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Michal Malý
Molstar
Commits
f028ad05
Commit
f028ad05
authored
6 years ago
by
David Sehnal
Browse files
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mol-model: Added Atom and Entity level custom props
parent
828c4dfd
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Changes
2
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2 changed files
src/mol-model-props/pdbe/structure-quality-report.ts
+2
-2
2 additions, 2 deletions
src/mol-model-props/pdbe/structure-quality-report.ts
src/mol-model/structure/model/properties/custom/indexed.ts
+159
-24
159 additions, 24 deletions
src/mol-model/structure/model/properties/custom/indexed.ts
with
161 additions
and
26 deletions
src/mol-model-props/pdbe/structure-quality-report.ts
+
2
−
2
View file @
f028ad05
...
@@ -140,7 +140,7 @@ function createIssueMapFromJson(modelData: Model, data: any): StructureQualityRe
...
@@ -140,7 +140,7 @@ function createIssueMapFromJson(modelData: Model, data: any): StructureQualityRe
}
}
}
}
return
IndexedCustomProperty
.
fromResidueMap
(
ret
,
Unit
.
Kind
.
Atomic
);
return
IndexedCustomProperty
.
fromResidueMap
(
ret
);
}
}
function
createIssueMapFromCif
(
modelData
:
Model
,
data
:
Table
<
typeof
StructureQualityReport
.
Schema
.
pdbe_structure_quality_report_issues
>
):
StructureQualityReport
.
IssueMap
|
undefined
{
function
createIssueMapFromCif
(
modelData
:
Model
,
data
:
Table
<
typeof
StructureQualityReport
.
Schema
.
pdbe_structure_quality_report_issues
>
):
StructureQualityReport
.
IssueMap
|
undefined
{
...
@@ -153,5 +153,5 @@ function createIssueMapFromCif(modelData: Model, data: Table<typeof StructureQua
...
@@ -153,5 +153,5 @@ function createIssueMapFromCif(modelData: Model, data: Table<typeof StructureQua
ret
.
set
(
idx
,
issues
.
value
(
i
));
ret
.
set
(
idx
,
issues
.
value
(
i
));
}
}
return
IndexedCustomProperty
.
fromResidueMap
(
ret
,
Unit
.
Kind
.
Atomic
);
return
IndexedCustomProperty
.
fromResidueMap
(
ret
);
}
}
\ No newline at end of file
This diff is collapsed.
Click to expand it.
src/mol-model/structure/model/properties/custom/indexed.ts
+
159
−
24
View file @
f028ad05
...
@@ -4,14 +4,85 @@
...
@@ -4,14 +4,85 @@
* @author David Sehnal <david.sehnal@gmail.com>
* @author David Sehnal <david.sehnal@gmail.com>
*/
*/
import
{
ResidueIndex
,
ChainIndex
,
ElementIndex
}
from
'
../../indexing
'
;
import
{
ResidueIndex
,
ChainIndex
,
ElementIndex
,
EntityIndex
}
from
'
../../indexing
'
;
import
{
Unit
,
Structure
,
StructureElement
}
from
'
../../../structure
'
;
import
{
Unit
,
Structure
,
StructureElement
}
from
'
../../../structure
'
;
import
{
Segmentation
}
from
'
mol-data/int
'
;
import
{
Segmentation
}
from
'
mol-data/int
'
;
import
{
UUID
}
from
'
mol-util
'
;
import
{
UUID
}
from
'
mol-util
'
;
import
{
CifWriter
}
from
'
mol-io/writer/cif
'
;
import
{
CifWriter
}
from
'
mol-io/writer/cif
'
;
import
{
Model
}
from
'
../../model
'
;
import
{
Model
}
from
'
../../model
'
;
export
class
IndexedCustomProperty
<
Idx
extends
IndexedCustomProperty
.
Index
,
T
=
any
>
{
export
interface
IndexedCustomProperty
<
Idx
extends
IndexedCustomProperty
.
Index
,
T
=
any
>
{
readonly
id
:
UUID
,
readonly
kind
:
Unit
.
Kind
,
readonly
level
:
IndexedCustomProperty
.
Level
,
has
(
idx
:
Idx
):
boolean
,
get
(
idx
:
Idx
):
T
|
undefined
,
getExportContext
(
structure
:
Structure
):
IndexedCustomProperty
.
