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InPrNa1.0.py
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InPrNa1.0.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys
# pymol lib
try:
from pymol import cmd
from pymol import *
#from cgo import *
except ImportError:
print 'Warning: pymol library cmd not found.'
sys.exit(1)
# external lib
try:
import Pmw
except ImportError:
print 'Warning: failed to import Pmw. Exit ...'
sys.exit(1)
try:
import ttk
import tkFileDialog
import tkColorChooser
except ImportError:
print 'Warning: failed to import ttk or tk. Exit ...'
try:
import numpy
except ImportError:
print 'Warning: failed to import numpy. Exit ...'
try:
import math
except ImportError:
print 'Warning: failed to import math. Exit ...'
try:
import Tkinter
from Tkinter import *
except:
import tkinter
import _tkinter
#from Tkinter import ScrolledText
try:
import ScrolledText as tkst
except:
import tkinter.scrolledtext as tkst
print 'Warning: failed to import ScrolledText. Exit ...'
def __init__(self):
self.menuBar.addmenuitem('Plugin', 'command',
'Interface Show', label='InPrNa1.0',
command=lambda s=self: start(s))
class start:
def __init__(self, app):
self.counter = 0.0
##interface information
self.pdbfile = ''
self.Resn_number = {'ALA': 0,
'ARG': 0,
'ASN': 0,
'ASP': 0,
'CYS': 0,
'GLN': 0,
'GLU': 0,
'GLY': 0,
'HIS': 0,
'ILE': 0,
'LEU': 0,
'LYS': 0,
'MET': 0,
'PHE': 0,
'PRO': 0,
'SER': 0,
'THR': 0,
'TRP': 0,
'TYR': 0,
'VAL': 0,
}
self.interface3_resn_number = {'ALA': 0,
'ARG': 0,
'ASN': 0,
'ASP': 0,
'CYS': 0,
'GLN': 0,
'GLU': 0,
'GLY': 0,
'HIS': 0,
'ILE': 0,
'LEU': 0,
'LYS': 0,
'MET': 0,
'PHE': 0,
'PRO': 0,
'SER': 0,
'THR': 0,
'TRP': 0,
'TYR': 0,
'VAL': 0,
}
self.interface35_resn_number = {'ALA': 0,
'ARG': 0,
'ASN': 0,
'ASP': 0,
'CYS': 0,
'GLN': 0,
'GLU': 0,
'GLY': 0,
'HIS': 0,
'ILE': 0,
'LEU': 0,
'LYS': 0,
'MET': 0,
'PHE': 0,
'PRO': 0,
'SER': 0,
'THR': 0,
'TRP': 0,
'TYR': 0,
'VAL': 0,
}
self.interface4_resn_number = {'ALA': 0,
'ARG': 0,
'ASN': 0,
'ASP': 0,
'CYS': 0,
'GLN': 0,
'GLU': 0,
'GLY': 0,
'HIS': 0,
'ILE': 0,
'LEU': 0,
'LYS': 0,
'MET': 0,
'PHE': 0,
'PRO': 0,
'SER': 0,
'THR': 0,
'TRP': 0,
'TYR': 0,
'VAL': 0,
}
self.interface45_resn_number = {'ALA': 0,
'ARG': 0,
'ASN': 0,
'ASP': 0,
'CYS': 0,
'GLN': 0,
'GLU': 0,
'GLY': 0,
'HIS': 0,
'ILE': 0,
'LEU': 0,
'LYS': 0,
'MET': 0,
'PHE': 0,
'PRO': 0,
'SER': 0,
'THR': 0,
'TRP': 0,
'TYR': 0,
'VAL': 0,
}
self.interface5_resn_number = {'ALA': 0,
'ARG': 0,
'ASN': 0,
'ASP': 0,
'CYS': 0,
'GLN': 0,
'GLU': 0,
'GLY': 0,
'HIS': 0,
'ILE': 0,
'LEU': 0,
'LYS': 0,
'MET': 0,
'PHE': 0,
'PRO': 0,
'SER': 0,
'THR': 0,
'TRP': 0,
'TYR': 0,
'VAL': 0,
}
self.interface55_resn_number = {'ALA': 0,
'ARG': 0,
'ASN': 0,
'ASP': 0,
'CYS': 0,
'GLN': 0,
'GLU': 0,
'GLY': 0,
'HIS': 0,
'ILE': 0,
'LEU': 0,
'LYS': 0,
'MET': 0,
'PHE': 0,
'PRO': 0,
'SER': 0,
'THR': 0,
'TRP': 0,
'TYR': 0,
'VAL': 0,
}
self.interface6_resn_number = {'ALA': 0,
'ARG': 0,
'ASN': 0,
'ASP': 0,
'CYS': 0,
'GLN': 0,
'GLU': 0,
'GLY': 0,
'HIS': 0,
'ILE': 0,
'LEU': 0,
'LYS': 0,
'MET': 0,
'PHE': 0,
