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AHA.py
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AHA.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
@author: justin
/media/justin/justin/neutron_water_orientation/protein/6eym/set_d/from_org_refined_no_wat
--pdb=6eym_del_D.pdb --out=adH.pdb --map=6eym_no_prot_D.ccp4 --pKa=no --wat=no --not_del=140 --EDIA=no
/media/justin/justin/neutron_water_orientation/protein/5ce4
--pdb=5ce4_noH_prot.pdb --out=adH.pdb --map=5ce4_2mFo-DFc_map.ccp4
/media/justin/justin/Acetylcholinesterase/2y2v_sort/2y2v_sort/P03
--pdb= P03.pdb --out=adH.pdb --map=P03_2mFo-DFc_map.ccp4 --pKa=no --wat=no --EDIA=yes
"""
import time
## set timer
time_start = time.time()
##load mandatory modules
import numpy as np
import argparse, sys
#import scipy as sc
import gemmi
mesh = 0.10
#defines if H or D labels are used
label_H="D"
##input variables:
parser=argparse.ArgumentParser()
parser.add_argument('--pdb', help='input pdb file',required=True)
parser.add_argument('--map', help='input ccp4 map',required=True)
parser.add_argument('--out', help='output file')
parser.add_argument('--wat', help='protonate water, yes or no')
parser.add_argument('--not_del',nargs='*', help='residues where hydrogends do not get delete')
parser.add_argument('--pKa', help='set jugment of hydrogens in hydrogen bond based on teh pKa value and not on the densety')
parser.add_argument('--EDIA',help='use EDIA yes or no')
parser.add_argument('--rad', help='rad file')
parser.add_argument('--rx', help='factor for integration radius')
args=parser.parse_args()
## process input
if args.pdb != None:
input_pdb=args.pdb
print("input pdb file is:", input_pdb)
else:
input_pdb="pdb"
print("input pdb file is:", input_pdb)
if args.map != None:
input_grid=args.map
map_ex=True
print("read from ", input_grid)
else:
input_grid="None"
map_ex= False
print("read from defalt ", input_grid)
if args.out != None:
out_file=args.out
print("output_file ",out_file)
else:
out_file="results"
print("default out_file ", out_file)
if args.wat != None:
wat=args.wat
if wat=="yes" or wat=="y" or wat=="YES" or wat=="Y" or wat=="True" :
wat_ex=True
print("water is getting protonatet")
else:
wat_ex=False
print("water is not getting protonatet")
else:
wat_ex=False
print("water is not getting protonatet")
if args.not_del != None:
not_del_l=args.not_del
for i in range(len(not_del_l)):
not_del_l[i]=int(not_del_l[i])
print("rsidues whre protons are not getting deletet ",not_del_l)
else:
not_del_l=[]
print("all hydgrogens are kept ")
if args.pKa != None:
pka=args.pKa
if pka=="yes" or pka=="y" or pka=="YES" or pka=="Y" or pka=="True" :
pka_ex=True
print("pKa values are used")
else:
pka_ex=False
print("pKa values are not used")
else:
pka_ex=False
print("pKa values are not used")
if args.EDIA != None:
EI=args.EDIA
if EI=="yes" or EI=="y" or EI=="YES" or EI=="Y" or EI=="True" :
EDIA_ex=True
print("EDIA is used")
else:
EDIA_ex=False
print("EDIA is not used")
else:
EDIA_ex=False
print("EDIA is not used")
if args.rad != None:
input_rad=args.rad
print("input rad file is:", input_rad)
else:
input_rad="/media/justin/justin/scripts/rad.csv"
print("input rad file is:", input_rad)
if args.rx != None:
rx=float(args.rx)
print("factor for the integration rx ",rx)
else:
rx=1
print("factor for the integration rx ",rx)
## reading and writeing rotines
def read_pdb(input_pdb):
## reads in pdb coordinates hardcodedt
##https://zhanglab.ccmb.med.umich.edu/BindProfX/pdb_atom_format.html
##COLUMNS DATA TYPE CONTENTS
##--------------------------------------------------------------------------------
##1 - 6 Record name "ATOM "
## 7 - 11 Integer Atom serial number.
##13 - 16 Atom Atom name.
##17 Character Alternate location indicator.
##18 - 20 Residue name Residue name.
##22 Character Chain identifier.
##23 - 26 Integer Residue sequence number.
##27 AChar Code for insertion of residues.
##31 - 38 Real(8.3) Orthogonal coordinates for X in Angstroms.
##39 - 46 Real(8.3) Orthogonal coordinates for Y in Angstroms.
##47 - 54 Real(8.3) Orthogonal coordinates for Z in Angstroms.
##55 - 60 Real(6.2) Occupancy.
##61 - 66 Real(6.2) Temperature factor (Default = 0.0).
##73 - 76 LString(4) Segment identifier, left-justified.
##77 - 78 LString(2) Element symbol, right-justified.
