LiteMol:SelectionAlgebra - Revision history

Matthew: edited by MJC

2017-05-05T12:23:12Z

edited by MJC

← Older revision		Revision as of 12:23, 5 May 2017
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	LiteMol has an atom selection language available, ~~similarly~~ to ~~the~~ other structure visualization tools such as VMD or PyMOL. The '''LiteMol selection algebra''' is inspired by our other service - [[PatternQuery:UserManual \| PatternQuery]]. While in the present version the selection syntax will be mainly used by method developers, syntax enabling the use of [[LiteMol:SelectionAlgebra#PyMOL \| PyMOL ]] and possibly [[LiteMol:SelectionAlgebra#VMD\| VMD]] selection algebra will be introduced in a near future.		LiteMol has an atom selection language available, similar to other structure visualization tools such as VMD or PyMOL. The '''LiteMol selection algebra''' is inspired by our other service - [[PatternQuery:UserManual \| PatternQuery]]. While in the present version the selection syntax will be mainly used by method developers, syntax enabling the use of [[LiteMol:SelectionAlgebra#PyMOL \| PyMOL ]] and possibly [[LiteMol:SelectionAlgebra#VMD\| VMD]] selection algebra will be introduced in the near future.


	=LiteMol selection algebra=		=LiteMol selection algebra=

	Molecular selections can be created in two different active contexts - [[LiteMol:Hierarchy#Molecule_Model_.28MM.29 \| model of molecule]] or [[LiteMol:Hierarchy#Molecule_Visual_.28VM.29 \| molecule visual]]. If either of the contexts is active in the entity tree, the right panel is populated with the '''Selection''' action. Next, you can create named selection using dedicated query language and further modify the visual part of your selection.		Molecular selections can be created in two different active contexts - [[LiteMol:Hierarchy#Molecule_Model_.28MM.29 \| model of molecule]] or [[LiteMol:Hierarchy#Molecule_Visual_.28VM.29 \| molecule visual]]. If either of the contexts is active in the entity tree, the right panel is populated with the '''Selection''' action. Next, you can create a named selection using the dedicated query language and further modify the visual part of your selection.


	{{large\| '''Notice:'''}} Arguments of LiteMol selection queries are '''case sensitive'''!		{{large\| '''Notice:'''}} Arguments of LiteMol selection queries are '''case sensitive'''!

	Meaning: '''GLY''' is a common non-polar residue found in PDB entries, whereas '''Gly''', '''gly''', or '''G''' ~~does~~ not exist.		Meaning: '''GLY''' is a common non-polar residue found in PDB entries, whereas '''Gly''', '''gly''', or '''G''' do not exist.

	==Basic queries==		==Basic queries==

Lukas at 13:56, 4 April 2017

2017-04-04T13:56:18Z

← Older revision		Revision as of 13:56, 4 April 2017
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	!Selection description		!Selection description
	\|-		\|-
	\| <code> or(Selection[]) </code>		\| <code> or(selections: Selection[]) </code>
	\| <code> or(residuesByName('HEM').ambientResidues(5), chainsById('A')) </code>		\| <code> or(residuesByName('HEM').ambientResidues(5), chainsById('A')) </code>
	\| Merges several selections.		\| Merges several selections.
	\|-		\|-
	\| <code> intersectWith(where: Selection, Selection) </code>		\| <code> intersectWith(where: Selection, sel: Selection) </code>
	\| <code> residuesByName('HEM').ambientResidues(5).intersectWith(chainsById('A')) </code>		\| <code> residuesByName('HEM').ambientResidues(5).intersectWith(chainsById('A')) </code>
	\| Finds intersection between two selections.		\| Finds intersection between two selections.

