Language Reference

Language Primitives
- Types
- Logic
- Control
- Relational
- Math
- Strings
- Lists
- Sets
- Flags
Structure Queries

Language Primitives

Types

bool

core.type.bool :: (Value) => Bool

Convert a value to boolean.

num

core.type.num :: (Value) => Number

Convert a value to number.

str

core.type.str :: (Value) => String

Convert a value to string.

regex

core.type.regex :: (
  String, (* Expression *)
  ?String (* Flags, e.g. 'i' for ignore case *)
) => Regex

Creates a regular expression from a string using the ECMAscript syntax.

list

core.type.list :: a* => List[a]

set

core.type.set :: a* => Set[a]

bitflags

core.type.bitflags :: (Number) => BitFlags

Interpret a number as bitflags.

composite-key

core.type.composite-key :: Value* => Value

Logic

not

core.logic.not :: (Bool) => Bool

and

core.logic.and :: Bool+ => Bool

or

core.logic.or :: Bool+ => Bool

Control

eval

core.ctrl.eval :: (Fn[a]) => a

Evaluate a function.

fn

core.ctrl.fn :: (a) => Fn[a]

Wrap an expression to a "lazy" function.

if

core.ctrl.if :: (
  Bool, (* Condition *)
  a, (* If true *)
  b (* If false *)
) => a | b

Relational

eq

core.rel.eq :: (a: Value, a: Value) => Bool

neq

core.rel.neq :: (a: Value, a: Value) => Bool

lt

core.rel.lt :: (Number, Number) => Bool

lte

core.rel.lte :: (Number, Number) => Bool

gr

core.rel.gr :: (Number, Number) => Bool

gre

core.rel.gre :: (Number, Number) => Bool

in-range

core.rel.in-range :: (
  Number, (* Value to test *)
  Number, (* Minimum value *)
  Number (* Maximum value *)
) => Bool

Check if the value of the 1st argument is >= 2nd and <= 3rd.

Math

add

core.math.add :: Number+ => Number

sub

core.math.sub :: Number+ => Number

mult

core.math.mult :: Number+ => Number

div

core.math.div :: (Number, Number) => Number

pow

core.math.pow :: (Number, Number) => Number

mod

core.math.mod :: (Number, Number) => Number

min

core.math.min :: Number+ => Number

max

core.math.max :: Number+ => Number

floor

core.math.floor :: (Number) => Number

ceil

core.math.ceil :: (Number) => Number

round-int

core.math.round-int :: (Number) => Number

abs

core.math.abs :: (Number) => Number

sqrt

core.math.sqrt :: (Number) => Number

sin

core.math.sin :: (Number) => Number

cos

core.math.cos :: (Number) => Number

tan

core.math.tan :: (Number) => Number

asin

core.math.asin :: (Number) => Number

acos

core.math.acos :: (Number) => Number

atan

core.math.atan :: (Number) => Number

sinh

core.math.sinh :: (Number) => Number

cosh

core.math.cosh :: (Number) => Number

tanh

core.math.tanh :: (Number) => Number

exp

core.math.exp :: (Number) => Number

log

core.math.log :: (Number) => Number

log10

core.math.log10 :: (Number) => Number

atan2

core.math.atan2 :: (Number, Number) => Number

Strings

concat

core.str.concat :: String+ => String

match

core.str.match :: (Regex, String) => Bool

Lists

get-at

core.list.get-at :: (List[a], Number) => a

Sets

has

core.set.has :: (Set[a], a) => Bool

Check if the the 1st argument includes the value of the 2nd.

is-subset

core.set.is-subset :: (Set[a], Set[a]) => Bool

Check if the the 1st argument is a subset of the 2nd.

Flags

has-any

core.flags.has-any :: (Flags[a], Flags[a]) => Bool

Check if the the 1st argument has at least one of the 2nd one's flags.

has-all

core.flags.has-all :: (Flags[a], Flags[a]) => Bool

Check if the the 1st argument has all 2nd one's flags.