##79 - 80 LString(2) Charge on the atom.
print(" read pdb file")
read_pdb = open(input_pdb, "r")
org_pdb =[]
work_pdb =[]
f_head=False
head=[]
for line in read_pdb:
idef = line[0:6].strip()
if idef=="ATOM" or idef=="HETATM":
f_head=True
l_pdb=[]
a = line[0:6].strip()
a_num = int(line[6:11].strip())
a_name = line[12:16].strip()
alter = line[16].strip()
res_name= line[17:20].strip()
chain = line[21].strip()
res_num = int(line[22:26].strip())
inser = line[26].strip()
x = float(line[30:38].strip())
y = float(line[38:46].strip())
z = float(line[46:54].strip())
occ = float(line[54:60].strip())
b_fac = float(line[60:66].strip())
seg_i = line[72:76].strip()
ele = line[76:78].strip()
charge = line[78:80].strip()
l_pdb.append(a)
l_pdb.append(a_num)
l_pdb.append(a_name)
l_pdb.append(alter)
l_pdb.append(res_name)
l_pdb.append(chain)
l_pdb.append(res_num)
l_pdb.append(inser)
l_pdb.append(x)
l_pdb.append(y)
l_pdb.append(z)
l_pdb.append(occ)
l_pdb.append(b_fac)
l_pdb.append(seg_i)
l_pdb.append(ele)
l_pdb.append(charge)
#[0, 1 , 2 , 3 , 4 , 5 , 6, , 7 , 8, 9,10
#[a, a_num, a_name, alter, res_name, chain, res_num, inser, x, y, z
#11 , 12 , 13 , 14 , 15
#occ, b_fac, seg_i, ele, charge]
org_pdb.append(l_pdb)
work_pdb.append(l_pdb)
# print(l_pdb)
if f_head==False:
head.append(line)
print("close file:", input_pdb)
return org_pdb, work_pdb, head
def atm_to_res(pdb_read):
## change pdb from list of atoms to list of res with atoms
pdb=[]
pdb.append([pdb_read[0]])
for i in range(1,len(pdb_read)):
if pdb_read[i][6] != pdb_read[i-1][6]:
pdb.append([pdb_read[i]])
if pdb_read[i][6] == pdb_read[i-1][6]:
pdb[len(pdb)-1].append(pdb_read[i])
return pdb
def read_grid(input_grid):
#read ccp4 map with gemmi
print(input_grid)
map= gemmi.read_ccp4_map(input_grid)
print(gemmi.InfoMap())
map_arr=np.array(map.grid,copy=False)
# x = np.linspace(0, map.grid.unit_cell.a, num=map_arr.shape[0], endpoint=False)
# y = np.linspace(0, map.grid.unit_cell.b, num=map_arr.shape[1], endpoint=False)
# z = np.linspace(0, map.grid.unit_cell.c, num=map_arr.shape[2], endpoint=False)
print("x,y,z",map.grid.unit_cell.a,map.grid.unit_cell.b,map.grid.unit_cell.c)
print("STD",np.std(map_arr))
map_std=np.std(map_arr)
map_ave=np.average(map_arr)
print("mean",np.mean(map_arr))
print("average",np.average(map_arr))
print("head",map.header_str)
print(map.__repr__())
# print(help(map))
print(" map is readet")
return map, map_std, map_ave
def write_pdb(pdb,head, output):
#writes out final pdb file with D atoms
res = open(output, "w")
atm_nr=0
for i in range(len(head)):
res.write(head[i])
for i in range(len(pdb)):
for k in range(len(pdb[i])):
atm_nr = atm_nr + 1
string = str('{:6}'.format(pdb[i][k][0]))
string = string + str('{:5.0f}'.format(atm_nr))
if len(list(str(pdb[i][k][2])))<4:
string = string + " "
string = string + str('{:3s}'.format(str(pdb[i][k][2])))
else:
string = string + " "
string = string + str('{:4s}'.format(str(pdb[i][k][2])))
# print( str('{:4s}'.format(str(pdb[i][k][2]))))
string = string + str('{:1}'.format(pdb[i][k][3]))
string = string + str('{:3}'.format(pdb[i][k][4]))
string = string + str('{:>2}'.format(pdb[i][k][5]))
string = string + str('{:4}'.format(pdb[i][k][6]))
string = string + str('{:1}'.format(pdb[i][k][7]))
string = string + " "
string = string + str('{:8.3f}'.format(pdb[i][k][8]))
string = string + str('{:8.3f}'.format(pdb[i][k][9]))
string = string + str('{:8.3f}'.format(pdb[i][k][10]))
string = string + str('{:6.2f}'.format(pdb[i][k][11]))
string = string + str('{:6.2f}'.format(pdb[i][k][12]))
string = string + str('{:>10}'.format(pdb[i][k][13]))
string = string + str('{:>2}'.format(pdb[i][k][14]))
string = string + "\n"
res.write(string)
res.write("END")
## work on pdb file
def treat_res(pdb,map):
#work on each residio seperatly
alerts=[["CH"],["NH"],["OH"],["SH"],["flip"],["wat"],["disordert"],[]]
# alerts =[CH,NH,OH,SH,flip]
# pdb, alerts = treat_n_nerm(pdb,map,alerts)
for res_num in range(len(pdb)):
# print("res",pdb[res_num][0][6])
if pdb[res_num][0][4]=="GLY":
