Module molTools

source code

Various structure related calculations.

Classes

[hide private]

Test
Test class

Functions

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[ 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

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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()