ExportCtx
<
T
>
}
export
namespace
IndexedCustomProperty
{
export
type
Index
=
ElementIndex
|
ResidueIndex
|
ChainIndex
|
EntityIndex
export
type
Level
=
'
atom
'
|
'
residue
'
|
'
chain
'
|
'
entity
'
export
interface
ExportCtx
<
T
>
{
elements
:
StructureElement
[],
property
(
index
:
number
):
T
}
export
function
getCifDataSource
<
Idx
extends
Index
,
T
>
(
structure
:
Structure
,
prop
:
IndexedCustomProperty
<
Idx
,
T
>
|
undefined
,
cache
:
any
):
CifWriter
.
Category
.
Instance
[
'
source
'
][
0
]
{
if
(
!
prop
)
return
{
rowCount
:
0
};
if
(
cache
&&
cache
[
prop
.
id
])
return
cache
[
prop
.
id
];
const
data
=
prop
.
getExportContext
(
structure
);
const
ret
=
{
data
,
rowCount
:
data
.
elements
.
length
};
if
(
cache
)
cache
[
prop
.
id
]
=
ret
;
return
ret
;
}
export
type
Atom
<
T
>
=
IndexedCustomProperty
<
ElementIndex
,
T
>
export
function
fromAtomMap
<
T
>
(
map
:
Map
<
ElementIndex
,
T
>
):
Atom
<
T
>
{
return
new
ElementMappedCustomProperty
(
map
);
}
export
function
fromAtomArray
<
T
>
(
array
:
ArrayLike
<
T
>
):
Atom
<
T
>
{
// TODO: create "array based custom property" as optimization
return
new
ElementMappedCustomProperty
(
arrayToMap
(
array
));
}
export
type
Residue
<
T
>
=
IndexedCustomProperty
<
ResidueIndex
,
T
>
const
getResidueSegments
=
(
model
:
Model
)
=>
model
.
atomicHierarchy
.
residueAtomSegments
;
export
function
fromResidueMap
<
T
>
(
map
:
Map
<
ResidueIndex
,
T
>
):
Residue
<
T
>
{
return
new
SegmentedMappedIndexedCustomProperty
(
'
residue
'
,
map
,
getResidueSegments
,
Unit
.
Kind
.
Atomic
);
}
export
function
fromResidueArray
<
T
>
(
array
:
ArrayLike
<
T
>
):
Residue
<
T
>
{
// TODO: create "array based custom property" as optimization
return
new
SegmentedMappedIndexedCustomProperty
(
'
residue
'
,
arrayToMap
(
array
),
getResidueSegments
,
Unit
.
Kind
.
Atomic
);
}
export
type
Chain
<
T
>
=
IndexedCustomProperty
<
ChainIndex
,
T
>
const
getChainSegments
=
(
model
:
Model
)
=>
model
.
atomicHierarchy
.
chainAtomSegments
;
export
function
fromChainMap
<
T
>
(
map
:
Map
<
ChainIndex
,
T
>
):
Chain
<
T
>
{
return
new
SegmentedMappedIndexedCustomProperty
(
'
chain
'
,
map
,
getChainSegments
,
Unit
.
Kind
.
Atomic
);
}
export
function
fromChainArray
<
T
>
(
array
:
ArrayLike
<
T
>
):
Chain
<
T
>
{
// TODO: create "array based custom property" as optimization
return
new
SegmentedMappedIndexedCustomProperty
(
'
chain
'
,
arrayToMap
(
array
),
getChainSegments
,
Unit
.
Kind
.
Atomic
);
}
export
type
Entity
<
T
>
=
IndexedCustomProperty
<
EntityIndex
,
T
>
export
function
fromEntityMap
<
T
>
(
map
:
Map
<
EntityIndex
,
T
>
):
Entity
<
T
>
{
return
new
EntityMappedCustomProperty
(
map
);
}
}
function
arrayToMap
<
Idx
extends
IndexedCustomProperty
.
Index
,
T
>
(
array
:
ArrayLike
<
T
>
):
Map
<
Idx
,
T
>
{
const
ret
=
new
Map
<
Idx
,
T
>
();
for
(
let
i
=
0
as
Idx
,
_i
=
array
.
length
;
i
<
_i
;
i
++
)
ret
.
set
(
i
,
array
[
i
]);
return
ret
;
}
class
SegmentedMappedIndexedCustomProperty
<
Idx
extends
IndexedCustomProperty
.
Index
,
T
=
any
>
implements
IndexedCustomProperty
<
Idx
,
T
>
{
readonly
id
:
UUID
=
UUID
.
create
();
readonly
id
:
UUID
=
UUID
.
create
();
readonly
kind
:
Unit
.
Kind
;
readonly
kind
:
Unit
.
Kind
;
has
(
idx
:
Idx
):
boolean
{
return
this
.
map
.
has
(
idx
);
}
has
(
idx
:
Idx
):
boolean
{
return
this
.
map
.
has
(
idx
);
}
...
@@ -25,7 +96,7 @@ export class IndexedCustomProperty<Idx extends IndexedCustomProperty.Index, T =
...
@@ -25,7 +96,7 @@ export class IndexedCustomProperty<Idx extends IndexedCustomProperty.Index, T =
const
unitGroups
=
structure
.
unitSymmetryGroups
;
const
unitGroups
=
structure
.
unitSymmetryGroups
;
const
loci
:
StructureElement
[]
=
[];
const
loci
:
StructureElement
[]
=
[];
const
segments
=
this
.
segmentGetter
(
models
[
0
])
const
segments
=
this
.
segmentGetter
(
models
[
0
])
;
for
(
const
unitGroup
of
unitGroups
)
{
for
(
const
unitGroup
of
unitGroups
)
{
const
unit
=
unitGroup
.
units
[
0
];
const
unit
=
unitGroup
.
units
[
0
];
...
@@ -52,37 +123,101 @@ export class IndexedCustomProperty<Idx extends IndexedCustomProperty.Index, T =
...
@@ -52,37 +123,101 @@ export class IndexedCustomProperty<Idx extends IndexedCustomProperty.Index, T =
return
{
elements
,
property
:
i
=>
this
.
get
(
index
[
elements
[
i
].
element
])
!
};
return
{
elements
,
property
:
i
=>
this
.
get
(
index
[
elements
[
i
].
element
])
!
};
}
}
constructor
(
private
map
:
Map
<
Idx
,
T
>
,
private
segmentGetter
:
(
model
:
Model
)
=>
Segmentation
<
ElementIndex
,
Idx
>
,
kind
:
Unit
.
Kind
)
{
constructor
(
public
level
:
'
residue
'
|
'
chain
'
,
private
map
:
Map
<
Idx
,
T
>
,
private
segmentGetter
:
(
model
:
Model
)
=>
Segmentation
<
ElementIndex
,
Idx
>
,
kind
:
Unit
.
Kind
)
{
this
.
kind
=
kind
;
this
.
kind
=
kind
;
}
}
}
}
export
namespace
IndexedCustomProperty
{
class
ElementMappedCustomProperty
<
T
=
any
>
implements
IndexedCustomProperty
<
ElementIndex
,
T
>
{
export
type
Index
=
ResidueIndex
|
ChainIndex
readonly
id
:
UUID
=
UUID
.
create
();
readonly
kind
:
Unit
.
Kind
;
readonly
level
=
'
atom
'
;
has
(
idx
:
ElementIndex
):
boolean
{
return
this
.
map
.
has
(
idx
);
}
get
(
idx
:
ElementIndex
)
{
return
this
.
map
.
get
(
idx
);
}
export
interface
ExportCtx
<
T
>
{
private
getStructureElements
(
structure
:
Structure
)
{
elements
:
StructureElement
[],
const
models
=
structure
.
models
;
property
(
index
:
number
):
T
if
(
models
.
length
!==
1
)
throw
new
Error
(
`Only works on structures with a single model.`
);
const
seenIndices
=
new
Set
<
ElementIndex
>
();
const
unitGroups
=
structure
.
unitSymmetryGroups
;
const
loci
:
StructureElement
[]
=
[];
for
(
const
unitGroup
of
unitGroups
)
{
const
unit
=
unitGroup
.
units
[
0
];
if
(
unit
.
kind
!==
this
.
kind
)
{
continue
;
}
}
export
function
getCifDataSource
<
Idx
extends
Index
,
T
>
(
structure
:
Structure
,
prop
:
IndexedCustomProperty
<
Idx
,
T
>
|
undefined
,
cache
:
any
):
CifWriter
.
Category
.
Instance
[
'
source
'
][
0
]
{
const
elements
=
unit
.
elements
;
if
(
!
prop
)
return
{
rowCount
:
0
};
for
(
let
i
=
0
,
_i
=
elements
.
length
;
i
<
_i
;
i
++
)
{
if
(
cache
&&
cache
[
prop
.
id
])
return
cache
[
prop
.
id
];
const
e
=
elements
[
i
];
const
data
=
prop
.
getExportContext
(
structure
)
;
if
(
!
this
.
has
(
e
)
||
seenIndices
.
has
(
e
))
continue
;
const
ret
=
{
data
,
rowCount
:
data
.
elements
.
length
}
;
seenIndices
.
