Package Biskit :: Module molTools
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Module molTools

source code

Various structure related calculations.

Classes [hide private]
  Test
Test class

Functions [hide private]
[ int, int, float, float ] hbonds(model)
Collect a list with all potential hydrogen bonds in model.
float OR None hbondCheck(angle, length)
A h-bond is longer that 2.4A but shorter that 3.5A, measuring from the nitrogen (donor) to the acceptor.
[float, float, float] xyzOfNearestCovalentNeighbour(i, model)
Closest atom in the same residue as atom with index i
string fasta(m, start=0, stop=None)
Extract fasta sequence from model.

Variables [hide private]
  test = Test()

Function Details [hide private]

hbonds(model)

source code 

Collect a list with all potential hydrogen bonds in model.
Parameters:
  • model (PDBModel) - PDBModel for which
Returns: [ int, int, float, float ]
a list of potential hydrogen bonds containing a lists with donor index, acceptor index, distance and angle.

hbondCheck(angle, length)

source code 

A h-bond is longer that 2.4A but shorter that 3.5A, measuring from the nitrogen (donor) to the acceptor. The corresponding length from the hydrogen (donor) to the acceptor (used here) is 1.4 and 2.5A.
  • the optimal length is about 2.8A (1.8A measured from the hydrogen).
  • long h-bond (>3.6A) should be quite linear angle >150
  • short h-bond (<3.6A) could be quite bent, but not more than 90-110
Parameters:
  • angle (float) - angle of bond to check
  • length (float) - lenght of bond to check (D-H...A)
Returns: float OR None
if the test is passed the cutoff angle for a hydrogen bond of the given length is returned, else None.

xyzOfNearestCovalentNeighbour(i, model)

source code 

Closest atom in the same residue as atom with index i
Parameters:
  • model (PDBModel) - PDBModel
  • i (int) - atom index
Returns: [float, float, float]
coordinates of the nearest atom

fasta(m, start=0, stop=None)

source code 

Extract fasta sequence from model.
Parameters:
  • m (PDBModel) - model
  • start (int) - first residue
  • stop (int) - last residue
Returns: string
fasta formated sequence and PDB code

Variables Details [hide private]

test

Value:
Test()