# -*- coding: utf-8 -*-
# !usr/bin/env python
import sys
import math
import numpy as np
np.random.seed(7)
seq_file = open('Protein_OXTR.txt', 'U') #input
abc_file = open('Music_OXTR.txt', 'w') #output
# Read the protein sequence #
heavychain = ''
##lightchain = ''
for eachline in seq_file:
if 'protseq' in eachline:
for seq in seq_file:
if seq.strip():
heavychain += seq.strip()
else:
break
# if 'light chain' in eachline:
# for seq in seq_file:
# if seq.strip():
# lightchain += seq.strip()
# else:
# break
# Read the protein properties #
dict_occurrence = {
'T': 'C',
'G': 'C',
'D': 'C',
'Y': 'C',
'L': 'D',
'N': 'D',
'K': 'E',
'Q': 'E',
'P': 'F',
'R': 'F',
'C': 'F',
'A': 'G',
'I': 'G',
'M': 'G',
'E': 'G',
'V': 'A',
'F': 'A',
'H': 'A',
'S': 'B',
'W': 'B'}
dict_aacomposition = {
'I': 'C',
'F': 'C',
'G': 'C',
'P': 'C',
'A': 'D',
'C': 'D',
'H': 'D',
'Y': 'E',
'K': 'E',
'V': 'F',
'D': 'F',
'E': 'G',
'Q': 'G',
'N': 'G',
'L': 'G',
'R': 'A',
'M': 'A',
'T': 'A',
'S': 'B',
'W': 'B'}
#property_file_netcharge = open('Property_NetCharge.txt', 'U')
#dict_netcharge = {}
#for eachline in property_file_netcharge:
# content = eachline.strip().split('\t')
# dict_netcharge[content[0]] = int(content[1])
dict_netcharge={"L":-1,"I":-1,"N":-1,"G":-1,"V":-1,"E":-1, "P":1,"H":1,"K":1,"A":1,"Y":1,"W":1,"Q":1,"M":1,"S":1,"C":1,"T":1,"F":1,"R":1,"D":1}
dict_hydropathy={"I":-1,"L":-1,"F":-1,"W":-1,"Y":-1,"V":-1,"A":1,"R":1,"N":1,"D":1,"C":1,"Q":1,"E":1,"G":1,"H":1,"K":1,"M":1,"P":1,"S":1,"T":1}
#property_file_size = open('Property_Size.txt', 'U')
#dict_size = {}
#for eachline in property_file_size:
# content = eachline.strip().split('\t')
# dict_size[content[0]] = float(content[1])
property_file_resvol = open('Property_ResidueVol.txt', 'U')
dict_resvol = {}
for eachline in property_file_resvol:
content = eachline.strip().split('\t')
dict_resvol[content[0]] = float(content[1])
#property_file_hydropathy = open('Property_Hydropathy.txt', 'U')
#dict_hydropathy = {}
#for eachline in property_file_hydropathy
# content = eachline.strip().split('\t')
# dict_hydropathy[content[0]] = float(content[1])
#########find main theme#################
noteM=[]
lengthM=[]
note_number={"C":1,"D":3,"E":5,"F":6,"G":8,"A":10,"B":12}
print(len(heavychain))
for i in range(0, len(heavychain)):
j= i-1
if j == -1:
j = len(heavychain)-1
note=note_number[dict_occurrence[heavychain[i]]]
if heavychain[j] in ["Y"]: lengthM.append(8)
elif heavychain[j] in ["W"]: lengthM.append(6)
elif heavychain[j] in ["F","M","Q","L"]: lengthM.append(4)
elif heavychain[j] in ["R"] : lengthM.append(3)
elif heavychain[j] in ["N","C","K","E"]: lengthM.append(2)
elif heavychain[j] in ["G","A","P","S","T","V","H","I","D"]: lengthM.append(1)
octave=4
if dict_netcharge[heavychain[i]] == 1 and heavychain[j] in ["R","L"] and octave < 6:
octave += 1
elif dict_netcharge[heavychain[i]] == 1 and heavychain[j] in ["R","L"] and octave == 6:
octave -= 1
elif dict_netcharge[heavychain[i]] == -1 and heavychain[j] in ["D","E"] and octave > 3:
octave -= 1
elif dict_netcharge[heavychain[i]] == -1 and heavychain[j] in ["D","E"] and octave == 3:
octave += 1
if heavychain[j] == 'P' and dict_occurrence[heavychain[i]] in ["A","C","D","F","G"]:
note +=1
noteM.append(note+12*octave)
max=0
maxs=0
maxe=0
for start in range(0, len(heavychain)-1):
for end in range(1,len(heavychain)):
totalNL=0
for int in range(start,end):
totalNL+=lengthM[int]
if totalNL == 16 or totalNL == 32 or totalNL == 64:
judge=1
for int in range(start,end):
if abs(noteM[int]-noteM[int+1])>5 :
judge=0
if judge == 1:
#print(start,end)
#break
if (end -start) >max:
max=end-start
maxs=start
maxe=end
#else:
# continue
#break
#print(noteM)
#print(lengthM)
print (maxs,maxe)
if (max == 0):
print ("no main theme found!")
# Generate ABC files #
abc_file.write('X: 1\nT: SMP RGS\nM: 4/4\nL: 1/16\nQ:1/4=80\nK:C % 0 sharps\n')
abc_main = ''
##j = 0
octave = 4
notelength = 0
abc_file.write('[V:1] ')
noteS=[]
#octaveS=[]
octS=[]
noOctaveS=[]
lengthS=[]
for i in range(0, len(heavychain)):
j= i-1
if j == -1:
j = len(heavychain)-1
# above reads light chain and loops #
note = dict_occurrence[heavychain[i]]
if heavychain[j] == 'P' and dict_occurrence[heavychain[i]] in ["A","C","D","F","G"]:
note = '^' + note
#if note == 'D': note = '[DGB]'
#elif note == 'A': note = '[ACF]'
#elif note == 'B': note = '[BDG]'
#elif note == 'G': note = '[GCE]'
#########chord section
if heavychain[i] in ["D", "Y"]:
rng=np.random.randint(1, 10)
if(rng >= 4):
note= '[CE]'
else:
note= '[CEG]'
if heavychain[i] in ["P", "R", "C"]:
rng=np.random.randint(1, 10)
if(rng >= 4):
note= '[FA]'
else:
note= '[FAC]'
if heavychain[i] == "M":
rng=np.random.randint(1, 10)
if(rng >= 4):
note= '[GC]'
else:
note= '[GCE]'
if heavychain[i] == "M" and i < len(heavychain)-1 and heavychain[i+1] in ["P","R","C"]: ###i+1 might have potential bug
note = '[CEF_B]'
if heavychain[i] in ["P","R","C"] and i >0 and heavychain[i-1] == "M":
note = '[FAC]'
if heavychain[i] in ["F", "H"]:
rng=np.random.randint(1, 10)
if(rng >= 4):
note= '[AC]'
else:
note= '[ACF]'
if heavychain[i] in ["F","H"] and i < len(heavychain)-1 and heavychain[i+1] in ["L"]: ###i+1 might have potential bug
note = '[A^CEG]'
if heavychain[i] in ["L"] and i >0 and heavychain[i-1] in ["F","H"]:
note = '[DFA]'
if heavychain[i] in ["L"]:
rng=np.random.randint(1, 10)
if(rng >= 4):
note= '[DF]'
else:
note= '[DFA]'
if heavychain[i] in ["L"] and i < len(heavychain)-1 and heavychain[i+1] in ["W"]: ###i+1 might have potential bug
rng=np.random.randint(1,2)
if(rng==1):
note='[D^FAC]'
elif(rng==2):
note='[D^FA]'
if heavychain[i] in ["W"] and i >0 and heavychain[i-1] in ["L"]:
note = '[GBD]'
if heavychain[i] in ["W"]:
rng=np.random.randint(1, 10)
if(rng >= 4):
note= '[BD]'
elif (rng >=2):
note= '[BDG]'