add
(
elements
[
i
])
;
if
(
cache
)
cache
[
prop
.
id
]
=
ret
;
loci
[
loci
.
length
]
=
StructureElement
.
create
(
unit
,
e
)
;
return
ret
;
}
}
}
export
type
Residue
<
T
>
=
IndexedCustomProperty
<
ResidueIndex
,
T
>
loci
.
sort
((
x
,
y
)
=>
x
.
element
-
y
.
element
);
const
getResidueSegments
=
(
model
:
Model
)
=>
model
.
atomicHierarchy
.
residueAtomSegments
;
return
loci
;
export
function
fromResidueMap
<
T
>
(
map
:
Map
<
ResidueIndex
,
T
>
,
kind
:
Unit
.
Kind
):
Residue
<
T
>
{
return
new
IndexedCustomProperty
(
map
,
getResidueSegments
,
kind
);
}
}
export
type
Chain
<
T
>
=
IndexedCustomProperty
<
ChainIndex
,
T
>
getExportContext
(
structure
:
Structure
):
IndexedCustomProperty
.
ExportCtx
<
T
>
{
const
getChainSegments
=
(
model
:
Model
)
=>
model
.
atomicHierarchy
.
chainAtomSegments
;
const
elements
=
this
.
getStructureElements
(
structure
);
export
function
fromChainMap
<
T
>
(
map
:
Map
<
ChainIndex
,
T
>
,
kind
:
Unit
.
Kind
):
Chain
<
T
>
{
return
{
elements
,
property
:
i
=>
this
.
get
(
elements
[
i
].
element
)
!
};
return
new
IndexedCustomProperty
(
map
,
getChainSegments
,
kind
);
}
constructor
(
private
map
:
Map
<
ElementIndex
,
T
>
)
{
this
.
kind
=
Unit
.
Kind
.
Atomic
;
}
}
class
EntityMappedCustomProperty
<
T
=
any
>
implements
IndexedCustomProperty
<
EntityIndex
,
T
>
{
readonly
id
:
UUID
=
UUID
.
create
();
readonly
kind
:
Unit
.
Kind
;
readonly
level
=
'
entity
'
;
has
(
idx
:
EntityIndex
):
boolean
{
return
this
.
map
.
has
(
idx
);
}
get
(
idx
:
EntityIndex
)
{
return
this
.
map
.
get
(
idx
);
}
private
getStructureElements
(
structure
:
Structure
)
{
const
models
=
structure
.
models
;
if
(
models
.
length
!==
1
)
throw
new
Error
(
`Only works on structures with a single model.`
);
const
index
=
models
[
0
].
atomicHierarchy
.
index
;
const
seenIndices
=
new
Set
<
EntityIndex
>
();
const
unitGroups
=
structure
.
unitSymmetryGroups
;
const
loci
:
StructureElement
[]
=
[];
const
segments
=
models
[
0
].
atomicHierarchy
.
chainAtomSegments
;
for
(
const
unitGroup
of
unitGroups
)
{
const
unit
=
unitGroup
.
units
[
0
];
if
(
unit
.
kind
!==
this
.
kind
)
{
continue
;
}
const
chains
=
Segmentation
.
transientSegments
(
segments
,
unit
.
elements
);
while
(
chains
.
hasNext
)
{
const
seg
=
chains
.
move
();
const
eI
=
index
.
getEntityFromChain
(
seg
.
index
);
if
(
!
this
.
has
(
eI
)
||
seenIndices
.
has
(
eI
))
continue
;
seenIndices
.
add
(
eI
);
loci
[
loci
.
length
]
=
StructureElement
.
create
(
unit
,
unit
.
elements
[
seg
.
start
]);
}
}
loci
.
sort
((
x
,
y
)
=>
x
.
element
-
y
.
element
);
return
loci
;
}
getExportContext
(
structure
:
Structure
):
IndexedCustomProperty
.
ExportCtx
<
T
>
{
const
elements
=
this
.
getStructureElements
(
structure
);
const
chainIndex
=
structure
.
model
.
atomicHierarchy
.
chainAtomSegments
.
index
;
const
index
=
structure
.
model
.
atomicHierarchy
.
index
;
return
{
elements
,
property
:
i
=>
this
.
get
(
index
.
getEntityFromChain
(
chainIndex
[
elements
[
i
].
element
]))
!
};
}
constructor
(
private
map
:
Map
<
EntityIndex
,
T
>
)
{
this
.
kind
=
Unit
.
Kind
.
Atomic
;
}
}
}
}
\ No newline at end of file
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