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== Basic Query Functions == ''Basic building blocks of the language - i.e. atoms, residues, and the like.'' === AminoAcids === <code>AminoAcids() -> Residues</code><br/> ''Sequence of all residues with the 20 basic amino acid names.''<br/> ;Options : ChargeType: String = "" - ''Specify type of the charge. Allowed values: Positive, Negative, Aromatic, Polar, NonPolar.'' ;Examples : <code>AminoAcids()</code> :: ''All amino acids.'' : <code>AminoAcids(ChargeType = "Polar")</code> :: ''Amino acids with polar charge.'' ---- === AtomIdRange === <code>AtomIdRange(minId: Integer, maxId: ?Integer) -> Atoms</code><br/> ''Sequence of atoms with minId <= atomId <= maxId.''<br/> ;Arguments : minId: Integer - ''Minimum id.'' : maxId: ?Integer - ''Maximum id. If not specified, maxId = minId.'' ;Examples : <code>AtomIdRange(152, 161)</code> :: ''Returns all atoms with id between 152 and 161 inclusive.'' ---- === AtomIds === <code>AtomIds(ids: Integer+) -> Atoms</code><br/> ''Sequence of atoms with specified identifiers.''<br/> ;Arguments : ids: Integer+ - ''Identifiers.'' ;Examples : <code>AtomIds(1, 2, 3)</code> :: ''Returns atoms with ids 1, 2, 3.'' ---- === AtomNames === <code>AtomNames(names: String+) -> Atoms</code><br/> ''Sequence of atoms with specified names.''<br/> ;Arguments : names: String+ - ''Allowed names.'' ;Examples : <code>AtomNames("O1","NH1")</code> :: ''Returns all atoms with names O1 or NH1.'' ---- === Atoms === <code>Atoms(symbols: String*) -> Atoms</code><br/> ''Sequence of atoms with specified element symbols. If no symbols are specified, yields all atoms one by one.''<br/> ;Arguments : symbols: String* - ''Allowed element symbols.'' ;Examples : <code>Atoms("Zn","Ca")</code> :: ''Returns all atoms with element symbol Zn or Ca'' ---- === Chains === <code>Chains(identifiers: Value*) -> PatternSeq</code><br/> ''Splits the structures into chains. If no identifiers are specified, all chains are returned.''<br/> ;Arguments : identifiers: Value* - ''Chain identifiers.'' ;Examples : <code>Chains()</code> :: ''Returns all chains.'' : <code>Chains("")</code> :: ''Returns chains without specific identifier.'' : <code>Chains("A", "B")</code> :: ''Returns chains A and B.'' ---- === Helices === <code>Helices() -> PatternSeq</code><br/> ''Returns all helices. This assumes the information about helices was present in the input structure.''<br/> ;Examples : <code>Helices()</code> :: ''Returns all helices.'' ---- === HetResidues === <code>HetResidues() -> Residues</code><br/> ''Sequence of all residues that contain HET atoms.''<br/> ;Options : NoWaters: Bool = True - ''Ignore water residues such as HOH.'' ;Examples : <code>HetResidues()</code> :: ''Returns all residues that contain HET atoms (ignores water).'' : <code>HetResidues(NoWaters=False)</code> :: ''Returns all residues that contain HET atoms (includes water).'' ---- === ModifiedResidues === <code>ModifiedResidues(parentNames: String*) -> Residues</code><br/> ''Sequence of modified residues that originate from the specified name. If no names are specified, yields all modified residues one by one.''<br/> ;Arguments : parentNames: String* - ''Parent residue names.'' ;Examples : <code>ModifiedResidues("MET")</code> :: ''Returns all residues modified from MET (for example MSE).'' ---- === Named === <code>Named(patterns: PatternSeq) -> PatternSeq</code><br/> '''Names' the pattern by its lowest atom id.''<br/> ;Arguments : patterns: PatternSeq - ''Patterns to name.'' ;Examples : <code>Atoms("Zn").Named().AmbientAtoms(7)</code> :: ''When exported, the result files will have names in the format '[parent id]_[pseudorandom number]_[zn atomid]'. If the Named function was not used, the name would be just '[parent id]_[pseudorandom number]'.'' ---- === NotAminoAcids === <code>NotAminoAcids() -> Residues</code><br/> ''Sequence of all residues that are not any of the 20 basic amino acids.''<br/> ;Options : NoWaters: Bool = True - ''Ignore water residues such as HOH.'' ;Examples : <code>NotAminoAcids()</code> :: ''Returns all residues that are not amino acids.'' ---- === NotAtomIds === <code>NotAtomIds(ids: Integer+) -> Atoms</code><br/> ''Sequence of atoms that do not have specified identifiers.''