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annotate merge_top.py @ 1:e8e3636338c8 draft default tip

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
author chemteam
date Mon, 24 Oct 2022 22:31:09 +0000
parents 7f64dd60f5d7
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7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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1 import argparse
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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3 import parmed as pmd
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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6 def merge_gro_files(prot_gro, lig_gro, cmplx_gro):
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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7 prot = pmd.load_file(prot_gro)
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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8 lig = pmd.load_file(lig_gro)
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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9 cmplx = prot + lig
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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10 cmplx.save(cmplx_gro)
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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13 def merge_top_files(prot_top, lig_top, cmplx_top):
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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14 with open(lig_top, 'r') as f:
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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15 lig_top_sections = f.read().split('\n[')
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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17 # open ligand topology
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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18 for n in range(len(lig_top_sections)):
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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19 if 'atomtypes' in lig_top_sections[n][:10]:
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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20 lig_atomtypes = lig_top_sections[n]
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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21 del lig_top_sections[n]
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22 break
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23 else:
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24 lig_atomtypes = None
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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25 lig_top_updated = '\n['.join(lig_top_sections)
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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27 # open protein topology
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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28 with open(prot_top, 'r') as f:
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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29 prot_top_combined = f.read()
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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30 if lig_atomtypes:
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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31 prot_top_sections = prot_top_combined.split('[ moleculetype ]\n')
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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32 prot_top_combined = (prot_top_sections[0] +
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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33 '; Include ligand atomtypes\n[' +
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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34 lig_atomtypes +
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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35 '\n[ moleculetype ]\n' +
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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36 prot_top_sections[1])
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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37 prot_top_sections = prot_top_combined.split('; Include water topology')
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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38 prot_top_combined = (prot_top_sections[0] +
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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39 '; Include ligand topology\n' +
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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40 lig_top_updated +
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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41 '\n; Include water topology' +
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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42 prot_top_sections[1])
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43 prot_top_combined += 'base 1\n'
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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44
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45 # save complex topology
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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46 with open(cmplx_top, 'w') as f:
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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47 f.write(prot_top_combined)
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48
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49
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50 def main():
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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51 parser = argparse.ArgumentParser(
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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52 description='Perform SMD runs for dynamic undocking')
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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53 parser.add_argument('--lig-top', help='Ligand TOP file.')
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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54 parser.add_argument('--prot-top', help='Protein TOP file.')
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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55 parser.add_argument('--lig-gro', help='Ligand GRO file.')
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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56 parser.add_argument('--prot-gro', help='Protein GRO file.')
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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57 parser.add_argument('--complex-top', help='Complex TOP file.')
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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58 parser.add_argument('--complex-gro', help='Complex GRO file.')
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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59 args = parser.parse_args()
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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60 merge_gro_files(args.prot_gro, args.lig_gro, args.complex_gro)
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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61 merge_top_files(args.prot_top, args.lig_top, args.complex_top)
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
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62
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63
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64 if __name__ == "__main__":
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65 main()