PatternQuery:Language Reference: Difference between revisions
HetResidues() query bugfix |
m Dave moved page MotiveQuery Language Reference to MotiveQuery:Language Reference |
(No difference)
|
Revision as of 15:20, 11 June 2014
Introduction
MotiveQuery (MQ) is a user friendly chemical language primarily designed for defining structural motifs. MQ combines the clarity and brevity of programming languages with the versatility of natural language, aiming for an efficient inclusion of chemical and biochemical knowledge into the definition of structural motifs. MQ allows definitions based on chemical connectivity and three-dimensional structure at the same time. Additionally, in the case of molecules based on residue chains (such as proteins, nucleic acids, saccharides, etc.), MQ allows the user to include any amount of information regarding the residue level structure directly into the definition of the motifs.
MotiveQuery is a subset of the Python programming language. Therefore, if you have experience with it, it should not be a problem to use MQ as well.
- The language is case sensitive - "filter" is NOT the same as "FiLtEr".
Some of the functions return Motives
while other only Motive
.
Motive
is a set of atoms.Motives
is a sequence ofMotive
(the sets of atoms).
When a molecule is queried, say using the expression Rings(5 * ["C"] + ["O"])
a sequences of motives each containing 6 atoms (5 C and 1 O) is returned. However, some functions such as Filter
need to operate on a single motive (the set of atoms) - not the whole sequences. The query Filter(Residues(), lambda r: r.Count(Atoms()) > 10)
first finds all residue Motives
(sequence) and then passes every single Motive
(set of atoms) to a function that counts the atoms in the motive and returns True if there is at least 11 of them. This is the reasoning behind these two types.
Using MotiveQuery in Silverlight applications
MotiveQuery can be used in SiteBinder, EEM Charges, and MotiveExplorer from the the corresponding UI elements. Moreover, it is possible to use MQ from the Scripting window. This is achieved using the MQ.Execute
function. The function takes two parameters: the query and an optional target structure list.
Examples
These examples can be executed from the Scripting window of SiteBinder, MotiveExplorer, or other Silverlight applications.
q = Atoms("Zn").ConnectedAtoms(2) MQ.Execute(q)
- This command finds all motifs specified by the query q in all loaded structures.
MQ.Execute(Residues("HEM"), [ Session.StructureMap["1tqn"], Session.StructureMap["2wer"] ])
- This command finds all HEM residues in structures 1tqn and 2wer (provided structures with these names are loaded).
q = AtomSimilarity(Motive("model"), Motive("1gtz_0")) MQ.Execute(q)
- This command computes the atom similarity (Jaccard coefficient) for structures model and 1gtz_0.
q = ResidueSimilarity(Motive("model"), Current()) MQ.Execute(q, Session.Structures)
- This command computes the residue similarity (Jaccard coefficient) for the structure with id 'model' (which is loaded using the Motive 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.
AminoAcids
AminoAcids() -> Residues
Sequence of all residues with the 20 basic amino acid names.
- Options
- ChargeType: String = "" - Specify type of the charge. Allowed values: Positive, Negative, Aromatic, Polar, NonPolar.
- Examples
AminoAcids()
- All amino acids.
AminoAcids(ChargeType = "Polar")
- Amino acids with polar charge.
AtomIdRange
AtomIdRange(minId: Integer, maxId: ?Integer) -> Atoms
Sequence of atoms with minId <= atomId <= maxId.
- Arguments
- minId: Integer - Minimum id.
- maxId: ?Integer - Maximum id. If not specified, maxId = minId.
- Examples
AtomIdRange(152, 161)
- Returns all atoms with id between 152 and 161 inclusive.
AtomIds
AtomIds(ids: Integer+) -> Atoms
Sequence of atoms with specified identifiers.
- Arguments
- ids: Integer+ - Identifiers.
- Examples
AtomIds(1, 2, 3)
- Returns atoms with ids 1, 2, 3.
AtomNames
AtomNames(names: String+) -> Atoms
Sequence of atoms with specified names.
- Arguments
- names: String+ - Allowed names.
- Examples
AtomNames("O1","NH1")
- Returns all atoms with names O1 or NH1.
Atoms
Atoms(symbols: String*) -> Atoms
Sequence of atoms with specified element symbols. If no symbols are specified, yields all atoms one by one. A single atom can be entered using the '@' operator.
