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MINT-lists.py
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#****************************************************************************
#* *
#* Copyright (C) 2013: University of Warsaw *
#* Author: Anna Gorska <[email protected]> *
#* Author: Maciej Jasinski <[email protected]> *
#* *
#* This program is free software; you can redistribute it and/or modify *
#* it under the terms of the GNU General Public License version 2, *
#* as published by the Free Software Foundation. *
#* *
#* This program is distributed in the hope that it will be useful, *
#* but WITHOUT ANY WARRANTY; without even the implied warranty of *
#* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
#* GNU General Public License for more details. *
#* *
#* You should have received a copy of the GNU General Public License *
#* along with this program; if not, write to the *
#* Free Software Foundation, Inc., *
#* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
#* *
#****************************************************************************/
#3
# !/usr/bin/python
import gzip
import math
import Bio
import sys
import os
from collections import Counter
import multiprocessing
import MDAnalysis
import pickle
import numpy as np
#import pandas as pd
from operator import itemgetter
#from pympler.asizeof import asizeof
sys.path.append(os.path.dirname(os.path.realpath(__file__)) + "/bin")
import rna_structure as RS
import RNAStructML as XML
import motif_cluster as MC
import csvToxls as cX
import colors_varna as Varna
import download_and_protonate as Download
import param_reader as ParamReader
import time
from Bio.PDB.MMCIFParser import MMCIFParser
#import warnings
#from Bio.PDB.PDBExceptions import PDBConstructionException, PDBConstructionWarning
#warnings.simplefilter('ignore', PDBConstructionWarning)
if len(sys.argv) < 2:
print "Specify CONFIG file!"
sys.exit()
elif len(sys.argv) > 2:
print "Too many arguments! Specify single configuration file!"
sys.exit()
def timer(f):
def g(*args, **kwargs):
start = time.clock()
result = f(*args, **kwargs)
open("../time.txt", 'a').write(f.__name__ + ": " +
str(time.clock() - start) + "\n")
return result
return
# warnings.simplefilter("error", RuntimeWarning)
aa = ["ALA", "ARG", "ASN", "ASP", "CYS", "GLU", "GLN", "GLY", "HIS", "HSD",
"ILE", "LEU", "LYS", "MET", "PHE", "PRO", "SER", "THR", "TRP", "TYR",
"VAL"]
NUCLEOTIDES = ["A", "U", "C", "G", "ADE", "URA", "CYT", "GUA", "RA", "RG",
"RC", "RU", "T", "DA", "DC", "DT", "DG", "G5", "G3", "A5",
"A3", "C3", "C5", "U5", "U3", "T5", "T3", "DG5", "DG3", "DA5",
"DA3", "DC3", "DC5", "DU5", "DU3", "DT5", "DT3", "LG5", "LG3",
"LA5", "LA3", "LC3", "LC5", "LU5", "LU3", "LT5", "LT3", "LA",
"LC", "LT", "LG", "LU", "TPN", "GPN", "CPN", "APN", "THY"]
a = [NUCLEOTIDES.extend([i+"5", i+"3"]) for i in ["RA", "RG", "RC", "RU"]]
ions = ["MG", "ZN", "NA", "K", "HOH", "SOD", "CLA", "TIP", "MN", "SO4", "WAT"]
possible_ps = ["O1P", "O2P", "OP1", "OP2"]
d = ["WC donor", "Hoogsteen donor", "Sugar donor"]
a = ["WC acceptor", "Hoogsteen acceptor", "Sugar acceptor"]
IF_MODIFIED = {}
UNKNOWN_NUC = []
HAVE_FORCE_FIELD = []
masses = {'C': 12.0, 'N': 14.0, 'O': 16.0, 'P': 15.0, 'H': 1.0}
# read csv file and create the table
def read_from_csv(filename):
table = []
f = open(filename, "r")
