# Copyright Notice # ================ # # The PyMOL Plugin source code in this file is copyrighted, but you can # freely use and copy it as long as you don't change or remove any of # the copyright notices. # # ---------------------------------------------------------------------- # This PyMOL Plugin is Copyright (C) 2017 by Marko Jukic # # All Rights Reserved # # Permission to use, copy and distribute # versions of this software and its documentation for any purpose and # without fee is hereby granted, provided that the above copyright # notice appear in all copies and that both the copyright notice and # this permission notice appear in supporting documentation, and that # the name(s) of the author(s) not be used in advertising or publicity # pertaining to distribution of the software without specific, written # prior permission. # # THE AUTHOR(S) DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, # INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN # NO EVENT SHALL THE AUTHOR(S) BE LIABLE FOR ANY SPECIAL, INDIRECT OR # CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF # USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR # OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR # PERFORMANCE OF THIS SOFTWARE. # ---------------------------------------------------------------------- # -*- coding: utf-8 -*- # ProBis_H2O # written for python 2.7.x # Not Yet Described at PyMOL wiki: / # Author : Marko Jukic # Date: October 2017 # License: chech http://insilab.org # Version: 0.93 __author__ = "Marko Jukic" __licence__ = "http://insilab.org" __version__ = "0.93" # Comments: Script is commented in Slovene language # import Tkinter, sys, re, gzip, os, urllib, urllib2 import fileinput, pymol, ttk, json, math, multiprocessing import numpy as np from pymol.cgo import * import tkMessageBox #tipicni python 2x tkFileDialog - v 3 je filedialog from tkFileDialog import askopenfilename from glob import glob from ftplib import FTP from collections import Counter from itertools import groupby # SCIKIT LEARN------------------------------------------------------------------ from sklearn.cluster import DBSCAN from sklearn.cluster import KMeans from sklearn import metrics from sklearn.datasets.samples_generator import make_blobs from sklearn.preprocessing import StandardScaler # /SCIKIR LEARN----------------------------------------------------------------- # ---------------------------------------INITIALIZE----------------------------- def __init__(self): """Add this Plugin to the PyMOL menu""" self.menuBar.addmenuitem('Plugin', 'command', 'ProBiS_H2O', label = 'ProBiS H2O', command = lambda: mainDialog(self.root)) red01 = '#ffe6e6' red02 = '#ffcccc' red03 = '#ffb3b3' red04 = '#ff9999' red05 = '#ff8080' red06 = '#ff6666' red07 = '#ff4d4d' red08 = '#ff3333' red09 = '#ff1a1a' red10 = '#ff0000' logo = """ iVBORw0KGgoAAAANSUhEUgAAAXgAAABeCAYAAAApHw85AAAAAXNSR0IArs4c6QAAAAlwSFlzAAAL 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w.pack() # ------------------------------------- ttk NoteBook --------------------------- global nb global p1 global p2 global p3 nb = ttk.Notebook(master, height=320, width=430) style = ttk.Style() style.configure("classicklook", foreground="black", background="#f2f1f0") p1 = Tkinter.Frame(nb) p2 = Tkinter.Frame(nb) p3 = Tkinter.Frame(nb) nb.add(p1, text='define system', ) nb.add(p2, text='cluster analysis', ) nb.add(p3, text=' About/Help ', ) group = Tkinter.LabelFrame(p1, text='define system') # group2 = Tkinter.LabelFrame(p2, text='ccluster analysis', bg = '#f2f1f0') nb.pack(padx=5, pady=5, fill=Tkinter.BOTH, expand=1) # ----------------------------- Water analysis TAB ----------------------------- group.pack(fill='both', expand=1, padx=5, pady=5) # group2.pack(fill='both', expand=1, padx=5, pady=5) # INPUT on tab p1 Tkinter.Label(group, text='PDB ID:').grid(row=2, column=0) Tkinter.Button(group, text="custom", command=custom_disk_file_get.load_file, justify=Tkinter.CENTER, padx=20).grid(row=2, column=5) global pdb_text pdb_text = Tkinter.StringVar(master=group) pdb_text.set("protein") def clearme(event): pdb_text.set("") global entry_pdb_text entry_pdb_text = Tkinter.Entry(group, textvariable=pdb_text, width=10) entry_pdb_text.bind("", clearme) entry_pdb_text.grid(row=2, column=1) entry_pdb_text.update() Tkinter.Label(group, text='Analyze binding site (default)').grid(row=3, column=1) global bsite_vicinity_setting global entry_bsite_vicinity_setting bsite_vicinity_setting = Tkinter.StringVar(master=group) entry_bsite_vicinity_setting = Tkinter.Checkbutton(group, variable=bsite_vicinity_setting, onvalue="yes", offvalue="not", justify=Tkinter.LEFT, padx=10) entry_bsite_vicinity_setting.grid(row=3, column=0) entry_bsite_vicinity_setting.select() entry_bsite_vicinity_setting.update() Tkinter.Label(group, text='Define water as binding site').grid(row=4, column=1) global water_binding_setting global entry_water_binding_setting water_binding_setting = Tkinter.StringVar(master=group) entry_water_binding_setting = Tkinter.Checkbutton(group, variable=water_binding_setting, onvalue="yes", offvalue="not", justify=Tkinter.LEFT, padx=10) entry_water_binding_setting.grid(row=4, column=0) entry_water_binding_setting.deselect() entry_water_binding_setting.update() Tkinter.Label(group, text='Compare whole chain').grid(row=5, column=1) global whole_chain_setting whole_chain_setting = Tkinter.StringVar(master=group) entry_whole_chain_setting = Tkinter.Checkbutton(group, variable=whole_chain_setting, onvalue="yes", offvalue="not", justify=Tkinter.LEFT, padx=10) entry_whole_chain_setting.grid(row=5, column=0) entry_whole_chain_setting.deselect() entry_whole_chain_setting.update() Tkinter.Label(group, text='Debye-Waller correction').grid(row=6, column=1) global debye_waller_setting debye_waller_setting = Tkinter.StringVar(master=group) entry_debye_waller_setting = Tkinter.Checkbutton(group, variable=debye_waller_setting, onvalue="yes", offvalue="not", justify=Tkinter.LEFT, padx=10) entry_debye_waller_setting.grid(row=6, column=0) entry_debye_waller_setting.deselect() entry_debye_waller_setting.update() Tkinter.Label(group, text='Single aligned chain per PDB entry').grid(row=7, column=1) global num_entity_chains_setting num_entity_chains_setting = Tkinter.StringVar(master=group) entry_num_entity_chains_setting = Tkinter.Checkbutton(group, variable=num_entity_chains_setting, onvalue="yes", offvalue="not", justify=Tkinter.LEFT, padx=10) entry_num_entity_chains_setting.grid(row=7, column=0) entry_num_entity_chains_setting.deselect() entry_num_entity_chains_setting.update() global seq_identity_value seq_identity_value = Tkinter.StringVar(master=group) seq_identity_value.set('Sequence identity: 95') seq_identity_options = ['Sequence identity: 95', 'Sequence identity: 90', 'Sequence identity: 70', 'Sequence identity: 50', 'blastclust: 30', 'blastclust: 40', 'blastclust: 50', 'blastclust: 70', 'blastclust: 90', 'blastclust: 95', 'blastclust: 100', 'custom_cluster'] seq_identity_menu = Tkinter.OptionMenu(group, seq_identity_value, *seq_identity_options) seq_identity_menu.grid(row=8, column=1) Tkinter.Label(group, text='Found').grid(row=9, column=0) global find_value find_value = Tkinter.StringVar(master=group) find_value.set(" ") entry_find_value = Tkinter.Entry(group, textvariable=find_value, width=25) entry_find_value.grid(row=9, column=1) entry_find_value.configure(state='disabled') entry_find_value.update() Tkinter.Label(group, text='Select\nBINDING SITE\n/ CHAIN').grid(row=10, column=0) global binding_listbox binding_listbox_scrollbar = Tkinter.Scrollbar(group, orient=Tkinter.VERTICAL) binding_listbox = Tkinter.Listbox(group, width=20, height=5, yscrollcommand=binding_listbox_scrollbar.set, selectmode=Tkinter.SINGLE) binding_listbox_scrollbar.config(command=binding_listbox.yview) binding_listbox_scrollbar.grid(row=10, column=2) binding_listbox.grid(row=10, column=1) binding_listbox.configure(state='normal') binding_listbox.update() bindng_listbox_scrollbar = Tkinter.Scrollbar(binding_listbox, orient=Tkinter.VERTICAL) # GO baby Tkinter.Button(group, text="Find", command=ClusterComplexManipulation.get_cluster_complexes, justify=Tkinter.CENTER, padx=30).grid(row=8, column=5) global enable_disable_download enable_disable_download = Tkinter.Button(group, text="Download", command=ClusterComplexManipulation.download_complexes, justify=Tkinter.CENTER, padx=13) enable_disable_download.grid(row=9, column=5) enable_disable_download.configure(state='disabled') global find_bsites find_bsites = Tkinter.Button(group, text="Identify", command=BindingSites.get_binding_sites, justify=Tkinter.CENTER, padx=18) find_bsites.grid(row=10, column=5) find_bsites.configure(state='normal') Tkinter.Button(p1, text="GO", command=h20Analysis.analyze_waters, justify=Tkinter.CENTER, padx=30).pack(side=Tkinter.RIGHT) Tkinter.Button(p1, text="SETUP DB", command=RSCB_contact.contact_rscb_pdb, justify=Tkinter.CENTER, padx=30).pack(side=Tkinter.LEFT) # -------------------------------Results TAB------------------------------------ group5 = Tkinter.LabelFrame(p2, borderwidth = 0, highlightthickness = 0) group5.pack(fill='both', expand=1, padx=5, pady=5) Tkinter.Label(group5, text='Info:').pack(anchor = Tkinter.W) global T1_text global T1 T1_text = Tkinter.StringVar(group5) T1_text.set(" ") s1 = Tkinter.Scrollbar(group5) T1 = Tkinter.Text(group5, height = 5) T1.focus_set() s1.pack(side="right", padx=2, pady=35, expand = False) T1.pack(side="left", padx=2, pady=8, expand = False) s1.config(command=T1.yview) T1.config(yscrollcommand=s1.set) T1.insert(Tkinter.END, T1_text.get()) #------------------- group56 = Tkinter.LabelFrame(p2, borderwidth = 0, highlightthickness = 0) group56.pack(fill='both', expand=1, padx=5, pady=1) Tkinter.Label(group56, text='Calculated clusters, conservation; keep selected display:').pack(side = Tkinter.LEFT) global display_setting display_setting = Tkinter.StringVar(master=group56) entry_display_setting = Tkinter.Checkbutton(group56, variable=display_setting, onvalue="yes", offvalue="not") entry_display_setting.pack(side = Tkinter.RIGHT, ipadx=15, expand = False) entry_display_setting.deselect() entry_display_setting.update() group6 = Tkinter.LabelFrame(p2, borderwidth = 0, highlightthickness = 0) group6.pack(fill='both', expand=1, padx=5, pady=1) global cluster_listbox cluster_listbox_scrollbar = Tkinter.Scrollbar(group6, orient=Tkinter.VERTICAL) cluster_listbox = Tkinter.Listbox(group6, width=50, height=7, yscrollcommand=cluster_listbox_scrollbar.set, selectmode=Tkinter.SINGLE) cluster_listbox_scrollbar.config(command=cluster_listbox.yview) cluster_listbox_scrollbar.pack(side="right", padx=2, pady=35, expand = False) cluster_listbox.pack(side="left", padx=2, pady=8, expand = False) cluster_listbox.configure(state='normal') cluster_listbox.update() cluster_listbox_scrollbar = Tkinter.Scrollbar(cluster_listbox, orient=Tkinter.VERTICAL) #---------------------- group7 = Tkinter.LabelFrame(p2, borderwidth = 0, highlightthickness = 0) group7.pack(fill='both', expand=1, padx=1, pady=1) Tkinter.Button(group7, text="display", command=pyMOLinterface.pyMOL_display_cluster, justify=Tkinter.CENTER, padx=10).pack(side=Tkinter.RIGHT) Tkinter.Button(group7, text="b-site", command=pyMOLinterface.pyMOL_bsite_cluster, justify=Tkinter.CENTER, padx=10).pack(side=Tkinter.RIGHT) Tkinter.Button(group7, text="contacts", command=pyMOLinterface.pyMOL_water_contacts, justify=Tkinter.CENTER, padx=10).pack(side=Tkinter.RIGHT) Tkinter.Button(group7, text="chain box", command=pyMOLinterface.pyMOL_chain_box, justify=Tkinter.CENTER, padx=10).pack(side=Tkinter.RIGHT) Tkinter.Button(group7, text="fetch/reset", command=pyMOLinterface.pyMOL_fetch_system, justify=Tkinter.CENTER, padx=10).pack(side=Tkinter.RIGHT) # -------------------------------HELP TAB--------------------------------------- inserted_helper_text = ''' ProBiS H2O plugin is a PyMOL gui tool using ProBiS for crystal complex water analysis. * Konc,J., Depolli,M., Trobec,R., Rozman,K., Janezic,D. Parallel-ProBiS: Fast parallel algorithm for local structural comparison of protein structures and binding sites. J. Comp. Chem., 2012, 33, 2199-2203. * Konc,J. and Janezic,D. ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment. Bioinformatics, 2010, 26, 1160-1168. * Jukic,M., Ilas,J., Brvar,M., Kikelj,D., Cesar,J., Anderluh,M. Linker-switch approach towards new ATP binding site inhibitors of DNA gyrase B. European Journal of Medicinal Chemistry, 2017, 125, 500-514. If You need help contact us at: marko.jukic@ffa.uni-lj.si konc@cmm.ki.si good luck! ''' s2 = Tkinter.Scrollbar(p3) T2 = Tkinter.Text(p3) s2.pack(side = "right", padx = 5, pady = 5, expand = False, fill = "y") T2.pack(side = "left", padx = 5, pady = 5, fill = "y") s2.config(command=T2.yview) T2.config(yscrollcommand=s2.set) T2.insert(Tkinter.END, inserted_helper_text) T2.tag_add("bluetag", "2.0", "2.10") T2.tag_add("bluetag", "2.44", "2.50") T2.tag_add("violettag", "9.0", "9.6") T2.tag_config("bluetag", background="white", foreground="dodger blue") T2.tag_config("violettag", background="ivory2", foreground="dark violet") # --------------------------------------------------- end main-loop ------------ # ----------------------------------------------------FUNCTIONS----------------- class custom_disk_file_get: @staticmethod def load_file(): fajlname = askopenfilename(filetypes=(("PDB files", "*.pdb"), ("All files", "*.*") )) if fajlname: try: print("File read.") print(str(fajlname)) except: tkMessageBox.showwarning(title='ProBiS H2O warning', parent=master, message="File error or \nFile not Found! \nplease investigate!") pdb_text = str(fajlname)[-8:-4] entry_pdb_text.delete(0, Tkinter.END) entry_pdb_text.insert(Tkinter.INSERT, pdb_text) entry_pdb_text.update() class RSCB_contact: """PDB database server setup""" lista_cluster_fajlov = ["clusters50.txt", "clusters70.txt", "clusters90.txt", "clusters95.txt", "bc-30.out", "bc-40.out", "bc-50.out", "bc-70.out", "bc-90.out", "bc-95.out", "bc-100.out"] @staticmethod def set_cluster_list(list): lista_cluster_fajlov = list @staticmethod def contact_rscb_pdb(): # initial setup current_path = str(os.getcwd()) if current_path == check_path: pass else: os.mkdir(check_path) os.chdir(check_path) """download fajlov""" print("Setting up the cluster database!") rscb_pdb_ftp_server = FTP("resources.rcsb.org") rscb_pdb_ftp_server.login() rscb_pdb_ftp_server.cwd('/sequence/clusters/') rscb_pdb_ftp_server.retrlines('LIST') for cluster_fajl in RSCB_contact.lista_cluster_fajlov: lokalni_fajl = open(str(cluster_fajl), 'wb') rscb_pdb_ftp_server.retrbinary('RETR ' + str(cluster_fajl), lokalni_fajl.write) lokalni_fajl.close rscb_pdb_ftp_server.quit() print("Database setup finished" + "\t thx RCSB protein data bank") if str(os.path.isfile("./.pro/probis")) == "False": os.system("mkdir ./.pro/") RSCB_contact.fetch_probis() os.system("mv ./probis ./.pro/") else: pass RSCB_contact.file_checks() return None # sys.exit() -crashes pymol sometimes ... # BOMO IMPLEMENTIRALI KASNEJE # pymol_path = "./Probis_H2O_database/" @staticmethod def fetch_probis(): urllib.urlretrieve ("http://insilab.org/files/probis-algorithm/probis", "probis") # + X + X + X :) @staticmethod def file_checks(): """preveri ce imamo instalirano bazo""" print("\nProBis_H2O: setting up...") check = "" for fajl in RSCB_contact.lista_cluster_fajlov: print(fajl + " present " + str(os.path.isfile(fajl))) if str(os.path.isfile(fajl)) == "False": print("ProBiS_H2O: please setup DB of rscb cluster files") break else: check += "a" if check == "aaaaaaaaaaa": print("ProBis_H2O: Database OK") if str(os.path.isfile("./.pro/probis")) == "False": print("ProBiS_H2O: please download probis using setup DB button in plugin GUI") else: try: if os.access("./.pro/probis", os.X_OK) == True: print("probis executable ok") else: print("probis executable present but no permissions set") print("Do not forget to set +x premission for probis in working directory: ") print("pymol_working_dir/ProBiS_H20/.pro/probis") except: pass # -------------------------------------------------file checks------------------ # initial setup check_path = str(os.getcwd()) + "/Probis_H2O/" if os.path.isdir(check_path) == False: print "please setup probis DB and Probis_H2O folder" else: os.chdir(check_path) RSCB_contact.file_checks() # ------------------------------------------------------------------------------ class ClusterComplexManipulation: """download and identification of cluster complexes from RCSB""" @staticmethod def get_cluster_unique_list(target_complex, ime_selekcije, sekvenca_id): #target complex: kater pdb #ime selekcije: "clusters" ali "bc-" #sekvenca katera je izbrana 50, 70, 90 vzorec = re.compile(target_complex, re.IGNORECASE) # lista z linijami ki vsebujejo iskani protein line_list = [] # lista z linijami ki so del clustra line_list_2 = [] # lista samo z imeni proteinov - ni unique - lahko je vec verig .... cluster_list = [] try: if ime_selekcije == "clusters": with open(ime_selekcije + sekvenca_id + ".txt", "rt") as infile: for linenumber, line in enumerate(infile): if vzorec.search(line) != None: line_list.append(line.rstrip('\n')) print("using cd-hit preclustering") print """ Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences, Weizhong Li & Adam Godzik (2006) Bioinformatics, 22:1658-9. """ print("Found entries in sequence file: ", line_list) print("Examined cluster number: ") print(line_list[0].split("\t")[0]) examined_cluster = line_list[0].split("\t")[0] # kljucen ^ na zacetku - zacetek linije !!! vzorec_2 = re.compile("^" + examined_cluster + "\t", re.IGNORECASE) with open(ime_selekcije + sekvenca_id + ".txt", "rt") as infile: for linenumber, line in enumerate(infile): if vzorec_2.search(line) != None: line_list_2.append(line.rstrip('\n')) for linija in line_list_2: a = linija.split("\t")[2][0:4] cluster_list.append(a) # make unique list set global cluster_list_unique cluster_list_unique = set(cluster_list) print("\nComplexes: ") print(cluster_list_unique) find_value.set(str(len(cluster_list_unique)) + " compl. in cluster no.:" + str(line_list[0].split("\t")[0])) print("Found num of entries in cluster: ", len(cluster_list_unique)) enable_disable_download.configure(state='active') binding_listbox.delete(0, Tkinter.END) return None else: with open(ime_selekcije + sekvenca_id + ".out", "rt") as infile: for linenumber, line in enumerate(infile): if vzorec.search(line) != None: line_list.append(line.rstrip('\n')) line_list_2 = line_list[0].split() for element in line_list_2: cluster_list.append(element[0:4]) global cluster_list_unique cluster_list_unique = set(cluster_list) print("\nComplexes: ") print(cluster_list_unique) find_value.set(str(len(cluster_list_unique)) + " compl. in blastclust cluster.") print("using blastclust pre-clustering") print""" Basic local alignment search tool, S.F. Altschul, W. Gish, W. Miller, E.W. Myers, & D.J. Lipman (1990) J. Mol. Biol. 215:403-410. """ print("Found num of entries in cluster: ", len(cluster_list_unique)) enable_disable_download.configure(state='active') binding_listbox.delete(0, Tkinter.END) return None except: tkMessageBox.showwarning(title='ProBiS H2O warning', parent=master, message="invalid PDB ID or \nDatabase File not Found! \nplease investigate!") print("Database File not Found!") @staticmethod def get_cluster_complexes(): wh_chain_setting = whole_chain_setting.get() if wh_chain_setting == "yes": entry_bsite_vicinity_setting.configure(state='disabled') entry_water_binding_setting.configure(state='disabled') else: entry_bsite_vicinity_setting.configure(state='active') entry_water_binding_setting.configure(state='active') #try: target_complex = str(pdb_text.get()) if len(target_complex) < 4: tkMessageBox.showwarning(title='ProBiS H2O warning', parent=master, message="invalid PDB ID!") elif len(target_complex) > 4: tkMessageBox.showwarning(title='ProBiS H2O warning', parent=master, message="invalid PDB ID!") else: # replaced by water definition in first stage # target_complex_chain = str(chain_id.get()) if str(seq_identity_value.get()) == "custom_cluster": selected_sequence = "_custom" ClusterComplexManipulation.get_cluster_unique_list(target_complex, "clusters", selected_sequence) elif str(seq_identity_value.get()) == "blastclust: 100": selected_sequence = "100" ClusterComplexManipulation.get_cluster_unique_list(target_complex, "bc-", selected_sequence) elif "blastclust" in str(seq_identity_value.get()): selected_sequence = str(seq_identity_value.get())[12:14] ClusterComplexManipulation.get_cluster_unique_list(target_complex, "bc-", selected_sequence) else: selected_sequence = str(seq_identity_value.get())[19:21] # print("hello" + target_complex + target_complex_chain + selected_sequence) ClusterComplexManipulation.get_cluster_unique_list(target_complex, "clusters", selected_sequence) #except: # tkMessageBox.showwarning(title='ProBiS H2O warning', parent=master, # message="Check all settings, \nplease investigate!") @staticmethod def download_complexes(): #za PDBje ki niso dostoni a imajo svoj entry nedostopni_datoteka = open("unavailable_pdb_list.txt", "w") try: def get_files_2(fajl): # ah lepse to kasneje !!! za download individualnih ent fajlov lokalni_fajl = open(fajl, 'wb') ftp_wwpdb_server.retrbinary('RETR ' + fajl, lokalni_fajl.write) lokalni_fajl.close() # unzip with gzip.open(fajl, 'rb') as compressed_f: lokalni_fajl_uncompressed = open(fajl_uncompressed, 'wb') lokalni_fajl_uncompressed.write(compressed_f.read()) lokalni_fajl_uncompressed.close() # ----- i = 1 for kompleks in cluster_list_unique: try: if os.path.isfile(str(kompleks).lower() + ".pdb"): i += 1 ftp_wwpdb_server = FTP("ftp.wwpdb.org") ftp_wwpdb_server.login() else: fajl = "pdb" + str(kompleks).lower() + ".ent.gz" fajl_uncompressed = str(kompleks).lower() + ".pdb" print("Downloading complex " + str(i) + " out of " + str(len(cluster_list_unique))) i += 1 ftp_wwpdb_server = FTP("ftp.wwpdb.org") ftp_wwpdb_server.login() ftp_wwpdb_server.cwd('/pub/pdb/data/structures/divided/pdb/' + str(kompleks[1:3]).lower() + "/") get_files_2(fajl) except: #i += 1 print("removing complex: " + str(kompleks)) nedostopni_datoteka.write(str(kompleks).lower() + "\n") pass ftp_wwpdb_server.quit() print("Download of complexes finished") return None except: tkMessageBox.showwarning(title='ProBiS H2O warning', parent=master, message="Check all settings, \nplease investigate!") nedostopni_datoteka.close() class BindingSites: """definiraj binding site""" bsite_unique_centers = [] @staticmethod def get_binding_sites(): wh_chain_setting = whole_chain_setting.get() if wh_chain_setting == "yes": entry_water_binding_setting.configure(state='disabled') entry_bsite_vicinity_setting.configure(state='disabled') else: entry_bsite_vicinity_setting.configure(state='active') entry_water_binding_setting.configure(state='active') try: binding_listbox.delete(0, Tkinter.END) water_sel = water_binding_setting.get() chain_sel = whole_chain_setting.get() target_complex_2 = str(pdb_text.get()).lower() vzorec_2 = re.compile("^" + "ATOM\s+\d+") # pazi na naslednji * ali + v re vzorec_3 = re.compile("^" + "HETATM\s*\d+") vzorec_4 = re.compile("HOH") # VSE LISTE--------------------------------------------------------- lista_za_heteroatome = [] lista_za_atome = [] lista_za_vode = [] lista_binding_sites = [] lista_water_binding_sites = [] lista_verige = [] lista_verige_konc = [] warning_lista = [] lista_verige_unique = [] bsite_unique = [] # podaj rezultate v tri glavne liste-------------------------------- try: with open(target_complex_2 + ".pdb", "rt") as infile: print(target_complex_2 + ".pdb") for linenumber, line in enumerate(infile): if vzorec_3.search(line) != None: if vzorec_4.search(line) != None: lista_za_vode.append(line.rstrip('\n')) else: lista_za_heteroatome.append(line.rstrip('\n')) if vzorec_2.search(line) != None: lista_za_atome.append(line.rstrip('\n')) else: pass except OSError: print("File not found!, please investigate.") # VKLJUCITEV CHAIN VOD global lista_za_atome_xyzchain lista_za_atome_xyzchain = [] for entry in lista_za_atome: test = [] try: entry2 = entry.split() # ATOM 477 CG2 ILE A 78 6.540 0.762 34.941 1.00 13.42 C test.append(entry2[6]) test.append(entry2[7]) test.append(entry2[8]) test.append(str(entry2[4]).upper()) lista_za_atome_xyzchain.append(test) except: pass if water_sel == "not": for linija in lista_za_heteroatome: #print(linija) #naslednja linija je pomembna za korekturo "posebnih" pdb (4bqp, ...), to je ze 123 korektura... if len(str(linija.split()[0])) > 6: unique_binding_site = str(linija.split()[2]) + "." + (str(linija.split()[3]))[1:] + "." + (str(linija.split()[3]))[0] lista_binding_sites.append(unique_binding_site) # prostorska definicija bsite bsite_unique.append([unique_binding_site, linija.split()[4], linija.split()[5], linija.split()[6]]) #naslednja linija je za korekturo "posebnih" pdb (1h00) #primer: #HETATM 2280 C22BFCP A1400 3.795 28.597 6.010 0.50 44.76 C elif len(str(linija.split()[2])) > 6: unique_binding_site = (str(linija.split()[2]))[-3:] + "." + (str(linija.split()[3]))[1:] + "." + (str(linija.split()[3]))[0] lista_binding_sites.append(unique_binding_site) # prostorska definicija bsite bsite_unique.append([unique_binding_site, linija.split()[4], linija.split()[5], linija.split()[6]]) #naslednja linija je za korekturo "posebnih" pdb (2v5z, 1l2s) #primer: #HETATM 8040 O2P FAD B1497 26.808 129.360 7.718 1.00 27.99 O elif len(str(linija.split()[4])) > 1: unique_binding_site = (str(linija.split()[3]))[-3:] + "." + (str(linija.split()[4]))[1:] + "." + (str(linija.split()[4]))[0] lista_binding_sites.append(unique_binding_site) # prostorska definicija bsite bsite_unique.append([unique_binding_site, linija.split()[5], linija.split()[6], linija.split()[7]]) else: unique_binding_site = str(linija.split()[3]) + "." + str(linija.split()[5]) + "." + str(linija.split()[4]) lista_binding_sites.append(unique_binding_site) # prostorska definicija bsite bsite_unique.append([unique_binding_site, linija.split()[6], linija.split()[7], linija.split()[8]]) else: for linija in lista_za_vode: #naslednja linija je pomembna za korekturo "posebnih" pdb (4bqp, ...), to je ze 123 korektura... if len(str(linija.split()[0])) > 6: unique_binding_site = str(linija.split()[2]) + "." + (str(linija.split()[3]))[1:] + "." + (str(linija.split()[3]))[0] lista_binding_sites.append(unique_binding_site) bsite_unique.append([unique_binding_site, linija.split()[4], linija.split()[5], linija.split()[6]]) else: unique_binding_site = str(linija.split()[3]) + "." + str(linija.split()[5]) + "." + str(linija.split()[4]) lista_binding_sites.append(unique_binding_site) bsite_unique.append([unique_binding_site, linija.split()[6], linija.split()[7], linija.split()[8]]) # priprava bsite --------------------------------------------------- # ok grupiranje ker zelimo UNIQUE for key, group in groupby(bsite_unique, lambda x: x[0]): bsx = [] bsy = [] bsz = [] for el in group: bsx.append(float(el[1])) bsy.append(float(el[2])) bsz.append(float(el[3])) # name of bsite, axerage x, average y, average z, min x, max x, min y, max y, min z, max z BindingSites.bsite_unique_centers.append([key, sum(bsx)/len(bsx), sum(bsy)/len(bsy), sum(bsz)/len(bsz), min(bsx), max(bsx), min(bsy), max(bsy), min(bsz), max(bsz)]) # priprava vode----------------------------------------------------- for linija in lista_za_vode: temp = [] if len(str(linija.split()[0])) > 6: water_binding_sites = str(linija.split()[2]) + "." + (str(linija.split()[3]))[1:] + "." + (str(linija.split()[3]))[0] lista_water_binding_sites.append(water_binding_sites) else: water_binding_sites = str(linija.split()[3]) + "." + str(linija.split()[5]) + "." + str(linija.split()[4]) lista_water_binding_sites.append(water_binding_sites) # debug: # print(lista_water_binding_sites) # priprava ostalo--------------------------------------------------- for linija in lista_za_atome: atom_site = [] try: atom_site.append(str(linija.split()[4])) atom_site.append(int(linija.split()[5])) lista_verige.append(atom_site) except: pass # priprava verige--------------------------------------------------- for key, group in groupby(lista_verige, lambda x: x[0]): temp_group = [] residue_number = 0 for el in group: # TO JE ZA STETJE UNIKATNIH AK OSTANKOV if el not in temp_group: temp_group.append(el) else: pass # uporbljeno za opcijo kjer se steje unikatne AK ostanke ins_str = str(temp_group[-1][0]) + " chain with " + str(len(temp_group)) + " residues" # ins_str = str(temp_group[-1][0]) + " chain with " + str(temp_group[-1][1]) + " residues" lista_verige_konc.append(ins_str) # print ins_str # debug line : # print lista_verige_konc # resevanje prolematicnih pdbjev - naj preveri uporabnik # v bodoce mogoce avtomatsko #------------------------------------------------------------------- if chain_sel == "not": for chainelement in lista_verige_konc: if float(chainelement.split()[3]) < 30.0: temp_str = "ONLY " + str(chainelement.split()[3]) + " resiues found in chain " + str(chainelement.split()[0]) # problemi v warning listi warning_lista.append(temp_str) else: pass if len(warning_lista) >= 1: tkMessageBox.showwarning(title='ProBiS H2O warning', parent=master, message="\n".join(warning_lista) + "\n" + "Try to compare whole chains instead of individual binding sites at the short chain location.") else: pass if water_sel == "not": for entry in sorted(list(set(lista_binding_sites))): binding_listbox.insert(0, entry) else: for entry in sorted(list(set(lista_binding_sites))): binding_listbox.insert(0, entry) for entry in sorted(list(set(lista_water_binding_sites))): binding_listbox.insert(0, entry) else: for entry in lista_verige_konc: binding_listbox.insert(0, entry) return None # flow out except------------------------------------------------------- except: tkMessageBox.showwarning(title='ProBiS H2O warning', parent=master, message="invalid PDB ID or \nDatabase File not Found! \n\nplease investigate!") print("Database File not Found!") print(sys.exc_info()) # class end # report lista 1---------------------------------------------------------------- report_list_1 = [] report_list_2 = [] report_list_1.append("ProBiS H2O REPORT file") report_list_1.append("-" * 25 + "\n\n") # ------------------------------------------------------------------------------ class h20Analysis: """collect, prepare, cluster, analyze, display, crystal h20 data""" @staticmethod def analyze_waters(): global SELECTED_SITE global SELECTED_SITE_CHAIN # NUM CPU: try: processors_available_local = str(multiprocessing.cpu_count()) except: processors_available_local = "1" # NUM_CPUS // nova_datoteka = open("report_" + str(pdb_text.get()).lower() + ".txt", "w") nova_datoteka.close() # za eno ali vec verig na primerjan protein one_or_multiple = num_entity_chains_setting.get() # get setting on superposition starting point analysis bsite_space_check = bsite_vicinity_setting.get() chain_sel = whole_chain_setting.get() vzorec_3 = re.compile("^" + "HETATM\s+\d+") vzorec_3_supp = re.compile("^" + "HETATM\d\d\d\d\d\s+") examined_list_unique = [] examined_list = list(cluster_list_unique) target_complex_2 = str(pdb_text.get()).lower() # to je za 1j4h kjer nastopajo nedosegljivi pdb-ji ki imajo svoje # entrije v bazi pdb: npr: 5GKY # za njih bomo tvorili bazo: unavailable_pdb_list.txt datoteka # ki se nahaja v delovnem okolju with open('unavailable_pdb_list.txt', 'r') as f: removed_list = f.read().splitlines() removed_list.append(target_complex_2.lower()) for element in examined_list: if str(element).lower() not in removed_list: examined_list_unique.append(str(element).lower()) else: pass try: bsite_selection = str(binding_listbox.get(binding_listbox.curselection())) chain_selection = str(binding_listbox.get(binding_listbox.curselection()))[-1] whole_chain_compare_selection = str(binding_listbox.get(binding_listbox.curselection()))[0] except: tkMessageBox.showwarning(title='ProBiS H2O warning', parent=master, message="invalid selection \n\nplease select b-site or chain!") return None if bsite_space_check == "yes": for element in BindingSites.bsite_unique_centers: if element[0] == bsite_selection: SELECTED_SITE = element SELECTED_SITE_CHAIN = str(chain_selection).upper() if bsite_space_check == "not": for element in BindingSites.bsite_unique_centers: if element[0] == bsite_selection: SELECTED_SITE = element SELECTED_SITE_CHAIN = str(chain_selection).upper() if str(chain_sel) == "yes": SELECTED_SITE = [] SELECTED_SITE.append("no binding site used in analysis") SELECTED_SITE_CHAIN = str(whole_chain_compare_selection).upper() else: pass #report 2,3,4,5,6,7,8,9, 10 report_list_1.append("\n\n\nExamined complex: " + target_complex_2) report_list_1.append("Whole chain setting used: " + str(chain_sel)) if str(chain_sel) == "yes": report_list_1.append("Whole chain selection: " + whole_chain_compare_selection) report_list_1.append("Binding site selection: / (not used)") report_list_1.append("Chain selection: " + whole_chain_compare_selection) else: report_list_1.append("Whole chain selection: / (not used)") report_list_1.append("Binding site selection: " + bsite_selection) report_list_1.append("Chain selection: " + chain_selection) report_list_1.append("Used PDB clusters with: " + str(seq_identity_value.get()) + " %") report_list_1.append("Unique structures in identified cluster: " + str(examined_list) + "\n\n\n") if chain_sel == "not": # for probis 2.4.7 os.system("./.pro/probis -ncpu " + processors_available_local + " -extract -bsite " + bsite_selection + " -dist 3.0 -f1 " + target_complex_2 + ".pdb -c1 " + chain_selection + " -srffile " + target_complex_2 + ".srf") # for probis 2.4.2 # os.system("./probis -extract -bsite " + bsite_selection + " -dist 3.0 -f1 " + target_complex_2 + ".pdb -c1 " + chain_selection + " > " + target_complex_2 + ".srf") else: os.system("./.pro/probis -ncpu " + processors_available_local + " -extract -f1 " + target_complex_2 + ".pdb -c1 " + whole_chain_compare_selection + " -srffile " + target_complex_2 + ".srf") master_chain_list = [] open("./srfs.txt", 'w').close() prot_list = [] print "aaaaaa" print examined_list_unique for element in examined_list_unique: unique_chain_list = [] # print element try: with open(element + ".pdb", "rt") as infile: for linenumber, line in enumerate(infile): if vzorec_3.search(line) != None: unique_chain = str(line.rstrip('\n').split()[4]) if len(unique_chain) == 1: unique_chain_list.append(unique_chain) elif len(unique_chain) == 2: #4WUC primer #: HETATM 2976 NA A NA A 403 8.964 15.893 -17.028 0.50 27.84 NA unique_chain = str(line.rstrip('\n').split()[5][0]) unique_chain_list.append(unique_chain) else: # naslednja linija [4][0] je za primer PDBJA: 4BRI # HETATM 5862 O2G UNP A1393 60.198 4.590 12.738 1.00 13.14 O # klasicen PDB: # HETATM 2769 N1 ARU A 1 35.314 25.889 32.623 1.00 60.17 N unique_chain = str(line.rstrip('\n').split()[4][0]) unique_chain_list.append(unique_chain) elif vzorec_3_supp.search(line) != None: # tretji problematicen primer: PDB ID: 4BRP # HETATM11092 BR BR A1394 19.400 -62.788 -5.889 1.00 49.48 BR unique_chain = str(line.rstrip('\n').split()[3][0]) unique_chain_list.append(unique_chain) else: pass unique_chain_list = list(set(unique_chain_list)) master_chain_list.append(unique_chain_list) for chain_id in unique_chain_list: # zacasna lista of unwanted unwanted_chain = [1, "1", 2, "2", 3, "3", 4, "4", 5, "5", 6, "6", 7, "7", 8, "8", 9, "9"] if chain_id in unwanted_chain: pass else: # for probis 2.4.2 # os.system("./probis -extract -f1 " + element + ".pdb -c1 " + chain_id + " > " + element + chain_id + ".srf") # for probis 2.4.7 os.system("./.pro/probis -ncpu " + processors_available_local + " -extract -f1 " + element + ".pdb -c1 " + chain_id + " -srffile " + element + chain_id + ".srf") # print("./probis -compare -super -f1 " + target_complex_2 + ".srf -c1 " + chain_selection + " -f2 " + element + chain_id + ".srf -c2 " + chain_id) srf_fajl = open("./srfs.txt", 'a') srf_fajl.write(element + chain_id + ".srf " + chain_id + "\n") srf_fajl.close() prot_list.append(element + " " + chain_id) pass except OSError: print("Database File not Found!, please investigate.") # ---------debug line----------------------------------------------------------- #print (master_chain_list) PAZI NA NASLEDNJO LINIJO srf_fajl.close() ############################## os.system("rm ./*.rota.pdb") os.system("rm ./AAA_NOSQL.nosql") ############################## if chain_sel == "not": # for probis 2.4.2 # os.system("./probis -surfdb -local -sfile srfs.txt -f1 " + target_complex_2 + ".srf -c1 " + chain_selection) # for probis 2.4.7 os.system("./.pro/probis -ncpu " + processors_available_local + " -surfdb -local -sfile srfs.txt -f1 " + target_complex_2 + ".srf -c1 " + chain_selection + " -nosql AAA_NOSQL.nosql") # get json of alignmnts for comparison of chains os.system("./.pro/probis -ncpu " + processors_available_local + " -results -f1 " + target_complex_2 + ".pdb -c1 " + chain_selection + " -nosql AAA_NOSQL.nosql -json AAA_NOSQL.json") else: os.system("./.pro/probis -ncpu " + processors_available_local + " -surfdb -sfile srfs.txt -f1 " + target_complex_2 + ".srf -c1 " + whole_chain_compare_selection + " -nosql AAA_NOSQL.nosql") os.system("./.pro/probis -ncpu " + processors_available_local + " -results -f1 " + target_complex_2 + ".pdb -c1 " + whole_chain_compare_selection + " -nosql AAA_NOSQL.nosql -json AAA_NOSQL.json") for element in prot_list: if chain_sel == "not": # for probis 2.4.2 # print (element.split(" ")[0] + " ---- " + element.split(" ")[1]) # os.system("./probis -align -alno 0 -f1 " + target_complex_2 + ".pdb -c1 " + chain_selection + " -f2 " + element.split(" ")[0] + ".pdb -c2 " + element.split(" ")[1]) # for probis 2.4.7 # -bkeep - DODANO NA NOVO os.system("./.pro/probis -ncpu " + processors_available_local + " -align -bkeep -alno 0 -nosql AAA_NOSQL.nosql -f1 " + target_complex_2 + ".pdb -c1 " + chain_selection + " -f2 " + element.split(" ")[0] + ".pdb -c2 " + element.split(" ")[1]) else: os.system("./.pro/probis -ncpu " + processors_available_local + " -align -bkeep -alno 0 -nosql AAA_NOSQL.nosql -f1 " + target_complex_2 + ".pdb -c1 " + whole_chain_compare_selection + " -f2 " + element.split(" ")[0] + ".pdb -c2 " + element.split(" ")[1]) print("Rotas