Lukas at 13:54, 4 April 2017

2017-04-04T13:54:20Z

← Older revision		Revision as of 13:54, 4 April 2017
Line 1:		Line 1:
	LiteMol has an atom selection language available, similarly to the other structure visualization tools such as VMD or PyMOL. The '''LiteMol selection algebra''' is inspired by our other service - [[PatternQuery:UserManual \| PatternQuery]]~~, although~~ in the present version the ~~amount of integrated queries is somewhat limited. Additionally~~, ~~as a feature LiteMol will contain a parser of~~ syntax enabling the use of [[LiteMol:SelectionAlgebra#PyMOL \| PyMOL ]] and possibly [[LiteMol:SelectionAlgebra#VMD\| VMD]] selection algebra.		LiteMol has an atom selection language available, similarly to the other structure visualization tools such as VMD or PyMOL. The '''LiteMol selection algebra''' is inspired by our other service - [[PatternQuery:UserManual \| PatternQuery]]. While in the present version the selection syntax will be mainly used by method developers, syntax enabling the use of [[LiteMol:SelectionAlgebra#PyMOL \| PyMOL ]] and possibly [[LiteMol:SelectionAlgebra#VMD\| VMD]] selection algebra will be introduced in a near future.


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	{{large\| '''Notice:'''}} Arguments of LiteMol selection queries are '''case sensitive'''!		{{large\| '''Notice:'''}} Arguments of LiteMol selection queries are '''case sensitive'''!

	Meaning: GLY is a common non-polar residue found in ~~the~~ PDB entries, whereas Gly, or ~~gly~~ does not exist.		Meaning: '''GLY''' is a common non-polar residue found in PDB entries, whereas '''Gly''', '''gly''', or '''G''' does not exist.