elif (rng ==1):
note= '[BDGF]'
if heavychain[i] in ["R"]:
if heavychain[j] in ["M","L"]:
note= '!ff!'+note
elif heavychain[j] in ["F", "I","A","C","V","W","T"]:
note = '!f!' + note
elif heavychain[j] in ["S"]:
note = '!mf!'+note
elif heavychain[j] in ["P","Y","G","Q","R"]:
note= "!p!"+ note
elif heavychain[j] in ["H","N","E","K","D"]:
note="!pp!"+note
noOctave=note
noOctaveS.append(noOctave)
if dict_netcharge[heavychain[i]] == 1 and heavychain[j] in ["R","L"] and octave < 6:
octave += 1
elif dict_netcharge[heavychain[i]] == 1 and heavychain[j] in ["R","L"] and octave == 6:
octave -= 1
elif dict_netcharge[heavychain[i]] == -1 and heavychain[j] in ["D","E"] and octave > 3:
octave -= 1
elif dict_netcharge[heavychain[i]] == -1 and heavychain[j] in ["D","E"] and octave == 3:
octave += 1
if octave == 1: note = note + ',,,'
elif octave == 2: note = note + ',,'
elif octave == 3: note = note + ','
elif octave == 4: note = note
elif octave == 5: note = note.lower()
octS.append(octave)
#if heavychain[j] == 'P': note = '^' + note
length = ''
if heavychain[j] in ["Y"]: length='8'
elif heavychain[j] in ["W"]: length='6'
elif heavychain[j] in ["F","M","Q","L"]: length='4'
elif heavychain[j] in ["R"] : length='3'
elif heavychain[j] in ["N","C","K","E"]: length='2'
# elif heavychain[j] in ["G","A","P","S","T","V","H","I","D"]: lengthM.append(1)
note += length
lengthS.append(length)
#######dynamics
noteS.append(note)
#if notelength == 10:
# notelength = 0
# abc_file.write(note + '| \\\n')
#else:
# abc_file.write(note)
#j += 1
#notelength += 1
#abc_file.write('\n')
notelength=0
i=0
while i <len(heavychain):
if heavychain[i] in ["W","Y"]:
for theme in range(maxs,maxe):
note=noOctaveS[theme]
if octS[i] == 1: note = note + ',,,'
elif octS[i] == 2: note = note + ',,'
elif octS[i] == 3: note = note + ','
elif octS[i] == 4: note = note
elif octS[i] == 5: note = note.lower()
note += lengthS[theme]
if notelength==10:
notelength=0
abc_file.write(note+'| \\\n')
else:
abc_file.write(note)
notelength +=1
if heavychain[i] in ["F","R"] and i <len(heavychain)-maxe+maxs:
for theme in range(maxs,maxe):
note=noOctaveS[i]
if octS[i] == 1: note = note + ',,,'
elif octS[i] == 2: note = note + ',,'
elif octS[i] == 3: note = note + ','
elif octS[i] == 4: note = note
elif octS[i] == 5: note = note.lower()
note += lengthS[theme]
if notelength==10:
notelength=0
abc_file.write(note+'| \\\n')
else:
abc_file.write(note)
notelength +=1
i+=1
else:
if notelength==10:
notelength=0
abc_file.write(noteS[i]+'| \\\n')
else:
abc_file.write(noteS[i])
notelength +=1
i+=1
####========left hand
abc_file.write('[V:2] ')
octave = 3
for i in range(0, len(heavychain)):
j= i-1
if j == -1:
j = len(heavychain)-1
# above reads light chain and loops #
note = dict_aacomposition[heavychain[i]]
if heavychain[j] == 'P' and dict_occurrence[heavychain[i]] in ["A","C","D","F","G"]:
