PatternQuery:Language Reference - Revision history

Lukas: /* Geometry Functions */

2016-07-11T12:38:24Z

Geometry Functions

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 : <code>Near(4, Atoms("Ca"), Atoms("Ca"), Rings(5 * ["C"] + ["O"]))</code>
 :: ''Finds all instance of a single ring with 5C and O atoms and two Ca atoms that are closer than 4 (angstroms).''
 <br/>
 == Meta-data Functions ==
 ''Functions dealing with meta-data about structures such as release date or authors.''

Lukas: Lukas moved page MotiveQuery:Language Reference to PatternQuery:Language Reference

2015-04-25T13:26:17Z

Lukas moved page MotiveQuery:Language Reference to PatternQuery:Language Reference

← Older revision	Revision as of 13:26, 25 April 2015
(No difference)

Dave at 20:48, 23 April 2015

2015-04-23T20:48:18Z

← Older revision		Revision as of 20:48, 23 April 2015
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	* '''<code>PatternSeq</code>''' is a sequence of '''<code>Pattern</code>''' (the sets of atoms).		* '''<code>PatternSeq</code>''' is a sequence of '''<code>Pattern</code>''' (the sets of atoms).

	When a molecule is queried, say using the expression <code>Rings(5 * ["C"] + ["O"])</code> a sequences of patterns each containing 6 atoms (5 C and 1 O) is returned. However, some functions such as <code>Filter</code> need to operate on a single pattern (the set of atoms) - not the whole sequences. The query <code>~~Filter(~~Residues(), lambda r: r.Count(Atoms()) > 10)</code> first finds all residue patterns ('''<code>PatternSeq</code>''') and then passes every single '''<code>Pattern</code>''' (set of atoms) to a function that counts the atoms in the pattern and returns True if there is at least 11 of them. This is the reasoning behind these two types.		When a molecule is queried, say using the expression <code>Rings(5 * ["C"] + ["O"])</code> a sequences of patterns each containing 6 atoms (5 C and 1 O) is returned. However, some functions such as <code>Filter</code> need to operate on a single pattern (the set of atoms) - not the whole sequences. The query <code>Residues().Filter(lambda r: r.Count(Atoms()) > 10)</code> first finds all residue patterns ('''<code>PatternSeq</code>''') and then passes every single '''<code>Pattern</code>''' (set of atoms) to a function that counts the atoms in the pattern and returns True if there is at least 11 of them. This is the reasoning behind these two types.

	== Basic Query Functions ==		== Basic Query Functions ==

Dave at 20:47, 23 April 2015

2015-04-23T20:47:45Z

← Older revision		Revision as of 20:47, 23 April 2015
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	* '''<code>PatternSeq</code>''' is a sequence of '''<code>Pattern</code>''' (the sets of atoms).		* '''<code>PatternSeq</code>''' is a sequence of '''<code>Pattern</code>''' (the sets of atoms).

	When a molecule is queried, say using the expression <code>Rings(5 * ["C"] + ["O"])</code> a sequences of patterns each containing 6 atoms (5 C and 1 O) is returned. However, some functions such as <code>Filter</code> need to operate on a single pattern (the set of atoms) - not the whole sequences. The query <code>Filter(Residues(), lambda r: r.Count(Atoms()) > 10)</code> first finds all residue patterns ('''<code>PatternSeq</code>''') and then passes every single '''<code>Pattern</code>''' (set of atoms) to a function that counts the atoms in the pattern and returns True if there is at least 11 of them. This is the reasoning behind these two types.== Basic Query Functions ==		When a molecule is queried, say using the expression <code>Rings(5 * ["C"] + ["O"])</code> a sequences of patterns each containing 6 atoms (5 C and 1 O) is returned. However, some functions such as <code>Filter</code> need to operate on a single pattern (the set of atoms) - not the whole sequences. The query <code>Filter(Residues(), lambda r: r.Count(Atoms()) > 10)</code> first finds all residue patterns ('''<code>PatternSeq</code>''') and then passes every single '''<code>Pattern</code>''' (set of atoms) to a function that counts the atoms in the pattern and returns True if there is at least 11 of them. This is the reasoning behind these two types.

			== Basic Query Functions ==
	''Basic building blocks of the language - i.e. atoms, residues, and the like.''		''Basic building blocks of the language - i.e. atoms, residues, and the like.''
	=== AminoAcids ===		=== AminoAcids ===

Dave at 20:46, 23 April 2015

2015-04-23T20:46:56Z

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Dave: /* RegularMotifs */

2015-01-07T21:35:02Z

RegularMotifs

← Older revision		Revision as of 21:35, 7 January 2015
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	<code>RegularMotifs(regex: Value) -> FragmentSeq</code><br/>		<code>RegularMotifs(regex: Value) -> FragmentSeq</code><br/>
	''Identifies regular motifs. The protein is split into individual chains and the residues are sorted by their Sequence Number before the motifs are identified. The query does not check if adjacent residues have consecutive Sequence Numbers. The query works in two modes: Amino and Nucleotide, on amino acids and nucleotides respectively. In the Amino mode, all the derivatives of standard residues are treated as the standard residues, as long as this information is properly annotated in MODRES or _pdbx_struct_mod_residue field. The default mode is 'Amino'''<br/>		''Identifies regular motifs. The protein is split into individual chains and the residues are sorted by their Sequence Number before the motifs are identified. The query does not check if adjacent residues have consecutive Sequence Numbers. The query works in two modes: Amino and Nucleotide, on amino acids and nucleotides respectively. In the Amino mode, all the derivatives of standard residues are treated as the standard residues, as long as this information is properly annotated in MODRES or _pdbx_struct_mod_residue field. The default mode is 'Amino'''<br/>


