Mercurial > repos > chemteam > biopdb_align_and_rmsd

annotate BioPDB_align_and_rmsd.py @ 0:6352d6dd74e2 draft default tip

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit b90c5ab8f15397299e8baf2e903a9911c44d7668
author chemteam
date Thu, 06 Jun 2024 07:09:14 +0000
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6352d6dd74e2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit b90c5ab8f15397299e8baf2e903a9911c44d7668
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1 #!/usr/bin/env python3
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2
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3 # The MIT License
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4 #
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5 # Copyright (c) 2010-2016 Anders S. Christensen
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6 #
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7 # Permission is hereby granted, free of charge, to any person obtaining a copy
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8 # of this software and associated documentation files (the "Software"), to deal
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9 # in the Software without restriction, including without limitation the rights
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10 # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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11 # copies of the Software, and to permit persons to whom the Software is
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12 # furnished to do so, subject to the following conditions:
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13 #
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14 # The above copyright notice and this permission notice shall be included in
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15 # all copies or substantial portions of the Software.
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16 #
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17 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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18 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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19 # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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20 # # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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21 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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22 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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23 # THE SOFTWARE.
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25 import argparse
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27 import Bio.PDB
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30 def __main__():
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31 parser = argparse.ArgumentParser(
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32 description='Residues to be aligned')
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33 parser.add_argument(
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34 '--start_residue', default=None,
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35 help='start residue')
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36 parser.add_argument(
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37 '--end_residue', default=None,
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38 help='end residue')
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39 parser.add_argument(
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40 '--ref_structure', default=None,
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41 help='reference structure')
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42 parser.add_argument(
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43 '--model', default=None,
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44 help='model structure')
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45 parser.add_argument(
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46 '--aligned_structure', default=None,
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47 help='aligned structure')
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48 parser.add_argument(
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49 '--rmsd', default=None,
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50 help='rmsd')
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51 args = parser.parse_args()
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52
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53 # Select what residues numbers you wish to align
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54 # and put them in a list
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55 start_id = int(args.start_residue)
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56 end_id = int(args.end_residue)
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57 atoms_to_be_aligned = range(start_id, end_id + 1)
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58
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59 # Start the parser
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60 pdb_parser = Bio.PDB.PDBParser(QUIET=True)
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61
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62 # Get the structures
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63 ref_structure = pdb_parser.get_structure("reference", args.ref_structure)
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64 sample_structure = pdb_parser.get_structure("sample", args.model)
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65
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66 # Use the first model in the pdb-files for alignment
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67 # Change the number 0 if you want to align to another structure
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68 ref_model = ref_structure[0]
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69 sample_model = sample_structure[0]
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70
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71 # Make a list of the atoms (in the structures) you wish to align.
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72 # In this case we use CA atoms whose index is in the specified range
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73 ref_atoms = []
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74 sample_atoms = []
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75
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76 # Iterate of all chains in the model in order to find all residues
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77 for ref_chain in ref_model:
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78 # Iterate of all residues in each model in order to find proper atoms
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79 for ref_res in ref_chain:
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80 # Check if residue number ( .get_id() ) is in the list
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81 if ref_res.get_id()[1] in atoms_to_be_aligned:
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82 # Append CA atom to list
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83 ref_atoms.append(ref_res['CA'])
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84
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85 # Do the same for the sample structure
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86 for sample_chain in sample_model:
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87 for sample_res in sample_chain:
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88 if sample_res.get_id()[1] in atoms_to_be_aligned:
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89 sample_atoms.append(sample_res['CA'])
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90
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91 # Now we initiate the superimposer:
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92 super_imposer = Bio.PDB.Superimposer()
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93 super_imposer.set_atoms(ref_atoms, sample_atoms)
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94 super_imposer.apply(sample_model.get_atoms())
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95
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96 # Save RMSD into an output file:
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97 with open(args.rmsd, 'w') as rmsd_out:
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98 rmsd_out.write(str(super_imposer.rms))
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99
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100 # Save aligned coordinates of the model:
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101 io = Bio.PDB.PDBIO()
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102 io.set_structure(sample_structure)
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103 io.save(args.aligned_structure)
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104
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105
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106 if __name__ == "__main__":
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107 __main__()