pdb, alerts = treat_GLY( pdb, res_num,alerts )
if pdb[res_num][0][4]=="PRO":
pdb, alerts = treat_PRO( pdb, res_num , alerts)
if pdb[res_num][0][4]=="PHE":
pdb, alerts = treat_PHE( pdb, res_num, alerts )
if pdb[res_num][0][4]=="ALA":
pdb, alerts = treat_ALA( pdb, res_num, alerts )
if pdb[res_num][0][4]=="VAL":
pdb, alerts = treat_VAL( pdb, res_num, alerts )
if pdb[res_num][0][4]=="LEU":
pdb, alerts = treat_LEU( pdb, res_num, alerts )
if pdb[res_num][0][4]=="ILE":
pdb, alerts = treat_ILE( pdb, res_num, alerts )
if pdb[res_num][0][4]=="MET":
pdb, alerts = treat_MET( pdb, res_num, alerts )
if pdb[res_num][0][4]=="ARG":
pdb, alerts = treat_ARG( pdb, res_num, alerts )
if pdb[res_num][0][4]=="TRP":
pdb, alerts = treat_TRP( pdb, res_num, alerts )
if pdb[res_num][0][4]=="ASN":
pdb, alerts = treat_ASN( pdb, res_num,map, alerts )
if pdb[res_num][0][4]=="GLN":
pdb, alerts = treat_GLN(pdb,res_num, map, alerts)
if pdb[res_num][0][4]=="ASP":
pdb, alerts = treat_ASP( pdb, res_num,map, alerts )
if pdb[res_num][0][4]=="GLU":
pdb, alerts = treat_GLU( pdb, res_num,map, alerts )
if pdb[res_num][0][4]=="HIS" or pdb[res_num][0][4]=="HID" or \
pdb[res_num][0][4]=="HIE" or pdb[res_num][0][4]=="HIP" :
pdb, alerts = treat_HIS(pdb,res_num, map, alerts)
if pdb[res_num][0][4]=="LYS":
pdb, alerts = treat_LYS( pdb, res_num, map, alerts )
if pdb[res_num][0][4]=="SER":
pdb, alerts = treat_SER( pdb, res_num ,map, alerts)
if pdb[res_num][0][4]=="THR":
pdb, alerts = treat_THR( pdb, res_num ,map, alerts)
if pdb[res_num][0][4]=="TYR":
pdb, alerts = treat_TYR( pdb, res_num ,map, alerts)
if pdb[res_num][0][4]=="CYS":
pdb, alerts = treat_CYS( pdb, res_num, map, alerts )
if pdb[res_num][0][4]=="WAT" or pdb[res_num][0][4]=="HOH" or pdb[res_num][0][4]=="DOD":
pdb, alerts = treat_WAT( pdb, res_num,map, alerts )
return pdb, alerts
######################################################
##All H well-defined
######################################################
def treat_GLY(pdb, res_num,alerts):
## add deteria to GLY
alter, alerts = find_alter(pdb,res_num,alerts)
pdb = ad_NH(pdb,res_num,alter)
# print(pdb[res_num])
pdb = ad_CH2(pdb, res_num,alter,"N","C","CA")
return pdb, alerts
def treat_PRO(pdb,res_num, alerts):
# ad hydrogen to standard psoitions at PRO
alter, alerts = find_alter(pdb,res_num,alerts)
pdb = ad_CH_R3(pdb, res_num,alter,"C","N","CA","CB")
pdb = ad_CH_R3(pdb, res_num,alter,"C","N","CA","CB")
pdb = ad_CH2(pdb, res_num,alter,"CA","CG","CB")
pdb = ad_CH2(pdb, res_num,alter,"CD","CB","CG")
pdb = ad_CH2(pdb, res_num,alter,"N","CG","CD")
return pdb, alerts
def treat_PHE(pdb,res_num, alerts):
# ad hydrogen to standard psoitions at PHE
alter, alerts = find_alter(pdb,res_num,alerts)
pdb = ad_NH(pdb,res_num,alter)
pdb = ad_CH_R3(pdb, res_num,alter,"C","N","CA","CB")
pdb = ad_CH2(pdb, res_num,alter,"CA","CG","CB")
pdb = ad_CH_ar(pdb, res_num,alter,"CG","CE2","CD2")
pdb = ad_CH_ar(pdb, res_num,alter,"CD2","CZ","CE2")
pdb = ad_CH_ar(pdb, res_num,alter,"CG","CE1","CD1")
pdb = ad_CH_ar(pdb, res_num,alter,"CD1","CZ","CE1")
pdb = ad_CH_ar(pdb, res_num,alter,"CE2","CE1","CZ")
return pdb, alerts
##############################################################
##CH3 in principle free, but uninteresting
#############################################################
def treat_ALA(pdb,res_num, alerts):
# ad hydrogen to standard psoitions at ALA
alter, alerts = find_alter(pdb,res_num,alerts)
pdb = ad_NH(pdb,res_num,alter)
pdb = ad_CH_R3(pdb, res_num,alter,"C","N","CA","CB")
pdb = ad_CH3(pdb, res_num,alter,"C","CA","CB")
return pdb, alerts
def treat_VAL(pdb,res_num, alerts):
# ad hydrogen to standard psoitions at VAL
alter, alerts = find_alter(pdb,res_num,alerts)
pdb = ad_NH(pdb,res_num,alter)
pdb = ad_CH_R3(pdb, res_num,alter,"C","N","CA","CB")
pdb = ad_CH_R3(pdb, res_num,alter,"CG2","CG1","CB","CA")
pdb = ad_CH3(pdb, res_num,alter,"CA","CB","CG1")
pdb = ad_CH3(pdb, res_num,alter,"CA","CB","CG2")
return pdb, alerts
def treat_LEU(pdb,res_num, alerts):