for i in f.readlines():
table.append(i.replace("\n", "").split(";"))
f.close()
return table
# function uncompressing the file
def uncompress(filename):
f_in = gzip.open(filename, 'rb')
pdb = filename.split(".")[0].replace("pdb", "") + ".ent"
f_out = open(pdb, "w")
f_out.write(f_in.read())
f_in.close()
f_out.close()
print "File with the strucuture: " + pdb
return pdb
def if_modified_list(nucs, PARMS, if_mod=False):
if if_mod is False:
if_mod = IF_MODIFIED
for i in nucs:
if_mod[i.get_id()] = if_modified(i, PARMS)
def if_modified(res, PARMS):
if not isinstance(res, str):
resname = res.get_resname()
else:
resname = res
resname = resname.strip()
if resname in NUCLEOTIDES:
return False
origin = check_origin(resname, PARMS)
if origin:
return origin
else:
return "Completly unknown Nucleotide ", resname
# #@timer
def get_nucleic_from_pdb(PARMS):
# Using BioPython to readin the PDB file
filename = PARMS["file_name"]
if filename.endswith(".cif"):
parser = MMCIFParser()
structure = parser.get_structure("1", filename)
else:
p = Bio.PDB.PDBParser(PERMISSIVE=1)
structure = p.get_structure("1", filename)
nucleotides = []
seq = ""
# searching for RNA
chains_names = PARMS["chains_names"]
if not chains_names:
for i in structure[0]:
chains_names.append(i.get_id())
for chain_name in chains_names:
for residue in structure[0][chain_name]:
name = residue.get_resname().replace(" ", "")
if name in NUCLEOTIDES:
nucleotides.append(residue)
seq += name + " "
elif name in UNKNOWN_NUC:
nucleotides.append(residue)
seq += name + " "
elif name not in aa and name not in ions:
w = "\nWARNING RESIDUE " + str(name) +\
"\ndoesn't seem to be nucleotide, amioacid or an ion."+\
"\nRunning the analysis without it."+\
"\nIf you wish for it to be analysed add parameters.\n"
print w
PARMS["OUT_FILE"].write(w)
tt = ("\n " + str(len(nucleotides)) +
" nucleotides, sequence: \n" + seq + "\n")
PARMS["OUT_FILE"].write(tt)
c = Counter(seq.split(" ")[:-1])
print "\nNucleotides statistics:"
PARMS["OUT_FILE"].write("Nucleotides statistics:\n")
k = c.keys()
if_modified_list(nucleotides, PARMS)
for i in k:
if i in NUCLEOTIDES:
tmp = str(i) + " "*(3-len(i)) + "-> " +\
str(c[i]) + " known parameters"
print tmp
PARMS["OUT_FILE"].write(tmp+"\n")
elif i in UNKNOWN_NUC:
tmp = str(i) + " "*(3-len(i)) +\
"-> " + str(c[i]) + " Unknown parameters"
PARMS["OUT_FILE"].write(tmp+"\n")
print tmp
return nucleotides
# read pdb, iter through its nucleotides:
# @timer
def read_in_charges(nucleotides, PARMS):
f = open(PARMS["table_charges"])
tmp = f.readlines()
f.close()
l = [i.replace("\n", "").split(";") for i in tmp[1:]]
column = 0
if PARMS["force_field"] == "AMBER":
column = [2, 5, 6]
elif PARMS["force_field"] == "CHARMM":
column = [3, 7, 8]
elif PARMS["force_field"] == "MY_OWN":
column = [4, 9, 10]
d = {}
nuc = list(set([names(n.get_resname(),PARMS) for n in nucleotides]))
for i in l:
# charge, vdw_radius, vdw_depth
try:
if i[0] in nuc: # and i[0] not in UNKNOWN_NUC:
d[i[0]+"_"+i[1]] = [float(i[column[0]]), float(i[column[1]]),
float(i[column[2]])]
except Exception:
print "We do not have data for ", i[0], " in ", i, " in"
print PARMS["force_field"], " force field."
suggested = [i for i in ["AMBER", "CHARMM"]
if i not in [PARMS["force_field"]]]
print "Try running with ", " ".join(suggested),
print " or defining your own field."