- Arguments
- symbols: String* - Allowed element symbols.
- Examples
Atoms("Zn","Ca")
- Returns all atoms with element symbol Zn or Ca
HetResidues
HetResidues() -> Residues
Sequence of all residues that contain HET atoms.
- Options
- NoWaters: Bool = True - Ignore water residues such as HOH.
- Examples
HetResidues()
- Returns all residues that contain HET atoms.
Named
Named(motives: Motives) -> Motives
'Names' the motive by its lowest atom id.
- Arguments
- motives: Motives - Motives to name.
- Examples
Atoms("Zn").Named().AmbientAtoms(7)
- 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
NotAminoAcids() -> Residues
Sequence of all residues that are not any of the 20 basic amino acids.
- Options
- NoWaters: Bool = True - Ignore water residues such as HOH.
- Examples
NotAminoAcids()
- Returns all residues that are not amino acids.
NotAtomIds
NotAtomIds(ids: Integer+) -> Atoms
Sequence of atoms that do not have specified identifiers.
- Arguments
- ids: Integer+ - Identifiers.
- Examples
NotAtomIds(1, 2, 3)
- Returns atoms that do not have id 1, 2, nor 3.
NotAtomNames
NotAtomNames(names: String+) -> Atoms
Sequence of atoms that do not have a specified name.
- Arguments
- names: String+ - Forbidden names.
- Examples
NotAtomNames("O4")
- Returns all atoms that are not called O4.
NotAtoms
NotAtoms(symbols: String+) -> Atoms
Sequence of atoms that are not particular elements.
- Arguments
- symbols: String+ - Forbidden element symbols.
- Examples
NotAtoms("O")
- Returns all atoms that are not O.
NotResidues
NotResidues(names: Value+) -> Residues
Sequence of residues that are not called by the specified names.
- Arguments
- names: Value+ - Forbidden residue names.
- Examples
NotResidues("THR","CYS")
- Returns all residues that are not THR or CYS.
RegularMotives
RegularMotives(regex: Value) -> Motives
Regular motives. The protein is split into individual chains and the residues are sorted by their Sequence Number before the motives are identified. The query does not check if adjacent residues have consecutive Sequence Numbers.
- Arguments
- regex: Value - Regular expression on one letter abbreviations of amino acids.
- Examples
RegularMotives("RGD")
- Finds all RGD motives.
RegularMotives(".HC.").Filter(lambda m: m.IsConnected())
- Finds all 4 residue motives with ?-HIS-CYS-? that are connected.
ResidueIdRange
ResidueIdRange(chain: String, min: Integer, max: ?Integer) -> Residues
Sequence of residues with specific chain and min <= sequence number <= max.
- 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
ResidueIdRange("A", 161, 165)
- Returns all residues on chain A with seq. number between 161 and 165 inclusive.
ResidueIds
ResidueIds(ids: String+) -> Residues
Sequence of residues with specific identifiers. If the structure does not contain a residue with the given identifier, it is skipped.
- Arguments
- ids: String+ - One or more identifiers in the form 'Chain Number InsertionCode', 'Chain Number', or 'Number'. Case sensitive (a != A).
- Examples
ResidueIds("A 123", "A 178")
- Returns residues A 123 and A 178 (provided the input structure contains them).
Residues
Residues(names: Value*) -> Residues
Sequence of residues with specified names. If no names are specified, yields all residues one by one. A single residue can be entered using the '#' operator.
- Arguments
- names: Value* - Allowed residue names.
- Examples
Residues("HIS", "CYS")
- Returns all HIS or CYS residues.
RingAtoms
RingAtoms(atom: Atoms, ring: ?Rings) -> Atoms
Returns all rings atoms.
- Arguments
- atom: Atoms - Atom types.
- ring: ?Rings - Specific ring.
- Examples
RingAtoms(Atoms("C"), Rings(4 * ["C"] + ["O"]))
- Returns all C atoms on a ring with 4C and O.
Rings
Rings(atoms: Value*) -> Rings
Sequence of rings with particular atoms. If no atoms are specified, yields all rings (cycles) one by one.
- Arguments
- atoms: Value* - Ring atoms.
- Examples
Rings(5 * ["C"] + ["O"])
- Returns all rings with 5C and 1O atoms.
Advanced Query Functions
Advanced building blocks of the language.