# ad hydrogen to standard psoitions at LEU
alter, alerts = find_alter(pdb,res_num,alerts)
# print("ALTER",alter)
pdb = ad_NH(pdb,res_num,alter)
pdb = ad_CH_R3(pdb, res_num,alter,"C","N","CA","CB")
pdb = ad_CH2(pdb, res_num,alter,"CA","CG","CB")
pdb = ad_CH_R3(pdb, res_num,alter,"CD2","CD1","CG","CB")
pdb = ad_CH3(pdb, res_num,alter,"CB","CG","CD1")
pdb = ad_CH3(pdb, res_num,alter,"CB","CG","CD2")
return pdb, alerts
def treat_ILE(pdb,res_num, alerts):
# ad hydrogen to standard psoitions at ILE
alter, alerts = find_alter(pdb,res_num,alerts)
pdb = ad_NH(pdb,res_num,alter)
pdb = ad_CH_R3(pdb, res_num,alter,"C","N","CA","CB")
pdb = ad_CH_R3(pdb, res_num,alter,"CG2","CG1","CB","CA")
pdb = ad_CH3(pdb, res_num,alter,"CA","CB","CG2")
pdb = ad_CH2(pdb, res_num,alter,"CD1","CB","CG1")
pdb = ad_CH3(pdb, res_num,alter,"CB","CG1","CD1")
return pdb, alerts
def treat_MET(pdb,res_num, alerts):
# ad hydrogen to standard psoitions at MET
alter, alerts = find_alter(pdb,res_num,alerts)
pdb = ad_NH(pdb,res_num,alter)
pdb = ad_CH_R3(pdb, res_num,alter,"C","N","CA","CB")
pdb = ad_CH2(pdb, res_num,alter,"CA","CG","CB")
pdb = ad_CH2(pdb, res_num,alter,"SD","CB","CG")
pdb = ad_CH3(pdb, res_num,alter,"CG","SD","CE")
return pdb, alerts
##############################################################
##All H well-defined
##############################################################
def treat_ARG(pdb,res_num, alerts):
# ad hydrogen to standard psoitions at ARG
alter, alerts = find_alter(pdb,res_num,alerts)
pdb = ad_NH(pdb,res_num,alter)
pdb = ad_CH_R3(pdb, res_num,alter,"C","N","CA","CB")
pdb = ad_CH2(pdb, res_num,alter,"CA","CG","CB")
pdb = ad_CH2(pdb, res_num,alter,"CD","CB","CG")
pdb = ad_CH2(pdb, res_num,alter,"CB","NE","CD")
pdb = ad_NH_s(pdb, res_num,alter,"CZ","CD","NE")
pdb = ad_NH2(pdb, res_num,alter,"NE","CZ","NH1")
pdb = ad_NH2(pdb, res_num,alter,"NE","CZ","NH2")
return pdb, alerts
##############################################################
## 1 well-defined H
##############################################################
def treat_TRP(pdb,res_num, alerts):
# ad hydrogen to standard psoitions at TRP
alter, alerts = find_alter(pdb,res_num,alerts)
pdb = ad_NH(pdb,res_num,alter)
pdb = ad_CH_R3(pdb, res_num,alter,"C","N","CA","CB")
pdb = ad_CH2(pdb, res_num,alter,"CA","CG","CB")
pdb = ad_CH_ar(pdb, res_num,alter,"CG","NE1","CD1")
pdb = ad_NH_s(pdb, res_num,alter,"CE2","CD1","NE1")
pdb = ad_CH_ar(pdb, res_num,alter,"CZ3","CD2","CE3")
pdb = ad_CH_ar(pdb, res_num,alter,"CE3","CH2","CZ3")
pdb = ad_CH_ar(pdb, res_num,alter,"CZ3","CZ2","CH2")
pdb = ad_CH_ar(pdb, res_num,alter,"CE2","CH2","CZ2")
return pdb, alerts
##############################################################
## Flip possible
##############################################################
def treat_ASN(pdb,res_num,map, alerts):
# ad hydrogen to standard psoitions at ASN and checks if O and N are
# fliped
alter, alerts = find_alter(pdb,res_num,alerts)
# print("Alter",alter)
if map_ex==True:
pdb,alerts = check_flip(pdb,res_num,alter,map,"ND2","OD1",alerts)
pdb = ad_NH(pdb,res_num,alter)
pdb = ad_CH_R3(pdb, res_num,alter,"C","N","CA","CB")
pdb = ad_CH2(pdb, res_num, alter,"CA","CG","CB")
pdb = ad_NH2(pdb, res_num,alter,"CB","CG","ND2")
return pdb, alerts
def treat_GLN(pdb,res_num,map, alerts):
# ad hydrogen to standard psoitions at GLN
# print("GLN!",pdb[res_num][0])
alter, alerts = find_alter(pdb,res_num,alerts)
if map_ex==True:
pdb,alerts = check_flip(pdb,res_num,alter,map,"NE2","OE1",alerts)
pdb = ad_NH(pdb,res_num,alter)
pdb = ad_CH_R3(pdb, res_num,alter,"C","N","CA","CB")
pdb = ad_CH2(pdb, res_num,alter,"CA","CG","CB")
pdb = ad_CH2(pdb, res_num,alter,"CD","CB","CG")
pdb = ad_NH2(pdb, res_num,alter,"CG","CD","NE2")
return pdb, alerts
#rotines for flip in ANS and GLN
def check_flip(pdb,res_num,alter,map,N,O,alerts):
#checks if HIS is fliped based on the map
#for this the map is integratet around CD2, CE1 and ND1, NE2. If the sum of the integrated values for carbon are smaller than for nitrogen the HIS is getting flipped.