note = '^' + note
#elif note == 'B': note = '[BDG]'
#elif note == 'G': note = '[GCE]'
if heavychain[i] in ["P", "F"]:
rng=np.random.randint(1, 10)
if(rng >= 4):
note= '[CE]'
else:
note= '[CEG]'
if heavychain[i] in ["C", "H"]:
rng=np.random.randint(1, 10)
if(rng >= 4):
note= '[DF]'
else:
note= '[DFA]'
if heavychain[i] in ["C","H"] and i < len(heavychain)-1 and heavychain[i+1] in ["W"]: ###i+1 might have potential bug
rng=np.random.randint(1,2)
if(rng==1):
note='[D^FAC]'
elif(rng==2):
note='[D^FA]'
if heavychain[i] in ["W"] and i >0 and heavychain[i-1] in ["C","H"]:
note = '[GBD]'
if heavychain[i] in ["Y"]:
rng=np.random.randint(1, 10)
if(rng >= 4):
note= '[EG]'
elif(rng>=2):
note= '[EGC]'
elif(rng==1):
note= '[EGBC]'
if heavychain[i] in ["D"]:
rng=np.random.randint(1, 10)
if(rng >= 4):
note= '[FA]'
else:
note= '[FAC]'
if heavychain[i] in ["L"]:
rng=np.random.randint(1, 10)
if(rng >= 4):
note= '[GB]'
elif(rng >=2):
note= '[GBD]'
elif(rng ==1):
note= '[GBDF]'
if heavychain[i] in ["R", "M"]:
rng=np.random.randint(1, 10)
if(rng >= 4):
note= '[AC]'
else:
note= '[ACF]'
if heavychain[i] in ["R","M"] and i < len(heavychain)-1 and heavychain[i+1] in ["H","C"]: ###i+1 might have potential bug
note = '[A^CEG]'
if heavychain[i] in ["H","C"] and i >0 and heavychain[i-1] in ["R","M"]:
note = '[DFA]'
if heavychain[i] in ["W"]:
rng=np.random.randint(1, 10)
if(rng >= 4):
note= '[BD]'
elif(rng >=2):
note= '[BDG]'
elif(rng ==1):
note= '[BDFG]'
if dict_hydropathy[heavychain[i]] == 1 and heavychain[j] in ["R","L"] and octave < 4:
octave += 1
elif dict_hydropathy[heavychain[i]] == -1 and heavychain[j] in ["R","L"] and octave > 1:
octave -= 1
elif dict_hydropathy[heavychain[i]] == 1 and heavychain[j] in ["I","V"] and octave == 4:
octave -= 1
elif dict_hydropathy[heavychain[i]] == -1 and heavychain[j] in ["I","V"] and octave == 1:
octave += 1
if octave == 1: note = note + ',,,'
elif octave == 2: note = note + ',,'
elif octave == 3: note = note + ','
elif octave == 4: note = note
elif octave == 5: note = note.lower()
length = ''
if heavychain[j] in ["G"]: length = '8'
elif heavychain[j] in ["S","A"] : length = '6'
elif heavychain[j] in ["D"]: length = '4'
elif heavychain[j] in ["C"]: length = '3'
elif heavychain[j] in ["M","H","Q","V","E","N","P","T"]: length ='2'
#elif heavychain[i] in ["W","Y","F","R","K","I","L"]: length='1'
note += length
#if note == 'D': note = '[DGB]'
#elif note == 'A': note = '[ACF]'
if heavychain[i] in ["R"]:
if heavychain[j] in ["M","L"]:
note= '!ff!'+note
elif heavychain[j] in ["F", "I","A","C","V","W","T"]:
note = '!f!' + note
elif heavychain[j] in ["S"]:
note = '!mf!'+note
elif heavychain[j] in ["P","Y","G","Q","R"]:
note= "!p!"+ note
elif heavychain[j] in ["H","N","E","K","D"]:
note="!pp!"+note
if notelength == 10:
notelength = 0
abc_file.write(note + '| \\\n')
else:
abc_file.write(note)
notelength += 1
abc_file.write('\n')