'PRO': 0,
'SER': 0,
'THR': 0,
'TRP': 0,
'TYR': 0,
'VAL': 0,
}
self.interface65_resn_number = {'ALA': 0,
'ARG': 0,
'ASN': 0,
'ASP': 0,
'CYS': 0,
'GLN': 0,
'GLU': 0,
'GLY': 0,
'HIS': 0,
'ILE': 0,
'LEU': 0,
'LYS': 0,
'MET': 0,
'PHE': 0,
'PRO': 0,
'SER': 0,
'THR': 0,
'TRP': 0,
'TYR': 0,
'VAL': 0,
}
self.interface7_resn_number = {'ALA': 0,
'ARG': 0,
'ASN': 0,
'ASP': 0,
'CYS': 0,
'GLN': 0,
'GLU': 0,
'GLY': 0,
'HIS': 0,
'ILE': 0,
'LEU': 0,
'LYS': 0,
'MET': 0,
'PHE': 0,
'PRO': 0,
'SER': 0,
'THR': 0,
'TRP': 0,
'TYR': 0,
'VAL': 0,
}
self.interface75_resn_number = {'ALA': 0,
'ARG': 0,
'ASN': 0,
'ASP': 0,
'CYS': 0,
'GLN': 0,
'GLU': 0,
'GLY': 0,
'HIS': 0,
'ILE': 0,
'LEU': 0,
'LYS': 0,
'MET': 0,
'PHE': 0,
'PRO': 0,
'SER': 0,
'THR': 0,
'TRP': 0,
'TYR': 0,
'VAL': 0,
}
self.interface8_resn_number = {'ALA': 0,
'ARG': 0,
'ASN': 0,
'ASP': 0,
'CYS': 0,
'GLN': 0,
'GLU': 0,
'GLY': 0,
'HIS': 0,
'ILE': 0,
'LEU': 0,
'LYS': 0,
'MET': 0,
'PHE': 0,
'PRO': 0,
'SER': 0,
'THR': 0,
'TRP': 0,
'TYR': 0,
'VAL': 0,
}
self.interface85_resn_number = {'ALA': 0,
'ARG': 0,
'ASN': 0,
'ASP': 0,
'CYS': 0,
'GLN': 0,
'GLU': 0,
'GLY': 0,
'HIS': 0,
'ILE': 0,
'LEU': 0,
'LYS': 0,
'MET': 0,
'PHE': 0,
'PRO': 0,
'SER': 0,
'THR': 0,
'TRP': 0,
'TYR': 0,
'VAL': 0,
}
self.interface9_resn_number = {'ALA': 0,
'ARG': 0,
'ASN': 0,
'ASP': 0,
'CYS': 0,
'GLN': 0,
'GLU': 0,
'GLY': 0,
'HIS': 0,
'ILE': 0,
'LEU': 0,
'LYS': 0,
'MET': 0,
'PHE': 0,
'PRO': 0,
'SER': 0,
'THR': 0,
'TRP': 0,
'TYR': 0,
'VAL': 0,
}
self.interface95_resn_number = {'ALA': 0,
'ARG': 0,
'ASN': 0,
'ASP': 0,
'CYS': 0,
'GLN': 0,
'GLU': 0,
'GLY': 0,
'HIS': 0,
'ILE': 0,
'LEU': 0,
'LYS': 0,
'MET': 0,
'PHE': 0,
'PRO': 0,
'SER': 0,
'THR': 0,
'TRP': 0,
'TYR': 0,
'VAL': 0,
}
self.interface10_resn_number = {'ALA': 0,
'ARG': 0,
'ASN': 0,
'ASP': 0,
'CYS': 0,
'GLN': 0,
'GLU': 0,
'GLY': 0,
'HIS': 0,
'ILE': 0,
'LEU': 0,
'LYS': 0,
'MET': 0,
'PHE': 0,
'PRO': 0,
'SER': 0,
'THR': 0,
'TRP': 0,
'TYR': 0,
'VAL': 0,
}
#interface pdb infotmation
self.interface3_lead = []
self.interface35_lead = []
self.interface4_lead = []
self.interface45_lead = []
self.interface5_lead = []
self.interface55_lead = []
self.interface6_lead = []
self.interface65_lead = []
self.interface7_lead = []
self.interface75_lead = []
self.interface8_lead = []
self.interface85_lead = []
self.interface9_lead = []
self.interface95_lead = []
self.interface10_lead = []
##############
self.DNA_atom = []
self.protein_atom = []
##############################################
self.bump_Classify_6 = {'valley':[],
'flat':[],
'peak':[]}
##############################################
self.INTERFACE_DIS_3 = []
self.INTERFACE_DIS_35 = []
self.INTERFACE_DIS_4 = []
self.INTERFACE_DIS_45 = []
self.INTERFACE_DIS_5 = []
self.INTERFACE_DIS_55 = []
self.INTERFACE_DIS_6 = []
self.INTERFACE_DIS_65 = []
self.INTERFACE_DIS_7 = []
self.INTERFACE_DIS_75 = []
self.INTERFACE_DIS_8 = []
self.INTERFACE_DIS_85 = []
self.INTERFACE_DIS_9 = []
self.INTERFACE_DIS_95 = []
self.INTERFACE_DIS_10 = []
self.app1 = app
self.parent = app.root
self.dialog = Pmw.Dialog(self.parent,
