first version

script/pymolbond.py

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+#!/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