sys.exit()
return d
def coords_and_charges_and_vdw(nuc, charges, TimeTable, N, PARMS):
out = {}
name = names(nuc.get_resname(),PARMS)
atoms_names = [i.split("_")[1] for i in charges.keys()
if (i.split("_")[0] == name)]
for at in atoms_names:
try:
out[at] = [charges[name+"_"+at],
TimeTable[nuc[at].get_full_id()][N], at]
except Exception:
try:
tmp = at[-1] + at[0:-1]
out[at] = [charges[name + "_" + at],
TimeTable[nuc[tmp].get_full_id()][N], at]
except Exception:
# print name+"_"+at, " ",charges[name+"_"+at]
pass
return out
def vdw_and_coulomb(base1, base2):
energy_c = 0.0
energy_vdw = 0.0
for i in base1:
for t in base2:
atom_distance = np.linalg.norm(base1[i][1] - base2[t][1])
# kcal/mol
energy_c += 332*base1[i][0][0]*base2[t][0][0]/atom_distance
# If you measure charge in units of the electron charge,
# and distance in Angstroms,
# then an electrostatic energy looks like:
# E (kcal/mol) = 332 * q1*q2/r
vdw_r = (base1[i][0][1] + base2[t][0][1])
energy_vdw += (np.sqrt(base1[i][0][2]*base2[t][0][2]) *
(((vdw_r/atom_distance)**12) -
2*((vdw_r/atom_distance)**6))) # kcal/mol
return (round(energy_c, 2),
round(energy_vdw, 2),
round(energy_c + energy_vdw, 2))
# measure distances
def pi_stacking(n1, n2, base1, base2, PARMS):
ps = {}
t1 = False
t2 = False
for t in possible_ps:
# bez wodorow
try:
t1 = atom_to_base_mas_center_distance(base2, base1[t])
t2 = atom_to_base_mas_center_distance(base1, base2[t])
if t1 and t1 < PARMS["OP_stacking_distance_cutoff"]:
ps[RS.resid_description(n2) + "_" +
RS.resid_description(n1) + ":" +
t] = [t1, vdw_and_coulomb(only_base(base2),
phosphate_group(base1))]
if t2 and t2 < PARMS["OP_stacking_distance_cutoff"]:
ps[RS.resid_description(n1) + "_" +
RS.resid_description(n2) + ":" +
t] = [t2, vdw_and_coulomb(only_base(base1),
phosphate_group(base2))]
except Exception:
pass
return ps
def phosphate_group(base):
phosphate = {}
ps = [i for i in base.keys() if "P" in i]
for i in ps:
phosphate[i] = base[i]
return phosphate
def only_base(base):
not_phosphate = {}
ps = [i for i in base.keys() if "P" not in i]
for i in ps:
not_phosphate[i] = base[i]
return not_phosphate
def atom_to_base_mas_center_distance(base, op):
mass_list = []
dist_list = []
for i in base:
if i not in possible_ps:
m = masses[i[0]]
dist_list.append(m*dist(base[i][1], op[1]))
mass_list.append(m)
return round(sum(dist_list)/float(sum(mass_list)), 2)
def atom_to_base_distance(base, op):
dist_list = []
for i in base:
if i not in possible_ps:
dist_list.append(dist(base[i][1], op[1]))
return round(sum(dist_list)/float(len(dist_list)), 2)
def vmd_for_dipole_selection(vdw_and_charges):
t = ["A", "C", "G", "U"]
o = {}
for m in t:
o[m] = [i.split("_")[1] for i in vdw_and_charges
if i.split("_")[0] == m]
return o
def measure_for_all(nucleotides, charges, PARMS, TimeTable, N):
table = PARMS["table_nuc_read"]
margin = int(PARMS["margin"])
h_bond_l = float(PARMS["h_bond_l"])
h_bond_angle = float(PARMS["h_bond_angle"])
# WCWC
WCWC_h_bonds = []
WCWC_clas = []
WCWC_conf = []
WCWC_nucs = []
# NON_SPEC
non_spec_h_bonds = []
non_spec_clas = []
non_spec_spec = []
non_spec_nucs = []
# STACKING
stacking_nucs = []
stacking_energies = []
stacking_pi = {}
# NUC CHAR
nucleotides_characteristics = {}
for i in nucleotides:
nucleotides_characteristics[i] = [[0], [None]]
# ALL TO ALL
for a in range(0, len(nucleotides)):
for b in range(a+1, len(nucleotides)):
i = nucleotides[a]
j = nucleotides[b]
if_a_WCWC_pair = False