	==Basic queries==		==Basic queries==
	{\| class="wikitable"		{\| class="wikitable"
	! colspan="3" \| List of selection queries		! colspan="3" \| List of selection queries
	\|-		\|-
	!		!Query definition
	Query		!Example
	!		!Selection description
	~~Examples~~
	!
	Selection description
	\|-		\|-
	\| <code> atomsByElement() </code >		\| <code> atomsByElement(elements: string[]) </code >
	\| <code> atomsByElement('C'), atomsByElement('C','O') </code>		\| <code> atomsByElement('C'), atomsByElement('C','O') </code>
	\| Atoms based on their element symbol (field ''_atom_site.type_symbol'').		\| Atoms based on their element symbol (field ''_atom_site.type_symbol'').
	\|-		\|-
	\| <code> atomsByName() </code>		\| <code> atomsByName(elements: string[]) </code>
	\| <code> atomsByName('C'), atomsByName('N','CA','C','O') </code>		\| <code> atomsByName('C'), atomsByName('N','CA','C','O') </code>
	\| Atoms based on their atom name (field ''_atom_site.label_atom_id'').		\| Atoms based on their atom name (field ''_atom_site.label_atom_id'').
	\|-		\|-
	\| <code> atomsById() </code>		\| <code> atomsById(numbers: number[]) </code>
	\| <code> atomsById(1), atomsById(1,2,3) </code>		\| <code> atomsById(1), atomsById(1,2,3) </code>
	\| Atoms based on their integer identifier (field ''_atom_site.id '').		\| Atoms based on their integer identifier (field ''_atom_site.id '').
	\|-		\|-
	\| <code> residuesByName() </code>		\| <code> residuesByName(elements: string[]) </code>
	\| <code> residuesByName('GLY'), residuesByName('ALA~~', 'HEM~~', 'PO4') </code>		\| <code> residuesByName('GLY'), residuesByName('ALA', 'PO4') </code>
	\| Residues based on their residue name (field ''_atom_site.label_comp_id'').		\| Residues based on their residue name (field ''_atom_site.label_comp_id'').
	\|-		\|-
	\| <code> residuesById() </code>		\| <code> residuesById(numbers: number[]) </code>
	\| <code> residuesById(100), residuesById(42,157,238) </code>		\| <code> residuesById(100), residuesById(42,157,238) </code>
	\| Residues based on integer identified (field ''_atom_site.auth_seq_id'').		\| Residues based on integer identified (field ''_atom_site.auth_seq_id'').
	\|-		\|-
	\| <code> chainsById() </code>		\| <code> chainsById(elements: string[]) </code>
	\| <code> chainsById('A'), chainsById('A', 'B') </code>		\| <code> chainsById('A'), chainsById('A', 'B') </code>
	\| Polymer chains based on their id (field ''_atom_site.auth_asym_id'').		\| Polymer chains based on their id (field ''_atom_site.auth_asym_id'').
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	\| <code> backbone() </code>		\| <code> backbone() </code>
	\| <code> backbone() </code>		\| <code> backbone() </code>
	\| Extracts structure backbone defined by certain atom names. '''Protein:''' ''N'', ''CA'', ''C'', ''O''. '''Nucleotide:''' ''P'', ''OP1'', ''OP2'', ''O3' '', ''O5' '', ''C3' '', ''C5' ''		\| Extracts structure backbone defined by certain atom names. '''Protein:''' ''N'', ''CA'', ''C'', ''O''. '''Nucleotide:''' ''P'', ''OP1'', ''OP2'', ''O3' '', ''O5' '', ''C3' '', ''C5' ''.
	\|-		\|-
	\| <code> sidechain() </code>		\| <code> sidechain() </code>
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	\|<code> cartoon() </code>		\|<code> cartoon() </code>
	\|<code> cartoon() </code>		\|<code> cartoon() </code>
	\| Extracts atoms vital for ''polymer'' cartoon visualization based on their names: ''CA'', ''O'', ''O5' '', ''C3' '', ''N3''		\| Extracts atoms vital for ''polymer'' cartoon visualization based on their names: ''CA'', ''O'', ''O5' '', ''C3' '', ''N3''.
	\|-		\|-
	\| <code> everything() </code>		\| <code> everything() </code>
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	Selection description		Selection description
	\|-		\|-
	\| <code> inside() </code>		\| <code> inside(where: Selection, sel: Selection) </code>
	\| <code> residuesByName('GLY').inside(chainsById('A')) </code>		\| <code> residuesByName('GLY').inside(chainsById('A')) </code>
	\| ~~All ''Gly'' residues on the ''A'' chain~~		\| Finds selection within another selection.
	\|-		\|-
	\| <code> ambientResidues() </code>		\| <code> ambientResidues(where: Selection, nmb: number ) </code>
	\| <code> residuesByName('HEM').ambientResidues(5) </code>		\| <code> residuesByName('HEM').ambientResidues(5) </code>
	\| ~~Blabla~~		\| Surrounds the inner selection by residues that have at least one atom within the given radius
	\|-		\|-
	\| <code> wholeResidues() </code>		\| <code> wholeResidues(where: Selection) </code>
	\| <code> atomsByElement('Pt').wholeResidues() </code>		\| <code> atomsByElement('Pt').wholeResidues() </code>
	\| ~~Blabla~~		\| Surrounds the inner selection by all atoms of residue's origin.
	\|-		\|-
	\|}		\|}
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	! colspan="3" \| List of selection queries		! colspan="3" \| List of selection queries
	\|-		\|-
	!		!Query
	Query		!Examples
	!		!Selection description
	Examples
	!
	Selection description
	\|-		\|-
	\| <code> or() </code>		\| <code> or(Selection[]) </code>
	\| <code> or() </code>		\| <code> or(residuesByName('HEM').ambientResidues(5), chainsById('A')) </code>
	\| ~~blabla~~		\| Merges several selections.
	\|-		\|-
	\| <code> intersectWith() </code>		\| <code> intersectWith(where: Selection, Selection) </code>
	\| <code> residuesByName('HEM').ambientResidues(5).intersectWith(chainsById('A')) </code>		\| <code> residuesByName('HEM').ambientResidues(5).intersectWith(chainsById('A')) </code>
	\| ~~All the ..~~.		\| Finds intersection between two selections.
	\|-		\|-
	\| <code> ~~wholeResidues~~() </code>		\| <code> complement(where: Selection) </code>
	\| <code> ~~atomsByElement~~('Pt').~~wholeResidues~~() </code>		\| <code> chainsById('A').complement() </code>
	\| ~~Blabla~~		\| Finds the complement of the inner selection to the active context.
	\|-		\|-
	\|}		\|}

