Parameter Options¶
The parameters to identify the interactions refer to those
used in PyPLIF, which
inspired by the IFP of Marcou and Rognan.
These parameters can be modified in .hippos/PARAMETERS.py in your home
directory after HIPPOS installed.
In general there are two rules that can be modified:
Maximum distance value.
Interaction angle limit (for hydrogen bond and aromatic interaction).
Here is the content of .hippos/PARAMETERS.py
'''
Parameter for interaction distance
Interaction exist if lower or equal
than these values
'''
HYDROPHOBIC = 4.5
AROMATIC = 4.0
HBOND = 3.5
ELECTROSTATIC = 4.0
'''
Parameter for minimum H bond angle.
Interaction exist if O --- H-D angle
higher or equal than HBOND_ANGLE value.
'''
HBOND_ANGLE = 135
'''
Parameter for aromatic interaction angle.
Face to Face if:
AROMATIC_ANGLE_LOW >= Angle between aromatic plane
Or AROMATIC_ANGLE_HIGH <= Angle between aromatic plane
Edge to Face if:
AROMATIC_ANGLE_LOW < Angle between aromatic plane <
AROMATIC_ANGLE_HIGH
'''
AROMATIC_ANGLE_LOW = 30.0
AROMATIC_ANGLE_HIGH = 150.0
The explanation of each value can be seen from the comment above the value assignment.
Simplified Bitstring Rule¶
HIPPOS provides simplified interaction bitstring to reduce unnecessary string in the output. The bitstring simplification rule can be seen in the table below. Number 1-7 in the header of the table correspond to the interaction type described in PyPLIF
1 Correspond to Hydrophobic
2 Correspond to Aromatic Face to Face
3 Correspond to Aromatic Edge to Face
4 Correspond to H-bond (protein is donor)
5 Correspond to H-bond (protein is acceptor)
6 Correspond to Electrostatic (protein +)
7 Correspond to Electrostatic (protein -)