Structure Queries

Types

element-symbol

structure.type.element-symbol :: (String) => ElementSymbol

Create element symbol representation from a string value.

atom-name

structure.type.atom-name :: (Value) => AtomName

Convert a value to an atom name.

entity-type

structure.type.entity-type :: (EntityType) => EntityType

Create normalized representation of entity type: non-polymer, polymer, unknown, water.

bond-flags

structure.type.bond-flags :: BondFlag* => BondFlags

Create bond flags representation from a list of strings. Allowed flags: aromatic, computed, covalent, hydrogen, ion, metallic, sulfide.

ring-fingerprint

structure.type.ring-fingerprint :: ElementSymbol+ => RingFingerprint

Create ring fingerprint from the supplied atom element list.

secondary-structure-flags

structure.type.secondary-structure-flags :: SecondaryStructureFlag* => SecondaryStructureFlag

Create secondary structure flags representation from a list of strings. Allowed flags: 3-10, alpha, beta, helix, none, pi, sheet, strand, turn.

auth-residue-id

structure.type.auth-residue-id :: (
  String, (* auth_asym_id *)
  Number, (* auth_seq_id *)
  ?String (* pdbx_PDB_ins_code *)
) => ResidueId

Residue identifier based on "auth_" annotation.

label-residue-id

structure.type.label-residue-id :: (
  String, (* label_entity_id *)
  String, (* label_asym_id *)
  Number, (* label_seq_id *)
  ?String (* pdbx_PDB_ins_code *)
) => ResidueId

Residue identifier based on mmCIF's "label_" annotation.

Iteration Slots

atom

structure.slot.atom :: () => AtomReference

A reference to the current atom.

atom-set-reduce

structure.slot.atom-set-reduce :: () => a: Value

Current value of the atom set reducer.

Generators

atom-groups

structure.generator.atom-groups :: {
  entity-test?: Bool = true, (* Test for the 1st atom of every entity *)
  chain-test?: Bool = true, (* Test for the 1st atom of every chain *)
  residue-test?: Bool = true, (* Test for the 1st atom every residue *)
  atom-test?: Bool = true, 
  group-by?: Any = atom-key (* Group atoms to sets based on this property. Default: each atom has its own set *)
} => AtomSelectionQuery

Return all atoms for which the tests are satisfied, grouped into sets.

rings

structure.generator.rings :: RingFingerprint* => AtomSelectionQuery

Return rings with the specified fingerprint(s). If no fingerprints are given, return all rings.

query-in-selection

structure.generator.query-in-selection :: {
  AtomSelectionQuery, 
  query: AtomSelectionQuery, 
  in-complement?: Bool = false
} => AtomSelectionQuery

Executes query only on atoms that are in the source selection.

empty

structure.generator.empty :: () => AtomSelectionQuery

Nada.

Selection Modifications

query-each

structure.modifier.query-each :: {
  AtomSelectionQuery, 
  query: AtomSelectionQuery
} => AtomSelectionQuery

Query every atom set in the input selection separately.

intersect-by

structure.modifier.intersect-by :: {
  AtomSelectionQuery, 
  by: AtomSelectionQuery
} => AtomSelectionQuery

Intersect each atom set from the first sequence from atoms in the second one.

except-by

structure.modifier.except-by :: {
  AtomSelectionQuery, 
  by: AtomSelectionQuery
} => AtomSelectionQuery

Remove all atoms from 'selection' that occur in 'by'.

union-by

structure.modifier.union-by :: {
  AtomSelectionQuery, 
  by: AtomSelectionQuery
} => AtomSelectionQuery

For each atom set A in the orginal sequence, combine all atoms sets in the target selection that intersect with A.

union

structure.modifier.union :: (AtomSelectionQuery) => AtomSelectionQuery

Collects all atom sets in the sequence into a single atom set.

cluster

structure.modifier.cluster :: {
  AtomSelectionQuery, 
  min-distance?: Number = 0, 
  max-distance: Number, 
  min-size?: Number = 2, (* Minimal number of sets to merge, must be at least 2 *)
  max-size?: Number (* Maximal number of sets to merge, if not set, no limit *)
} => AtomSelectionQuery

Combines atom sets that have mutual distance in the interval [min-radius, max-radius]. Minimum/maximum size determines how many atom sets can be combined.

include-surroundings

structure.modifier.include-surroundings :: {
  AtomSelectionQuery, 
  radius: Number, 
  atom-radius?: Number = 0, (* Value added to each atom before the distance check, for example VDW radius. Using this argument is computationally demanding. *)
  as-whole-residues?: Bool
} => AtomSelectionQuery

For each atom set in the selection, include all surrouding atoms/residues that are within the specified radius.

include-connected

structure.modifier.include-connected :: {
  AtomSelectionQuery, 
  bond-test?: Bool = true for covalent bonds, 
  layer-count?: Number = 1, (* Number of bonded layers to include. *)
  as-whole-residues?: Bool
} => AtomSelectionQuery

Pick all atom sets that are connected to the target.

expand-property

structure.modifier.expand-property :: {
  AtomSelectionQuery, 
  property: Value
} => AtomSelectionQuery

To each atom set in the selection, add all atoms that have the same property value that was already present in the set.

