ParserOptionsSpec

Parser options specification. Used to specify the options of a GLModel. Depending on the input file format, not all fields may be defined.

Members

altLoc :string

which alternate location to select, if present; '*' to load all ; supported by pdb

Type:
  • string

assemblyIndex :number

index of the assembly in symmetry ; supported by mmtf

Type:
  • number

assignBonds :boolean

for formats without explicit bonds (e.g. PDB, xyz) infer bonding (default true).

Type:
  • boolean

doAssembly :boolean

boolean dictating weather or not to do assembly ; supported by mcif, pdb

Type:
  • boolean

dontConnectDuplicatedAtoms :boolean

do not detect bonds between symmetries generated with duplicateAssemblyAtoms (cif only - other formats never make bonds between symmetries)

Type:
  • boolean

duplicateAssemblyAtoms :boolean

Set to true if you wish to duplicate assembly atoms otherwise false ; supported by all formats with symmetries. Not duplicating will result in faster rendering but it will not be possible to individually style symmetries.

Type:
  • boolean

frames :boolean

true if you want to add to a new frame and false otherwise ; supported by all

Type:
  • boolean

hbondCutoff :number

maximum distance used for identifying hydrogen bonds when computing secondary structure; supported by pdb, mmtf, cif

Type:
  • number

keepH :boolean

do not strip hydrogens ; supported by sdf,mol2

Type:
  • boolean

multimodel :boolean

specifies whether or not multiple models are being defined ; supported by xyz,sdf, or mol2

Type:
  • boolean

noComputeSecondaryStructure :boolean

do not compute ss ; supported by pdb, mmtf, cif

Type:
  • boolean

noSecondaryStructure :boolean

boolean dictating the presence of a secondary structure ; supported by pdb

Type:
  • boolean

normalizeAssembly :boolean

shift symmetry mates so their centroid is in the unit cell

Type:
  • boolean

onemol :boolean

specifies weather or not the model is of one molecule ; Supported by xyz , sdf , mol2

Type:
  • boolean

parseStyle :unknown

used to define ChemDoodle styles ; supported by cdjson

Type:
  • unknown

style :AtomStyleSpec

set model to this style after parsing

unboundCations :boolean

for formats without explicit bonds, if assigning bonds to not assign bonds to common cations

Type:
  • boolean

vibrate :object

object specifying the vibration behavior ; supported by all

Type:
  • object
Properties
NameTypeAttributesDescription
framesnumber<optional>

vibrate.frames - number of frames to be created, default to 10 ; supported by all

amplitudenumber<optional>

vibrate.amplitude -amplitude of distortion, default to 1 (full) ; supported by all

wrapAtoms :boolean

Set to true with duplicateAssemblyAtoms to individually wrap atoms (from symmetries) into unit cell

Type:
  • boolean