buttons=('Browse', 'load PDB', 'Cancel'),
command=self.Ask_Dialog_Cmd)
# pdb_load_Ent = Entry(self.dialog.interior(), textvariable=self.pdb_file_path, width=35)
self.pdb_load_Ent = Text(self.dialog.interior(),height=1, width=30)
# pdb_load_Ent.delete()
self.pdb_load_Ent.grid(sticky='E')
def Ask_Dialog_Cmd(self, cmd ):
if cmd == 'Browse':
self.GetPDBFilePath()
# self.pdb_file_path.set(self.pdbfile)
self.pdb_load_Ent.delete(1.0,Tkinter.END)
self.pdb_load_Ent.insert(END,self.pdbfile)
elif cmd == 'load PDB':
# print 'hello'
self.LoadPDB(self.pdbfile)
self.dialog.withdraw()
self.plugin = Plugin(self.app1, self.pdbfile)
self.plugin.Resn_number = self.Resn_number
self.plugin.interface6_resn_number = self.interface6_resn_number
self.plugin.interface3_resn_number = self.interface3_resn_number
self.plugin.interface35_resn_number = self.interface35_resn_number
self.plugin.interface4_resn_number = self.interface4_resn_number
self.plugin.interface45_resn_number = self.interface45_resn_number
self.plugin.interface5_resn_number = self.interface5_resn_number
self.plugin.interface55_resn_number = self.interface55_resn_number
self.plugin.interface6_resn_number = self.interface6_resn_number
self.plugin.interface65_resn_number = self.interface65_resn_number
self.plugin.interface7_resn_number = self.interface7_resn_number
self.plugin.interface75_resn_number = self.interface75_resn_number
self.plugin.interface8_resn_number = self.interface8_resn_number
self.plugin.interface85_resn_number = self.interface85_resn_number
self.plugin.interface9_resn_number = self.interface9_resn_number
self.plugin.interface95_resn_number = self.interface95_resn_number
self.plugin.interface10_resn_number = self.interface10_resn_number
self.plugin.bump_Classify_6 = self.bump_Classify_6
self.plugin.bump_Classify_3 = self.bump_Classify_3
self.plugin.bump_Classify_35 = self.bump_Classify_35
self.plugin.bump_Classify_4 = self.bump_Classify_4
self.plugin.bump_Classify_45 = self.bump_Classify_45
self.plugin.bump_Classify_all = self.bump_Classify_all
self.plugin.bump_Classify_set["all_protein"] = self.bump_Classify_all
self.plugin.bump_Classify_set["3angstrom"] = self.bump_Classify_3
self.plugin.bump_Classify_set["3.5angstrom"] = self.bump_Classify_35
self.plugin.bump_Classify_set["4angstrom"] = self.bump_Classify_4
self.plugin.bump_Classify_set["4.5angstrom"] = self.bump_Classify_45
self.plugin.bump_Classify_set["6angstrom"] = self.bump_Classify_6
self.plugin.interface3_lead = self.interface3_lead
self.plugin.interface35_lead = self.interface35_lead
self.plugin.interface4_lead = self.interface4_lead
self.plugin.interface45_lead = self.interface45_lead
self.plugin.interface5_lead = self.interface5_lead
self.plugin.interface55_lead = self.interface55_lead
self.plugin.interface6_lead = self.interface6_lead
self.plugin.interface65_lead = self.interface65_lead
self.plugin.interface7_lead = self.interface7_lead
self.plugin.interface75_lead = self.interface75_lead
self.plugin.interface8_lead = self.interface8_lead
self.plugin.interface85_lead = self.interface85_lead