Flatten
Flatten(motives: Motives, selector: Motive->Motives) -> Motives
Converts a sequence of sequence of motifs into a single 'flat' sequence.
- Arguments
- motives: Motives - Motives to project.
- selector: Motive->Motives - The selector.
- Examples
Residues("HIS").Flatten(lambda m: m.Find(Atoms("C")))
- Returns all C atoms on HIS residues.
Inside
Inside(motives: Motives, where: Motives) -> Motives
Finds motives within another motive. Equivalent to where.SelectMany(lambda m: m.Find(motives))
- Arguments
- motives: Motives - Motives to find.
- where: Motives - Where to find them.
- Examples
Atoms("C").Inside(Residues("HIS"))
- Returns all C atoms on HIS residues.
Or
Or(motives: Motives+) -> Motives
Merges several motive sequences into one.
- Arguments
- motives: Motives+ - Motives to merge.
- Examples
Or(Atoms("Zn").ConnectedResidues(1), Rings())
- Finds all zincs and their connected residues or rings.
ToAtoms
ToAtoms(motives: Motives) -> Motives
Collects all 'inner' motives and yields all unique atoms one by one.
- Arguments
- motives: Motives - Motives to split.
- Examples
Residues("HIS").ToAtoms()
- Returns all atoms on HIS residues one by one.
ToResidues
ToResidues(motives: Motives) -> Motives
Collects all 'inner' motives and yields all unique residues one by one. The residues contain only the atoms that have been yielded by the inner query.
- Arguments
- motives: Motives - Motives to split.
- Examples
ToResidues(Atoms("C"))
- Returns all C atoms grouped by residues.
Union
Union(motives: Motives) -> Motives
Collects all 'inner' motives and yields one created from their unique atoms.
- Arguments
- motives: Motives - Motives to merge.
- Examples
Rings().Union()
- Creates a single motive that contains all rings.
Filter Functions
Functions useful for filtering motifs.
Contains
Contains(where: Motive, what: Motives) -> Bool
Checks if a motif is contained within another one. Equivalent to where.Count(motives) > 0.
- Arguments
- where: Motive - Where to look.
- what: Motives - What to find.
- Examples
HetResidues().Filter(lambda m: m.Contains(Rings(5*['C']+['O'])).Not())
- Returns all HET residues that do not contain a 5CO ring.
Count
Count(where: Motive, what: Motives) -> Integer
Counts all occurrences of motive 'what' in motive 'where'.
- Arguments
- where: Motive - Where to count it.
- what: Motives - What motive to count.
- Examples
m.Count(Residues("HIS"))
- Returns the count of HIS residues in the motive m. Where m is a Motive (for example when using the Filter function or returned by the ToMotive() function). This example will not work directly and is here to illustrate a concept.
Atoms("Zn").ConnectedResidues(1).Filter(lambda m: m.Count(Residues("HIS")) == 2)
- Motifs with Zn atoms and its connected residues with exactly 2 HIS residues.
ExecuteIf
ExecuteIf(query: Motives, condition: Motive->Bool) -> Motives
Executes a query only if the condition is met. Otherwise, return an empty sequence of motifs.
- Arguments
- query: Motives - Query to execute.
- condition: Motive->Bool - Condition that must be satisfied for the parent structure/motif.
- Examples
Residues().ExecuteIf(lambda p: p.Metadata('PdbResolution') <= 2.0)
- Returns residues in structures that have resolution lower than 2.0ang.
AminoAcids().ExecuteIf(lambda p: p.Count(Atoms('Fe')) > 3)
- Returns all amino acids in structures that have at least 3 Fe atoms.
Filter
Filter(motives: Motives, filter: Motive->Bool) -> Motives
Filters a sequence of motives with a given predicate.
- Arguments
- motives: Motives - Motives to filter.
- filter: Motive->Bool - Filter predicate.
- Examples
Residues().Filter(lambda m: m.Count(Atoms("C")) >= 3)
- Returns all residues that contain at least 3 C atoms.
IsConnected
IsConnected(motive: Motive) -> Bool
Checks if a particular motive is a connected graph.
- Arguments
- motive: Motive - A motive to test.
- Examples
Atoms("Zn").AmbientResidues(3).Filter(lambda m: m.IsConnected())
- Finds all motives with a Zn and residues within 3 ang, where all the ambient residues are connected to the central atom.
