PatternQuery:Use Cases - Revision history

Lukas at 13:42, 25 April 2015

2015-04-25T13:42:53Z

← Older revision		Revision as of 13:42, 25 April 2015
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	(m.Count(Residues("His")) == 2) & (m.Count(Residues("Cys")) == 2)) </syntaxhighlight>		(m.Count(Residues("His")) == 2) & (m.Count(Residues("Cys")) == 2)) </syntaxhighlight>

	At first the zinc atoms are selected together with their bonded residues. Additionally, these ~~motives~~ are filtered according to the content of their amino acids.		At first the zinc atoms are selected together with their bonded residues. Additionally, these patterns are filtered according to the content of their amino acids.

	====Identify all the residues, which contain a sugar ring====		====Identify all the residues, which contain a sugar ring====
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	.Filter(lambda l: l.Count(Atoms("P")) == 0)</syntaxhighlight>		.Filter(lambda l: l.Count(Atoms("P")) == 0)</syntaxhighlight>

	At first we select all the pairs of calcium atoms, if they are in a vicinity of 4Å and less by <syntaxhighlight lang="python">Near(4, Atoms("Ca"), Atoms("Ca"))</syntaxhighlight> Subsequently all the bonded residues are checked if they contain either pyranose or furanose ring. only the ~~motives~~ containing either pentose <syntaxhighlight lang="python">(Rings(5 * ["C"] + ["O"]))</syntaxhighlight> or furanose <syntaxhighlight lang="python">(Rings(4 * ["C"] + ["O"]))</syntaxhighlight> are returned. Since a sugar moiety is an integral part of nucleotides, there is a final simple check, assuring, that no ~~fragments~~ containing phosphorus, i.e. nucleotide are retained.		At first we select all the pairs of calcium atoms, if they are in a vicinity of 4Å and less by <syntaxhighlight lang="python">Near(4, Atoms("Ca"), Atoms("Ca"))</syntaxhighlight> Subsequently all the bonded residues are checked if they contain either pyranose or furanose ring. only the patterns containing either pentose <syntaxhighlight lang="python">(Rings(5 * ["C"] + ["O"]))</syntaxhighlight> or furanose <syntaxhighlight lang="python">(Rings(4 * ["C"] + ["O"]))</syntaxhighlight> are returned. Since a sugar moiety is an integral part of nucleotides, there is a final simple check, assuring, that no patterns containing phosphorus, i.e. nucleotide are retained.

Lukas: Lukas moved page MotiveQuery:Use Cases to PatternQuery:Use Cases

2015-04-25T12:57:32Z

Lukas moved page MotiveQuery:Use Cases to PatternQuery:Use Cases

← Older revision	Revision as of 12:57, 25 April 2015
(No difference)

Lukas at 15:20, 20 April 2015

2015-04-20T15:20:26Z

← Older revision		Revision as of 15:20, 20 April 2015
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	==== Find all post-translational modified aminoacids ====		==== Find all post-translational modified aminoacids ====
	*i.e. Those ~~incodporated~~ in the protein backbone and not hetero atoms		*i.e. Those incorporated in the protein backbone and not hetero atoms
	<syntaxhighlight lang="python">		<syntaxhighlight lang="python">
	NotAminoAcids().		NotAminoAcids().

Lukas: /* Identify all binding sites of PA-IIL lectin in different organisms */

2014-12-23T22:42:42Z

Identify all binding sites of PA-IIL lectin in different organisms

← Older revision		Revision as of 22:42, 23 December 2014
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	====Identify all binding sites of PA-IIL lectin in different organisms====		====Identify all binding sites of PA-IIL lectin in different organisms====
	*Binding sites of this type of lectin comprise of two calcium atoms close to each other and a binded sugar residue.		*Binding sites of this type of lectin comprise of two calcium atoms close to each other and a binded sugar residue.
	<syntaxhighlight lang="python">Near(4, Atoms("Ca"), Atoms("Ca"))~~.Filter(lambda m: m.Count(Atoms("Ca")) == 2)~~.ConnectedResidues(1).Filter(lambda m: (m.Count(Rings(5 * ["C"] + ["O"])~~) > 0) \| (m.Count(~~Rings(4 * ["C"] + ["O"])) > 0)) </syntaxhighlight>		<syntaxhighlight lang="python">
			Near(4, Atoms("Ca"), Atoms("Ca"))
			.ConnectedResidues(1)
			.Filter(lambda l:
			l.Count(Or(Rings(5 * ["C"] + ["O"]), Rings(4 * ["C"] + ["O"]))) > 0)
			.Filter(lambda l: l.Count(Atoms("P")) == 0)</syntaxhighlight>