done ... (alignment 0 !)") # correction of multiple or one chain per protein allignment aligned_unique = [] aligned_discard = [] helper = [] if str(one_or_multiple) == "yes": with open("AAA_NOSQL.json") as json_fajl: z_data = json.load(json_fajl) for aligned in z_data: if str(aligned["pdb_id"]) in helper: aligned_discard.append(str(aligned["pdb_id"]) + str(aligned["chain_id"])) else: helper.append(str(aligned["pdb_id"])) aligned_unique.append(str(aligned["pdb_id"]) + str(aligned["chain_id"])) if chain_sel == "not": for discarded in aligned_discard: os.system("rm ./" + target_complex_2 + chain_selection + "_" + str(discarded) + ".0.rota.pdb") else: for discarded in aligned_discard: os.system("rm ./" + target_complex_2 + whole_chain_compare_selection + "_" + str(discarded) + ".0.rota.pdb") else: pass # ----------------START WATER COLLECTION------------------------------------ # vzorci vod v PDB # linija1 = "HETATM 3315 O HOH A 653 6.657 0.611 50.201 1.00 22.92 O" # linija2 = "HETATM 6180 O HOH A1063 46.720 3.111 27.787 1.00 51.91 O" # linija3 = "HETATM 3046 O AHOH A 562 19.114 37.882 -1.866 0.50 24.61 O" # linija4 = "HETATM 3047 O BHOH A 562 20.241 36.438 -1.021 0.50 30.54 O" # linija5 = "HETATM11839 O HOH A2001 45.529 16.939 64.867 1.00 20.76 O" PDB_master_file_list = [] imena_fajlov = glob("*.rota.pdb") # ZADNJI JE KOMPLEKS imena_fajlov.append(target_complex_2 + ".pdb") #print(imena_fajlov) vzorec_water_mining1 = re.compile("^" + "HETATM\s+\d+\s+\S+\s+" + "HOH" + "\s+\D\s+\d+\s+") # ok za linijo 1 vzorec_water_mining2 = re.compile("^" + "HETATM\s+\d+\s+\S+\s+" + "HOH" + "\s+\D\d{4}\s+") # ok za linijo 2 vzorec_water_mining3 = re.compile("^" + "HETATM\s+\d+\s+\S+\s+" + "\wHOH" + "\s+\D\s+\d+\s+") # ok za linijo 3,4 vzorec_water_mining4 = re.compile("^" + "HETATM\d+\s+\S+\s+" + "HOH" + "\s+\D\d{4}\s+") # za linijo 5 # VZOREC ZA END MODELA: VSAK *.rota.pdb ima MODEL2 zacetni kompleks vzorec_water_only_model_1 = re.compile("^" + "ENDMDL") # DEBUG LINE # print(imena_fajlov) for ime_fajla in imena_fajlov: # print (ime_fajla) lista_h2o = [] with open(ime_fajla, 'r') as brani_fajl: for linija in brani_fajl: if vzorec_water_mining1.search(linija) != None: voda = linija.split() voda.append(ime_fajla) # print voda lista_h2o.append(voda) elif vzorec_water_mining2.search(linija) != None: voda = linija.split() voda.insert(5, voda[4][1:]) voda[4] = voda[4].strip("1234567890") voda.append(ime_fajla) lista_h2o.append(voda) elif vzorec_water_mining3.search(linija) != None: voda = linija.split() voda[3] = voda[3][1:] voda.append(ime_fajla) lista_h2o.append(voda) elif vzorec_water_mining4.search(linija) != None: voda = linija.split() voda.insert(4, voda[3][1:]) voda[3] = voda[3].strip("1234567890") voda.insert(1, voda[0][6:]) voda[0] = voda[0].strip("1234567890") voda.append(ime_fajla) lista_h2o.append(voda) # naslednja linija je kljucna zaradi 2 modelov v *.rota.pdb elif vzorec_water_only_model_1.search(linija) != None: break else: pass PDB_master_file_list.append(lista_h2o) # ----debug----------------------------------------------------------------- # print (PDB_master_file_list) MASTER_h2o_list = [] fajl_list = [] for PDB_water_fajl in PDB_master_file_list: try: for het, stev, atom, molekula, veriga, zapor, x, y, z, occ, R, atom2, fajl in PDB_water_fajl: test = [] # test.append(het), test.append(stev), test.append(x), test.append(y), test.append(z) test.append(x), test.append(y), test.append(z), test.append(fajl), test.append(R), test.append(zapor) MASTER_h2o_list.append(test) fajl_list.append(fajl) except (RuntimeError, TypeError, NameError, ValueError): pass entities = int(len(set(fajl_list))) #print ("AAA") #print (set(fajl_list)) # naslednja linija je debug line # print (MASTER_h2o_list) T1.delete(1.0, Tkinter.END) T1_text.set("Master water list includes %r molecules\n" % (len(MASTER_h2o_list))) # REPORT list 11,12 report_list_1.append(str(find_value.get()) + " (sequence identity pre-cluster)") report_list_1.append("Master water list includes %r waters" % (len(MASTER_h2o_list))) T1.insert(Tkinter.END, T1_text.get()) T1_text.set("Superimposed chains: %r\n" % (entities)) T1.insert(Tkinter.END, T1_text.get()) # print "Master lista vod narejena in vsebuje %r vod" % (len(MASTER_h2o_list)) print "writing H2O master list" nova_datoteka = open("master_water_list.txt", "w") for tocka in MASTER_h2o_list: nova_datoteka.write("%s\n" % tocka) nova_datoteka.close() print "done..." nb.select(p2) # DBSCAN formatting----------------------------------------------------- # binding site clustering # BindingSites.bsite_unique_centers master_bsite_lista_vod = [] master_bsite_lista_vod_koordinata_x = [] master_bsite_lista_vod_koordinata_y = [] master_bsite_lista_vod_koordinata_z = [] master_lista_vod = [] master_lista_vod_koordinata_x = [] master_lista_vod_koordinata_y = [] master_lista_vod_koordinata_z = [] # POPRAVA VOD DA NE SEGAJO IZVEN CHAINA correction_x = [] correction_y = [] correction_z = [] for element in lista_za_atome_xyzchain: if SELECTED_SITE_CHAIN == element[3]: correction_x.append(float(element[0])) correction_y.append(float(element[1])) correction_z.append(float(element[2])) global atom_max_x global atom_min_x global atom_max_y global atom_min_y global atom_max_z global atom_min_z atom_max_x = max(correction_x) + 4 atom_min_x = min(correction_x) - 4 atom_max_y = max(correction_y) + 4 atom_min_y = min(correction_y) - 4 atom_max_z = max(correction_z) + 4 atom_min_z = min(correction_z) - 4 global boundingBox boundingBox = [LINEWIDTH, 2.0, BEGIN, LINES, COLOR, float(1), float(0), float(0), VERTEX, atom_min_x, atom_min_y, atom_min_z, #1 VERTEX, atom_min_x, atom_min_y, atom_max_z, #2 VERTEX, atom_min_x, atom_max_y, atom_min_z, #3 VERTEX, atom_min_x, atom_max_y, atom_max_z, #4 VERTEX, atom_max_x, atom_min_y, atom_min_z, #5 VERTEX, atom_max_x, atom_min_y, atom_max_z, #6 VERTEX, atom_max_x, atom_max_y, atom_min_z, #7 VERTEX, atom_max_x, atom_max_y, atom_max_z, #8 VERTEX, atom_min_x, atom_min_y, atom_min_z, #1 VERTEX, atom_max_x, atom_min_y, atom_min_z, #5 VERTEX, atom_min_x, atom_max_y, atom_min_z, #3 VERTEX, atom_max_x, atom_max_y, atom_min_z, #7 VERTEX, atom_min_x, atom_max_y, atom_max_z, #4 VERTEX, atom_max_x, atom_max_y, atom_max_z, #8 VERTEX, atom_min_x, atom_min_y, atom_max_z, #2 VERTEX, atom_max_x, atom_min_y, atom_max_z, #6 VERTEX, atom_min_x, atom_min_y, atom_min_z, #1 VERTEX, atom_min_x, atom_max_y, atom_min_z, #3 VERTEX, atom_max_x, atom_min_y, atom_min_z, #5 VERTEX, atom_max_x, atom_max_y, atom_min_z, #7 VERTEX, atom_min_x, atom_min_y, atom_max_z, #2 VERTEX, atom_min_x, atom_max_y, atom_max_z, #4 VERTEX, atom_max_x, atom_min_y, atom_max_z, #6 VERTEX, atom_max_x, atom_max_y, atom_max_z, #8 END ] # ---------------------------------------------------------------------- # cluster TESTING # mlv_datoteka = open("random_water_list5.txt", "r") mlv_datoteka = open("master_water_list.txt", "r") for linija in mlv_datoteka: vmesna_lista = [] linija2 = linija.replace("[", "") linija3 = linija2.replace("]", "") linija4 = linija3.replace(" ", "") linija5 = linija4.replace("'", "") linija_lista = linija5.split(",") x = float(linija_lista[0]) y = float(linija_lista[1]) z = float(linija_lista[2]) vmesna_lista.append(x) vmesna_lista.append(y) vmesna_lista.append(z) if bsite_space_check == "yes" and chain_sel == "not": # print("drugo mesto") # print(lista_za_atome_xyzchain) if SELECTED_SITE[4] - 4 <= vmesna_lista[0] <= SELECTED_SITE[5] + 4: if SELECTED_SITE[6] - 4 <= vmesna_lista[1] <= SELECTED_SITE[7] + 4: if SELECTED_SITE[8] - 4 <= vmesna_lista[2] <= SELECTED_SITE[9] + 4: master_bsite_lista_vod.append(vmesna_lista) x2 = float(vmesna_lista[0]) master_bsite_lista_vod_koordinata_x.append(x2) y2 = float(vmesna_lista[1]) master_bsite_lista_vod_koordinata_y.append(y2) z2 = float(vmesna_lista[2]) master_bsite_lista_vod_koordinata_z.append(z2) else: pass else: pass else: pass if bsite_space_check == "not" and chain_sel == "not": if atom_min_x <= vmesna_lista[0] <= atom_max_x: if atom_min_y <= vmesna_lista[1] <= atom_max_y: if atom_min_z <= vmesna_lista[2] <= atom_max_z: master_lista_vod_koordinata_x.append(x) master_lista_vod_koordinata_y.append(y) master_lista_vod_koordinata_z.append(z) master_lista_vod.append(vmesna_lista) if chain_sel == "yes": if atom_min_x <= vmesna_lista[0] <= atom_max_x: if atom_min_y <= vmesna_lista[1] <= atom_max_y: if atom_min_z <= vmesna_lista[2] <= atom_max_z: master_lista_vod_koordinata_x.append(x) master_lista_vod_koordinata_y.append(y) master_lista_vod_koordinata_z.append(z) master_lista_vod.append(vmesna_lista) else: pass mlv_datoteka.close() # naslednja linija je samo za debug namen (odkomentiraj po potrebi) # print(master_bsite_lista_vod) # /DBSCAN formatting---------------------------------------------------- def display_cluster_info(mlist, mlist_x, mlist_y, mlist_z): x_dim = max(mlist_x) - min(mlist_x) y_dim = max(mlist_y) - min(mlist_y) z_dim = max(mlist_z) - min(mlist_z) system_volume = round(x_dim * y_dim * z_dim) T1_text.set("System volume is: %d cubic A\n" % (system_volume)) T1.insert(Tkinter.END, T1_text.get()) # report list 13,14,15 report_list_1.append("System volume is: %d cubic A\n" % (system_volume)) report_list_1.append("IDENTIFIED CLUSTERS: \n") report_list_1.append("-" * 25) def calculate_clusters(lista, sample_size): lista_np_array = np.array(lista) db3D = DBSCAN(eps=0.9, min_samples=sample_size).fit(lista_np_array) labels3D = db3D.labels_ # print(labels3D) # Number of clusters in labels, ignoring noise if present. n_clusters_3D = len(set(labels3D)) - (1 if -1 in labels3D else 0) return int(n_clusters_3D) cluster_listbox.delete(0, Tkinter.END) start_population = 2 clus_num = calculate_clusters(mlist, start_population) cluster_collate_list = [] max_population = 0 while clus_num >= 1: consv = round((float(start_population)/float(entities)), 2) # limita ena je overloaded ker je lahko teoreticno prisotnih vec molekul vode na istem mestu v istem kristalu # glede na to da je smisel tega orodja v eksperimentalnih podatkih bi bile taksne vode na lokaciji manjsi od 1 A # nesmiselne in korigirane s strani kristalografa # zato lahko komot v skrajno nenavadno ali eksp-nekorigiranem primeru vrednost consv presega 1 # taksne primere tukaj reduciramo na vrednost 1 kar pomeni, da je voda na tej lokaciji nastopa v vseh eksperimentalnih entitetah if consv > 1: consv = 1.0 else: pass # za report list------------------------------------------------ text_consv = int(round(consv*10)) * "*" st = 10 - len(text_consv) text_consv += st * " " # print consv if str(clus_num) == "1": text = (str(clus_num) + " cluster with " + str(start_population) + " H2O molecules. " + "consv. " + str(consv)) else: text = (str(clus_num) + " clusters with " + str(start_population) + " H2O molecules. " + "consv. " + str(consv)) num_spaces = 55 - len(text) report_list_1.append(text + + num_spaces * " " + "[" + text_consv + "]") # REPORT LIST APPEND-------------------------------------------- cluster_collate_list.append([clus_num, start_population, text]) start_population += 1 clus_num = calculate_clusters(mlist, start_population) max_population = start_population temp_collate = [] for cluster_num, start_population, list_text in reversed(cluster_collate_list): if cluster_num not in temp_collate: cluster_listbox.insert(Tkinter.END, list_text) temp_collate.append(cluster_num) else: pass for i, listbox_entry in enumerate(cluster_listbox.get(0, Tkinter.END)): if 0.9 <= float(listbox_entry.split()[7]): cluster_listbox.itemconfig(i, {'bg':red10}) elif 0.8 <=float(listbox_entry.split()[7]) < 0.9: cluster_listbox.itemconfig(i, {'bg':red09}) elif 0.7 <=float(listbox_entry.split()[7]) < 0.8: cluster_listbox.itemconfig(i, {'bg':red08}) elif 0.6 <=float(listbox_entry.split()[7]) < 0.7: cluster_listbox.itemconfig(i, {'bg':red07}) elif 0.5 <=float(listbox_entry.split()[7]) < 0.6: cluster_listbox.itemconfig(i, {'bg':red06}) elif 0.4 <=float(listbox_entry.split()[7]) < 0.5: cluster_listbox.itemconfig(i, {'bg':red05}) elif 0.3 <=float(listbox_entry.split()[7]) < 0.4: cluster_listbox.itemconfig(i, {'bg':red04}) elif 0.2 <=float(listbox_entry.split()[7]) < 0.3: cluster_listbox.itemconfig(i, {'bg':red03}) elif 0.1 <=float(listbox_entry.split()[7]) < 0.2: cluster_listbox.itemconfig(i, {'bg':red02}) else: cluster_listbox.itemconfig(i, {'bg':red01}) # report list 15 report_list_1.append("-" * 25) max_pop_text = "Maximum occupied cluster contains %d H2O molecules \n binding site: %s" % (max_population - 1, SELECTED_SITE[0]) T1_text.set(max_pop_text) T1.insert(Tkinter.END, T1_text.get()) report_list_1.insert(10, max_pop_text) if chain_sel == "yes": display_cluster_info(master_lista_vod, master_lista_vod_koordinata_x, master_lista_vod_koordinata_y, master_lista_vod_koordinata_z) else: if bsite_space_check == "yes": display_cluster_info(master_bsite_lista_vod, master_bsite_lista_vod_koordinata_x, master_bsite_lista_vod_koordinata_y, master_bsite_lista_vod_koordinata_z) else: display_cluster_info(master_lista_vod, master_lista_vod_koordinata_x, master_lista_vod_koordinata_y, master_lista_vod_koordinata_z) # cleanup os.system("rm ./*.ent.gz") os.system("rm ./*.srf") os.system("rm ./*.rota.pdb") os.system("rm ./AAA_NOSQL*") os.system("rm ./query.json") os.system("rm ./info.json") os.system("rm ./srfs.txt") return None class pyMOLinterface: """use wonderful pyMol for visualisation of collected results""" """thanks! Warren L. DeLano!""" @staticmethod def pyMOL_water_contacts(): target_complex_3 = str(pdb_text.get()).lower() # za H-bond mejno razdajo kar 4 A pymol.cmd.do("select protein, polymer and %s" % (target_complex_3)) pymol.cmd.do("select ligand, organic and %s" % (target_complex_3)) pymol.cmd.do("select conserved_waters, H2O*") pymol.cmd.do("select donors, (elem n,o and (neighbor hydro)) and %s" % (target_complex_3)) pymol.cmd.do("select acceptors, (elem o or (elem n and not (neighbor hydro))) and %s" % (target_complex_3)) pymol.cmd.do("distance prot_acceptors, (protein and acceptors), conserved_waters, 4.0") pymol.cmd.do("distance prot_donors, (protein and donors), conserved_waters, 4.0") pymol.cmd.do("distance ligand_acceptors, (ligand and acceptors), conserved_waters, 4.0") pymol.cmd.do("distance ligand_donors, (ligand and donors), conserved_waters, 4.0") pymol.cmd.do("distance inter_conserved_H2O, conserved_waters, conserved_waters, 4.0") pymol.cmd.do("delete donors") pymol.cmd.do("delete acceptors") pymol.cmd.do("set dash_color, magenta") pymol.cmd.do("set dash_gap, 0.2") pymol.cmd.do("set dash_length, 0.2") pymol.cmd.do("set dash_round_ends, on") pymol.cmd.do("set dash_width, 3") @staticmethod def pyMOL_fetch_system(): target_complex_3 = str(pdb_text.get()).lower() # print(target_complex_3) pymol.cmd.do("delete all") pymol.cmd.do("fetch %s" % (target_complex_3)) pymol.cmd.do("center %s" % (target_complex_3)) pymol.cmd.do("center %s" % (target_complex_3)) pymol.cmd.do("hide everything, %s" % (target_complex_3)) pymol.cmd.do("show cartoon, %s" % (target_complex_3)) pymol.cmd.do("set cartoon_color, %s" % ("white")) pymol.cmd.do("hide lines, all") pymol.cmd.do("util.cbag") pymol.cmd.do("show surface, %s" % (target_complex_3)) pymol.cmd.do("set transparency, 0.9") pymol.cmd.do("set surface_color, %s" % ("white")) pymol.cmd.do("show sticks, organic") pymol.cmd.do("color