self.plugin.interface9_lead = self.interface9_lead
self.plugin.interface95_lead = self.interface95_lead
self.plugin.interface10_lead = self.interface10_lead
# print "flat"
self.plugin.bump_Classify_flat=self.bump_Classify_all
self.plugin.bump_Classify_peak=self.bump_Classify_all
self.plugin.bump_Classify_valley=self.bump_Classify_all
self.plugin.INTERFACE_DIS_3 = self.INTERFACE_DIS_3
self.plugin.INTERFACE_DIS_35 = self.INTERFACE_DIS_35
self.plugin.INTERFACE_DIS_4 = self.INTERFACE_DIS_4
self.plugin.INTERFACE_DIS_45 = self.INTERFACE_DIS_45
self.plugin.INTERFACE_DIS_5 = self.INTERFACE_DIS_5
self.plugin.INTERFACE_DIS_55 = self.INTERFACE_DIS_55
self.plugin.INTERFACE_DIS_6 = self.INTERFACE_DIS_6
self.plugin.INTERFACE_DIS_65 = self.INTERFACE_DIS_65
self.plugin.INTERFACE_DIS_7 = self.INTERFACE_DIS_7
self.plugin.INTERFACE_DIS_75 = self.INTERFACE_DIS_75
self.plugin.INTERFACE_DIS_8 = self.INTERFACE_DIS_8
self.plugin.INTERFACE_DIS_85 = self.INTERFACE_DIS_85
self.plugin.INTERFACE_DIS_9 = self.INTERFACE_DIS_9
self.plugin.INTERFACE_DIS_95 = self.INTERFACE_DIS_95
self.plugin.INTERFACE_DIS_10 = self.INTERFACE_DIS_10
self.plugin.INTERFACE_CONTENT = self.INTERFACE_DIS_6
elif cmd == 'Cancel':
print('Exiting Plugin ...')
if __name__ == '__main__':
self.parent.destroy()
else:
self.dialog.withdraw()
print('Done.')
else:
self.dialog.withdraw()
def GetPDBFilePath(self):
self.pdbfile = tkFileDialog.askopenfilename()
def LoadPDB(self, pdbfile):
if pdbfile is not None:
cmd.load(pdbfile)
cmd.color('gray')
cmd.show('sphere')
############
## Main
###########
atom_content_dir = self.Open_PDB_content(pdbfile)
self.All_protein_Atom = self.calcu_durg_pdb_interface(pdbfile)
self.bump_Classify_all = self.BumpClassify(self.protein_atom,atom_content_dir)
self.bump_Classify_6 = self.BumpClassify(self.INTERFACE_DIS_6, atom_content_dir)
self.bump_Classify_3 = self.BumpClassify(self.INTERFACE_DIS_3, atom_content_dir)
self.bump_Classify_35 = self.BumpClassify(self.INTERFACE_DIS_35, atom_content_dir)
self.bump_Classify_4 = self.BumpClassify(self.INTERFACE_DIS_4, atom_content_dir)
self.bump_Classify_45 = self.BumpClassify(self.INTERFACE_DIS_45, atom_content_dir)
self.progress_window.destroy()
#SELECT INTERFACE
cmd.select('Nucleic', 'resn DA+DC+DG+DT+DU+A+T+G+C+I+U+5IU')
# cmd.select("interface", resn + ' and ' + resi + ' and ' + chain,)
self.selector(self.INTERFACE_DIS_6,"interface")
cmd.create("INTERFACE1", "interface")
# cmd.hide()
self.selector(self.All_protein_Atom,"protein")
# cmd.hide("everything", "protein")
# cmd.show("surface","protein")
# cmd.create("PROTEIN", "protein")
# cmd.hide("everything", "protein")
cmd.select('Nucleic', 'resn DA+DC+DG+DT+DU+A+T+G+C+I+U+5IU')
#cmd.extract("protein","proteins")
#cmd.extract("Nucleic","Nucleics")
else:
print ('NO Path Input')
def calcu_dis(self, coord_1, coord_2):
coord_1_X = float(coord_1[0])
coord_1_Y = float(coord_1[1])
coord_1_Z = float(coord_1[2])
coord_2_X = float(coord_2[0])
coord_2_Y = float(coord_2[1])
coord_2_Z = float(coord_2[2])
Euclid_Dis = math.sqrt(
