Mercurial > repos > jay > pdaug_peptide_core_functions
annotate PDAUG_Peptide_Structure_Builder/PDAUG_Peptide_Structure_Builder.py @ 6:6822d43a5f84 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
author | jay |
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date | Sun, 31 Jan 2021 02:17:01 +0000 |
parents | e743e76b8991 |
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e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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1 import tempfile |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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2 import pandas as pd |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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3 import shutil |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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4 import sys |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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5 import glob |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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6 import fragbuilder |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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7 import openbabel |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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8 from fragbuilder import peptide |
e743e76b8991
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9 |
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10 import os |
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11 |
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12 |
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13 def read_pep_file(pep_infile): |
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15 file = open(pep_infile) |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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16 lines = file.readlines() |
e743e76b8991
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17 |
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18 Index = [] |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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19 list_pep_name = [] |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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20 |
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21 for line in lines: |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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22 if '>' in line: |
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23 Index.append(line.strip('\n')) |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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24 else: |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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25 line = line.strip('\n') |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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26 line = line.strip('\r') |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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27 list_pep_name.append(line.strip('\n')) |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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28 |
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29 return list_pep_name |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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30 |
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31 def structure_gen(pep_seq, out_dir): |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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32 |
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33 if not os.path.exists(os.path.join(out_dir, 'DataFile')): |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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34 os.makedirs(os.path.join(out_dir, 'DataFile')) |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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35 |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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36 b = len(pep_seq) |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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37 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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38 for seq in pep_seq: |
e743e76b8991
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39 |
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40 pep = peptide.Peptide(seq, nterm = "charged", cterm = "neutral") |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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41 pep.regularize() |
e743e76b8991
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42 pep.write_pdb(os.path.join(out_dir, 'DataFile', seq+".pdb")) |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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43 |
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44 obConversion = openbabel.OBConversion() |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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45 obConversion.SetInAndOutFormats("pdb", "sdf") |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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46 mol = openbabel.OBMol() |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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47 obConversion.ReadFile(mol, os.path.join(out_dir, 'DataFile', seq+".pdb")) |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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48 |
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49 mol.AddHydrogens() |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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50 |
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51 |
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52 def main_process(str_pep_file, out_dir): |
e743e76b8991
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53 |
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54 my_pep = read_pep_file(str_pep_file) |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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55 structure_gen(my_pep, out_dir) |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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56 |
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57 |
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58 if __name__=="__main__": |
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59 |
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61 import argparse |
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62 parser = argparse.ArgumentParser() |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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64 parser.add_argument("-p", "--pep", required=True, default=None, help="pep file") |
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65 parser.add_argument("-o", "--OutDir", required=None, default=os.getcwd(), help="Path to out file") |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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67 args = parser.parse_args() |
e743e76b8991
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68 main_process(args.pep, args.OutDir) |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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