if whether_not_too_far_simple(i, j, PARMS["cutoff"], TimeTable, N):
potential_h_bonds = detect_H_bonds(i, j, table,
h_bond_l, h_bond_angle,
PARMS, TimeTable, N)
h_bonds = [t for t in potential_h_bonds
if (t[3][0] != -1 and t[3][1] != -1) and
t[3][0] >= h_bond_angle and t[3][1] <= h_bond_l]
if len(h_bonds) > 0:
clas = classify_H_bonds(i, j, h_bonds, table, PARMS)
tmp = clas.split("/")
nucleotides_characteristics[i][0].append(len(h_bonds))
nucleotides_characteristics[i][1].append(j)
nucleotides_characteristics[j][0].append(len(h_bonds))
nucleotides_characteristics[j][1].append(i)
if_a_WCWC_pair = True
if tmp[0] == tmp[1] == "WC":
WCWC_h_bonds.append(h_bonds)
WCWC_clas.append(clas)
WCWC_conf.append(nucleotides_conformation(i, j,
TimeTable, N))
WCWC_nucs.append([a, b])
else:
non_spec_nucs.append([a, b])
non_spec_h_bonds.append(h_bonds)
non_spec_clas.append(clas)
non_spec_spec.append(nucleotides_conformation(i, j,
TimeTable, N))
else:
h_bonds_margin = [t for t in potential_h_bonds if
(t[3][0] >= h_bond_angle *
(1.0 - margin) and
t[3][1] <= h_bond_l*(1.0 + margin))]
if len(h_bonds_margin) > 0:
non_spec_nucs.append([a, b])
non_spec_h_bonds.append(h_bonds_margin)
non_spec_clas.append("")
non_spec_spec.append("Large margin")
# stacking
ccvi = coords_and_charges_and_vdw(i, charges, TimeTable, N, PARMS)
ccvj = coords_and_charges_and_vdw(j, charges, TimeTable, N, PARMS)
if (i != j and not if_a_WCWC_pair and
whether_not_too_far_simple(i, j, PARMS["cutoff_stacking"],
TimeTable, N)):
base1 = only_base(ccvi)
base2 = only_base(ccvj)
stacking = vdw_and_coulomb(base1, base2)
if stacking[1] <= PARMS["vdw_cutoff_stacking"]:
stacking_nucs.append([i, j])
stacking_energies.append(stacking)
# distance from OPs
stacking_pi.update(pi_stacking(i, j, ccvi, ccvj, PARMS))
out_dicti = {
"WCWC_h_bonds": WCWC_h_bonds,
"WCWC_clas": WCWC_clas,
"WCWC_conf": WCWC_conf,
"WCWC_nucs": WCWC_nucs,
"non_spec_h_bonds": non_spec_h_bonds,
"non_spec_clas": non_spec_clas,
"non_spec_spec": non_spec_spec,
"non_spec_nucs": non_spec_nucs,
"translated_nucleotides":
translate_nucleotides_characteristics(nucleotides_characteristics),
"stacking_nucs": stacking_nucs,
"stacking_energies": stacking_energies,
"stacking_pi": stacking_pi}
return out_dicti
def base_atoms(residue):
# print [at for at in residue if at.get_name]
out = []
for at in residue:
name = at.get_name()
if "'" not in name and "P" not in name:
out.append(at)
return out
def check_origin(resname, PARMS):
try:
return PARMS["dicti_modified_nucs"][resname]
except Exception:
return False
def translate_nucleotides_characteristics(nucleotides_characteristics):
out = {}
for i in nucleotides_characteristics.keys():
out[RS.resid_description(i)] = [sum(nucleotides_characteristics[i][0]),
" ".join([RS.resid_description(nuc)
for nuc in
nucleotides_characteristics[i][1]])]
return out
# return cis/trans - nucleotide conformation for a bond
def nucleotides_conformation(i, j, TimeTable, N):
atoms_coords = []
for n in [i, j]:
if if_exists(n, "C1'"):
atoms_coords.append(TimeTable[n["C1'"].get_full_id()][N])
elif if_exists(n, "C1*"):
atoms_coords.append(TimeTable[n["C1*"].get_full_id()][N])
elif if_exists(n, "C8*"): #PNA in Amber
atoms_coords.append(TimeTable[n["C8*"].get_full_id()][N])
# elif if_exists(n, "N1*"):
# atoms_coords.append(TimeTable[n["N1*"].get_full_id()][N])
elif if_exists(n, "C4'"): #PNA in CHARMM
atoms_coords.append(TimeTable[n["C4'"].get_full_id()][N])
else:
print "No c1/n1 in", n
if if_exists(n, "N9"):
