packmol-memgen-minimal 1.1.16__py3-none-any.whl

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Files changed (71) hide show
  1. packmol_memgen/__init__.py +2 -0
  2. packmol_memgen/__version__.py +34 -0
  3. packmol_memgen/data/LICENSE.Apache-2.0 +201 -0
  4. packmol_memgen/data/extra_solvents.lib +789 -0
  5. packmol_memgen/data/frcmod.lipid_ext +97 -0
  6. packmol_memgen/data/frcmod.solvents +129 -0
  7. packmol_memgen/data/insane_lipids.txt +138 -0
  8. packmol_memgen/data/insane_solvents.txt +45 -0
  9. packmol_memgen/data/leaprc.extra_solvents +42 -0
  10. packmol_memgen/data/leaprc.lipid_ext +48 -0
  11. packmol_memgen/data/lipid_ext.lib +12312 -0
  12. packmol_memgen/data/martini_v3.0.0.itp +356605 -0
  13. packmol_memgen/data/memgen.parm +4082 -0
  14. packmol_memgen/data/pdbs.tar.gz +0 -0
  15. packmol_memgen/data/solvent.parm +14 -0
  16. packmol_memgen/example/example.sh +31 -0
  17. packmol_memgen/lib/__init__.py +0 -0
  18. packmol_memgen/lib/amber.py +77 -0
  19. packmol_memgen/lib/charmmlipid2amber/__init__.py +0 -0
  20. packmol_memgen/lib/charmmlipid2amber/charmmlipid2amber.csv +7164 -0
  21. packmol_memgen/lib/charmmlipid2amber/charmmlipid2amber.py +225 -0
  22. packmol_memgen/lib/pdbremix/LICENSE +21 -0
  23. packmol_memgen/lib/pdbremix/__init__.py +0 -0
  24. packmol_memgen/lib/pdbremix/_version.py +1 -0
  25. packmol_memgen/lib/pdbremix/amber.py +1103 -0
  26. packmol_memgen/lib/pdbremix/asa.py +227 -0
  27. packmol_memgen/lib/pdbremix/data/aminoacid.pdb +334 -0
  28. packmol_memgen/lib/pdbremix/data/binaries.json +26 -0
  29. packmol_memgen/lib/pdbremix/data/charmm22.parameter +2250 -0
  30. packmol_memgen/lib/pdbremix/data/charmm22.topology +1635 -0
  31. packmol_memgen/lib/pdbremix/data/color_b.py +682 -0
  32. packmol_memgen/lib/pdbremix/data/hin.lib +130 -0
  33. packmol_memgen/lib/pdbremix/data/hydroxide.lib +88 -0
  34. packmol_memgen/lib/pdbremix/data/make_chi.py +92 -0
  35. packmol_memgen/lib/pdbremix/data/opls.parameter +1108 -0
  36. packmol_memgen/lib/pdbremix/data/opls.topology +1869 -0
  37. packmol_memgen/lib/pdbremix/data/phd.frcmod +82 -0
  38. packmol_memgen/lib/pdbremix/data/phd.leaprc +4 -0
  39. packmol_memgen/lib/pdbremix/data/phd.prepin +35 -0
  40. packmol_memgen/lib/pdbremix/data/template.pdb +334 -0
  41. packmol_memgen/lib/pdbremix/data/znb.frcmod +24 -0
  42. packmol_memgen/lib/pdbremix/data/znb.leaprc +7 -0
  43. packmol_memgen/lib/pdbremix/data/znb.lib +69 -0
  44. packmol_memgen/lib/pdbremix/data.py +264 -0
  45. packmol_memgen/lib/pdbremix/fetch.py +102 -0
  46. packmol_memgen/lib/pdbremix/force.py +627 -0
  47. packmol_memgen/lib/pdbremix/gromacs.py +978 -0
  48. packmol_memgen/lib/pdbremix/lib/__init__.py +0 -0
  49. packmol_memgen/lib/pdbremix/lib/docopt.py +579 -0
  50. packmol_memgen/lib/pdbremix/lib/pyqcprot.py +305 -0
  51. packmol_memgen/lib/pdbremix/namd.py +1078 -0
  52. packmol_memgen/lib/pdbremix/pdbatoms.py +543 -0
  53. packmol_memgen/lib/pdbremix/pdbtext.py +120 -0
  54. packmol_memgen/lib/pdbremix/protein.py +311 -0
  55. packmol_memgen/lib/pdbremix/pymol.py +480 -0
  56. packmol_memgen/lib/pdbremix/rmsd.py +203 -0
  57. packmol_memgen/lib/pdbremix/simulate.py +420 -0
  58. packmol_memgen/lib/pdbremix/spacehash.py +73 -0
  59. packmol_memgen/lib/pdbremix/trajectory.py +286 -0
  60. packmol_memgen/lib/pdbremix/util.py +273 -0
  61. packmol_memgen/lib/pdbremix/v3.py +16 -0
  62. packmol_memgen/lib/pdbremix/v3array.py +482 -0
  63. packmol_memgen/lib/pdbremix/v3numpy.py +350 -0
  64. packmol_memgen/lib/pdbremix/volume.py +155 -0
  65. packmol_memgen/lib/utils.py +1017 -0
  66. packmol_memgen/main.py +2827 -0
  67. packmol_memgen_minimal-1.1.16.dist-info/METADATA +664 -0
  68. packmol_memgen_minimal-1.1.16.dist-info/RECORD +71 -0
  69. packmol_memgen_minimal-1.1.16.dist-info/WHEEL +4 -0
  70. packmol_memgen_minimal-1.1.16.dist-info/entry_points.txt +2 -0
  71. packmol_memgen_minimal-1.1.16.dist-info/licenses/LICENSE +338 -0
packmol_memgen/data/extra_solvents.lib ADDED
@@ -0,0 +1,789 @@
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+ !!index array str
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+ "ACN"
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+ "ACT"
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+ "BNZ"
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+ "CL3"
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+ "DMS"
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+ "IPH"
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+ "MOH"
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+ "NMA"
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+ "TFE"
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+ !entry.ACN.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
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+ "C1" "CT" 0 1 131072 1 6 -0.550300
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+ "H11" "HC" 0 1 131072 2 1 0.190400
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+ "H12" "HC" 0 1 131072 3 1 0.190400
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+ "H13" "HC" 0 1 131072 4 1 0.190400
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+ "C2" "YK" 0 1 131072 5 6 0.491700
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+ "N3" "YN" 0 1 131072 6 7 -0.512600
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+ !entry.ACN.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
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+ "C1" "CT" 0 -1 0.0
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+ "H11" "HC" 0 -1 0.0
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+ "H12" "HC" 0 -1 0.0
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+ "H13" "HC" 0 -1 0.0
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+ "C2" "YK" 0 -1 0.0
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+ "N3" "YN" 0 -1 0.0
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+ !entry.ACN.unit.boundbox array dbl
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+ -1.000000
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+ 0.0
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+ 0.0
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+ 0.0
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+ 0.0
