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== Geometry Functions == ''Functions that rely on the geometry of patterns.'' === AmbientAtoms === <code>AmbientAtoms(pattern: PatternSeq, r: Number) -> PatternSeq</code><br/> ''Surrounds the inner pattern by atoms that within the given radius from the inner pattern.''<br/> ;Arguments : pattern: PatternSeq - ''Basic pattern.'' : r: Number - ''Radius.'' ;Options : ExcludeBase: Bool = False - ''Exclude the central original pattern.'' : NoWaters: Bool = True - ''Ignore water residues such as HOH.'' : YieldNamedDuplicates: Bool = False - ''Yield duplicate patterns if they have a different name.'' ;Examples : <code>Atoms("Fe").AmbientAtoms(4)</code> :: ''Finds Fe atoms and all atoms within 4 (angstroms) from each of them.'' ---- === AmbientResidues === <code>AmbientResidues(pattern: PatternSeq, r: Number) -> PatternSeq</code><br/> ''Surrounds the inner pattern by residues that have at least one atom within the given radius from the inner pattern.''<br/> ;Arguments : pattern: PatternSeq - ''Basic pattern.'' : r: Number - ''Radius.'' ;Options : ExcludeBase: Bool = False - ''Exclude the central original pattern.'' : NoWaters: Bool = True - ''Ignore water residues such as HOH.'' : YieldNamedDuplicates: Bool = False - ''Yield duplicate patterns if they have a different name.'' ;Examples : <code>Rings(6 * ["C"]).AmbientResidues(4)</code> :: ''Finds rings with 6C atoms and all residues within 4 (angstroms) from each of them.'' ---- === Cluster === <code>Cluster(r: Number, patterns: PatternSeq+) -> PatternSeq</code><br/> ''Clusters all patterns that are pairwise closer than r (angstroms).''<br/> ;Arguments : r: Number - ''Maximum distance between two patterns in the cluster.'' : patterns: PatternSeq+ - ''Patterns to cluster.'' ;Examples : <code>Cluster(4, Atoms("Ca"), Rings(5 * ["C"] + ["O"]))</code> :: ''Finds all instance of one or more rings with 5C and O atoms and one or more Ca atoms that are closer than 4 (angstroms).'' ---- === Filled === <code>Filled(pattern: PatternSeq) -> PatternSeq</code><br/> ''Adds all atoms that fall within the circumsphere (with radius multiplied by the factor) of the basic pattern.''<br/> ;Arguments : pattern: PatternSeq - ''Basic pattern.'' ;Options : NoWaters: Bool = True - ''Ignore water residues such as HOH.'' : RadiusFactor: Number = 0.75 - ''Circumsphere radius factor.'' ;Examples : <code>Cluster(4, Residues("HIS")).Filled(RadiusFactor = 0.75)</code> :: ''Finds clusters of HIS residues and all atoms within the circumsphere.'' ---- === Near === <code>Near(r: Number, patterns: PatternSeq+) -> PatternSeq</code><br/> ''Clusters all patterns that are pairwise closer than r (angstroms) and checks if the "counts" match.''<br/> ;Arguments : r: Number - ''Maximum distance between two sub-patterns in the pattern.'' : patterns: PatternSeq+ - ''Patterns to 'cluster'.'' ;Examples : <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).'' ---- === Spherify === <code>Spherify(pattern: PatternSeq, r: Number) -> PatternSeq</code><br/> ''Identifies the geometrical center of the base pattern and then includes all atoms within the specified radius.'' ;Arguments : pattern: PatternSeq - ''Basic pattern.'' : r: Number - ''Radius.'' ;Options : ExcludeBase: Bool = False - ''Exclude the central original pattern.'' : NoWaters: Bool = True - ''Ignore water residues such as HOH.'' : YieldNamedDuplicates: Bool = False - ''Yield duplicate patterns if they have a different name.'' ;Examples <code>Rings(6 * ["C"]).Spherify(5)</code><br/> ''Finds benzene moiety, computes centroid of each pattern, and includes all atoms within 5 angstroms from it. <br/>
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