	;Arguments		;Arguments

Lukas: /* RegularMotifs */

2015-01-07T21:29:12Z

RegularMotifs

← Older revision		Revision as of 21:29, 7 January 2015
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	=== RegularMotifs ===		=== RegularMotifs ===
	<code>RegularMotifs(regex: Value) -> FragmentSeq</code><br/>		<code>RegularMotifs(regex: Value) -> FragmentSeq</code><br/>
	''Identifies regular motifs. The protein is split into individual chains and the residues are sorted by their Sequence Number before the motifs are identified. The query does not check if adjacent residues have consecutive Sequence Numbers. The query works in two modes: Amino and Nucleotide, on amino acids and nucleotides respectively. The default mode is 'Amino'''<br/>		''Identifies regular motifs. The protein is split into individual chains and the residues are sorted by their Sequence Number before the motifs are identified. The query does not check if adjacent residues have consecutive Sequence Numbers. The query works in two modes: Amino and Nucleotide, on amino acids and nucleotides respectively. In the Amino mode, all the derivatives of standard residues are treated as the standard residues, as long as this information is properly annotated in MODRES or _pdbx_struct_mod_residue field. The default mode is 'Amino'''<br/>


	;Arguments		;Arguments
	: regex: Value - ''Regular expression on one letter abbreviations of amino acids.''		: regex: Value - ''Regular expression on one letter abbreviations of amino acids.''
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	:: ''Finds all 4 residue motifs with ?-HIS-CYS-? that are connected.''		:: ''Finds all 4 residue motifs with ?-HIS-CYS-? that are connected.''
	----		----

	=== ResidueIdRange ===		=== ResidueIdRange ===
	<code>ResidueIdRange(chain: String, min: Integer, max: ?Integer) -> Residues</code><br/>		<code>ResidueIdRange(chain: String, min: Integer, max: ?Integer) -> Residues</code><br/>

Lukas: /* Using MotiveQuery in Silverlight applications */

2014-12-26T20:32:45Z

Using MotiveQuery in Silverlight applications

← Older revision		Revision as of 20:32, 26 December 2014
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	<pre>q = ResidueSimilarity(Fragment("model"), Current())		<pre>q = ResidueSimilarity(Fragment("model"), Current())
	MQ.Execute(q, Session.Structures)</pre>		MQ.Execute(q, Session.Structures)</pre>
	: ''This command computes the residue similarity (Jaccard coefficient) for the structure with id 'model' (which is loaded using the Fragment function) and all other loaded structures (computed one by one using the function Current()). The result is returned in CSV format.''== Basic Query Functions ==		: ''This command computes the residue similarity (Jaccard coefficient) for the structure with id 'model' (which is loaded using the Fragment function) and all other loaded structures (computed one by one using the function Current()). The result is returned in CSV format.''

			== Basic Query Functions ==
	''Basic building blocks of the language - i.e. atoms, residues, and the like.''		''Basic building blocks of the language - i.e. atoms, residues, and the like.''
	=== AminoAcids ===		=== AminoAcids ===
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	:: ''Returns all sheets.''		:: ''Returns all sheets.''
	<br/>		<br/>

	== Advanced Query Functions ==		== Advanced Query Functions ==
	''Advanced building blocks of the language.''		''Advanced building blocks of the language.''

Dave at 20:23, 17 December 2014

2014-12-17T20:23:38Z

← Older revision		Revision as of 20:23, 17 December 2014
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	<pre>q = ResidueSimilarity(Fragment("model"), Current())		<pre>q = ResidueSimilarity(Fragment("model"), Current())
	MQ.Execute(q, Session.Structures)</pre>		MQ.Execute(q, Session.Structures)</pre>
	: ''This command computes the residue similarity (Jaccard coefficient) for the structure with id 'model' (which is loaded using the Fragment function) and all other loaded structures (computed one by one using the function Current()). The result is returned in CSV format.''		: ''This command computes the residue similarity (Jaccard coefficient) for the structure with id 'model' (which is loaded using the Fragment function) and all other loaded structures (computed one by one using the function Current()). The result is returned in CSV format.''== Basic Query Functions ==
	== Basic Query Functions ==
	''Basic building blocks of the language - i.e. atoms, residues, and the like.''		''Basic building blocks of the language - i.e. atoms, residues, and the like.''
	=== AminoAcids ===		=== AminoAcids ===
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	: <code>Atoms().Filter(lambda m: m.NearestDistanceTo(Residues("ASP")) >= 5)</code>		: <code>Atoms().Filter(lambda m: m.NearestDistanceTo(Residues("ASP")) >= 5)</code>
	:: ''Finds all atoms that are at least 5 (angstroms) away from any ASP residue.''		:: ''Finds all atoms that are at least 5 (angstroms) away from any ASP residue.''
			----
			=== SeqCount ===
			<code>SeqCount(what: FragmentSeq) -> Integer</code><br/>
			''Counts the length of a sequence of motifs.''<br/>
			;Arguments
			: what: FragmentSeq - ''What fragment sequence to count.''
			;Examples
			: <code>Atoms("Zn").AmbientResidues(3).Filter(lambda m: m.Find(Residues("HIS")).SeqCount() > 1)</code>
			:: ''Returns a sequence of fragments with Zn atom and residues within 3ang if the fragment contains at least 2 HIS residues.''
	<br/>		<br/>
	== Topology Functions ==		== Topology Functions ==

Dave at 22:08, 15 December 2014

2014-12-15T22:08:42Z

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