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+ !entry.ACN.unit.childsequence single int
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+ 2
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+ !entry.ACN.unit.connect array int
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+ 0
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+ 0
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+ !entry.ACN.unit.connectivity table int atom1x int atom2x int flags
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+ 1 2 1
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+ 1 3 1
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+ 1 4 1
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+ 1 5 1
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+ 5 6 1
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+ !entry.ACN.unit.hierarchy table str abovetype int abovex str belowtype int belowx
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+ "U" 0 "R" 1
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+ "R" 1 "A" 1
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+ "R" 1 "A" 2
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+ "R" 1 "A" 3
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+ "R" 1 "A" 4
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+ "R" 1 "A" 5
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+ "R" 1 "A" 6
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+ !entry.ACN.unit.name single str
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+ "ACN"
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+ !entry.ACN.unit.positions table dbl x dbl y dbl z
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+ 0.190004 0.390525 1.095384
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+ 1.251140 0.527201 1.257559
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+ -0.188272 -0.326916 1.811747
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+ -0.315243 1.336343 1.240788
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+ -0.046680 -0.095944 -0.269115
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+ -0.229653 -0.472016 -1.323959
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+ !entry.ACN.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
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+ 0 0 0 0 0 0
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+ !entry.ACN.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
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+ "ACN" 1 7 1 "w" 0
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+ !entry.ACN.unit.residuesPdbSequenceNumber array int
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+ 0
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+ !entry.ACN.unit.solventcap array dbl
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+ -1.000000
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+ 0.0
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+ 0.0
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+ 0.0
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+ !entry.ACN.unit.velocities table dbl x dbl y dbl z
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+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
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+ !entry.ACT.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
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+ "C1" "PC" 0 1 131072 1 6 -0.180000
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+ "H11" "PH" 0 1 131072 2 1 0.060000
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+ "H12" "PH" 0 1 131072 3 1 0.060000
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+ "H13" "PH" 0 1 131072 4 1 0.060000
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+ "C2" "PK" 0 1 131072 5 6 0.500000
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+ "O3" "O" 0 1 131072 6 8 -0.500000
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+ "C4" "PC" 0 1 131072 7 6 -0.180000
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+ "H41" "PH" 0 1 131072 8 1 0.060000
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+ "H42" "PH" 0 1 131072 9 1 0.060000
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+ "H43" "PH" 0 1 131072 10 1 0.060000
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+ !entry.ACT.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
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+ "C1" "PC" 0 -1 0.0
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+ "H11" "PH" 0 -1 0.0
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+ "H12" "PH" 0 -1 0.0
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+ "H13" "PH" 0 -1 0.0
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+ "C2" "PK" 0 -1 0.0
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+ "O3" "O" 0 -1 0.0
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+ "C4" "PC" 0 -1 0.0
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+ "H41" "PH" 0 -1 0.0
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+ "H42" "PH" 0 -1 0.0
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+ "H43" "PH" 0 -1 0.0
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+ !entry.ACT.unit.boundbox array dbl
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+ -1.000000
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+ 0.0
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+ 0.0
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+ 0.0
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+ !entry.ACT.unit.childsequence single int
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+ 2
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+ !entry.ACT.unit.connect array int
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+ 0
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+ 0
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+ !entry.ACT.unit.connectivity table int atom1x int atom2x int flags
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+ 1 2 1
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+ 1 3 1
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+ 1 5 1
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+ 5 6 1
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+ 5 7 1
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+ 7 8 1
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+ 7 9 1
