Electric Field

Briefs

The electric_field_strength_at_along function calculates the electric field strength at a specified point between two atoms based on their coordinates and charge, optionally considering a specified direction, and supports different units for the result.

Input/Output

Input

Params: The stru, p1, p2, d1, and region_pattern are required input

• stru:

  A Structure() object which represents the structure of the target enzyme. MUST have charges assigned for ligands. (See examples).

  How to obtain

  A protein strutcuture object can be obtained by this APIs.

  Normally, the EF is calculated based on structures sampled from MD or other sampling methods.

• p1, p2 and d1:

  Specify where is the field strength is calculated.

  (p1,p2) - by 2 points (default: the center of them) and calculate along p1 -> p2

  (p1,d1) - by 1 point and along direction d1

  
  

  p1 and p2 can be Atom() objects or Cartesian coordinates.

  For example, a cartesian coordinates can be the center of an aromatic ring.

  How to obtain

  Atom() objects can be obtained by these APIs.

  Cartesian coordinate can be defined as a tuple (e.g.: (1.0, 2.0, 3.0) )

region_pattern:

The specified region within the structure serves as the origin of field charges.

How to obtain

The region_pattern uses the StructureSelection syntax defined here.

Normally people exclude the solvent and substrate, which the target bond is in, from the selection region.

Output

Output: A specified field strength in default unit kcal/(mol*e*Ang). The direction is from p1 to p2 or along the d1 direction

Arguments

stru:

The target enzyme’s structure must be initialized with charges. (See Input/Output)

p1, p2 and d1:

To calculate the electric field within an enzyme, input a location and either a direction (d1) or two points (p1, p2), ensuring enzyme charges are included; d1 defines the field strength projection direction. (See Input/Output)

location:

The location of the measurement when 2 points are specified.

Supported keywords: [center, p1, p2] (default: center)

Reference

REF: EnzyHTP: A High-Throughput Computational Platform for Enzyme Modeling (https://pubs.acs.org/doi/full/10.1021/acs.jcim.1c01424)

region_pattern:

The specified region within the structure serves as the origin of field charges, utilizing PyMOL selection syntax. Users should exclude the solvent or substrate from the selection region if they intend to measure a bond within the same molecule. The instruction can be founded as APIs.

unit:

The unit of the result.

Supported keywords: [kcal/(mol*e*Ang), MV/cm] (default: kcal/(mol*e*Ang))

Example code

In this example, we will use the script to calculate the electric field between the breaking C-H of the substrate in a KE07 variant.

How input is prepared

stru

obtained by reading from a PDB file using PDBParser().get_structure() Note that we also assigned the charge and spin using .assign_ncaa_chargespin() method. (See Details)

p1, p2

They are obtained by the .get() method from Structure

region_pattern

we excluded the reacting residue (A.101) and the substrate (B.254)

import os
import numpy as np
from enzy_htp.analysis import ele_field_strength_at_along
from enzy_htp import PDBParser

# Initialize PDB parser
sp = PDBParser()

# Load structure from PDB file
stru_obj = sp.get_structure("KE.pdb")

# Assign charges to the structure
stru_obj.assign_ncaa_chargespin({"H5J" : (0,1)})

# Define the target bond as p1, p2
p1 = test_stru.get("B.254.CAE")
p2 = test_stru.get("B.254.H2")

# Calculate electric field strength along the bond
result = ele_field_strength_at_along(stru_obj, p1, p2, region_pattern="chain A and (not resi 101)",)

print("Electric field strength:", result)

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Author: Xinchun Ran <xinchun.ran@vanderbilt.edu>