	At first we select all the calcium atoms ~~and clusters them~~, if they are in a vicinity of 4Å and less~~. Additionally~~, ~~we check if there are exactly 2 such atoms.~~ Subsequently all the ~~binded~~ residues are ~~found and finally,~~ only the motives containing either pentose <syntaxhighlight lang="python">(Rings(5 * ["C"] + ["O"]))</syntaxhighlight> or furanose <syntaxhighlight lang="python">(Rings(4 * ["C"] + ["O"]))</syntaxhighlight> are returned.		At first we select all the pairs of calcium atoms, if they are in a vicinity of 4Å and less by <syntaxhighlight lang="python">Near(4, Atoms("Ca"), Atoms("Ca"))</syntaxhighlight> Subsequently all the bonded residues are checked if they contain either pyranose or furanose ring. only the motives containing either pentose <syntaxhighlight lang="python">(Rings(5 * ["C"] + ["O"]))</syntaxhighlight> or furanose <syntaxhighlight lang="python">(Rings(4 * ["C"] + ["O"]))</syntaxhighlight> are returned. Since a sugar moiety is an integral part of nucleotides, there is a final simple check, assuring, that no fragments containing phosphorus, i.e. nucleotide are retained.

	~~Equivalently:~~

	~~<syntaxhighlight lang="python">Near(4~~, ~~Atoms("Ca")~~, ~~Atoms("Ca"))~~.~~Filter(lambda m: m~~.~~Count(Atoms("Ca")) == 2)~~.~~ConnectedResidues(1).Filter(lambda m: m.Contains(Or((Rings(5 * ["C"] + ["O"])), Rings(4 * ["C"] + ["O"]))))</syntaxhighlight>~~

Lukas: /* Identify all the residues, which contain a sugar ring */

2014-12-23T22:35:33Z

Identify all the residues, which contain a sugar ring

← Older revision		Revision as of 22:35, 23 December 2014
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	* This task can be decomposed to two individual subtasks, since sugars contain either pentose or furanose ring. Pentose ring contains 4 carbon and an oxygen atom. Similarly, furanose ring is composed of 5 carbon atoms and an oxygen atom.		* This task can be decomposed to two individual subtasks, since sugars contain either pentose or furanose ring. Pentose ring contains 4 carbon and an oxygen atom. Similarly, furanose ring is composed of 5 carbon atoms and an oxygen atom.

	<syntaxhighlight lang="python">Or(Rings(4 * ["C"] + ["O"]).ConnectedResidues(0), Rings(5 * ["C"] + ["O"]).ConnectedResidues(0)) </syntaxhighlight>		<syntaxhighlight lang="python">
			Or(Rings(4 * ["C"] + ["O"]).ConnectedResidues(0),
			Rings(5 * ["C"] + ["O"]).ConnectedResidues(0)) </syntaxhighlight>

	By specifying the <code>Ring()</code> queries, we select only the ring part of the molecule. By extending the <code>Ring()</code> query with <syntaxhighlight lang="python">ConnectedResidues(0)</syntaxhighlight> only the residue which includes this ring is selected. Last but not least we can join both queries with <syntaxhighlight lang="python">Or()</syntaxhighlight> in order to merge results.		By specifying the <code>Ring()</code> queries, we select only the ring part of the molecule. By extending the <code>Ring()</code> query with <syntaxhighlight lang="python">ConnectedResidues(0)</syntaxhighlight> only the residue which includes this ring is selected. Last but not least we can join both queries with <syntaxhighlight lang="python">Or()</syntaxhighlight> in order to merge results.

Lukas: /* Identify Zinc fingers */

2014-12-23T22:34:31Z

Identify Zinc fingers

← Older revision		Revision as of 22:34, 23 December 2014
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	*There is a variety of different zinc fingers based on the surrounding residues, in our example we will focus on those comprising two zinc and two his residues (Cys2His2).		*There is a variety of different zinc fingers based on the surrounding residues, in our example we will focus on those comprising two zinc and two his residues (Cys2His2).