for alt in range(len(alter)):
com=ceck_bond_atoms_2(pdb,res_num,alter[alt],N,O)
if com==False:
continue
N_coord=anam_to_coord(pdb,res_num,alter[alt],N)
O_coord=anam_to_coord(pdb,res_num,alter[alt],O)
int_N=int_around_point(N_coord,map,def_r_int("N"),mesh)
int_O=int_around_point(O_coord,map,def_r_int("N"),mesh)
# print("sum_C", sum_C)
# print("sum_N", sum_N)
if int_O > int_N:
# print(alter[alt])
# print(pdb[res_num][0])
# print(pdb[res_num][1])
# print("N and C are getting fliped for" ,pdb[res_num][0][5],pdb[res_num][0][4],pdb[res_num][0][6])
pdb = del_NH2(pdb,res_num, alter[alt],N_coord)
string = str(pdb[res_num][0][4])+" "+str(pdb[res_num][0][6])+" "+str(pdb[res_num][0][5])+" got flipped"
alerts[4].append(string)
for i in range(len(pdb[res_num])):
if pdb[res_num][i][3]==alter[alt]:
if pdb[res_num][i][2]==N:
# print("¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤")
# print(pdb[res_num][i][8],pdb[res_num][i][9],pdb[res_num][i][10])
pdb[res_num][i][8]=O_coord[0]
pdb[res_num][i][9]=O_coord[1]
pdb[res_num][i][10]=O_coord[2]
# print(pdb[res_num][i][8],pdb[res_num][i][9],pdb[res_num][i][10])
# print("##################")
if pdb[res_num][i][2]==O:
pdb[res_num][i][8]=N_coord[0]
pdb[res_num][i][9]=N_coord[1]
pdb[res_num][i][10]=N_coord[2]
# print(pdb[res_num][i])
return pdb, alerts
def ceck_bond_atoms_2(pdb,res_num,alt, A1, A2):
## cecks if all needet atoms to ad a D are existing in residue
com = True
res = []
for i in range(len(pdb[res_num])):
# print(len(list(pdb[res_num][i][3])))
if pdb[res_num][i][3]==alt or\
len(list(pdb[res_num][i][3]))==0:
# print(pdb[res_num][i][3],len(list(pdb[res_num][i][3])))
res.append(pdb[res_num][i][2])
elif len(list(alt))==0:
if pdb[res_num][i][3]=="A":
res.append(pdb[res_num][i][2])
# print("A1, A2, A3",A1, A2, A3)
# print("res",res)
if A1 not in res or A2 not in res:
com=False
return com
def del_NH2(pdb,res_num,alt,A_coord):
##find CH bond du A3
# H_coord=[]
ele1="N"
atom1=A_coord
cov1=ele_to_cov_rad(ele1)
for i in range(len(pdb[res_num])):
if pdb[res_num][i][3]==alt or len(list(pdb[res_num][i][3]))==0:
atom2 =np.array([pdb[res_num][i][8],pdb[res_num][i][9],pdb[res_num][i][10]])
ele2 = pdb[res_num][i][14]
cov2=ele_to_cov_rad(ele2)
d = CDist2(atom1,atom2)
dmax= cov1+cov2+0.4
if 0.5 <= d <= dmax:
if pdb[res_num][i][14] == "H" or pdb[res_num][i][14]=="D":
del pdb[res_num][i]
return pdb
##############################################################
## No on charged, 4 posible position on neutral
##############################################################
def treat_ASP(pdb,res_num,map, alerts):
# ad hydrogen to standard psoitions at ASP and chek if it is
# protonatet or unprotonatet based on the mp
alter, alerts = find_alter(pdb,res_num,alerts)
pdb = ad_NH(pdb,res_num,alter)
pdb = ad_CH_R3(pdb, res_num,alter,"C","N","CA","CB")
pdb = ad_CH2(pdb, res_num,alter,"CA","CG","CB")
if map_ex==True:
av_CH, std_CH= int_CH(pdb,res_num,alter,map,mesh)
pdb,alerts = ad_CO2H_map(pdb, res_num,alter,map,"OD1", "CG","OD2",av_CH, std_CH, alerts)
return pdb, alerts
def treat_GLU(pdb,res_num,map, alerts):
# ad hydrogen to standard psoitions at GLU
alter, alerts = find_alter(pdb,res_num,alerts)
pdb = ad_NH(pdb,res_num,alter)
pdb = ad_CH_R3(pdb, res_num,alter,"C","N","CA","CB")
pdb = ad_CH2(pdb, res_num,alter,"CA","CG","CB")
pdb = ad_CH2(pdb, res_num,alter,"CD","CB","CG")
if map_ex==True:
av_CH, std_CH= int_CH(pdb,res_num,alter,map,mesh)
pdb,alerts=ad_CO2H_map(pdb,res_num,alter,map,"OE1","CD","OE2",av_CH, std_CH,alerts)
return pdb, alerts
def ad_CO2H_map(pdb, res_num,alter,map, A1, A2, A3,av_CH,std_CH,alerts):
# chekc if CO2- group is protonatet
for alt in range(len(alter)):
com = check(pdb,res_num, alter[alt],A1, A2, A3, 2)
if com == False:
return pdb
r = 0.997
Ad_l=[106.2,114.9]
Dd_l=[0,180]
A1xyz = anam_to_coord(pdb,res_num,alter[alt],A1)
A2xyz = anam_to_coord(pdb,res_num,alter[alt],A2)
A3xyz = anam_to_coord(pdb,res_num,alter[alt],A3)
H_coords=[]
for k in range(len(Dd_l)):