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+ 7 10 1
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+ !entry.ACT.unit.hierarchy table str abovetype int abovex str belowtype int belowx
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+ "U" 0 "R" 1
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+ "R" 1 "A" 1
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+ "R" 1 "A" 2
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+ "R" 1 "A" 3
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+ "R" 1 "A" 4
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+ "R" 1 "A" 5
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+ "R" 1 "A" 6
129
+ "R" 1 "A" 7
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+ "R" 1 "A" 8
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+ "R" 1 "A" 9
132
+ "R" 1 "A" 10
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+ !entry.ACT.unit.name single str
134
+ "ACT"
135
+ !entry.ACT.unit.positions table dbl x dbl y dbl z
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+ 1.288219 -0.607661 0.0
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+ 1.335519 -1.250375 -0.874415
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+ 1.335520 -1.250373 0.874416
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+ 2.133758 0.065905 -1.000000E-06
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+ 0.0 0.187496 0.0
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+ -1.335519 -1.250375 0.874415
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+ -1.335519 -1.250374 -0.874416
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+ -2.133757 0.065905 0.0
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+ !entry.ACT.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
147
+ 0 0 0 0 0 0
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+ !entry.ACT.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
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+ "ACT" 1 11 1 "w" 0
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+ !entry.ACT.unit.residuesPdbSequenceNumber array int
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+ 0
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+ !entry.ACT.unit.solventcap array dbl
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+ -1.000000
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+ 0.0
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+ 0.0
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+ 0.0
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+ !entry.ACT.unit.velocities table dbl x dbl y dbl z
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+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
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+ !entry.BNZ.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
170
+ "C1" "PA" 0 1 131072 1 6 -0.115000
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+ "H1" "PI" 0 1 131072 2 1 0.115000
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+ "C2" "PA" 0 1 131072 3 6 -0.115000
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+ "H2" "PI" 0 1 131072 4 1 0.115000
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+ "C3" "PA" 0 1 131072 5 6 -0.115000
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+ "H3" "PI" 0 1 131072 6 1 0.115000
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+ "C4" "PA" 0 1 131072 7 6 -0.115000
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+ "H4" "PI" 0 1 131072 8 1 0.115000
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+ "C5" "PA" 0 1 131072 9 6 -0.115000
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+ "H5" "PI" 0 1 131072 10 1 0.115000
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+ "C6" "PA" 0 1 131072 11 6 -0.115000
181
+ "H6" "PI" 0 1 131072 12 1 0.115000
182
+ !entry.BNZ.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
183
+ "C1" "PA" 0 -1 0.0
184
+ "H1" "PI" 0 -1 0.0
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+ "C2" "PA" 0 -1 0.0
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+ "H2" "PI" 0 -1 0.0
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+ "C3" "PA" 0 -1 0.0
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+ "H3" "PI" 0 -1 0.0
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+ "C4" "PA" 0 -1 0.0
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+ "H4" "PI" 0 -1 0.0
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+ "C5" "PA" 0 -1 0.0
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+ "H5" "PI" 0 -1 0.0
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+ "C6" "PA" 0 -1 0.0
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+ "H6" "PI" 0 -1 0.0
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+ !entry.BNZ.unit.boundbox array dbl
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+ -1.000000
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+ 0.0
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+ 0.0
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+ 0.0
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+ 0.0
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+ !entry.BNZ.unit.childsequence single int
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+ 2
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+ !entry.BNZ.unit.connect array int
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+ 0
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+ 0
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+ !entry.BNZ.unit.connectivity table int atom1x int atom2x int flags
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+ 1 2 1
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+ 3 5 1
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+ 5 6 1
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+ 5 7 1
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+ 7 8 1
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+ 7 9 1
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+ 9 10 1
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+ 9 11 1
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+ 11 12 1
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+ !entry.BNZ.unit.hierarchy table str abovetype int abovex str belowtype int belowx
220
+ "U" 0 "R" 1
221
+ "R" 1 "A" 1
222
+ "R" 1 "A" 2
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+ "R" 1 "A" 3