Selection Filters

pick

structure.filter.pick :: {
  AtomSelectionQuery, 
  test: Bool
} => AtomSelectionQuery

Pick all atom sets that satisfy the test.

with-same-atom-properties

structure.filter.with-same-atom-properties :: {
  AtomSelectionQuery, 
  source: AtomSelectionQuery, 
  property: Any
} => AtomSelectionQuery

Pick all atom sets for which the set of given atom properties is a subset of the source properties.

intersected-by

structure.filter.intersected-by :: {
  AtomSelectionQuery, 
  by: AtomSelectionQuery
} => AtomSelectionQuery

Pick all atom sets that have non-zero intersection with the target.

within

structure.filter.within :: {
  AtomSelectionQuery, 
  target: AtomSelectionQuery, 
  min-radius?: Number = 0, 
  max-radius: Number, 
  atom-radius?: Number = 0, (* Value added to each atom before the distance check, for example VDW radius. Using this argument is computationally demanding. *)
  invert?: Bool = false (* If true, pick only atom sets that are further than the specified radius. *)
} => AtomSelectionQuery

Pick all atom sets from selection that have any atom within the radius of any atom from target.

is-connected-to

structure.filter.is-connected-to :: {
  AtomSelectionQuery, 
  target: AtomSelectionQuery, 
  bond-test?: Bool = true for covalent bonds, 
  disjunct?: Bool = true, (* If true, there must exist a bond to an atom that lies outside the given atom set to pass test. *)
  invert?: Bool = false (* If true, return atom sets that are not connected. *)
} => AtomSelectionQuery

Pick all atom sets that are connected to the target.

Selection Combinators

intersect

structure.combinator.intersect :: AtomSelectionQuery* => AtomSelectionQuery

Return all unique atom sets that appear in all of the source selections.

merge

structure.combinator.merge :: AtomSelectionQuery* => AtomSelectionQuery

Merges multiple selections into a single one. Only unique atom sets are kept.

distance-cluster

structure.combinator.distance-cluster :: {
  matrix: List[List[Number]], (* Distance matrix, represented as list of rows (num[][])). Lower triangle is min distance, upper triangle is max distance. *)
  selections: List[AtomSelectionQuery] (* A list of held selections. *)
} => AtomSelectionQuery

Pick combinations of atom sets from the source sequences that are mutually within distances specified by a matrix.

Atom Sets

atom-count

structure.atom-set.atom-count :: () => Number

count-query

structure.atom-set.count-query :: (AtomSelectionQuery) => Number

Counts the number of occurences of a specific query inside the current atom set.

reduce

structure.atom-set.reduce :: {
  initial: a: Value, (* Initial value assigned to slot.atom-set-reduce. Current atom is set to the 1st atom of the current set for this. *)
  value: a: Value (* Expression executed for each atom in the set *)
} => a: Value

Execute the value expression for each atom in the current atom set and return the result. Works the same way as Array.reduce in JavaScript (result = value(value(...value(initial))))

property-set

structure.atom-set.property-set :: (a) => Set[a]

Returns a set with all values of the given property in the current atom set.

Atom Properties

Core Properties

element-symbol

structure.atom-property.core.element-symbol :: (?AtomReference = slot.current-atom) => ElementSymbol

vdw

structure.atom-property.core.vdw :: (?AtomReference = slot.current-atom) => Number

Van der Waals radius

x

structure.atom-property.core.x :: (?AtomReference = slot.current-atom) => Number

Cartesian X coordinate

y

structure.atom-property.core.y :: (?AtomReference = slot.current-atom) => Number

Cartesian Y coordinate

z

structure.atom-property.core.z :: (?AtomReference = slot.current-atom) => Number

Cartesian Z coordinate

atom-key

structure.atom-property.core.atom-key :: (?AtomReference = slot.current-atom) => Value

Unique value for each atom. Main use case is grouping of atoms.

bond-count

structure.atom-property.core.bond-count :: {
  ?AtomReference = slot.current-atom, 
  flags?: BondFlags = covalent
} => Number

Number of bonds (by default only covalent bonds are counted).

connected-component-key

structure.atom-property.topology.connected-component-key :: (?AtomReference = slot.current-atom) => Value

Unique value for each connected component.