<br/> ;Arguments : ids: Integer+ - ''Identifiers.'' ;Examples : <code>NotAtomIds(1, 2, 3)</code> :: ''Returns atoms that do not have id 1, 2, nor 3.'' ---- === NotAtomNames === <code>NotAtomNames(names: String+) -> Atoms</code><br/> ''Sequence of atoms that do not have a specified name.''<br/> ;Arguments : names: String+ - ''Forbidden names.'' ;Examples : <code>NotAtomNames("O4")</code> :: ''Returns all atoms that are not called O4.'' ---- === NotAtoms === <code>NotAtoms(symbols: String+) -> Atoms</code><br/> ''Sequence of atoms that are not particular elements.''<br/> ;Arguments : symbols: String+ - ''Forbidden element symbols.'' ;Examples : <code>NotAtoms("O")</code> :: ''Returns all atoms that are not O.'' ---- === NotResidues === <code>NotResidues(names: Value+) -> Residues</code><br/> ''Sequence of residues that are not called by the specified names.''<br/> ;Arguments : names: Value+ - ''Forbidden residue names.'' ;Examples : <code>NotResidues("THR","CYS")</code> :: ''Returns all residues that are not THR or CYS.'' ---- === RegularMotifs === <code>RegularMotifs(regex: Value) -> PatternSeq</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/> ;Arguments : regex: Value - ''Regular expression on one letter abbreviations of amino acids.'' ;Options : Type: String = "Amino" - ''Determines the type of the query. Allowed values: Amino, Nucleotide.'' ;Examples : <code>RegularMotifs("RGD")</code> :: ''Finds all RGD motifs.'' : <code>RegularMotifs("ACGTU", Type = 'Nucleotide')</code> :: ''Finds all consecutive occurrences of the ACGTU nucleotides.'' : <code>RegularMotifs(".HC.").Filter(lambda m: m.IsConnected())</code> :: ''Finds all 4 residue motifs with ?-HIS-CYS-? that are connected.'' ---- === ResidueIdRange === <code>ResidueIdRange(chain: String, min: Integer, max: ?Integer) -> Residues</code><br/> ''Sequence of residues with specific chain and min <= sequence number <= max.''<br/> ;Arguments : chain: String - ''Chain identifier. Case sensitive (a != A).'' : min: Integer - ''Minimum sequence number.'' : max: ?Integer - ''Maximum sequence number. If not specified, max = min.'' ;Examples : <code>ResidueIdRange("A", 161, 165)</code> :: ''Returns all residues on chain A with seq. number between 161 and 165 inclusive.'' ---- === ResidueIds === <code>ResidueIds(ids: String+) -> Residues</code><br/> ''Sequence of residues with specific identifiers. If the structure does not contain a residue with the given identifier, it is skipped.''<br/> ;Arguments : ids: String+ - ''One or more identifiers in the format 'NUMBER [CHAIN] [i:INSERTIONCODE]' (parameters in [] are optional, for example '175 i:12' or '143 B'). Case sensitive (a != A).'' ;Examples : <code>ResidueIds("132 A", "178 A")</code> :: ''Returns residues A 123 and A 178 (provided the input structure contains them).'' ---- === Residues === <code>Residues(names: String*) -> Residues</code><br/> ''Sequence of residues with specified names. If no names are specified, yields all residues one by one.''<br/> ;Arguments : names: String* - ''Allowed residue names.'' ;Examples : <code>Residues("HIS", "CYS")</code> :: ''Returns all HIS or CYS residues.'' ---- === RingAtoms === <code>RingAtoms(atom: Atoms, ring: ?Rings) -> Atoms</code><br/> ''Returns all rings atoms.''<br/> ;Arguments : atom: Atoms - ''Atom types.'' : ring: ?Rings - ''Specific ring.'' ;Examples : <code>RingAtoms(Atoms("C"), Rings(4 * ["C"] + ["O"]))</code> :: ''Returns all C atoms on a ring with 4C and O.'' ---- === Rings === <code>Rings(atoms: Value*) -> Rings</code><br/> ''Sequence of rings with particular atoms. If no atoms are specified, yields all rings (cycles) one by one. The order of atoms matters.''<br/> ;Arguments : atoms: Value* - ''Ring atoms.'' ;Examples : <code>Rings()</code> :: ''Returns all rings.'' : <code>Rings(5 * ["C"] + ["O"])</code> :: ''Returns all rings with 5C and 1O atoms.'' : <code>Rings(["C", "C", "N", "C", "N"])</code> :: ''Returns all rings with C-C-N-C-N atoms.'' : <code>Or(Rings(["C", "C", "N", "C", "N"]), Rings(["C", "C", "C", "N", "N"]))</code> :: ''Returns all rings with C-C-N-C-N or C-C-C-N-N atoms.'' ---- === Sheets === <code>Sheets() -> PatternSeq</code><br/> ''Returns all sheets. This assumes the information about sheets was present in the input structure.''<br/> ;Examples : <code>Sheets()</code> :: ''Returns all sheets.'' <br/>
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