cif
'
:
case
'
cif
'
:
...
...
This diff is collapsed.
Click to expand it.
src/mol-plugin/state/transforms/model.ts
+
2
−
2
View file @
320144b3
...
@@ -108,7 +108,7 @@ const TrajectoryFromPDB = PluginStateTransform.BuiltIn({
...
@@ -108,7 +108,7 @@ const TrajectoryFromPDB = PluginStateTransform.BuiltIn({
})({
})({
apply
({
a
})
{
apply
({
a
})
{
return
Task
.
create
(
'
Parse PDB
'
,
async
ctx
=>
{
return
Task
.
create
(
'
Parse PDB
'
,
async
ctx
=>
{
const
parsed
=
await
parsePDB
(
a
.
data
).
runInContext
(
ctx
);
const
parsed
=
await
parsePDB
(
a
.
data
,
a
.
label
).
runInContext
(
ctx
);
if
(
parsed
.
isError
)
throw
new
Error
(
parsed
.
message
);
if
(
parsed
.
isError
)
throw
new
Error
(
parsed
.
message
);
const
models
=
await
trajectoryFromPDB
(
parsed
.
result
).
runInContext
(
ctx
);
const
models
=
await
trajectoryFromPDB
(
parsed
.
result
).
runInContext
(
ctx
);
const
props
=
{
label
:
models
[
0
].
label
,
description
:
`
${
models
.
length
}
model
${
models
.
length
===
1
?
''
:
'
s
'
}
`
};
const
props
=
{
label
:
models
[
0
].
label
,
description
:
`
${
models
.
length
}
model
${
models
.
length
===
1
?
''
:
'
s
'
}
`
};
...
@@ -222,7 +222,7 @@ const StructureAssemblyFromModel = PluginStateTransform.BuiltIn({
...
@@ -222,7 +222,7 @@ const StructureAssemblyFromModel = PluginStateTransform.BuiltIn({
const
base
=
Structure
.
ofModel
(
model
);
const
base
=
Structure
.
ofModel
(
model
);
if
(
!
asm
)
{
if
(
!
asm
)
{
await
ensureSecondaryStructure
(
base
)
await
ensureSecondaryStructure
(
base
)
const
label
=
{
label
:
a
.
data
.
label
,
description
:
structureDesc
(
base
)
};
const
label
=
{
label
:
'
Deposited
'
,
description
:
structureDesc
(
base
)
};
return
new
SO
.
Molecule
.
Structure
(
base
,
label
);
return
new
SO
.
Molecule
.
Structure
(
base
,
label
);
}
}
...
...
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