IsConnectedTo
IsConnectedTo(current: Motive, motive: Motives) -> Bool
Checks if a particular motive is connected to any other specified motive. The motives must have empty intersection for this function to return true.
- Arguments
- current: Motive - A motive to test.
- motive: Motives - Motive sequence to test against.
- Examples
Atoms().Filter(lambda a: a.IsConnectedTo(Rings()))
- Finds all atoms that are connected to a ring they do not belong to.
IsNotConnectedTo
IsNotConnectedTo(current: Motive, motive: Motives) -> Bool
Checks if a particular motive is not connected to any other specified motive. The motives must have empty intersection for this function to return true.
- Arguments
- current: Motive - A motive to test.
- motive: Motives - Motive sequence to test against.
- Examples
Residues().Filter(lambda r: r.IsNotConnectedTo(Atoms("Ca")))
- Finds all residues that are not connected to Ca atoms. The residue itself can still contain Ca atoms.
NearestDistanceTo
NearestDistanceTo(current: Motive, motive: Motives) -> Real
Finds the distance to a particular motive.
- Arguments
- current: Motive - A motive to test.
- motive: Motives - Motive sequence to test against.
- Examples
Atoms().Filter(lambda m: m.NearestDistanceTo(Residues("ASP")) >= 5)
- Finds all atoms that are at least 5 (angstroms) away from any ASP residue.
Topology Functions
Functions that rely on the topology of motifs.
ConnectedAtoms
ConnectedAtoms(motive: Motives, n: Integer) -> Motives
Surrounds the inner motive by n layers of atoms.
- Arguments
- motive: Motives - Basic motive.
- n: Integer - Number of atom layers to connect.
- Options
- YieldNamedDuplicates: Bool = False - Yield duplicate motifs if they have a different name.
- Examples
Residues("MAN").ConnectedAtoms(2)
- Finds all MAN residues and then adds two connected levels of atoms to them.
ConnectedResidues
ConnectedResidues(motive: Motives, n: Integer) -> Motives
Surrounds the inner motive by n layers of residues.
- Arguments
- motive: Motives - Basic motive.
- n: Integer - Number of residue layers to connect.
- Options
- YieldNamedDuplicates: Bool = False - Yield duplicate motifs if they have a different name.
- Examples
Atoms("Zn").ConnectedResidues(1)
- Finds all Zn atoms and adds all residues that are connected to them.
Path
Path(motives: Motives+) -> Motives
Creates a new motif from 'connected' parts.
- Arguments
- motives: Motives+ - Motifs to path.
- Examples
Path(Atoms("O"), Atoms("C"), Atoms("O"))
- Finds motifs with two O and one C atoms where the C atoms is connected to the O ones.
Star
Star(center: Motives, motives: Motives+) -> Motives
Creates a new motif from a central one and connected parts.
- Arguments
- center: Motives - Center motif.
- motives: Motives+ - Motifs to chain.
- Examples
Star(Atoms("C"), Atoms("O"), Atoms("O"))
- Finds motifs with two O atoms and one C atom in the center.
Atoms("C").Star(Atoms("O"), Atoms("O"))
- Finds motifs with two O atoms and one C atom in the center.
Geometry Functions
Functions that rely on the geometry of motifs.
AmbientAtoms
AmbientAtoms(motive: Motives, r: Number) -> Motives
Surrounds the inner motive by atoms that within the given radius from the inner motive.
- Arguments
- motive: Motives - Basic motive.
- r: Number - Radius.
- Options
- ExcludeBase: Bool = False - Exclude the central original motif.
- NoWaters: Bool = True - Ignore water residues such as HOH.
- YieldNamedDuplicates: Bool = False - Yield duplicate motifs if they have a different name.
- Examples
Atoms("Fe").AmbientAtoms(4)
- Finds Fe atoms and all atoms within 4 (angstroms) from each of them.
AmbientResidues
AmbientResidues(motive: Motives, r: Number) -> Motives
Surrounds the inner motive by residues that have at least one atom within the given radius from the inner motive.
- Arguments
- motive: Motives - Basic motive.
- r: Number - Radius.
- Options
- ExcludeBase: Bool = False - Exclude the central original motif.
- NoWaters: Bool = True - Ignore water residues such as HOH.
- YieldNamedDuplicates: Bool = False - Yield duplicate motifs if they have a different name.