H_coords.append([ZtoXYZ(A1xyz,A2xyz,A3xyz,r,Ad_l[k],Dd_l[k]),A3])
H_coords.append([ZtoXYZ(A3xyz,A2xyz,A1xyz,r,Ad_l[k],Dd_l[k]),A1])
r_int=def_r_int("H")
int_H_l=[]
for k in range(len(H_coords)):
int_H_l.append([H_coords[k][0],int_around_point(H_coords[k][0],map,r_int,mesh),H_coords[k][1]])
test_H=[0,0,0]
# print("int_H_l",int_H_l)
for i in range(len(int_H_l)):
if int_H_l[i][1]> test_H[1]:
test_H[0]=int_H_l[i][0]
test_H[1]=int_H_l[i][1]
test_H[2]=int_H_l[i][2]
# print("av_CH std_CH test_H[1]",av_CH, std_CH, test_H[1])
if (av_CH -1*std_CH) <= test_H[1] and test_H[1]> 0:
# print("test_H[2]",test_H[1],av_CH,std_CH)
nam=list(test_H[2])
if len(nam)<=2:
name=nam[1]
else:
name = nam[1]#+nam[2]
name1 = label_H+name+"2"
# name1 ="H"+test_H[2]
# print("!!!!!!!!!!!!!!!!!!!!!!!!!!!!",nam[2],"######################################")
pdb = add_to_pdb(pdb,res_num,alter[alt], test_H[2], test_H[0], name1,test_H[1])
#
if nam[2]=="1":
for i in range(len(pdb[res_num])):
if pdb[res_num][i][2]==A1 and pdb[res_num][i][3]==alter[alt]:
O1=i
if pdb[res_num][i][2]==A3 and pdb[res_num][i][3]==alter[alt]:
O2=i
pdb[res_num][O1][2]=A3
pdb[res_num][O2][2]=A1
# print(name1 ,"is addet to ",test_H[2],res_num)
string=str(name1)+" is addet to "+str(pdb[res_num][0][4])+" "+str(pdb[res_num][0][6])+" "+str(pdb[res_num][0][5])
alerts[2].append(string)
# else:
# string=str(pdb[res_num][0][4])+" "+str(pdb[res_num][0][6])+" "+str(pdb[res_num][0][5])+" is charged"
# alerts[2].append(string)
return pdb, alerts
##############################################################
## Hid, Hie, Hip and flip
##############################################################
def treat_HIS(pdb,res_num,map, alerts):
# ad hydrogen to standard psoitions at HIS
alter, alerts = find_alter(pdb,res_num,alerts)
if map_ex==True:
pdb,alerts =check_flip_HIS(pdb,res_num,alter,map,alerts)
proto = pdb[res_num][0][4]
pdb = ad_NH(pdb,res_num,alter)
pdb = ad_CH_R3(pdb, res_num,alter,"C","N","CA","CB")
pdb = ad_CH2(pdb, res_num,alter,"CA","CG","CB")
pdb = ad_CH_ar(pdb, res_num,alter,"ND1","NE2","CE1")
pdb = ad_CH_ar(pdb, res_num,alter,"CG","NE2","CD2")
if map_ex==True:
av_CH,sig_CH= int_CH(pdb,res_num,alter,map,mesh)
pdb,alerts = ad_NH_s_map(pdb, res_num,alter,map,"CE1","CD2","NE2",av_CH,sig_CH,alerts)
pdb,alerts = ad_NH_s_map(pdb, res_num,alter,map,"CE1","CG","ND1",av_CH,sig_CH,alerts)
else:
if proto == "HIS" or\
proto == "HIE" or proto == "HIP":
pdb = ad_NH_s(pdb, res_num,alter,"CE1","CD2","NE2")
if proto == "HID" or proto == "HIP":
pdb = ad_NH_s(pdb, res_num,alter,"CE1","CG","ND1")
return pdb, alerts
##############################################################
## 3 H on a ring; may be deprotonated
##############################################################
def treat_LYS(pdb,res_num, map, alerts):
# ad hydrogen to standard psoitions at LYS
alter, alerts = find_alter(pdb,res_num,alerts)
pdb = ad_NH(pdb,res_num,alter)
pdb = ad_CH_R3(pdb, res_num,alter,"C","N","CA","CB")
pdb = ad_CH2(pdb, res_num,alter,"CA","CG","CB")
pdb = ad_CH2(pdb, res_num,alter,"CD","CB","CG")
pdb = ad_CH2(pdb, res_num,alter,"CE","CG","CD")
pdb = ad_CH2(pdb, res_num,alter,"NZ","CD","CE")
if map_ex==True:
av_CH,sig_CH= int_CH(pdb,res_num,alter,map,mesh)
pdb = ad_NH3_map(pdb,res_num,alter,"CD","CE","NZ",map,av_CH,sig_CH)
else:
pdb = ad_NH3(pdb, res_num,alter,"CD","CE","NZ")
return pdb, alerts
def treat_n_nerm(pdb,map,alerts):
## protonates NH3 as Nterminal
res_num=0
alter, alerts = find_alter(pdb,res_num,alerts)
if map_ex==True:
pdb = ad_NH3_map_ter(pdb,res_num,alter,"C","CA","N",map)
else:
pdb = ad_NH3(pdb, res_num,alter,"C","CA","N")
return pdb, alerts
##############################################################
## 1 H on a ring
##############################################################
def treat_SER(pdb,res_num,map, alerts):
# ad hydrogen to standard psoitions at SER
alter, alerts = find_alter(pdb,res_num,alerts)
pdb = ad_NH(pdb,res_num,alter)
pdb = ad_CH_R3(pdb, res_num,alter,"C","N","CA","CB")
