Interface

ParserOptionsSpec

ParserOptionsSpec

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

View Source parsers/ParserOptionsSpec.ts, line 6

Members

string

# altLoc Optional

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

View Source parsers/ParserOptionsSpec.ts, line 78

number

# assemblyIndex Optional

index of the assembly in symmetry ; supported by mmtf

View Source parsers/ParserOptionsSpec.ts, line 83

boolean

# assignBonds Optional

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

View Source parsers/ParserOptionsSpec.ts, line 88

boolean

# doAssembly Optional

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

View Source parsers/ParserOptionsSpec.ts, line 43

boolean

# dontConnectDuplicatedAtoms Optional

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

View Source parsers/ParserOptionsSpec.ts, line 58

boolean

# duplicateAssemblyAtoms Optional

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.

View Source parsers/ParserOptionsSpec.ts, line 48

boolean

# frames Optional

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

View Source parsers/ParserOptionsSpec.ts, line 11

number

# hbondCutoff Optional

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

View Source parsers/ParserOptionsSpec.ts, line 73

boolean

# keepH Optional

do not strip hydrogens ; supported by sdf,mol2

View Source parsers/ParserOptionsSpec.ts, line 33

boolean

# multimodel Optional

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

View Source parsers/ParserOptionsSpec.ts, line 23

boolean

# noComputeSecondaryStructure Optional

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

View Source parsers/ParserOptionsSpec.ts, line 68

boolean

# noSecondaryStructure Optional

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

View Source parsers/ParserOptionsSpec.ts, line 63

boolean

# normalizeAssembly Optional

shift symmetry mates so their centroid is in the unit cell

View Source parsers/ParserOptionsSpec.ts, line 53

boolean

# onemol Optional

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

View Source parsers/ParserOptionsSpec.ts, line 28

unknown

# parseStyle Optional

used to define ChemDoodle styles ; supported by cdjson

View Source parsers/ParserOptionsSpec.ts, line 38

AtomStyleSpec

# style Optional

set model to this style after parsing

View Source parsers/ParserOptionsSpec.ts, line 93

object

# vibrate Optional

object specifying the vibration behavior ; supported by all

Properties:
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

View Source parsers/ParserOptionsSpec.ts, line 16