- Examples
Rings(6 * ["C"]).AmbientResidues(4)
- Finds rings with 6C atoms and all residues within 4 (angstroms) from each of them.
Cluster
Cluster(r: Number, motives: Motives+) -> Motives
Clusters all motives that are pairwise closer than r (angstroms).
- Arguments
- r: Number - Maximum distance between two motives in the cluster.
- motives: Motives+ - Motives to cluster.
- Examples
Cluster(4, Atoms("Ca"), Rings(5 * ["C"] + ["O"]))
- 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
Filled(motive: Motives) -> Motives
Adds all atoms that fall within the circumsphere (with radius multiplied by the factor) of the basic motive.
- Arguments
- motive: Motives - Basic motive.
- Options
- NoWaters: Bool = True - Ignore water residues such as HOH.
- RadiusFactor: Number = 0.75 - Circumsphere radius factor.
- Examples
Cluster(4, Residues("HIS")).Filled(RadiusFactor = 0.75)
- Finds clusters of HIS residues and all atoms within the circumsphere.
Near
Near(r: Number, motives: Motives+) -> Motives
Clusters all motives that are pairwise closer than r (angstroms) and checks if the "counts" match.
- Arguments
- r: Number - Maximum distance between two sub-motives in the motive.
- motives: Motives+ - Motives to 'cluster'.
- Examples
Near(4, Many(Atoms("Ca"), 2), Rings(5 * ["C"] + ["O"]))
- Finds all instance of a single ring with 5C and O atoms and two Ca atoms that are closer than 4 (angstroms).
Miscellaneous Functions
Various useful functions. These function often require a special setup (i.e. only useful in Scripting window or in specific applications).
AminoSequenceString
AminoSequenceString(motive: Motive) -> String
Returns a string of single-letter amino acids contained in the motive.
Note: This function cannot be used directly to query motifs from MotiveExplorer or MotiveQuery service.
- Arguments
- motive: Motive - Motive to convert.
- Examples
Motive("1tqn_12").AminoSequenceString()
- Returns a string representing amino acids in the motive '1tqn_12'.
RegularMotives(Motive("1tqn_12").AminoSequenceString())
- Returns all regular motives that correspond to the AMK sequence in 1tqn_12.
AtomProperty
AtomProperty(atomMotive: Motive, name: String) -> ?
If the property exists and the motive consists of a single atom, returns the property. Otherwise, returns Nothing.
Note: This function cannot be used directly to query motifs from MotiveExplorer or MotiveQuery service.
- Arguments
- atomMotive: Motive - Single atom motive.
- name: String - Property name.
- Examples
a.Property("charge")
- Gets the 'charge' property of the atom a. Where a is a single atom Motive. This example will not work directly.
Atoms().Filter(lambda a: a.Property("charge") >= 2)
- All atoms with the charge property greater or equal to 2. This example will only work in cases where a suitable property is defined. For example in Scripting window in the Charges app.
AtomSimilarity
AtomSimilarity(a: Motive, b: Motive) -> Real
Computes Jaccard/Tanimoto coefficient on atoms (element symbols) of both structures.
Note: This function cannot be used directly to query motifs from MotiveExplorer or MotiveQuery service.
- Arguments
- a: Motive - First motive.
- b: Motive - Second motive.
- Examples
AtomSimilarity(Current(),Motive("1tqn_12"))
- Computes the atom similarity between the current motif and 1tqn_12. This example can be used in SiteBinder to create a descriptor (assuming a structure with id '1tqn_12' is loaded).
CommonAtoms
CommonAtoms(modelId: String) -> Motives
Returns a single motive with atoms common with the model. Properties checked: atom id, element symbol, chain, residue number. This query is useful for example for atom selection in SiteBinder.
Note: This function cannot be used directly to query motifs from MotiveExplorer or MotiveQuery service.
- Arguments
- modelId: String - Id of the model.
- Examples
CommonAtoms("1tqn_12")
- Returns a motive formed by atoms common with the '1tqn_12' structure.
CSA
CSA() -> Motives
Entries from Catalytic Site Atlas represented as motifs. Works only if used from the command line version of MotiveQuery and property configured.
Note: This function cannot be used directly to query motifs from MotiveExplorer or MotiveQuery service.
- Examples
CSA()
- All CSA sites for the given structure. This example will only work if used from the command line version of MotiveQuery and property configured.