	~~==PyMOL==~~
	~~In preparation...~~

	~~==VMD==~~
	~~In preparation...~~

Lukas at 17:23, 3 April 2017

2017-04-03T17:23:45Z

@@ Line 10: / Line 10: @@
 Meaning: GLY is a common non-polar residue found in the PDB entries, whereas Gly, or gly does not exist.
+==Basic queries==
 {| class="wikitable"
 ! colspan="3" | List of selection queries
@@ Line 32: / Line 32: @@
 | <code>  atomsById(1), atomsById(1,2,3) </code>
 | Atoms based on their integer identifier (field ''_atom_site.id '').
 |-
 | <code>  residuesByName() </code>
@@ Line 45: / Line 41: @@
 | Residues based on integer identified (field ''_atom_site.auth_seq_id'').
 |-
-| <code>  chains() </code>
+| <code>  chainsById() </code>
-| <code>  chains('A'), chains('A','B','C') </code>
+| <code>  chainsById('A'), chainsById('A', 'B') </code>
 | Polymer chains based on their id (field ''_atom_site.auth_asym_id'').
 |}
-{{huge | TODO inside query and logical combinations}}
+==Logical queries==
 ==PyMOL==

Lukas: Created page with "LiteMol has an atom selection language available, similarly to the other structure visualization tools such as VMD or PyMOL. The '''LiteMol selection algebra''' is inspired by..."

2016-07-21T14:56:12Z

Created page with "LiteMol has an atom selection language available, similarly to the other structure visualization tools such as VMD or PyMOL. The '''LiteMol selection algebra''' is inspired by..."

New page

LiteMol has an atom selection language available, similarly to the other structure visualization tools such as VMD or PyMOL. The '''LiteMol selection algebra''' is inspired by our other service - [[PatternQuery:UserManual | PatternQuery]], although in the present version the amount of integrated queries is somewhat limited. Additionally, as a feature LiteMol will contain a parser of syntax enabling the use of [[LiteMol:SelectionAlgebra#PyMOL | PyMOL ]] and possibly [[LiteMol:SelectionAlgebra#VMD| VMD]] selection algebra.

=LiteMol selection algebra=

Molecular selections can be created in two different active contexts - [[LiteMol:Hierarchy#Molecule_Model_.28MM.29 | model of molecule]] or [[LiteMol:Hierarchy#Molecule_Visual_.28VM.29 | molecule visual]]. If either of the contexts is active in the entity tree, the right panel is populated with the '''Selection''' action. Next, you can create named selection using dedicated query language and further modify the visual part of your selection.

{{large| '''Notice:'''}} Arguments of LiteMol selection queries are '''case sensitive'''!

Meaning: GLY is a common non-polar residue found in the PDB entries, whereas Gly, or gly does not exist.

{| class="wikitable"
! colspan="3" | List of selection queries
|-
!
Query
!
Examples
!
Selection description
|-
| <code> atomsByElement() </code >
| <code> atomsByElement('C'), atomsByElement('C','O') </code>
| Atoms based on their element symbol (field ''_atom_site.type_symbol'').
|-
| <code> atomsByName() </code>
| <code> atomsByName('C'), atomsByName('N','CA','C','O') </code>
| Atoms based on their atom name (field ''_atom_site.label_atom_id'').
|-
| <code> atomsById() </code>
| <code> atomsById(1), atomsById(1,2,3) </code>
| Atoms based on their integer identifier (field ''_atom_site.id '').
|-
| <code> atomsByName() </code>
| <code> atomsByName('C'), atomsByName('N', 'CA', 'C', 'O') </code>
| Atoms based on their atom name (field ''_atom_site.label_atom_id'').
|-
| <code> residuesByName() </code>
| <code> residuesByName('GLY'), residuesByName('ALA', 'HEM', 'PO4') </code>
| Residues based on their residue name (field ''_atom_site.label_comp_id'').
|-
| <code> residuesById() </code>
| <code> residuesById(100), residuesById(42,157,238) </code>
| Residues based on integer identified (field ''_atom_site.auth_seq_id'').
|-
| <code> chains() </code>
| <code> chains('A'), chains('A','B','C') </code>
| Polymer chains based on their id (field ''_atom_site.auth_asym_id'').
|}

{{huge | TODO inside query and logical combinations}}

==PyMOL==
In preparation...

==VMD==
In preparation...