pdb = ad_CH2(pdb, res_num,alter,"CA","OG","CB")
if map_ex==True:
pdb, alerts = ad_OH_map(pdb, res_num,alter,"CA","CB","OG",map, alerts)
else:
pdb = ad_OH(pdb, res_num,alter,"CA","CB","OG")
return pdb, alerts
def treat_THR(pdb,res_num,map, alerts):
# ad hydrogen to standard psoitions at THR
alter, alerts = find_alter(pdb,res_num,alerts)
pdb = ad_NH(pdb,res_num,alter)
pdb = ad_CH_R3(pdb, res_num,alter,"C","N","CA","CB")
pdb = ad_CH_R3(pdb, res_num,alter,"CG2","OG1","CB","CA")
pdb = ad_CH3(pdb, res_num,alter,"CA","CB","CG2")
if map_ex==True:
pdb, alerts = ad_OH_map(pdb, res_num,alter,"CA","CB","OG1",map, alerts)
else:
pdb = ad_OH(pdb, res_num,alter,"CA","CB","OG1")
return pdb, alerts
def treat_TYR(pdb,res_num,map, alerts):
# ad hydrogen to standard psoitions at TYR
alter, alerts = find_alter(pdb,res_num,alerts)
pdb = ad_NH(pdb,res_num,alter)
pdb = ad_CH_R3(pdb, res_num,alter,"C","N","CA","CB")
pdb = ad_CH2(pdb, res_num, alter,"CA","CG","CB")
pdb = ad_CH_ar(pdb, res_num,alter,"CE2","CG","CD2")
pdb = ad_CH_ar(pdb, res_num,alter,"CZ","CD2","CE2")
pdb = ad_CH_ar(pdb, res_num,alter,"CD1","CZ","CE1")
pdb = ad_CH_ar(pdb, res_num,alter,"CG","CE1","CD1")
if map_ex==True:
pdb, alerts = ad_OH_map(pdb, res_num,alter,"CE1","CZ","OH",map, alerts)
else:
pdb = ad_OH(pdb, res_num,alter,"CE1","CZ","OH")
return pdb, alerts
##############################################################
## 1 H on a ring; may be deprotonated
##############################################################
def treat_CYS(pdb,res_num, map, alerts):
# ad hydrogen to standard psoitions at CYS
alter, alerts = find_alter(pdb,res_num,alerts)
pdb = ad_NH(pdb,res_num,alter)
pdb = ad_CH_R3(pdb, res_num,alter,"C","N","CA","CB")
pdb = ad_CH2(pdb, res_num,alter,"CA","SG","CB")
if map_ex==True:
pdb, alerts = ad_SH_map(pdb, res_num,alter,"CA","CB","SG",map,alerts)
else:
pdb = ad_SH(pdb, res_num,alter,"CA","CB","SG")
return pdb, alerts
##############################################################
## 2 H on a sphere
##############################################################
def treat_WAT(pdb,res_num,map, alerts):
# ad hydrogen to standard psoitions at WAT
if map_ex==True and wat_ex==True:
alter, alerts = find_alter(pdb,res_num,alerts)
# print("alter",alter)
sphere=def_sphere(0.98, 20)
r_int=def_r_int("H")
coord_O=[pdb[res_num][0][8],pdb[res_num][0][9],pdb[res_num][0][10]]
# print(pdb[res_num])
# print(coord_O)
int_sphere_l=int_sphere(sphere,map,coord_O,r_int)
best_fit=find_best_fit(int_sphere_l,coord_O)
if best_fit[2]<= best_fit[0][2]:
print("integratet value is to small hydrogens are not aded")
return pdb , alerts
print("best_fit","sum",best_fit[2],"H1",best_fit[0][1],"H2",best_fit[1][1],"O",best_fit[0][2])
pdb = add_to_pdb(pdb,res_num,alter[0], "O", best_fit[0][0], "H2",best_fit[1][1])
pdb = add_to_pdb(pdb,res_num,alter[0], "O", best_fit[1][0], "H1",best_fit[0][1])
# for i in range(len(pdb[res_num])):
# print("water atom",i,pdb[res_num][i])
return pdb, alerts
def find_best_fit(l_int, coord_O):
# finds atom pair with best fit in 104,5 +- 5 degree
pairs=[]
# bes_fit=[]
g_opt=104.5
g_sig=10
int_sum=-1000
for i in range(len(l_int)):
v1=twoP_to_vec(coord_O,l_int[i][0])
for k in range(i,len(l_int)):
v2=twoP_to_vec(coord_O,l_int[k][0])
ang=C2Angle(v1,v2)
if g_opt-g_sig <= ang <= g_opt+g_sig:
pairs.append([l_int[i],l_int[k],l_int[i][1]+l_int[k][1]])
print("len(pairs)",len(pairs))
for i in range(len(pairs)):
if int_sum < pairs[i][2]:
int_sum=pairs[i][2]
best_fit=pairs[i]
return best_fit
def int_sphere(sphere,map,coord_O,r_int):
#integrates for all points in list sphere on map
int_sphere_l=[]
# r_int_O=ele_to_cov_rad("O")
int_O=int_around_point(coord_O,map,r_int, mesh)
for i in range(len(sphere)):
H=[sphere[i][0]+coord_O[0],sphere[i][1]+coord_O[1],sphere[i][2]+coord_O[2]]
int_H=int_around_point(H,map,r_int, mesh)
int_sphere_l.append([H,int_H,int_O])
return int_sphere_l
def def_sphere(r,deg):
#defines sphere wit radius r around 0,0,0
sphere=[]
for teth in range(0,180,deg):
for phi in range(0,360,deg):
x=r*np.sin(np.radians(teth))*np.cos(np.radians(phi))
y=r*np.sin(np.radians(teth))*np.sin(np.radians(phi))
z=r*np.cos(np.radians(teth))
sphere.append([x,y,z])
print("len(sphere)",len(sphere))
return sphere
## rotiens to work on residues
def find_alter(pdb,res_num,alerts):
## finds alternative conformations in residue
alter=[]
for i in range(len(pdb[res_num])):
alter.append(pdb[res_num][i][3])
alter=list(dict.fromkeys(alter))
if len(alter)>=2:
string=str(pdb[res_num][0][4])+" "+str(pdb[res_num][0][6])+" "+str(pdb[res_num][0][5])+" is disordert"
alerts[6].append(string)
# print("alter",alter)
return alter, alerts
def ad_NH(pdb,res_num,alter):
## ad HN if a naiboring resiue is existing
# print("ad_NH_print alter",alter,pdb[res_num][0][6])
for alt in range(len(alter)):
# res=pdb[res_num][0][6]
## print("RES",res)
# for i in range(len(pdb)):
# for k in range(len(pdb[res_num])):
# if pdb[i][k][6]== res-1 and pdb[i][k][2].strip()=="C" and pdb[res_num][0][5]==pdb[i][k][5]:
# print("¤¤¤¤¤¤¤¤¤¤¤¤¤¤1")
# print(pdb[res_num][0])
com = ceck_bond_atoms_N(pdb,res_num,res_num-1,alter[alt],"N","CA", "C")
# print("com",com)
# print("¤¤¤¤¤¤¤¤¤¤¤¤¤¤2")
# if len(alter)>1:
# print("alter[alt],com",alter[alt],com)
if com == False:
print("missing atoms to locate NH")
return pdb
# print(pdb[res_num])
# print("alter,res:num", alter[alt],res_num)
# nr_b=nr_bonds(pdb,res_num,alter[alt],"N")
# ext_H=False
# print("alter",alter)
ext_H=check_extH_N(pdb,res_num,"N",alter[alt])
if ext_H == True:
print("NH not, H is already existing!!!!!!!!!!!!!!!!")
# print("at residue",pdb[res_num][0][6])
# if alter[alt]=="B":
# print("BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB")
# print("Res_num",pdb[i][k][6])
return pdb
int_H=0
Nxyz = anam_to_coord(pdb,res_num,alter[alt],"N")
# print(pdb[res_num])
CAxyz = anam_to_coord(pdb,res_num,alter[alt],"CA")
Cxyz = anam_to_coord(pdb,res_num-1,alter[alt],"C")
r=1.016
Ad=117.7
Dd=180
# if alter[alt]=="B":
# print("BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB")
# print("Res_num",pdb[i][k][6])
# if alter[alt]=="A":
# print("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA")
# print("res:num",pdb[i][k][6])
H = ZtoXYZ(Cxyz,CAxyz,Nxyz,r,Ad,Dd)
if map_ex==True:
int_H=int_around_point(H,map,def_r_int("H"), mesh)
pdb = add_to_pdb(pdb,res_num,alter[alt],"N",H,label_H,int_H)
return pdb
def check_extH_N(pdb,res_num,atom,alt):
# cheks if H of NH is existing
ext=False
atom1, ele1 =anam_to_coord_ele(pdb,res_num,alt,atom)
cov1=ele_to_cov_rad(ele1)
# print("atom1, ele1",atom1, ele1,alt)
# print("find NH ex", pdb[res_num][0])
for i in range(len(pdb[res_num])):
if pdb[res_num][i][3]==alt:# or len(list(pdb[res_num][i][3]))==0:
# print(alt)
# print("test alt",alt)
if pdb[res_num][i][14]=="H" or pdb[res_num][i][14]=="D":
atom2 =np.array([pdb[res_num][i][8],pdb[res_num][i][9],pdb[res_num][i][10]])
ele2 = pdb[res_num][i][14]
cov2=ele_to_cov_rad(ele2)
d = CDist2(atom1,atom2)
dmax= cov1+cov2+0.4
if 0.5 <= d <= dmax:
ext=True
# print("ATOM2", pdb[res_num][i])
return ext
def ad_CA(pdb,res_num,alter):
#add HCA at standard positons
for alt in range(len(alter)):
com= check(pdb,res_num,alter[alt],"C","N","CA", 3)
print("ALTER",alter)
print("len(alter",len(alter))
if len(alter)>1:
print("alter,com,QQQQQQQQQQQQ", alter,com)
if com == False:
return pdb
if len(alter)>1:
print("QQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ")
CAxyz = anam_to_coord(pdb,res_num,alter[alt],"CA")
Nxyz = anam_to_coord(pdb,res_num,alter[alt],"N")
Cxyz = anam_to_coord(pdb,res_num,alter[alt],"C")
r = 1.095
Ad = 109
Dd= -121.5
HCA = ZtoXYZ(Nxyz,Cxyz,CAxyz,r,Ad,Dd)
int_H=0
if map_ex==True:
int_H=int_around_point(HCA,map,def_r_int("H"), mesh)
pdb = add_to_pdb(pdb,res_num,alter[alt],"CA",HCA,"HA",int_H)
return pdb
def ad_CH3(pdb, res_num,alter, A1, A2, A3):
# ad 3H as CH3 group to A3
for alt in range(len(alter)):
# print("alter[alt]",alter[alt])