((coord_1_X - coord_2_X) ** 2) + ((coord_1_Y - coord_2_Y) ** 2) + ((coord_1_Z - coord_2_Z) ** 2))
return Euclid_Dis
#no DNA
def Open_PDB_content(self, pdb_file_name):
file_handle = open(pdb_file_name, 'r')
counter = 0
atom_content_dir = {}
for file_content in file_handle:
if file_content[0:4] == 'ATOM':
if file_content[17:20] != ' DA' and \
file_content[17:20] != ' DT' and \
file_content[17:20] != ' DG' and \
file_content[17:20] != ' DC' and \
file_content[17:20] != ' A' and \
file_content[17:20] != ' C' and \
file_content[17:20] != ' G' and \
file_content[17:20] != ' T' and \
file_content[17:20] != ' U' and \
file_content[17:20] != ' I':
atom_content_dir[counter] = file_content
counter = counter + 1
# print counter
return atom_content_dir
def Calcu_PDB_CA_SI(self, Valid_ATOM_Num):
Vint = Valid_ATOM_Num * 20.1
Vsphere = 4 * math.pi * 12 ** 3 / 3
Vext = Vsphere - Vint
CX = (Vext - Vint) / Vsphere
return CX
def calcu_durg_pdb_interface(self, pdb_file_name):
ATOM_content = []
DX_content = []
pdb_content_handle = open(pdb_file_name, 'r')
for DX_Cell in pdb_content_handle:
if DX_Cell[0:4] == 'ATOM':
self.counter += 1
if DX_Cell[17:20] == ' DA' or \
DX_Cell[17:20] == ' DT' or \
DX_Cell[17:20] == ' DG' or \
DX_Cell[17:20] == ' DC' or \
DX_Cell[17:20] == ' A' or \
DX_Cell[17:20] == ' C' or \
DX_Cell[17:20] == ' G' or \
DX_Cell[17:20] == ' T' or \
DX_Cell[17:20] == ' U' or \
DX_Cell[17:20] == ' I' :
# and DX_Cell[13:15] == 'CA':
# print DX_Cell
DX_content.append(DX_Cell)
else:
if DX_Cell[13:15] == 'CA':
self.Resn_number[DX_Cell[17:20]] += 1
ATOM_content.append(DX_Cell)
pdb_content_handle.close()
self.protein_atom = ATOM_content
self.DNA_atom = DX_content
# progress tk window
self.progress_window = Tk()
self.progress_window.title('Calculating')
self.progress_window.geometry('630x150')
## 设置进度条
ttk.Label(self.progress_window, text='Progress:', ).place(x=45, y=60)
self.canvas = Canvas(self.progress_window, width=465, height=22, bg="white")
self.fill_line = self.canvas.create_rectangle(1.5, 1.5, 0, 23, width=0, fill="green")
self.canvas.place(x=110, y=60)
x = self.counter # 未知变量，可更改
self.progress_counters = float(465.0/self.counter) # 是矩形填充满的次数
# print n
##################################
for Atom in ATOM_content:
min_dis = 9999
Atom_cood = [Atom[30:38], Atom[38:46], Atom[46:54]]
interface_flag = 0
####progress
self.progress_counters = float(self.progress_counters + 465.0 / x)
info_6 = ""
for Dx in DX_content:
DX_cood = [Dx[30:38], Dx[38:46], Dx[46:54]]
dis = self.calcu_dis(Atom_cood, DX_cood)
info = Atom[:26] + " --- " + Dx[:26]
if min_dis > dis:
min_dis = dis
info_6 = Atom[:26] + " --- " + Dx[:26]
if min_dis < 6:
self.INTERFACE_DIS_6.append(Atom)
self.interface6_lead.append(info_6)
if Atom[13:15] == 'CA':
self.interface6_resn_number[Atom[17:20]] += 1
if min_dis < 3:
self.INTERFACE_DIS_3.append(Atom)
self.interface3_lead.append(info_6)
if Atom[13:15] == 'CA':
self.interface3_resn_number[Atom[17:20]] += 1
if min_dis < 3.5:
self.INTERFACE_DIS_35.append(Atom)
self.interface35_lead.append(info_6)
