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PatternQuery:Language Reference

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Revision as of 17:18, 16 October 2013 by Dave (talk | contribs)

Introduction

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 of Motive (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.

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

LogicalNot(x: Bool) -> Bool
Computes 'LogicalNot' of the input value.

Arguments
x: Bool - Argument.
Examples
Not(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

LogicalXor(xs: Bool+) -> Bool
Computes 'LogicalXor' of the input values.

Arguments
xs: Bool+ - Arguments.
Examples
LogicalXor(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.


Basic Query Functions

Basic building blocks of the language - i.e. atoms, residues, and the like.

AminoAcids

AminoAcids -> Residues
Sequence of all amino acids in a given protein.

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.

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

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 numner]_[zn atomid]'. If the Named function was not used, the name would be just '[parent id]_[pseudorandom numner]'.

NotAminoAcids

NotAminoAcids -> Residues
Sequence of all residues resudies that are not amino acids.

Options
NoWaters: Bool = True - Ignore water residues such as HOH.
Examples
NotAminoAcids()
Returns all residues that are not amino acids.

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: String) -> Motives
Regular motives. The protein is split into individual chains before the motives are identified.

Arguments
regex: String - Regular expression on one letter abbreviations of amino acids.
Examples
RegularMotives("RGD")
Finds all RGD motives.

ResidueIdRange

ResidueIdRange(chain: String, min: Integer, max: ?Integer) -> Residues
Sequence of residues with specific chain and min <= sequence number <= max.

Arguments
chain: String - Chain idetifier. 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.

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 - i.e. filters and unions.

Count

Count(where: Motive, what: Motives) -> Integer
Counts all occurences 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.

Current

Current -> Motive
A variable that is assigned by the application environment.

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.

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.

Find

Find(source: Motive, motives: Motives) -> Motives
Converts the source motive to a structure and finds motives within it.

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).

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.

Motive

Motive(structureName: String) -> Motive
Returns a structure represented a motive.

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).

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.

SelectMany

SelectMany(motives: Motives, selector: Motive->Motives) -> Motives
Projects a sequence of motives to another.

Arguments
motives: Motives - Motives to project.
selector: Motive->Motives - The selector.
Examples
Residues("HIS").SelectMany(lambda m: m.Find(Atoms("C")))
Returns all C atoms on HIS residues.

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.

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.

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.

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.


Topology Functions

Functions that manipulate the topology of motives.

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.

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.


Geometry Functions

Functions that manipulate the geometry of motives.

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).

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.


Miscellaneous Functions

Various useful functions.

AtomProperty

AtomProperty(atomMotive: Motive, name: String) -> ?
If the property exists and the motive consits of a single atom, returns the property. Otherwise, returns Nothing.

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.

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).

Descriptor

Descriptor(motive: Motive, name: String) -> ?
Returns the descriptor. If the descriptor does not exist, 'null' is returned.

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.

ResidueSimilarity

ResidueSimilarity(a: Motive, b: Motive) -> Real
Computes Jaccard/Tanimoto coefficient on residue names of both structures.

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).


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