Mercurial > repos > bgruening > rdock_rbcavity

annotate select_points_SDF.py @ 6:744a777e9f90 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit dff183f4eb2d3df42917ec4fed0fbdb2ea11e19a"
author bgruening
date Thu, 21 May 2020 10:56:13 -0400
parents 82193638d0c5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
parents:
diff changeset
1 import argparse
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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2
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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diff changeset
3 def get_coordinates(lines):
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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4 version = lines[3][34:39]
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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5 molecule = []
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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6 if version == 'V2000':
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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7 natom = int(lines[3][:3].strip())
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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8 for i in range(1, natom + 1):
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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9 temp = []
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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10 j = 3 + i
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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11 x = float(lines[j][:10].strip())
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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12 y = float(lines[j][11:20].strip())
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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13 z = float(lines[j][21:30].strip())
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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14 temp.extend([x, y, z])
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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15 molecule.append(temp)
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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16 else:
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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17 read = 0
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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18 for line in lines:
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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19 if "END ATOM" in line:
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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20 read = 0
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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21 break
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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22 if read:
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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23 temp = []
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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24 a = line.split(" ")
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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25 x, y, z = float(a[5]), float(a[6]), float(a[7])
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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26 temp.extend([x, y, z])
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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27 molecule.append(temp)
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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28 if "BEGIN ATOM" in line:
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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29 read = 1
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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30 return molecule
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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31
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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32
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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33 def select_points(all_coordinates):
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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34 tol = 1.5
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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35 select = []
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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36
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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37 for molecule in all_coordinates:
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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38 for coordinates in molecule:
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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39 tv = 0
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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40 temp = []
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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41 x, y, z = coordinates
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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42 for record in select:
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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43 xr, yr, zr = record
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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44 if xr-tol < x and x < xr+tol and \
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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45 yr-tol < y and y < yr+tol and \
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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46 zr-tol < z and z < zr+tol:
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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47 tv = 1
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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48 break
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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49 if tv == 1:
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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50 continue
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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51 temp.extend([x, y, z])
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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52 select.append(temp)
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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53 return select
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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54
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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55
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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56 def sdfout(centers, writer):
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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57 n = len(centers)
6
744a777e9f90 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit dff183f4eb2d3df42917ec4fed0fbdb2ea11e19a"
bgruening
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diff changeset
58 writer.write("Frankenstein ligand\n00000000000000000000 3D\nCreated in Galaxy\n")
5
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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59 writer.write("%3d 0 0 0 0 0 0 0 0 0999 V2000\n" % n)
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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60 for record in centers:
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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61 x, y, z = record
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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62 writer.write("%10.4f%10.4f%10.4f C 0 0 0 0 0 0 0 0 0 0 0 0\n" % (x, y, z))
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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63
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64 writer.write("M END\n$$$$\n")
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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65
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66
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67 def main():
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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68 parser = argparse.ArgumentParser(description='RDKit screen')
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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69 parser.add_argument('-i', '--input',
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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70 help="Input file")
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71 parser.add_argument('-o', '--output',
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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72 help="Base name for output file (no extension).")
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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73 args = parser.parse_args()
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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74
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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75 mol_coordinates = []
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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76 all_coordinates = []
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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77 with open(args.input) as file:
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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78 for line in file:
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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79 if line.strip() == '$$$$':
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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80 temp = get_coordinates(mol_coordinates)
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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81 all_coordinates.append(temp)
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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82 mol_coordinates.clear()
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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83 else:
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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84 mol_coordinates.append(line)
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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85 centers = select_points(all_coordinates)
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
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86 with open(args.output, 'w+') as writer:
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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87 sdfout(centers, writer)
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
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88
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
parents:
diff changeset
89 if __name__ == "__main__":
82193638d0c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
bgruening
parents:
diff changeset
90 main()