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simulateplots.py
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simulateplots.py
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import csv
import sys
import os
import matplotlib.pyplot as plt
import pandas as pd
from nmrutil import *
def make_plots(cp, project):
datapath=cp.get('datadir')
fp = open(datapath+os.sep+project+os.sep+'result'+os.sep+cp.get('predictionoutput'),'r')
spectra_simulated_dicts = []
spectrum_simulated_dict = {}
line=fp.readline().strip()
while line:
if line == '/':
spectra_simulated_dicts.append(spectrum_simulated_dict)
#spectrum_simulated=[]
spectrum_simulated_dict = {}
else:
peaks_string=line.split(",")
peak_y = float(peaks_string[0])
peak_x = float(peaks_string[1])
peak_type = peaks_string[2]
#peak_c = int(peaks_string[3])
#peak_h = int(peaks_string[4]) q: [], [] || m: [], [] || t: [], y: []
if peak_type in spectrum_simulated_dict:
spectrum_simulated_dict[peak_type][0].append(peak_x)
spectrum_simulated_dict[peak_type][1].append(peak_y)
else:
spectrum_simulated_dict[peak_type] = [[peak_x], [peak_y]]
line=fp.readline().strip()
#spectra_simulated.append(spectrum_simulated)
#print(spectra_simulated)
fp.close()
fp = open(datapath+os.sep+project+os.sep+cp.get('msmsinput'),'r')
line=fp.readline().strip()
smiles=[]
while line:
smiles.append(line)
line = fp.readline().strip()
usehsqctocsy = cp.get('usehsqctocsy')
usehmbc = cp.get('usehmbc')
if os.path.exists(datapath+os.sep+project+os.sep+cp.get('msmsinput')[0:len(cp.get('msmsinput'))-4]+'names.txt'):
with open(datapath+os.sep+project+os.sep+cp.get('msmsinput')[0:len(cp.get('msmsinput'))-4]+'names.txt') as f:
linesnames = f.read().splitlines()
i = 0
for name in linesnames:
plt_w = 15
plt_h = 30
mosaic = """A;Q"""
if usehmbc == 'true':
if usehsqctocsy == 'true':
mosaic = "AAA;BQC"
plt_w = 45
else:
mosaic = "AA;BQ"
plt_w = 30
elif usehmbc == 'false' and usehsqctocsy == 'true':
mosaic = "AA;QC"
plt_w = 30
fig = plt.figure(figsize=(plt_w, plt_h))
ax_dict = fig.subplot_mosaic(mosaic)
try:
skeletal_structure = plt.imread(datapath+os.sep+project+os.sep+"reports"+os.sep+name+".jpg")
except:
print("Structure image not found for " + name)
pass
ax_dict['A'].axis('off')
ax_dict['A'].imshow(skeletal_structure)
ax_dict['Q'].set_xlim([10, 0])
ax_dict['Q'].set_ylim([200, 0])
ax_dict['Q'].scatter(spectra_simulated_dicts[i]['q'][0], spectra_simulated_dicts[i]['q'][1], c='blue', label='Simulated HSQC', alpha=0.6, edgecolors='none', s=50)
ax_dict['Q'].legend()
ax_dict['Q'].grid(True)
if usehmbc != 'false':
ax_dict['B'].set_xlim([10, 0])
ax_dict['B'].set_ylim([200, 0])
ax_dict['B'].scatter(spectra_simulated_dicts[i]['b'][0], spectra_simulated_dicts[i]['b'][1], c='blue', label='Simulated HMBC', alpha=0.6, edgecolors='none', s=50)
ax_dict['B'].legend()
ax_dict['B'].grid(True)
if usehsqctocsy != 'false':
ax_dict['C'].set_xlim([10, 0])
ax_dict['C'].set_ylim([200, 0])
ax_dict['C'].scatter(spectra_simulated_dicts[i]['t'][0], spectra_simulated_dicts[i]['t'][1], c='blue', label='Simulated HSQCTOCSY', alpha=0.6, edgecolors='none', s=50)
ax_dict['C'].legend()
ax_dict['C'].grid(True)
save_path = datapath+os.sep+project+os.sep+'sim_plots'
if not os.path.exists(save_path):
os.makedirs(save_path)
fig.savefig(save_path+os.sep+name+'.png', transparent=False, dpi=80, bbox_inches="tight")
i+=1
plt.close()
if __name__ == '__main__':
project = sys.argv[1]
cp = readprops(project)
print("Plotting spectra..")
make_plots(cp, project)