	<syntaxhighlight lang="python">Atoms("Zn").ConnectedResidues(1).Filter(lambda m: (m.Count(Residues("His")) == 2) & (m.Count(Residues("Cys")) == 2)) </syntaxhighlight>		<syntaxhighlight lang="python">
			Atoms("Zn").
			ConnectedResidues(1).
			Filter(lambda m:
			(m.Count(Residues("His")) == 2) & (m.Count(Residues("Cys")) == 2)) </syntaxhighlight>

	At first the zinc atoms are selected together with their bonded residues. Additionally, these motives are filtered according to the content of their amino acids.		At first the zinc atoms are selected together with their bonded residues. Additionally, these motives are filtered according to the content of their amino acids.



	====Identify all the residues, which contain a sugar ring====		====Identify all the residues, which contain a sugar ring====

Lukas: /* Find all heteroatoms, which are not covalently bonded to the protein structure */

2014-12-23T22:32:32Z

Find all heteroatoms, which are not covalently bonded to the protein structure

← Older revision		Revision as of 22:32, 23 December 2014
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	====Find all heteroatoms, which are not covalently bonded to the protein structure====		====Find all heteroatoms, which are not covalently bonded to the protein structure====
	* Takes all the heteroatoms and queries them for being connected to any amino acid of a given protein		* Takes all the heteroatoms and queries them for being connected to any amino acid of a given protein
	<syntaxhighlight lang="python">HetResidues().Filter(lambda m: m.IsNotConnectedTo(AminoAcids()))</syntaxhighlight>		<syntaxhighlight lang="python">
			HetResidues().
			Filter(lambda m: m.IsNotConnectedTo(AminoAcids()))</syntaxhighlight>

	====Identify Zinc fingers====		====Identify Zinc fingers====

Lukas: /* Find all post-translational modified aminoacids */

2014-12-23T22:32:15Z

Find all post-translational modified aminoacids

← Older revision		Revision as of 22:32, 23 December 2014
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	==== Find all post-translational modified aminoacids ====		==== Find all post-translational modified aminoacids ====
	*i.e. Those incodporated in the protein backbone and not hetero atoms		*i.e. Those incodporated in the protein backbone and not hetero atoms
	<syntaxhighlight lang="python">NotAminoAcids().Filter(lambda m: m.Count(HetResidues()) == 0) </syntaxhighlight>		<syntaxhighlight lang="python">
	This query queries all the non-standard amino acids for their presence among Hetatom entries. Equivalently:<syntaxhighlight lang="python">NotAminoAcids().Filter(lambda m: m.Contains(HetResidues()).Not())</syntaxhighlight>		NotAminoAcids().
			Filter(lambda m: m.Count(HetResidues()) == 0) </syntaxhighlight>
			This query queries all the non-standard amino acids for their presence among Hetatom entries. Equivalently:<syntaxhighlight lang="python">
			NotAminoAcids().
			Filter(lambda m: m.Contains(HetResidues()).Not())</syntaxhighlight>

	====Find all heteroatoms, which are not covalently bonded to the protein structure====		====Find all heteroatoms, which are not covalently bonded to the protein structure====

Lukas at 15:55, 16 December 2014

2014-12-16T15:55:10Z

Show changes

Lukas: /* Find all post-translational modified aminoacids */

2014-12-12T10:28:50Z

Find all post-translational modified aminoacids

← Older revision		Revision as of 10:28, 12 December 2014
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	*i.e. Those incodporated in the protein backbone and not hetero atoms		*i.e. Those incodporated in the protein backbone and not hetero atoms
	<pre>NotAminoAcids().Filter(lambda m: m.Count(HetResidues()) == 0) </pre>		<pre>NotAminoAcids().Filter(lambda m: m.Count(HetResidues()) == 0) </pre>
	This query queries all the non-standard amino acids for their presence among Hetatom entries. Equivalently:**<pre>NotAminoAcids().Filter(lambda m: m.Contains(HetResidues()).Not())</pre>		This query queries all the non-standard amino acids for their presence among Hetatom entries. Equivalently:<pre>NotAminoAcids().Filter(lambda m: m.Contains(HetResidues()).Not())</pre>



	====Find all heteroatoms, which are not covalently bonded to the protein structure====		====Find all heteroatoms, which are not covalently bonded to the protein structure====