first version

2024-09-07 09:12:14 +08:00
commit bc8cc22a9c
27 changed files with 2530 additions and 0 deletions
--- a/script/show_protein_protein_interaction.py
+++ b/script/show_protein_protein_interaction.py
@@ -0,0 +1,92 @@
+from pymol import cmd
+from pymol.cmd import util
+import sys
+from pymol_color_plugin import colorp
+
+
+def HBond(ChA,ChB):
+    name = f'Hbond'
+    dist = cmd.distance(name, ChA,ChB, '3.5', '2')
+    return name
+
+def Pi_Pi_interaction(ChA,ChB):
+    name = f'PI_PI'
+    cmd.distance(name,ChA, ChB,'5.5','6')
+    return name
+
+def Cation_Pi_interaction(ChA,ChB):
+    name = f'PI_Cation'
+    cmd.distance(name, ChA, ChB, '5.5', '7')
+    return name
+
+def Salt_bridge_positive(ChA,ChB):
+    name = f'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
+
+def Salt_bridge_negative(ChA,ChB):
+    name = f'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
+
+# def T_stacking(ChA, ChB):
+#     name = 'T_stacking'
+#     # 添加适当的距离和选择标准
+#     cmd.distance(name, ChA, ChB, '5.5', '2')
+#     return name
+
+# def Hydrophobic_interaction(ChA, ChB):
+#     name = 'Hydrophobic'
+#     # 添加适当的距离和选择标准
+#     cmd.distance(name, ChA, ChB, '7.0', '2')
+#     return name
+
+# def VDW_interaction(ChA, ChB):
+#     name = 'VDW'
+#     # 添加适当的距离和选择标准
+#     cmd.distance(name, ChA, ChB, '4.0', '2')
+#     return name
+
+def show_label_name(obj:str):
+    cmd.label(f'name CA and {obj}', 'oneletter+resi')
+    cmd.set('label_bg_color', -7, '', 0)
+    cmd.set('label_size', 18, '', 0)
+    cmd.set('label_font_id', '7')
+
+def interact(obj:str='epitope', distance:int=5):
+    cmd.show('stick',f'{obj}')
+    cmd.set('stick_radius', '0.3', f'{obj}')
+    colorp.color_mole(obj)
+    #show_label_name(obj)
+    cmd.select('nearby',f'byres {obj} around {distance}')
+    cmd.show('stick','nearby')
+    cmd.set('stick_radius', '0.1', 'nearby')
+    cmd.set('cartoon_transparency', 0.7, selection='nearby')
+    Hbond = HBond(obj, 'nearby')
+    PI = Pi_Pi_interaction(obj, 'nearby')
+    C_PI = Cation_Pi_interaction(obj, 'nearby')
+    SBP = Salt_bridge_positive(obj, 'nearby')
+    SBN = Salt_bridge_negative(obj, 'nearby')
+    cmd.set('dash_color', 'yellow', Hbond)
+    cmd.set('dash_color', 'blue', PI)
+    cmd.set('dash_color', 'blue', C_PI)
+    cmd.set('dash_color', 'orange', SBP)
+    cmd.set('dash_color', 'orange', SBN)
+    cmd.set('dash_radius', '0.07')
+    cmd.set('dash_gap', '0.3')
+    #cmd.remove('e. h and  neighbor(name C*)')
+    cmd.zoom('Hbond')
+
+def main():
+    cmd.reinitialize()
+    cmd.fetch('5sws',type='pdb')
+    colorp.pretty()
+    cmd.select('epitope','chain C and resi 1-9')
+    cmd.zoom('nearby')
+    interact()
+    cmd.save(f'5sws_interaction.pse')