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
- string
assemblyIndex :number
index of the assembly in symmetry ; supported by mmtf
- number
assignBonds :boolean
for formats without explicit bonds (e.g. PDB, xyz) infer bonding (default true).
- boolean
doAssembly :boolean
boolean dictating weather or not to do assembly ; supported by mcif, pdb
- boolean
dontConnectDuplicatedAtoms :boolean
do not detect bonds between symmetries generated with duplicateAssemblyAtoms (cif only - other formats never make bonds between symmetries)
- 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.
- boolean
frames :boolean
true if you want to add to a new frame and false otherwise ; supported by all
- boolean
hbondCutoff :number
maximum distance used for identifying hydrogen bonds when computing secondary structure; supported by pdb, mmtf, cif
- number
keepH :boolean
do not strip hydrogens ; supported by sdf,mol2
- boolean
multimodel :boolean
specifies whether or not multiple models are being defined ; supported by xyz,sdf, or mol2
- boolean
noComputeSecondaryStructure :boolean
do not compute ss ; supported by pdb, mmtf, cif
- boolean
noSecondaryStructure :boolean
boolean dictating the presence of a secondary structure ; supported by pdb
- boolean
normalizeAssembly :boolean
shift symmetry mates so their centroid is in the unit cell
- boolean
onemol :boolean
specifies weather or not the model is of one molecule ; Supported by xyz , sdf , mol2
- boolean
parseStyle :unknown
used to define ChemDoodle styles ; supported by cdjson
- 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
- boolean
vibrate :object
object specifying the vibration behavior ; supported by all
- object
| Name | Type | Attributes | Description |
|---|---|---|---|
frames | number | <optional> | vibrate.frames - number of frames to be created, default to 10 ; supported by all |
amplitude | number | <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
- boolean