atoms_coords.append(TimeTable[n["N9"].get_full_id()][N])
elif if_exists(n, "N1"):
atoms_coords.append(TimeTable[n["N1"].get_full_id()][N])
else:
print "No n9/n1 in", n
angle = measure_torsion_angle(atoms_coords)
if angle > -90 and angle < 90:
return "Cis"
else:
return "Trans"
def get_atoms_of_the_rest(res):
out = []
for i in res:
name = i.get_name()
if "'" not in name and "*" not in name and "H" not in name:
out.append(i)
out.sort()
return out
def measure_torsion_angle(list_of_arrays):
v1_2 = list_of_arrays[0] - list_of_arrays[1]
v3_2 = list_of_arrays[3] - list_of_arrays[1]
v3_4 = list_of_arrays[3] - list_of_arrays[2]
il_skal_1_2_3_2 = np.dot(v1_2, v3_2)
il_skal_3_4_3_2 = np.dot(v3_4, v3_2)
mian_1 = np.dot(v3_2, v3_2)
v1 = v1_2 - (il_skal_1_2_3_2/mian_1)*v3_2
v2 = -v3_4 + (il_skal_3_4_3_2/mian_1)*v3_2
cos_dih = np.dot(v1, v2/(np.linalg.norm(v1)*np.linalg.norm(v2)))
#added because of python inaccuracy in the floating point operations
if cos_dih > 1:
cos_dih = 1
else:
if cos_dih < -1:
cos_dih = -1
dih_rad = np.arccos(cos_dih)
znak_dih = math.copysign(1, np.dot(v1_2, (np.cross(v3_2, v3_4))))
dih = math.degrees(dih_rad)*int(znak_dih)
return dih
# Cutoff - simple
def whether_not_too_far_simple(i, j, cutoff, TimeTable, N):
coords = []
for n in [i, j]:
if if_exists(n, "C1'"):
coords.append(list(TimeTable[n["C1'"].get_full_id()][N]))
elif if_exists(n, "C1*"):
coords.append(list(TimeTable[n["C1*"].get_full_id()][N]))
elif if_exists(n, "C8*"): #PNA in Amber
coords.append(list(TimeTable[n["C8*"].get_full_id()][N]))
elif if_exists(n, "C4'"): #PNA in CHARMM
coords.append(list(TimeTable[n["C4'"].get_full_id()][N]))
# elif if_exists(n, "N1*"):
# coords.append(list(TimeTable[n["N1*"].get_full_id()][N]))
# elif if_exists(n, "N4'"):
# coords.append(list(TimeTable[n["N4'"].get_full_id()][N]))
else:
return False
if dist(coords[0], coords[1]) < cutoff:
return True
return False
def purine_or_pyrimidyne(nuc):
if names(nuc.get_resname(),PARMS) in ["A", "G"]:
return "purine"
else:
return "pyrimidyne"
def classify_H_bonds(i, j, h_bonds, table, PARMS):
atoms_i = [t[0] for t in h_bonds]
atoms_j = [t[2] for t in h_bonds]
return "/".join([classify_list_of_atoms(i.get_resname(),
atoms_i, table,
PARMS),
classify_list_of_atoms(j.get_resname(),
atoms_j, table,
PARMS),
str(len(h_bonds))])
# * means corner
def classify_list_of_atoms(res_name, atoms, table, PARMS):
tmp = []
modi = False
if if_modified(res_name, PARMS):
modi = True
res_name = check_origin(res_name.strip(), PARMS)
for i in atoms:
a = what_site_atom(res_name, i, table,PARMS)
if a == [] and modi:
a = ["Modified"]
tmp.append(a)
if len(tmp) > 1:
t = list(reduce(lambda x, y: x & y, (set(i) for i in tmp)))
if not t:
return " or ".join(a)
return t[0]
else:
return "*".join(tmp[0])
def what_site_atom(res_name, atom, table,PARMS):
row = table[[i[0] for i in table].index(names(res_name,PARMS))]
sites = []
for i in range(0, len(row)):
if atom in row[i].split():
tmp = table[0][i].split()[0]
if tmp not in sites:
sites.append(tmp)
return sites
def atom_coords(res, at, TimeTable, N, PARMS):
at = at.replace(" ", "")
try:
return TimeTable[res[at].get_full_id()][N]
except Exception:
try:
at = at.replace("'", "*")
return TimeTable[res[at].get_full_id()][N]
except Exception:
try:
at = at + "'"
return TimeTable[res[at].get_full_id()][N]
except Exception:
#If and elif below are an ugly solution for two different names for the methyl C in PNA TPN residue in Amber and CHARMM.