if Atom[13:15] == 'CA':
self.interface35_resn_number[Atom[17:20]] += 1
if min_dis < 4:
self.INTERFACE_DIS_4.append(Atom)
self.interface4_lead.append(info_6)
if Atom[13:15] == 'CA':
self.interface4_resn_number[Atom[17:20]] += 1
if min_dis < 4.5:
self.INTERFACE_DIS_45.append(Atom)
self.interface45_lead.append(info_6)
if Atom[13:15] == 'CA':
self.interface45_resn_number[Atom[17:20]] += 1
if min_dis < 5.5:
self.INTERFACE_DIS_55.append(Atom)
self.interface55_lead.append(info_6)
if Atom[13:15] == 'CA':
self.interface55_resn_number[Atom[17:20]] += 1
if min_dis < 6.5:
self.INTERFACE_DIS_65.append(Atom)
self.interface65_lead.append(info_6)
if Atom[13:15] == 'CA':
self.interface65_resn_number[Atom[17:20]] += 1
if min_dis < 7:
self.INTERFACE_DIS_7.append(Atom)
self.interface7_lead.append(info_6)
if Atom[13:15] == 'CA':
self.interface7_resn_number[Atom[17:20]] += 1
if min_dis < 7.5:
self.INTERFACE_DIS_75.append(Atom)
self.interface75_lead.append(info_6)
if Atom[13:15] == 'CA':
self.interface75_resn_number[Atom[17:20]] += 1
if min_dis < 8:
self.INTERFACE_DIS_8.append(Atom)
self.interface8_lead.append(info_6)
if Atom[13:15] == 'CA':
self.interface8_resn_number[Atom[17:20]] += 1
if min_dis < 8.5:
self.INTERFACE_DIS_85.append(Atom)
self.interface85_lead.append(info_6)
if Atom[13:15] == 'CA':
self.interface85_resn_number[Atom[17:20]] += 1
if min_dis < 9:
self.INTERFACE_DIS_9.append(Atom)
self.interface9_lead.append(info_6)
if Atom[13:15] == 'CA':
self.interface9_resn_number[Atom[17:20]] += 1
if min_dis < 9.5:
self.INTERFACE_DIS_95.append(Atom)
self.interface95_lead.append(info_6)
if Atom[13:15] == 'CA':
self.interface95_resn_number[Atom[17:20]] += 1
if min_dis < 10:
self.INTERFACE_DIS_10.append(Atom)
self.interface10_lead.append(info_6)
if Atom[13:15] == 'CA':
self.interface10_resn_number[Atom[17:20]] += 1
self.canvas.coords(self.fill_line, (0, 0, self.progress_counters, 60))
self.progress_window.update()
return ATOM_content
# print Interface_content
def calcu_dis(self, coord_1, coord_2):
coord_1_X = float(coord_1[0])
coord_1_Y = float(coord_1[1])
coord_1_Z = float(coord_1[2])
coord_2_X = float(coord_2[0])
coord_2_Y = float(coord_2[1])
coord_2_Z = float(coord_2[2])
Euclid_Dis = numpy.sqrt(
((coord_1_X - coord_2_X) ** 2) + ((coord_1_Y - coord_2_Y) ** 2) + ((coord_1_Z - coord_2_Z) ** 2))
return Euclid_Dis
def BumpClassify(self, Atom_content, atom_content_dir):
bump_Classify = {'valley':[],
'flat':[],
'peak':[]}
for Cell in Atom_content:
# print Cell
ca_cood = (Cell[30:38], Cell[38:46], Cell[46:54])
atom_counter = 0
for key in atom_content_dir:
coord_2 = (atom_content_dir[key][30:38], atom_content_dir[key][38:46], atom_content_dir[key][46:54])
dis = self.calcu_dis(ca_cood, coord_2)
if dis < 12:
atom_counter = atom_counter + 1
CX = self.Calcu_PDB_CA_SI(atom_counter)
# print CX
if CX < -0.2:
shape = "valley"
bump_Classify['valley'].append(Cell)
# self.valleyCell.append(Cell)
elif CX < 0.2:
shape = 'flat'
bump_Classify['flat'].append(Cell)
# self.flatCell.append(Cell)
else:
shape = "peak"