blue, organic") pymol.cmd.do("select %s_waters, resn hoh" % (target_complex_3)) pymol.cmd.do("show nonbonded, %s_waters" % (target_complex_3)) pymol.cmd.deselect() @staticmethod def pyMOL_chain_box(): pymol.cmd.load_cgo(boundingBox, "box") @staticmethod def pyMOL_bsite_cluster(): # display binding sites of clusters pymol.cmd.do("select bsites, H2O* around 6") pymol.cmd.do("select byres bsites") pymol.cmd.do("show sticks, byres bsites") pymol.cmd.do("util.cbay byres bsites") pymol.cmd.do("set_bond stick_radius, 0.1, byres bsites") pymol.cmd.do("select sele, name ca and byres bsites") pymol.cmd.do("label sele,\"%s-%s\" % (resn,resi)") pymol.cmd.do("set label_size, 18") pymol.cmd.do("set label_font_id, 7") pymol.cmd.do("show sticks, organic") pymol.cmd.do("color blue, organic") pymol.cmd.do("util.cnc organic") pymol.cmd.do("set_bond stick_radius, 0.25, organic") @staticmethod def pyMOL_display_cluster(): display_clusters_setting = display_setting.get() bsite_space_check = bsite_vicinity_setting.get() chain_sel = whole_chain_setting.get() # za korekcijo in pogled R faktorja debye_waller_check = debye_waller_setting.get() # DBSCAN formatting----------------------------------------------------- # binding site clustering # BindingSites.bsite_unique_centers master_bsite_lista_vod = [] master_bsite_lista_vod_koordinata_x = [] master_bsite_lista_vod_koordinata_y = [] master_bsite_lista_vod_koordinata_z = [] master_lista_vod = [] master_lista_vod_koordinata_x = [] master_lista_vod_koordinata_y = [] master_lista_vod_koordinata_z = [] # za Debye Waller master_bsite_lista_atom_iso_displacement = [] master_lista_atom_iso_displacement = [] # master_lista_names = [] master_bsite_lista_info = [] master_lista_info = [] mlv_datoteka = open("master_water_list.txt", "r") for linija in mlv_datoteka: vmesna_lista = [] linija2 = linija.replace("[", "") linija3 = linija2.replace("]", "") linija4 = linija3.replace(" ", "") linija5 = linija4.replace("'", "") linija_lista = linija5.split(",") x = float(linija_lista[0]) y = float(linija_lista[1]) z = float(linija_lista[2]) B = float(linija_lista[4]) if B < 0: B = 0 info = str(linija_lista[3]) + " location: " + str(linija_lista[5].strip("\n")) # anizotropni displcement bomo implementirali v V2 hopefully # + 1.4 je zaradi r H2O isotropni_displacement = math.sqrt(B/(8*((math.pi)**2))) + 1.4 # master_lista_names.append(ime) vmesna_lista.append(x) vmesna_lista.append(y) vmesna_lista.append(z) if bsite_space_check == "yes" and chain_sel == "not": if SELECTED_SITE[4] - 4 <= vmesna_lista[0] <= SELECTED_SITE[5] + 4: if SELECTED_SITE[6] - 4 <= vmesna_lista[1] <= SELECTED_SITE[7] + 4: if SELECTED_SITE[8] - 4 <= vmesna_lista[2] <= SELECTED_SITE[9] + 4: master_bsite_lista_vod.append(vmesna_lista) x2 = float(vmesna_lista[0]) master_bsite_lista_vod_koordinata_x.append(x2) y2 = float(vmesna_lista[1]) master_bsite_lista_vod_koordinata_y.append(y2) z2 = float(vmesna_lista[2]) master_bsite_lista_vod_koordinata_z.append(z2) master_bsite_lista_atom_iso_displacement.append(isotropni_displacement) master_bsite_lista_info.append(info) if bsite_space_check == "not" and chain_sel == "not": if atom_min_x <= vmesna_lista[0] <= atom_max_x: if atom_min_y <= vmesna_lista[1] <= atom_max_y: if atom_min_z <= vmesna_lista[2] <= atom_max_z: master_lista_vod_koordinata_x.append(x) master_lista_vod_koordinata_y.append(y) master_lista_vod_koordinata_z.append(z) master_lista_vod.append(vmesna_lista) master_lista_atom_iso_displacement.append(isotropni_displacement) master_lista_info.append(info) if chain_sel == "yes": if atom_min_x <= vmesna_lista[0] <= atom_max_x: if atom_min_y <= vmesna_lista[1] <= atom_max_y: if atom_min_z <= vmesna_lista[2] <= atom_max_z: master_lista_vod_koordinata_x.append(x) master_lista_vod_koordinata_y.append(y) master_lista_vod_koordinata_z.append(z) master_lista_vod.append(vmesna_lista) master_lista_atom_iso_displacement.append(isotropni_displacement) master_lista_info.append(info) else: pass # /DBSCAN formatting---------------------------------------------------- # BSITE LOKALNO ALI GLOBALNO NA VERIGI if bsite_space_check == "yes" and chain_sel == "not": master_lista_vod = master_bsite_lista_vod master_lista_atom_iso_displacement = master_bsite_lista_atom_iso_displacement master_lista_info = master_bsite_lista_info else: pass mlv_datoteka.close() try: # example: # 2 clusters with 14 H2O molecules consv. 0.67 cluster_selection = int(cluster_listbox.get(cluster_listbox.curselection()).split()[3]) consv_of_cluster = float(cluster_listbox.get(cluster_listbox.curselection()).split()[7]) # print (cluster_selection) # report list report_list_1.append("\nBinding site info (name, avg x, y, z, min x, max x, min y, max y, min z, max z; box 4 A around extremes): \n" + str(SELECTED_SITE)) report_list_1.append("\nExamined cluster with " + str(cluster_selection) + " H2O molecules\n") report_list_1.append("-" * 25) except: tkMessageBox.showwarning(title='ProBiS H2O warning', parent=master, message="please select clusters to display") return db3D = DBSCAN(eps=0.9, min_samples=cluster_selection).fit(np.array(master_lista_vod)) labels3D = db3D.labels_ #debug line: #print(labels3D) # Number of clusters in labels, ignoring noise if present. n_clusters_3D = len(set(labels3D)) - (1 if -1 in labels3D else 0) i = 0 clustri_tock = [] tocke = [] for element in labels3D: temp = [] if element != -1: temp.append(master_lista_vod[i]) temp.append(element) temp.append(master_lista_atom_iso_displacement[i]) temp.append(master_lista_info[i]) # temp.append(master_lista_names[i]) # report list report_list_1.append(temp) tocke.append(temp) # report list else: pass i += 1 if debye_waller_check == "not": if display_clusters_setting == "not": pymol.cmd.do("delete H2O*") else: pass for element in list(set(labels3D)): cluster_temp = [] # print element for sub_element in tocke: if sub_element[1] == element: cluster_temp.append(sub_element[0]) # print cluster_temp try: # k_means_test = KMeans(n_clusters = 1).fit(cluster_temp) # print ("means je ") # print (k_means_test.cluster_centers_[0]) # koordinate = k_means_test.cluster_centers_[0][0] print cluster_temp[0][0] pymol.cmd.do("set_color clus_color, [%f, %f, %f]" % (1.0, (1.0 - consv_of_cluster), (1.0 - consv_of_cluster))) pymol.cmd.do("pseudoatom H2O_clus-%d_%.2f, vdw=1, color=clus_color, pos=[%f, %f, %f]" % (element, consv_of_cluster, cluster_temp[0][0], cluster_temp[0][1], cluster_temp[0][2])) pymol.cmd.do("show spheres, H2O_clus-%d*" % (element)) # pymol.cmd.do("pseudoatom H2O_mined_cluster %d, vdw=1, color=tv_blue, pos=[%f, %f, %f]" % (cluster_selection, element[0][0], element[0][1], element[0][2])) except IndexError: pass else: pymol.cmd.do("delete H2O*") pymol.cmd.do("delete iso_disp") for element in list(set(labels3D)): cluster_temp = [] # print element for sub_element in tocke: if sub_element[1] == element: sub_element[0].append(sub_element[2]) cluster_temp.append(sub_element[0]) # print (cluster_temp) try: print cluster_temp[0][0] pymol.cmd.do("pseudoatom H2O_clus, vdw=1, color=red, pos=[%f, %f, %f]" % (cluster_temp[0][0], cluster_temp[0][1], cluster_temp[0][2])) pymol.cmd.do("show spheres, H2O_clus") for tocka in cluster_temp: print(tocka) pymol.cmd.do("pseudoatom iso_disp, vdw=%f, color=red, pos=[%f, %f, %f]" % (cluster_temp[0][3], cluster_temp[0][0], cluster_temp[0][1], cluster_temp[0][2])) pymol.cmd.do("show dots, iso_disp") except IndexError: pass # report on cluster nova_datoteka = open("report_" + str(pdb_text.get()).lower() + ".txt", "w") for linija in report_list_1: nova_datoteka.write("%s\n" % linija) nova_datoteka.close() print "report created..." # thanks Janez for Support!