#Will work probably also for the DNA Thymine
if PARMS["force_field"] == "AMBER" and "C5M" in at:
return False
elif PARMS["force_field"] == "CHARMM" and "C7" in at:
return False
else:
print "There is no atom ", at, " in resid :",
print res.get_resname(), RS.resid_description(res)
return False
# Function detecting all possible H-Bonds between two residues
def detect_H_bonds(res1, res2, table, h_bond_l, h_bond_angle,
PARMS, TimeTable, N):
Hbonds = []
for at_donor in donor_acceptor_list(res1, "d", table, if_modified(res1,
PARMS),PARMS):
for at_acceptor in donor_acceptor_list(res2, "a",
table, if_modified(res2, PARMS),PARMS):
for hydrogen in hydrogens_names_for_donor_name(res1, at_donor):
tmp = if_hbond(atom_coords(res1, at_donor, TimeTable, N, PARMS),
TimeTable[res1[hydrogen].get_full_id()][N],
atom_coords(res2, at_acceptor, TimeTable, N, PARMS),
h_bond_l, h_bond_angle, PARMS)
Hbonds.append([at_donor, hydrogen, at_acceptor, tmp])
for at_donor in donor_acceptor_list(res2, "d", table, if_modified(res2,
PARMS),PARMS):
for at_acceptor in donor_acceptor_list(res1, "a",
table, if_modified(res1, PARMS),PARMS):
for hydrogen in hydrogens_names_for_donor_name(res2, at_donor):
tmp = if_hbond(atom_coords(res2, at_donor, TimeTable, N, PARMS),
TimeTable[res2[hydrogen].get_full_id()][N],
atom_coords(res1, at_acceptor, TimeTable, N, PARMS),
h_bond_l, h_bond_angle, PARMS)
Hbonds.append([at_acceptor, hydrogen, at_donor, tmp])
return Hbonds
# Function to check whether there is a h_bood
def if_hbond(donor_coord, hydrogen_coord,
acceptor_coord, h_bond_l, h_bond_angle, PARMS):
try:
kat = f_angl([donor_coord, hydrogen_coord, acceptor_coord])
if PARMS["h_bond_atom"] == "donor":
dlugosc = dist(donor_coord, acceptor_coord)
else:
dlugosc = dist(hydrogen_coord, acceptor_coord)
return (kat, dlugosc)
except Exception:
return (-1, -1)
# Function to compte the distance
def dist(coord1, coord2):
return ((coord1[0] - coord2[0])**2 +
(coord1[1] - coord2[1])**2 +
(coord1[2] - coord2[2])**2)**0.5
# Function to compute the angle
def f_angl(list_of_arrays):
a = list_of_arrays[0] - list_of_arrays[1]
b = list_of_arrays[2] - list_of_arrays[1]
cos = np.dot(a, b)/(np.linalg.norm(a)*np.linalg.norm(b))
#added because of python inaccuracy in the floating point operations
if cos > 1:
cos = 1
else:
if cos < -1:
cos = -1
try:
ang_rad = math.degrees(np.arccos(cos))
except RuntimeWarning:
print "Cosinus, wrong ", cos
ang_rad = math.degrees(ang_rad)
return ang_rad
# Checking if the atom exists
def if_exists(res, at_name):
try:
res[at_name].get_coord()
return True
except Exception:
return False
# Creating list of the hydrogensnames names
def hydrogens_names_for_donor_name(res, at_donor):
inki = ["1", "2", "3"]
hs = []
k = at_donor[2:]
# pusty
h = "H" + at_donor[1] + k
if if_exists(res, h) and h not in hs:
hs.append(h)
for i in inki:
# beginning
h = i + "H" + at_donor[1] + k
if if_exists(res, h) and h not in hs:
hs.append(h)
# ending
h = "H" + at_donor[1] + i + k
if if_exists(res, h) and h not in hs:
hs.append(h)
return hs
# function gives list of atoms - acceptors or donors
def donor_acceptor_list(resid, da, table, modify,PARMS):
if not modify:
n = names(resid.get_resname(),PARMS)
t = table[[i[0] for i in table].index(n)]
tmp = ""
if da == "a":
for i in a:
tmp += " " + t[table[0].index(i)]
if da == "d":
for i in d:
tmp += " " + t[table[0].index(i)]
# PODMIENIC
out = []
for i in tmp.split():
if i not in out:
out.append(i)
return out
elif modify:
atoms_base = base_atoms(resid)
hydrogens = [i for i in atoms_base if "H" in i.get_name()]
nums = [j.get_name()[1] for j in hydrogens]
out = []
for n in [i.get_name() for i in atoms_base]:
if "H" not in n and len(n) > 1:
if da == "d" and list(n)[1] in nums:
out.append(n)
elif da == "a" and list(n)[1] not in nums:
out.append(n)
return out
def number_first(s):
num = [i for i in s if i.isdigit()]
letters = [i for i in s if not i.isdigit()]
return "".join(num)+"".join(letters)
# changing name for residue
def names(resname,PARMS):
resname = resname.replace(" ", "")
if resname in ["G", "U", "A", "C"]:
return resname
elif resname in ["GUA", "URA", "CYT", "ADE",
"G5", "G3", "A5", "A3", "C3",
"C5", "U5", "U3", "T5", "T3",
""]:
if PARMS["all_nucs_DNA"] == 1:
return "D"+resname[0]
else:
return resname[0]
elif resname in ["DG5", "DG3", "DA5", "DA3", "DC3",
"DC5", "DU5", "DU3", "DT5", "DT3"]:
return resname[:2]
elif resname in ["THY"]:
return "DT"
elif (resname.startswith("R") or
resname.startswith("L")):
return resname[1]
else:
return resname
# margin in %
def chcek_if_close_to_value(x, ref, margin):
if (ref - ref*(1-margin) < x) and (ref*(1 + margin) > x):
return True
else:
return False
# save to csv file
def list_to_csv_file(file_name, list_out):
f = open(file_name + ".csv", "w")
for i in range(0, len(list_out)):
f.write(str(i) + " ; " + str(list_out[i]) + "\n")
f.close()
print "Saved csv file " + file_name + ".csv in directory: "
def nicely_print(l, LINE_LENGTH):
out = ""
word = " ".join(l)
if len(l) > LINE_LENGTH:
number_of_lines = len(l)/LINE_LENGTH
for i in range(0, number_of_lines):
out += str(i*LINE_LENGTH + 1) +\
" "*(8 - len(str(i*LINE_LENGTH + 1))) +\
word[i*LINE_LENGTH:(i + 1)*LINE_LENGTH] +\
" " + str((i + 1)*LINE_LENGTH) + "\n"
# Adding ending
last_one = number_of_lines*LINE_LENGTH+1
out += str(last_one) + " "*(8-len(str(last_one))) +\
word[last_one:] + " " + str(len(word)+1)+"\n"
else:
out += "1 " + word + " " + str(len(l))
return out
# @timer
def create_reps(l, color_number):
trip = ""
if l:
for i in l:
if i and "vmd" not in i:
try:
tmp = i.split("]")[1]
except Exception:
tmp = i
tt = tmp.split("chain")[1:]
if len(tt) == 1:
tt = "chain " + tt[0]
else:
tt = "or ".join(["chain " + j for j in tt])
trip += "mol selection {" + tt +\
"}\nmol color ColorID " +\
str(color_number) +\
"\nmol rep Licorice \nmol addrep top\n"
return trip
return " "
# @timer
def vmd_run(vmd, filename, PARMS):
f = open(filename, "w")
text = """mol load pdb """ + os.path.realpath(PARMS["file_name"]) + """
mol delrep 0 top
mol rep Lines
mol color colorID 2
mol addrep top \n""" + create_reps(vmd[0], 4) + create_reps(vmd[1], 5) +\
create_reps(vmd[2], 6) + create_reps(vmd[3], 7)
f.write(text)
f.close()
def stacking_presentation(stacking_nucs, stacking_energies):
out = " qn1 n2 Coul VDW sum\n"
per_nucleotide = {}
for i, n in enumerate(stacking_nucs):
m = RS.resid_description(n[0]) + " " + RS.resid_description(n[1])
add_safely_to_dicti(per_nucleotide,
RS.resid_description(n[0]),
stacking_energies[i])
add_safely_to_dicti(per_nucleotide,
RS.resid_description(n[1]),
stacking_energies[i])
if not IF_MODIFIED[n[0].get_id()] and not IF_MODIFIED[n[1].get_id()]:
out += m + " "*(10 - len(m)) + str(stacking_energies[i]) + "\n"
