| flat | In `radiate` drawing mode, redraws the whole structure, aligning to a baseline the base featured on the exterior loops (aka "dangling ends") | False |
[^1]: Since there is no canonical definition of pseudoknotted portions, a maximal planar subset is extracted from the input structure, defined to be the planar portion, and used as a scaffold for the drawing algorithms.
| bpIncrement | float | In linear drawing mode, defines the vertical increment used to separate two successive, nested base-pairs |
| periodNum | int | Sets the interval between two successive base numbers. More specifically, if `k` is the period, then the first and last bases of the RNA are numbered, along with each base whose number is a multiple of `k` |
| resolution | float | Chooses the resolution of a bitmap export, _i.e._ the multiplier in the number of pixels in each dimension of the exported picture. |
| rotation | float | Rotates the whole RNA of a certain angular increment |
| spaceBetweenBases | float | Sets the distance between consecutive bases |
| zoom | float | Defines the level of zoom and zoom increment used to display the RNA within this panel |
| flat | In `radiate` drawing mode, redraws the whole structure, aligning to a baseline the base featured on the exterior loops (aka "dangling ends") | False |
[^1]: Since there is no canonical definition of pseudoknotted portions, a maximal planar subset is extracted from the input structure, defined to be the planar portion, and used as a scaffold for the drawing algorithms.
"""
forkey,valueinkwargs.items():
...
...
@@ -263,8 +324,16 @@ class VARNA:
self.options=kwargs
defset_numeric_params(self,**kwargs):
"""Change value of numeric parameters in one function.
This is equivalent to use setting function of each parameter,
such as [set_bp_increment][varnaapi.VARNA.set_bp_increment].
Args:
**kwargs (dict): See [NUMERIC_PARAMS][varnaapi.NUMERIC_PARAMS] for allowed keywords.
"""
forkey,valueinkwargs.items():
ifkeynotinNUMERIC_OPTIONS:
ifkeynotinNUMERIC_PARAMS:
raiseException("{} is not a valid keyword".format(key))
assert_is_number(value)
ifkey=="periodNum":
...
...
@@ -273,6 +342,8 @@ class VARNA:
self.params[key]=float(value)
defformat_structure(self):
"""Return secondary structure in dot-brackaet notation
"""
defgreedy_fill(c1,c2,res,ss,i,j):
ifi<=j:
k=ss[i]
...
...
@@ -312,27 +383,45 @@ class VARNA:
self.params['border']="\"{}\"".format(border)
defset_bp_style(self,style:str):
"""Set default style for base-pairs rendering, chosen among: