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gen_syst1.py
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gen_syst1.py
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#!/usr/bin/env python3
#######!/software/sse/easybuild/prefix/software/Anaconda3/5.3.0-extras-nsc1/bin-wrapped/python
# -*- coding: utf-8 -*-
# run with protonation: gen_syst1.py qm.tex pdb P
# run without protonation: gen_syst1.py qm.tex pdb
## program to automatise teh generation
#of the syst1 file for quantum refinment
import time
## set timer
time_start = time.time()
import sys
##load mandatory modules
import numpy as np
#import numpy as np
print(sys.argv)
if len(sys.argv)>=2:
qm=sys.argv[1]
print("read from line 1")
else:
qm="qm.txt"
if len(sys.argv)>=3:
input_pdb=sys.argv[2]
print("read from line 2")
else:
input_pdb="comqum.pdb"
f_p=False
if len(sys.argv)>=4:
pq=sys.argv[3]
print(pq)
if pq == "P" or pq == "p":
f_p=True
print("protonation is on")
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 read_qm(qm):
## read in atoms or resiodues for the qm system
## inly actueal atoms trancuation ateoms are definem on it own
## ATOM in PDB formart
## RESI only one number
## ANAM atom name with chain and residue
## ANUM atom number
print(" read qm file")
read_qm_f = open(qm, "r")
qm_atom = []
qm_resi = []
qm_anam = []
qm_anum = []
qm_rnum = []
for line in read_qm_f:
idef = line[0:6].strip()
idef2= line.split()
if idef=="ATOM" or idef=="HETATM":
l_pdb=[]
a = line[0:6]
a_num = int(line[6:11].strip())
a_name = line[12:16]
alter = line[16]
res_name= line[17:20]
chain = line[21]
res_num = int(line[22:26].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)
qm_atom.append(l_pdb)
if len(idef2)>=1:
if idef=="RESI" or idef2[0]=="RESI":
s_line=line.split()
l_resi=[]
l_resi.append(s_line[1])
l_resi.append(int(s_line[2]))
qm_resi.append(l_resi)
if idef=="ANAM" or idef2[0]=="ANAM":
s_line=line.split()
l_resi=[]
l_resi.append(s_line[1])
l_resi.append(int(s_line[2]))
if len(s_line)<4:
s_line.append(" ")
l_resi.append((s_line[3]))
qm_anam.append(l_resi)
if idef=="ANUM" or idef2[0]=="ANUM":
s_line=line.split()
l_resi=[]
l_resi.append(int(s_line[1]))
qm_anum.append(l_resi)
if idef=="RNUM" or idef2[0]=="RNUM":
s_line=line.split()
l_resi=[]
l_resi.append(int(s_line[1]))
l_resi.append(int(s_line[2]))
qm_rnum.append(l_resi)
print("close file:", qm)
return qm_atom, qm_resi, qm_anam, qm_anum, qm_rnum
def assign_atm_nr(qm_atom, qm_resi, qm_anum, qm_anam, qm_rnum ,pdb):
atm_nr=[]
atm_qm=[]
if len(qm_atom)>0:
for i in range(len(qm_atom)):
res_num= qm_atom[i][6]
chain = qm_atom[i][5].strip()
a_name = qm_atom[i][2].strip()
for j in range(len(pdb)):
for k in range(len(pdb[j])):
res_num_pdb = pdb[j][k][6]
chain_pdb = pdb[j][k][5].strip()
a_name_pdb = pdb[j][k][2].strip()
if res_num == res_num_pdb and chain == chain_pdb and a_name == a_name_pdb:
atm_nr.append(pdb[j][k][1])
atm_qm.append(pdb[j][k])
if len(qm_resi)>0:
for i in range(len(qm_resi)):
res_num= qm_resi[i][1]
chain = qm_resi[i][0].strip()
for j in range(len(pdb)):
for k in range(len(pdb[j])):
res_num_pdb = pdb[j][k][6]
chain_pdb = pdb[j][k][5].strip()
# print(res_num, res_num_pdb)
if res_num == res_num_pdb and chain == chain_pdb:
# print(work_pdb[j][1])
atm_nr.append(pdb[j][k][1])
atm_qm.append(pdb[j][k])
if len(qm_anum)>0:
for i in range(len(qm_anum)):
a_num=qm_anum[i][0]
for j in range(len(pdb)):
for k in range(len(pdb[j])):
a_num_pdb=pdb[j][k][1]
if a_num == a_num_pdb:
atm_nr.append(pdb[j][k][1])
atm_qm.append(pdb[j][k])
if len(qm_anam)>0:
for i in range(len(qm_anam)):
res_num= qm_anam[i][1]
chain = qm_anam[i][2].strip()
a_name = qm_anam[i][0].strip()
for j in range(len(pdb)):
for k in range(len(pdb[j])):
res_num_pdb = pdb[j][k][6]
chain_pdb = pdb[j][k][5].strip()
a_name_pdb = pdb[j][k][2].strip()
if res_num == res_num_pdb and chain == chain_pdb and a_name == a_name_pdb:
atm_nr.append(pdb[j][k][1])
atm_qm.append(pdb[j][k])
if len(qm_rnum)>0:
for i in range(len(qm_rnum)):
low = qm_rnum[i][0]
up = qm_rnum[i][1]
# print(low,up)
for j in range(len(pdb)):
a_num_pdb=pdb[j][k][1]
# print(a_num_pdb, low,up)
if low <= a_num_pdb <= up:
atm_nr.append(pdb[j][k][1])
atm_qm.append(pdb[j][k])
atm_nr = list(set(atm_nr))
atm_nr= sorted(atm_nr)
atom_qm=[]
# print(atm_nr)
# print(atm_qm)
for i in range(len(atm_nr)):
for j in range(len(atm_qm)):
# print(atm_qm[j])
if atm_nr[i]== atm_qm[j][1]:
atom_qm.append(atm_qm[j])
break
return atm_nr, atom_qm
def len3dvec(vec):
## calculates lengh of a 3D vecor
## input as list
a = np.sqrt(vec[0]**2 + vec[1]**2 + vec[2]**2)
return a
def find_truncation(atm_nr, atom_qm, pdb):
## serche for trancuation atoms in radius aof 1.8 A around atoms
trunc_nr = []
trunc_atm= []
print(atom_qm)
for i in range(len(atom_qm)):
vec1=[0,0,0]
vec1[0] = atom_qm[i][8]
vec1[1] = atom_qm[i][9]
vec1[2] = atom_qm[i][10]
for j in range(len(pdb)):
for k in range(len(pdb[j])):
vec2=[0,0,0]
vec2[0] = pdb[j][k][8]
vec2[1] = pdb[j][k][9]
vec2[2] = pdb[j][k][10]
vec=[0,0,0]
for h in range(len(vec)):
vec[h]=vec1[h]-vec2[h]
lenvec= len3dvec(vec)
if 0.5 < lenvec <= 1.8:
trunc_nr.append(pdb[j][k][1])
trunc_atm.append(pdb[j][k])
# print("trunc_nr",trunc_nr)
trunc_nr=sorted(list(set(trunc_nr)))
# print(len(trunc_nr),"trunc_nr2",trunc_nr)
# print("atm_nr",atm_nr)
trunc_nr = list(set(trunc_nr)-set(atm_nr))
trunc_atom=[]
# print("trunc_atm",trunc_atm)
# print("trunc_nr",trunc_nr)
for i in range(len(trunc_nr)):
for j in range(len(trunc_atm)):
if trunc_nr[i]==trunc_atm[j][1]:
trunc_atom.append(trunc_atm[j])
break
return trunc_nr, trunc_atom
def sum_list(atm_nr, atom_qm, trunc_nr, trunc_atm):
## define list of QM atom and truncation atoms
f_trunc=[]
f_all= atm_nr + trunc_nr
for i in range(len(trunc_atm)):
if trunc_atm[i][14].strip() != "H":
f_trunc.append(trunc_atm[i][1])
# if trunc_atm[i][2].strip() != "H":
# f_trunc.append(trunc_atm[i][1])
f_all = sorted(list(set(f_all)))
f_trunc=sorted(list(set(f_trunc)))
f_qm=list(set(f_all)-set(f_trunc))
f_qm = sorted(list(set(f_qm)))
return f_all, f_qm, f_trunc
def write_syst1(f_all,f_trunc):
syst1=open("syst1","w")
syst1.write("coment \n")
f_comp=compress_list(f_all)
for i in range(len(f_comp)):
if len(f_comp[i])==1:
string=str(f_comp[i][0])+" \n"
if len(f_comp[i])==2:
string = str(f_comp[i][0])+"-"+str(f_comp[i][1])+" \n"
syst1.write(string)
syst1.write(" \n")
for i in range(len(f_trunc)):
string=str(f_trunc[i])+" \n"
syst1.write(string)
syst1.write(" \n \n \n")
syst1.close()
print("syst1 file is ready")
def compress_list(list_in):
list_out=[]
# print("len(list_in)",len(list_in))
second = False
for i in range(len(list_in)):
# print(second, i, )
if i == 0:
pm = -1
pp = list_in[i+1]-1
p = list_in[i]
if 0 < i < len(list_in)-1:
pm = list_in[i-1]+1
pp = list_in[i+1]-1
p = list_in[i]
if i == len(list_in)-1:
pm = list_in[i-1]+1
pp = -1
p = list_in[i]
# print(i, list_in[i],p,pm,pp, second)
if second == False:
if p != pm and p == pp:
list_out.append([list_in[i]])
second = True
if p != pm and p != pp:
list_out.append([list_in[i]])
second = False
continue
if second == True :
if p == pm and p == pp :
# print("###############")
continue
if p == pm and p != pp :
# print("!!!!!!!!!!!")
list_out[len(list_out)-1].append(list_in[i])
second = False
if p != pm and p != pp :
# print("¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤")
list_out.append([list_in[i]])
second = False
# print("len(list_out)",len(list_out))
return list_out
def write_restart_anam(f_qm,work_pdb):
## write input to restart this programm
r_anam=open("restart_anam","w")
w_pdb=open("pdb_syst1","w")
# w_label=open("label_vis.sh","w")
atm_nr=0
for i in range(len(f_qm)):
for j in range(len(work_pdb)):
if f_qm[i]==work_pdb[j][1]:
# print(work_pdb[j])
string="ANAM "+ work_pdb[j][2]+" "+str(work_pdb[j][6])+" " + work_pdb[j][5] + "\n"
s_pdb, atm_nr= write_pdbi_line(work_pdb[j], atm_nr)
# s_label=prep_vis(work_pdb[j])
r_anam.write(string)
w_pdb.write(s_pdb)
# w_label.write(s_label)
def write_rename(f_all,f_trunc,work_pdb):
w_label=open("label_vis.sh","w")
for i in range(len(f_all)):
for j in range(len(work_pdb)):
if f_all[i]==work_pdb[j][1]:
ele=work_pdb[j][14]
if f_all[i] in f_trunc:
ele="H"
s_label=prep_vis(work_pdb[j],ele)
w_label.write(s_label)
def prep_vis(pdb,ele):
#preper bash file for the corect labeling of the pdb file from mimic
#[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]
res_nam= pdb[4]
res_num= pdb[6]
chain= pdb[5]
string="sed -i \"0,/"
string = string + str('{:2}'.format(ele))
# string = string + " ??? 1/s//"
string = string + " ??? 1/s/"
string = string + str('{:2}'.format(ele))
string = string + " ??? 1/"
string = string + str('{:2}'.format(ele))
string = string + " "
string = string + str(res_nam) + " "
string = string + str(chain)#+ " "
string = string + str('{:4}'.format(res_num))
string = string + "/g\" pdb"
string = string + "\n"
return string
def write_pdbi_line(pdb, atm_nr):
## wite out PDB file
atm_nr = atm_nr + 1
string = str('{:6}'.format(pdb[0]))
string = string + str('{:5.0f}'.format(atm_nr))
string = string + " "
string = string + str('{:3s}'.format(str(pdb[2])))
string = string + str('{:1}'.format(pdb[3]))
string = string + str('{:3}'.format(pdb[4]))
string = string + str('{:>2}'.format(pdb[5]))
string = string + str('{:4}'.format(pdb[6]))
string = string + str('{:1}'.format(pdb[7]))
string = string + " "
string = string + str('{:8.3f}'.format(pdb[8]))
string = string + str('{:8.3f}'.format(pdb[9]))
string = string + str('{:8.3f}'.format(pdb[10]))
string = string + str('{:6.2f}'.format(pdb[11]))
string = string + str('{:6.2f}'.format(pdb[12]))
string = string + str('{:>7}'.format(pdb[13]))
string = string + str('{:>5}'.format(pdb[14]))
string = string + "\n"
return string, atm_nr
def atm_to_res(pdb_read):
# sort pdb in residues
pdb=[]
pdb.append([pdb_read[0]])
for i in range(1,len(pdb_read)):
if pdb_read[i][6] != pdb_read[i-1][6]:
# print(len(pdb))
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 proto_qm(pdb,atom_qm,f_p):
# protonates qm system if protons are not existing
# print("protonate syst1")
if f_p== False:
return pdb
print("protonate syst1")
for i in range(len(atom_qm)):
# print("protonate syst1")
# print(atom_qm[i])
xyz=[atom_qm[i][8],atom_qm[i][9],atom_qm[i][10]]
# print(xyz)
ele=atom_qm[i][14]
# print(ele)
# print(atom_qm[i])
if ele=="C":
pdb=prot_c(pdb,xyz,ele,atom_qm[i])
if ele=="N":
pdb=prot_n(pdb,xyz,ele,atom_qm[i])
if ele=="O":
pdb=prot_o(pdb,xyz,ele,atom_qm[i])
return pdb
def prot_n(pdb,xyz,ele,atom_qm):
## identyfy atom pype and protanes it
bond_atom=f_bond_atoms(pdb,atom_qm)
n_bonds=def_n_bonds(xyz,ele,bond_atom)
if 1.5< n_bonds <= 2.5 and len(bond_atom)==2:
pdb= ad_NH_s(pdb,bond_atom[0],bond_atom[1],atom_qm)
return pdb
if n_bonds==1 and len(bond_atom)==1:
pdb=ad_NH2(pdb,bond_atom[0],atom_qm)
return pdb
return pdb
def ad_NH2(pdb, A2, A3):
# ad 2H as NH2 group to A3
# print("¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤")
r = 1.012
Ad = 120
Dd = 180
Dd1 = 0
A1=find_A1(pdb,A3,A2)
A3xyz = [A3[8],A3[9],A3[10]]
A2xyz = [A2[8],A2[9],A2[10]]
A1xyz = [A1[8],A1[9],A1[10]]
adH1 = ZtoXYZ(A1xyz,A2xyz,A3xyz,r,Ad,Dd)
adH2 = ZtoXYZ(A1xyz,A2xyz,A3xyz,r,Ad,Dd1)
nam=list(A3[2])
name = str(nam[0])
name1 = "H1"+name
name2 = "H2"+name
pdb = add_to_pdb(pdb, A3, adH1, name1)
pdb = add_to_pdb(pdb, A3, adH2, name2)
return pdb
def ad_NH_s(pdb, A1, A2, A3):
# ad H as NH (SP2) group to A3
# print("atoms treatet")
# print("A3",A3)
# print("A2",A2)
# print("A1",A1)
r = 1.032
Ad = 120
Dd = 180
A3xyz = [A3[8],A3[9],A3[10]]
A2xyz = [A2[8],A2[9],A2[10]]
A1xyz = [A1[8],A1[9],A1[10]]
adH1 = ZtoXYZ(A1xyz,A2xyz,A3xyz,r,Ad,Dd)
nam=list(A3[2])
if len(nam)<=2:
name=nam[0]
else:
name = nam[1]+nam[2]
name1 = "H"+name
# print("name1",name1)
# print(adH1)
# print(A3)
# print("next step ad to pdb")
pdb = add_to_pdb(pdb, A3, adH1, name1)
# print("addet to pdb")
# print("&&&&&&&&&&&&&&&TEST&&&&&&&&&&&&")
return pdb
def prot_o(pdb,xyz,ele,atom_qm):
## identyfy atom pype and protanes it
bond_atom=f_bond_atoms(pdb,atom_qm)
n_bonds=def_n_bonds(xyz,ele,bond_atom)
# print("atom_qm",n_bonds,len(bond_atom), atom_qm)
# if atom_qm[4]=="HOH":
# print(bond_atom)
if n_bonds >= 2:
return pdb
if n_bonds==1 and len(bond_atom)==1:
pdb=ad_OH(pdb,bond_atom[0],atom_qm)
if n_bonds==0 and atom_qm[4]=="HOH":
pdb = ad_OH_water(pdb,atom_qm)
return pdb
def ad_OH_water(pdb,atom_qm):
## protonates water in direction of posible hydrogen bonds
print(atom_qm)
l_vdw=vdw()
l_h_bonds=find_h_bond(atom_qm,pdb,l_vdw)
# for i in range(len(l_h_bonds)):
# print("l_h_bonds",l_h_bonds[i])
if len(l_h_bonds)>=1:
# print("######################adH1#######################")
adH1=find_short_H(atom_qm,l_h_bonds)
if adH1[0]==0:
return pdb
name1 ="H1"+atom_qm[2]
pdb = add_to_pdb(pdb, atom_qm, adH1, name1)
if len(l_h_bonds)>=2:
# print("______________________________adH2_______________________")
adH2=find_short_H(atom_qm,l_h_bonds)
if adH2[0]==0:
return pdb
name2 ="H2"+atom_qm[2]
pdb = add_to_pdb(pdb, atom_qm, adH2, name2)
return pdb
def find_short_H(atom_qm,l_h_bonds):
## finds shortest istace in list of coordinates
P1=[atom_qm[8],atom_qm[9],atom_qm[10]]
d_min=1000000
for i in range(len(l_h_bonds)):
P2=[l_h_bonds[i][8],l_h_bonds[i][9],l_h_bonds[i][10]]
dist=CDist2(P1,P2)
if dist< d_min:
exist=f_ex_h(pdb, P1, P2)
# print("exist",exist)
# if exist == True:
# print("l_h_bonds[i]",l_h_bonds[i])
if exist == False:
d_min=dist
atom_min=l_h_bonds[i]
P_s=[atom_min[8],atom_min[9],atom_min[10]]
vec=twoP_to_vec(P1,P_s)
# print("len3Dvec(vec)",len3dvec(vec))
h_vec=resize_vec(vec,0.98)
# print("len3Dvec(h_vec)",len3dvec(h_vec))
coord=[P1[0]+h_vec[0],P1[1]+h_vec[1],P1[2]+h_vec[2]]
if coord == P1:
coord= [0]
return coord
def f_ex_h(pdb, A1, A2):
#check if hydrogen is positiond in 30 deree to OHO distance
## false if proton not existing true if existing
flag=False
dh=1.5
max_dist=0.6
for j in range(len(pdb)):
for k in range(len(pdb[j])):
if pdb[j][k][14]=="H" or pdb[j][k][14]=="D" :
p0=[pdb[j][k][8],pdb[j][k][9],pdb[j][k][10]]
d1= CDist2(A1,p0)
d2=CDist2(A2,p0)
ang=CAngle(A1,p0,A2)
if d1 <= dh or d2 <=dh:
if 120 <= ang <= 220:
# print("ATOM H",pdb[j][k])
# print("ang",ang)
flag=True
return flag
def d_p_to_line(p0,p1,p2):
## calculate distance between a point0 and a line between p1 and p2
if (p1[0] == p2[0] and p1[1] == p2[1] and p1[2] == p2[2]):
d=0
else:
if (p2[0]-p1[0] != 0):
t=-((p1[0]-p0[0])*(p2[0]-p1[0]))/((abs(p2[0]-p1[0]))**2)
elif (p2[1]-p1[2] != 0 ):
t=-((p1[1]-p0[1])*(p2[1]-p1[1]))/((abs(p2[1]-p1[1]))**2)
elif ( p2[2]-p1[2] != 0):
t=-((p1[2]-p0[2])*(p2[2]-p1[2]))/((abs(p2[2]-p1[2]))**2)
d2=((p1[0]-p0[0])+(p2[0]-p1[0])*t)**2+((p1[1]-p0[1])+(p2[1]-p1[1])*t)**2+((p1[2]-p0[2])+(p2[2]-p1[2])*t)**2
d=d2**(0.5)
return d
def resize_vec(vec,r):
vec=Normlz(vec)
# print("len3Dvec(vec)",len3dvec(vec))
new_vec=[vec[0]*r,vec[1]*r,vec[2]*r]
return new_vec
def find_h_bond(atom_qm,pdb,l_vdw):
OO=l_vdw[3][1]+l_vdw[3][1]
ON=l_vdw[3][1]+l_vdw[4][1]
h_bond=[]
O=[atom_qm[8],atom_qm[9],atom_qm[10]]
for j in range(len(pdb)):
for k in range(len(pdb[j])):
if pdb[j][k][14]=="O" or pdb[j][k][14]=="N" :
# print(pdb[k][6],l_water[i][j][6])
if pdb[j][k][6]!=atom_qm[6]:
acc=[pdb[j][k][8],pdb[j][k][9],pdb[j][k][10]]
dist=CDist2(O,acc)
if pdb[j][k][14]=="O":
if dist <= OO:
h_bond.append(pdb[j][k])
if pdb[j][k][14]=="N":
if dist <= ON:
h_bond.append(pdb[j][k])
return h_bond
def vdw():
l_vdw=[["H",1.20],["D",1.20],["C",1.70],["O",1.52],["N",1.55],["CL",1.75],["F",1.47],["BR",1.85]]
# h_vdw=1.20
# c_vdw=1.70
# o_vdw=1.52
# n_vdw=1.55
# s_vdw=1.80
# cl_vdw= 1.75
# f_vdw=1.47
# br_vdw= 1.85
return l_vdw
def ad_OH(pdb, A2, A3):
# ad H as OH group to A3
r = 0.978
Ad = 106
Dd = 180
A1=find_A1(pdb,A3,A2)
A3xyz = [A3[8],A3[9],A3[10]]
A2xyz = [A2[8],A2[9],A2[10]]
A1xyz = [A1[8],A1[9],A1[10]]
adH1 = ZtoXYZ(A1xyz,A2xyz,A3xyz,r,Ad,Dd)
name1 ="H"+A3[2]
pdb = add_to_pdb(pdb, A3, adH1, name1)
return pdb
def prot_c(pdb,xyz,ele,atom_qm):
## identyfy atom pype and protanes it
bond_atom=f_bond_atoms(pdb,atom_qm)
# print(bond_atom)
# print("xyz###",xyz)
n_bonds=def_n_bonds(xyz,ele,bond_atom)
res_num=atom_qm[6]
alter=atom_qm[3]
if n_bonds >= 4:
return pdb
if n_bonds==1:
pdb = ad_CH3(pdb,res_num,alter,bond_atom[0],atom_qm)
if n_bonds<=2.5 and len(bond_atom)==2:
pdb = ad_CH2(pdb, res_num, alter, bond_atom[0], bond_atom[1], atom_qm)
if 2.5< n_bonds<= 3.5 and len(bond_atom)==2:
pdb = ad_CH_ar(pdb, bond_atom[0], bond_atom[1], atom_qm)
if 2.5< n_bonds<= 3.5 and len(bond_atom)==3:
pdb = ad_CH_R3(pdb, bond_atom[0], bond_atom[1], atom_qm, bond_atom[2])
# print("n_bonds",ele,n_bonds)
return pdb
def ad_CH_R3(pdb, A1, A2, A3, A4):
r = 1.032
Ad = 109
Dd = 116
A3xyz = [A3[8],A3[9],A3[10]]
A2xyz = [A2[8],A2[9],A2[10]]
A1xyz = [A1[8],A1[9],A1[10]]
A4xyz = [A4[8],A4[9],A4[10]]
adH1 = H_tert(A1xyz, A2xyz, A3xyz, A4xyz,r)
name1 ="H"+A3[2]
pdb = add_to_pdb(pdb, A3, adH1, name1)
return pdb
def H_tert(A1, A2, A3, A4,r):
## set terzier H to A3 in dinstace r
v1=twoP_to_vec(A3,A1)
v2=twoP_to_vec(A3,A2)
v3=twoP_to_vec(A3,A4)
v_sum=[0,0,0]
for i in range(len(v_sum)):
v_sum[i]=-(v1[i]+v2[i]+v3[i])
len_v_sum=len3dvec(v_sum)
H_vec=[0,0,0]
for i in range(len(v_sum)):
H_vec[i]=(r*v_sum[i])/len_v_sum
H_pos=[0,0,0]
for i in range(len(H_vec)):
H_pos[i]=A3[i]+H_vec[i]
return H_pos
def ad_CH_ar(pdb, A1, A2, A3):
# ad H as CH (SP2) group to A3
r = 1.014
Ad = 120
Dd = 180
A3xyz = [A3[8],A3[9],A3[10]]
A2xyz = [A2[8],A2[9],A2[10]]
A1xyz = [A1[8],A1[9],A1[10]]
adH1 = ZtoXYZ(A1xyz,A2xyz,A3xyz,r,Ad,Dd)
name1 ="H"+A3[2]
nam=list(A3[2])
if len(nam)<=2:
name=nam[1]
else:
name = nam[1]+nam[2]
name1 = "H"+name
pdb = add_to_pdb(pdb, A3, adH1, name1)
return pdb
def ad_CH2(pdb, res_num, alter, A1, A2, A3):
# ad 2H as CH2 group to A3
r = 1.095
Ad = 109
Dd= -121.5
A3xyz = [A3[8],A3[9],A3[10]]
A2xyz = [A2[8],A2[9],A2[10]]
A1xyz = [A1[8],A1[9],A1[10]]
adH1 = ZtoXYZ(A1xyz,A2xyz,A3xyz,r,Ad,Dd)
adH2 = ZtoXYZ(A1xyz,A2xyz,A3xyz,r,Ad,-Dd)
nam=list(A3[2])
if len(nam)<=2:
name=nam[1]
else:
name = nam[1]+nam[2]
name1 = "1H"+name
name2 = "2H"+name
pdb = add_to_pdb(pdb, A3, adH1, name1)
pdb = add_to_pdb(pdb, A3, adH2, name2)
return pdb
def ad_CH3(pdb, res_num,alter, A2, A3):
# ad 3H as CH3 group to A3
# for alt in range(len(alter)):
# print("alter[alt]",alter[alt])
# com = check(pdb,res_num,alter[alt],A1, A2, A3, 1)
# print(com)
# if com == False:
# return pdb
# print( pdb[res_num])
# print("A2", A2)
A1=find_A1(pdb,A3,A2)
# print("A1",A1)
r = 1.095
Ad = 109
Dd = 180
Dd1 = 60
A3xyz = [A3[8],A3[9],A3[10]]
A2xyz = [A2[8],A2[9],A2[10]]
A1xyz = [A1[8],A1[9],A1[10]]
adH1 = ZtoXYZ(A1xyz,A2xyz,A3xyz,r,Ad,Dd)
adH2 = ZtoXYZ(A1xyz,A2xyz,A3xyz,r,Ad,Dd1)
adH3 = ZtoXYZ(A1xyz,A2xyz,A3xyz,r,Ad,-Dd1)
nam=list(A3[2])
if len(nam)<=2:
name=nam[0]
else:
name = nam[0]+nam[1]
name1 = "H1"+name
name2 = "H2"+name
name3 = "H3"+name
pdb = add_to_pdb(pdb, A3, adH1, name1)
pdb = add_to_pdb(pdb, A3, adH2, name2)
pdb = add_to_pdb(pdb, A3, adH3, name3)
return pdb
def add_to_pdb(pdb,old_atm,new_koord,new_nam):
## ad a new deuterium atom to behind an existing atom in the pdb list
atom=0
new_nam="H"
for i in range(len(pdb)):
for k in range(len(pdb[i])):
# print("ALT",alt)
# atom=0
# print(pdb[res_num][i][3])
# print(pdb[res_num][i][2].strip())
if pdb[i][k][2].strip()==old_atm[2].strip() and\
pdb[i][k][3].strip()==old_atm[3].strip() and\
pdb[i][k][5].strip()==old_atm[5].strip() and\
pdb[i][k][6]==old_atm[6]:
atom=pdb[i][k]
indice = k+1
res_num=i
if atom == 0:
return pdb
l_pdb=[]
l_pdb.append(atom[0])
l_pdb.append(atom[1])
l_pdb.append(new_nam)
l_pdb.append(atom[3])
l_pdb.append(atom[4])
l_pdb.append(atom[5])
l_pdb.append(atom[6])
l_pdb.append(atom[7])
l_pdb.append(new_koord[0])
l_pdb.append(new_koord[1])
l_pdb.append(new_koord[2])
l_pdb.append(atom[11])
l_pdb.append(atom[12])
l_pdb.append(atom[13])
l_pdb.append("H")
l_pdb.append(" ")
# print("old_atom",old_atm)
# print("atom",atom)
# print("l_pdb",l_pdb)
# print("???????????????????????????????????????????")
pdb[res_num].insert(indice, l_pdb)
# pdb[res_num].append(l_pdb)
return pdb
def find_A1(pdb,A3,A2):
# find atom bond to A2 to define dihedral to A3
# print("A3",A3)
# print("A2",A2)
bond_atoms=f_bond_atoms(pdb,A2)
# print(bond_atoms)
for i in range(len(bond_atoms)):
if bond_atoms[i][2]!= A3[2]:
A1=bond_atoms[i]
return A1
def CAngle(x,y,z):
# calculate angle between a,b,c in degree
x1=[0,0,0]
x2=[0,0,0]
for i in range(len(x)):
x1[i]=y[i]-x[i]
x2[i]=y[i]-z[i]
Cangle=C2Angle(x1,x2)
return Cangle
def C2Angle(x,y):
#Calculates the angle between x and y
#Answer in degrees