#!/usr/bin/env python
# -*- encoding: utf-8 -*-
'''
@file               :pymolbond.py
@Description:       :
@Date               :2023/09/01 16:57:02
@Author             :lyzeng
@Email              :pylyzeng@gmail.com
@version            :1.0
'''

class Bond():
    """
    This class contains static methods for identifying various types of molecular interactions.
    """

    @staticmethod
    def HBond(ChA, ChB):
        """Identifies hydrogen bonds between two chains."""
        name = 'Hbond'
        cmd.distance(name, ChA, ChB, '3.5', '2')
        return name

    @staticmethod
    def Pi_Pi_interaction(ChA, ChB):
        """Identifies pi-pi interactions between two chains."""
        name = 'PI_PI'
        cmd.distance(name, ChA, ChB, '5.5', '6')
        return name

    @staticmethod
    def Cation_Pi_interaction(ChA, ChB):
        """Identifies cation-pi interactions between two chains."""
        name = 'PI_Cation'
        cmd.distance(name, ChA, ChB, '5.5', '7')
        return name

    @staticmethod
    def Salt_bridge_positive(ChA, ChB):
        """Identifies salt bridges from positive residues in one chain to negative residues in another chain."""
        name = 'SBP'
        selection_1 = f'{ChB} and ((resn LYS and name NZ) or (resn ARG and name NE+NH*))'
        selection_2 = f'{ChA} and resn ASP+GLU and name OD*+OE*'
        cmd.distance(name, selection_1, selection_2, '5.0', '0')
        return name

    @staticmethod
    def Salt_bridge_negative(ChA, ChB):
        """Identifies salt bridges from negative residues in one chain to positive residues in another chain."""
        
        name = 'SBN'
        selection_1 = f'{ChA} and ((resn LYS and name NZ) or (resn ARG and name NE+NH*))'
        selection_2 = f'{ChB} and resn ASP+GLU and name OD*+OE*'
        cmd.distance(name, selection_1, selection_2, '5.0', '0')
        return name

    @staticmethod
    def Van_der_Waals(ChA, ChB): # not tested
        """Identifies Van der Waals interactions between two chains."""
        name = 'VDW'
        cmd.distance(name, ChA, ChB, '0.6', '0')
        return name

    @staticmethod
    def Hydrophobic_interaction(ChA, ChB): # not tested
        """Identifies hydrophobic interactions between two chains."""
        name = 'Hydrophobic'
        cmd.distance(name, ChA, ChB, '0.6', '0')
        return name

    @staticmethod
    def Electrostatic_interaction(ChA, ChB): # not tested
        """Identifies electrostatic interactions between two chains."""
        name = 'Electrostatic'
        cmd.distance(name, ChA, ChB, '0.6', '0')
        return name

    @staticmethod
    def Metal_coordination(ChA, ChB): # not tested
        """Identifies metal coordination bonds between two chains."""
        name = 'MetalCoord'
        cmd.distance(name, ChA, ChB, '0.2', '0')
        return name

    @staticmethod
    def Disulfide_bond(ChA, ChB): # not tested
        """Identifies disulfide bonds between two chains."""
        name = 'Disulfide'
        cmd.distance(name, ChA, ChB, '0.2', '0')
        return name