Current
Current() -> Motive
A variable that is assigned by the application environment.
Note: This function cannot be used directly to query motifs from MotiveExplorer or MotiveQuery service.
- Examples
AtomSimilarity(Current(), Motive("model"))
- Returns the atom similarity of the current motive and the model. This example will work for example when defining a structure descriptor in SiteBinder and there is a structure with id 'model' loaded.
Descriptor
Descriptor(motive: Motive, name: String) -> ?
Returns the descriptor. If the descriptor does not exist, 'null' is returned.
Note: This function cannot be used directly to query motifs from MotiveExplorer or MotiveQuery service.
- Arguments
- motive: Motive - Motive that represents entire structure.
- name: String - Descriptor name.
- Examples
Current().Descriptor("similarity") >= 0.75
- Returns True if 'similarity' descriptor of the current motif is at least 0.75. This example will work for example in SiteBinder's structure selection if the 'similarity' descriptor has been previously defined.
DynamicInvoke
DynamicInvoke(value: Value, name: String, isProperty: Bool, args: Value) -> Value
Dynamically invoke a member. (internal)
Note: This function cannot be used directly to query motifs from MotiveExplorer or MotiveQuery service.
- Arguments
- value: Value - InnerQuery.
- name: String - Member name.
- isProperty: Bool - Is this a property.
- args: Value - Array of arguments.
Find
Find(source: Motive, motives: Motives) -> Motives
Converts the source motive to a structure and finds motives within it.
Note: This function cannot be used directly to query motifs from MotiveExplorer or MotiveQuery service.
- Arguments
- source: Motive - Where to look.
- motives: Motives - Motives to find.
- Examples
AtomSimilarity(Current().Find(NotAtoms("N")).ToMotive(), Motive("model").Find(NotAtoms("N")).ToMotive())
- Computes the atom similarity of the 'current' and 'model' motives, but ignores N atoms. This example can be used in SiteBinder to create a descriptor (assuming a structure with id 'model' is loaded).
Metadata
Metadata(motive: Motive, name: String) -> Value
Get a metadata from the parent structure of the motif. For example resolution. If the given property is not present, null value is returned. For more information for available metadata, visit the general MotiveQuery wiki page.
Note: This function cannot be used directly to query motifs from MotiveExplorer or MotiveQuery service.
- Arguments
- motive: Motive - Motive.
- name: String - Property name.
- Examples
Residues().ExecuteIf(lambda p: p.Metadata('PdbResolution') <= 2.0)
- Returns residues in structures that have resolution lower than 2.0ang.
Motive
Motive(structureName: String) -> Motive
Returns a structure represented a motive.
Note: This function cannot be used directly to query motifs from MotiveExplorer or MotiveQuery service.
- Arguments
- structureName: String - Name of a structure.
- Examples
Motive("1tqn_12")
- Returns the structure '1tqn_12' represented as a motive. Usable in defining descriptors or in Scripting window (using MQ.Execute).
ResidueSimilarity
ResidueSimilarity(a: Motive, b: Motive) -> Real
Computes Jaccard/Tanimoto coefficient on residue names of both structures.
Note: This function cannot be used directly to query motifs from MotiveExplorer or MotiveQuery service.
- Arguments
- a: Motive - First motive.
- b: Motive - Second motive.
- Examples
ResidueSimilarity(Current(), Motive("1tqn_12"))
- Computes the residue similarity between the current motif and 1tqn_12. This example can be used in SiteBinder to create a descriptor (assuming a structure with id '1tqn_12' is loaded).
ToMotive
ToMotive(motives: Motives) -> Motive
Converts a sequence of Motives to a single motive. The Motive type is required by some function such as AtomSimilarity.
Note: This function cannot be used directly to query motifs from MotiveExplorer or MotiveQuery service.
- Arguments
- motives: Motives - Motives to convert.
- Examples
Residues("HIS").ToMotive()
- Converts a sequence of HIS residue Motives to a single Motive.
AtomSimilarity(Current().Find(NotAtoms("N")).ToMotive(), Motive("model").Find(NotAtoms("N")).ToMotive())
- Computes the atom similarity of the 'current' and 'model' motives, but ignores N atoms.
Value Functions
Functions such as addition or comparison of numbers.
Abs
Abs(x: Number) -> Number
Computes the 'Abs' function of the argument.