else:
out += m + " "*(10 - len(m)) + " MODIFIED NUCLEOTIDES" + "\n"
return (out, per_nucleotide)
def add_safely_to_dicti(dicti, k, v):
if k in dicti.keys():
tmp = dicti[k]
dicti[k] = add_tuples(tmp, v)
else:
dicti[k] = v
def add_tuples(t1, t2):
n = []
for i in range(min(len(t1), len(t2))):
n.append(round(t1[i]+t2[i], 2))
return tuple(n)
# @timer
# file_name, cutoff, cutoff_stacking, h_bond_l, h_bond_angle, vmd
def single_frame_analysis(PARMS):
nucleotides = get_nucleic_from_pdb(PARMS)
if len(nucleotides) <= 1:
PARMS["OUT_FILE"].write("Are there any nucleotides in the structure?\n")
sys.exit()
charges = read_in_charges(nucleotides, PARMS)
TimeTable = TimeTable_from_nucleotides(nucleotides)
megalist = measure_for_all(nucleotides, charges, PARMS, TimeTable, 0)
struct_analysis = RS.analysis(megalist, nucleotides, True, IF_MODIFIED)
filename = PARMS["out_name"] + "_vmd_run.tcl"
out_file = (struct_analysis["fileText"] + "\n\nStacking pairs:" +
stacking_presentation(megalist["stacking_nucs"],
megalist["stacking_energies"])[0] +
"\n\nStacking pi pairs\n" +
stacking_pi_description(megalist["stacking_pi"]))
vmd_run(struct_analysis["vmd"], filename, PARMS)
if PARMS["vmd"]:
print "Trying to run VMD ... "
os.system("vmd -e "+filename)
print " "
LISTS = {}
for i in ["arches", "dot_bracket", "trajectory", "translated_nucleotides",
"stacking_pi", "pairs_in_time", "stacking"]:
LISTS[i] = {}
traj_len = 1
frames = {1: (megalist, struct_analysis, out_file)}
out_file_text = ""
for key in frames.keys():
frame = frames[key]
out_file_text += frame[2] + "\n"
for i in ["arches", "dot_bracket", "trajectory"]:
LISTS[i][key] = frame[1][i]
for i in ["translated_nucleotides", "stacking_pi"]:
LISTS[i][key] = frame[0][i]
LISTS["stacking"][key] = (frame[0]["stacking_nucs"],
frame[0]["stacking_energies"])
LISTS["pairs_in_time"][key] = frame[0]
create_outputs(LISTS, traj_len, nucleotides,
struct_analysis["dot_bracket"], PARMS)
PARMS["OUT_FILE"].write(out_file_text)
return LISTS
def stacking_pi_description(l):
out = ""
for i in l:
out += i + " " + " ".join([str(m) for m in l[i]]) + "\n"
return out
# @timer
def single_frame_in_traj_analysis(nucleotides, charges,
PARMS, TimeTable, N):
megalist = measure_for_all(nucleotides, charges, PARMS, TimeTable, N)
struct_analysis = [None]*10
try:
struct_analysis = RS.analysis(megalist, nucleotides,
False, IF_MODIFIED)
out_file = struct_analysis["fileText"] +\
"\n\nStacking pairs:" +\
stacking_presentation(megalist["stacking_nucs"],
megalist["stacking_energies"])[0] +\
"\n\nStacking pi pairs\n" +\
stacking_pi_description(megalist["stacking_pi"])
except Exception:
f = open("error"+str(N), "w")
f.write("problem in single_frame_in_traj")
f.close()
out_file = "Problem with frame"
return (megalist, struct_analysis, out_file)
# @timer
def for_a_sub_traj(universe, nucleotides, index, CAT, NAME, charges,
PARMS, TimeTable):
d = {}
number_of_pickles = 0
num_of_frames = float(len(index))
for i, N in enumerate(index):
print "frame number ", N, " "*(10-len(str(a))),\
100*round((i+1)/num_of_frames, 3), "%\n"
d[N] = single_frame_in_traj_analysis(nucleotides, charges,
PARMS, TimeTable, N)
if float(sys.getsizeof(d)/1024**3) > PARMS["max_memory_GB"]:
pickle_file_name = (CAT + "/" + NAME + "_out_dictionary_pickle_" +
str_index(index) +
"_" + str(number_of_pickles))