Macromolecular Properties (derived from the mmCIF format)

auth-residue-id

structure.atom-property.macromolecular.auth-residue-id :: (?AtomReference = slot.current-atom) => ResidueId

type.auth-residue-id symbol executed on current atom's residue

label-residue-id

structure.atom-property.macromolecular.label-residue-id :: (?AtomReference = slot.current-atom) => ResidueId

type.label-residue-id symbol executed on current atom's residue

residue-key

structure.atom-property.macromolecular.residue-key :: (?AtomReference = slot.current-atom) => Value

Unique value for each tuple (label_entity_id,auth_asym_id,auth_seq_id,pdbx_PDB_ins_code), main use case is grouping of atoms

chain-key

structure.atom-property.macromolecular.chain-key :: (?AtomReference = slot.current-atom) => Value

Unique value for each tuple (label_entity_id,auth_asym_id), main use case is grouping of atoms

entity-key

structure.atom-property.macromolecular.entity-key :: (?AtomReference = slot.current-atom) => Value

Unique value for each tuple label_entity_id, main use case is grouping of atoms

is-het

structure.atom-property.macromolecular.is-het :: (?AtomReference = slot.current-atom) => Bool

Equivalent to atom_site.group_PDB !== ATOM

id

structure.atom-property.macromolecular.id :: (?AtomReference = slot.current-atom) => Number

_atom_site.id

label_atom_id

structure.atom-property.macromolecular.label_atom_id :: (?AtomReference = slot.current-atom) => AtomName

label_alt_id

structure.atom-property.macromolecular.label_alt_id :: (?AtomReference = slot.current-atom) => String

label_comp_id

structure.atom-property.macromolecular.label_comp_id :: (?AtomReference = slot.current-atom) => String

label_asym_id

structure.atom-property.macromolecular.label_asym_id :: (?AtomReference = slot.current-atom) => String

label_entity_id

structure.atom-property.macromolecular.label_entity_id :: (?AtomReference = slot.current-atom) => String

label_seq_id

structure.atom-property.macromolecular.label_seq_id :: (?AtomReference = slot.current-atom) => Number

auth_atom_id

structure.atom-property.macromolecular.auth_atom_id :: (?AtomReference = slot.current-atom) => AtomName

auth_comp_id

structure.atom-property.macromolecular.auth_comp_id :: (?AtomReference = slot.current-atom) => String

auth_asym_id

structure.atom-property.macromolecular.auth_asym_id :: (?AtomReference = slot.current-atom) => String

auth_seq_id

structure.atom-property.macromolecular.auth_seq_id :: (?AtomReference = slot.current-atom) => Number

pdbx_PDB_ins_code

structure.atom-property.macromolecular.pdbx_PDB_ins_code :: (?AtomReference = slot.current-atom) => String

pdbx_formal_charge

structure.atom-property.macromolecular.pdbx_formal_charge :: (?AtomReference = slot.current-atom) => Number

occupancy

structure.atom-property.macromolecular.occupancy :: (?AtomReference = slot.current-atom) => Number

B_iso_or_equiv

structure.atom-property.macromolecular.B_iso_or_equiv :: (?AtomReference = slot.current-atom) => Number

entity-type

structure.atom-property.macromolecular.entity-type :: (?AtomReference = slot.current-atom) => EntityType

Type of the entity as defined in mmCIF (polymer, non-polymer, water, unknown)

secondary-structure-key

structure.atom-property.macromolecular.secondary-structure-key :: (?AtomReference = slot.current-atom) => Value

Unique value for each secondary structure element.

secondary-structure-flags

structure.atom-property.macromolecular.secondary-structure-flags :: (?AtomReference = slot.current-atom) => SecondaryStructureFlag

is-modified

structure.atom-property.macromolecular.is-modified :: (?AtomReference = slot.current-atom) => Bool

True if the atom bolongs to modification of a standard residue.

modified-parent-name

structure.atom-property.macromolecular.modified-parent-name :: (?AtomReference = slot.current-atom) => String

'3-letter' code of the modifed parent residue.

Bond Properties

flags

structure.bond-property.flags :: () => BondFlags

order

structure.bond-property.order :: () => Number

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Language Reference

Language Primitives

Types

bool

num

str

regex

list

set

bitflags

composite-key

Logic

not

and

or

Control

eval

fn

if

Relational

eq

neq

lt

lte

gr

gre

in-range

Math

add

sub

mult

div

pow

mod

min

max

floor

ceil

round-int

abs

sqrt

sin

cos

tan

asin

acos

atan

sinh

cosh

tanh

exp

log

log10

atan2

Strings

concat

match

Lists

get-at

Sets

has

is-subset

Flags

has-any

has-all

Structure Queries

Types

element-symbol

atom-name

entity-type

bond-flags

ring-fingerprint

secondary-structure-flags

auth-residue-id