- Arguments
- x: Number - Argument.
- Examples
Abs(x)
- Evaluates the expression.
Divide (/)
Divide(x: Number, y: Number) -> Number
Computes the 'Divide' function of the values.
- Arguments
- x: Number - Left argument.
- y: Number - Right argument.
- Examples
x / y
- Evaluates the expression.
Equal (==)
Equal(x: Value, y: Value) -> Bool
Determines the 'Equal' relation between two values.
- Arguments
- x: Value - Left argument.
- y: Value - Right argument.
- Examples
x == y
- Evaluates to True or False based on the value of x and y.
Greater (>)
Greater(x: Number, y: Number) -> Bool
Determines the 'Greater' relation between two values.
- Arguments
- x: Number - Left argument.
- y: Number - Right argument.
- Examples
x > y
- Evaluates to True or False based on the value of x and y.
GreaterEqual (>=)
GreaterEqual(x: Number, y: Number) -> Bool
Determines the 'GreaterEqual' relation between two values.
- Arguments
- x: Number - Left argument.
- y: Number - Right argument.
- Examples
x >= y
- Evaluates to True or False based on the value of x and y.
Less (<)
Less(x: Number, y: Number) -> Bool
Determines the 'Less' relation between two values.
- Arguments
- x: Number - Left argument.
- y: Number - Right argument.
- Examples
x < y
- Evaluates to True or False based on the value of x and y.
LessEqual (<=)
LessEqual(x: Number, y: Number) -> Bool
Determines the 'LessEqual' relation between two values.
- Arguments
- x: Number - Left argument.
- y: Number - Right argument.
- Examples
x <= y
- Evaluates to True or False based on the value of x and y.
LogicalAnd (&)
LogicalAnd(xs: Bool+) -> Bool
Computes 'LogicalAnd' of the input values.
- Arguments
- xs: Bool+ - Arguments.
- Examples
x & y
- Evaluates to True or False based on the values of x and y.
LogicalNot (Not)
LogicalNot(x: Bool) -> Bool
Computes 'LogicalNot' of the input value. This function can be called using the shorthand 'Not'.
- Arguments
- x: Bool - Argument.
- Examples
LogicalNot(x)
- Evaluates to True or False based on the value of x.
x.Not()
- Evaluates to True or False based on the value of x.
LogicalOr (|)
LogicalOr(xs: Bool+) -> Bool
Computes 'LogicalOr' of the input values.
- Arguments
- xs: Bool+ - Arguments.
- Examples
x | y
- Evaluates to True or False based on the values of x and y.
LogicalXor (Xor)
LogicalXor(xs: Bool+) -> Bool
Computes 'LogicalXor' of the input values. This function can be called using the shorthand 'Xor'.
- Arguments
- xs: Bool+ - Arguments.
- Examples
LogicalXor(x, y)
- Evaluates to True or False based on the values of x and y.
Xor(x, y)
- Evaluates to True or False based on the values of x and y.
Minus (-)
Minus(x: Number) -> Number
Computes the arithmetic negation of the argument.
- Arguments
- x: Number - Argument.
- Examples
-x
- Arithmetic negation of x.
NotEqual (!=)
NotEqual(x: Value, y: Value) -> Bool
Determines the 'NotEqual' relation between two values.
- Arguments
- x: Value - Left argument.
- y: Value - Right argument.
- Examples
x != y
- Evaluates to True or False based on the value of x and y.
Plus (+)
Plus(x: Number, y: Number) -> Number
Computes the 'Plus' function of the values.
- Arguments
- x: Number - Left argument.
- y: Number - Right argument.
- Examples
x + y
- Evaluates the expression.
Power (^)
Power(x: Number, y: Number) -> Number
Computes the 'Power' function of the values.
- Arguments
- x: Number - Left argument.
- y: Number - Right argument.
- Examples
x ^ y
- Evaluates the expression.
Subtract (-)
Subtract(x: Number, y: Number) -> Number
Computes the 'Subtract' function of the values.
- Arguments
- x: Number - Left argument.
- y: Number - Right argument.
- Examples
x - y
- Evaluates the expression.
Times (*)
Times(x: Number, y: Number) -> Number
Computes the 'Times' function of the values.
- Arguments
- x: Number - Left argument.
- y: Number - Right argument.
- Examples
x * y
- Evaluates the expression.