bump_Classify['peak'].append(Cell)
# self.peakCell.append(Cell)
return bump_Classify
def selector(self,content,sele_name):
for i in content:
# con_list.append(i[17:20])
cmd.select(sele_name, ' resn ' +i[17:20]+ ' and resi' + i[22:26] + ' and chain ' +i[21],merge=1)
#################
# GUI related
#################
class Plugin:
def __init__(self, app, pdbfile):
self.parent = app.root
self.pdb_file_path = pdbfile
self.DIS = 6
self.interface_mod = "spheres"
self.protein_mod = "spheres"
self.INTERFACE_CONTENT = []
###############################
#dafault all_protein
self.bump_Classify_valley = {'valley': [],
'flat': [],
'peak': []}
self.bump_Classify_flat = {'valley': [],
'flat': [],
'peak': []}
self.bump_Classify_peak = {'valley': [],
'flat': [],
'peak': []}
self.bump_Classify_all={'valley': [],
'flat': [],
'peak': []}
self.bump_Classify_3={'valley': [],
'flat': [],
'peak': []}
self.bump_Classify_35={'valley': [],
'flat': [],
'peak': []}
self.bump_Classify_4={'valley': [],
'flat': [],
'peak': []}
self.bump_Classify_45={'valley': [],
'flat': [],
'peak': []}
self.bump_Classify_6={'valley': [],
'flat': [],
'peak': []}
# defalut set all_protein
self.bump_Classify_set = {}
self.valleyCell = []
self.flatCell = []
self.peakCell = []
self.valley_range_get = ''
################################
self.INTERFACE_DIS_3 = []
self.INTERFACE_DIS_35 = []
self.INTERFACE_DIS_4 = []
self.INTERFACE_DIS_45 = []
self.INTERFACE_DIS_5 = []
self.INTERFACE_DIS_55 = []
self.INTERFACE_DIS_6 = []
self.INTERFACE_DIS_7 = []
self.INTERFACE_DIS_75 = []
self.INTERFACE_DIS_8 = []
self.INTERFACE_DIS_85 = []
self.INTERFACE_DIS_9 = []
self.INTERFACE_DIS_95 = []
self.INTERFACE_DIS_10 = []
################################
# COLOR VAR
self.surf_col = '#7CFC00'
self.protein_col = '#666666'
self.nucleic_col = '#666666'
self.bump_col = '#FF3030'
self.valley_col = '#FF0000'
self.peak_col = '#0000FF'
self.flat_col = '#00FF00'
self.property_col = '#7CFC00'
self.surf_col_tuple = (124, 252, 0)
self.valley_col_tuple = (255, 0, 0)
self.flat_col_tuple = (0, 255, 0)
self.peak_col_tuple = (0, 0, 255)
self.property_col_tuple = (125, 250, 0)
self.protein_col_tuple = (88, 87, 86)
self.nucleic_col_tuple = (88, 87, 86)
cmd.set_color('valley_col', self.valley_col_tuple)
cmd.set_color('flat_col', self.flat_col_tuple)
cmd.set_color('peak_col', self.peak_col_tuple)
#info
self.interface3_lead = []
self.interface35_lead = []
self.interface4_lead = []
self.interface45_lead = []
self.interface5_lead = []
self.interface55_lead = []
self.interface6_lead = []
self.interface65_lead = []
self.interface7_lead = []
self.interface75_lead = []
self.interface8_lead = []
self.interface85_lead = []
self.interface9_lead = []
self.interface95_lead = []
self.interface10_lead = []
################################
self.Resn_number = {'ALA': 0,
'ARG': 0,
'ASN': 0,
'ASP': 0,
'CYS': 0,
'GLN': 0,
'GLU': 0,
'GLY': 0,
'HIS': 0,
'ILE': 0,
'LEU': 0,
'LYS': 0,
'MET': 0,
'PHE': 0,
'PRO': 0,
'SER': 0,
'THR': 0,
'TRP': 0,
'TYR': 0,
'VAL': 0,
}
self.interface3_resn_number = {'ALA': 0,
'ARG': 0,