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+ "R" 1 "A" 4
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+ "R" 1 "A" 5
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+ "R" 1 "A" 6
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+ "R" 1 "A" 7
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+ "R" 1 "A" 8
229
+ "R" 1 "A" 9
230
+ "R" 1 "A" 10
231
+ "R" 1 "A" 11
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+ "R" 1 "A" 12
233
+ !entry.BNZ.unit.name single str
234
+ "BNZ"
235
+ !entry.BNZ.unit.positions table dbl x dbl y dbl z
236
+ 0.562381 1.214422 0.361091
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+ 0.998762 2.156756 0.641280
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+ -0.779445 1.146099 0.020041
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+ -1.384257 2.035418 0.035592
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+ -1.341825 -0.068323 -0.341050
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+ -2.383019 -0.121338 -0.605688
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+ -0.562381 -1.214422 -0.361090
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+ -0.998762 -2.156756 -0.641280
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+ 0.779445 -1.146099 -0.020041
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+ 1.384257 -2.035417 -0.035592
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+ 1.341826 0.068323 0.341049
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+ 2.383019 0.121338 0.605688
248
+ !entry.BNZ.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
249
+ 0 0 0 0 0 0
250
+ !entry.BNZ.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
251
+ "BNZ" 1 13 1 "w" 0
252
+ !entry.BNZ.unit.residuesPdbSequenceNumber array int
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+ 0
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+ !entry.BNZ.unit.solventcap array dbl
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+ -1.000000
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+ 0.0
257
+ 0.0
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+ 0.0
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+ 0.0
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+ !entry.BNZ.unit.velocities table dbl x dbl y dbl z
261
+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
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+ !entry.CL3.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
274
+ "H1" "HZ" 0 1 131072 1 1 0.265900
275
+ "C1" "CZ" 0 1 131072 2 6 -0.384700
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+ "CL1" "CL" 0 1 131072 3 6 0.039600
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+ "CL2" "CL" 0 1 131072 4 6 0.039600
278
+ "CL3" "CL" 0 1 131072 5 6 0.039600
279
+ !entry.CL3.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
280
+ "H1" "HZ" 0 -1 0.0
281
+ "C1" "CZ" 0 -1 0.0
282
+ "CL1" "CL" 0 -1 0.0
283
+ "CL2" "CL" 0 -1 0.0
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+ "CL3" "CL" 0 -1 0.0
285
+ !entry.CL3.unit.boundbox array dbl
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+ -1.000000
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+ 0.0
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+ 0.0
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+ 0.0
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+ 0.0
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+ !entry.CL3.unit.childsequence single int
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+ 2
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+ !entry.CL3.unit.connect array int
294
+ 0
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+ 0
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+ !entry.CL3.unit.connectivity table int atom1x int atom2x int flags
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+ 1 2 1
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+ 2 3 1
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+ 2 4 1
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+ 2 5 1
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+ !entry.CL3.unit.hierarchy table str abovetype int abovex str belowtype int belowx
302
+ "U" 0 "R" 1
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+ "R" 1 "A" 1
304
+ "R" 1 "A" 2
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+ "R" 1 "A" 3
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+ "R" 1 "A" 4
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+ "R" 1 "A" 5
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+ !entry.CL3.unit.name single str
309
+ "CL3"
310
+ !entry.CL3.unit.positions table dbl x dbl y dbl z
311
+ 5.572900 14.270900 6.777400
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+ 5.808900 13.674900 7.671400
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+ 6.074900 11.951900 7.100400
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+ 7.346900 14.214900 8.395400
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+ 4.387900 13.808900 8.718400
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+ !entry.CL3.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
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+ 0 0 0 0 0 0
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+ !entry.CL3.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
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+ "CL3" 1 6 1 "w" 0
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+ !entry.CL3.unit.residuesPdbSequenceNumber array int
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+ 0
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+ !entry.CL3.unit.solventcap array dbl
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+ -1.000000
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+ 0.0
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+ 0.0
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+ 0.0
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+ !entry.CL3.unit.velocities table dbl x dbl y dbl z
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+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
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+ 0.0 0.0 0.0
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+ !entry.DMS.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
335
+ "C1" "SK" 0 1 131072 1 6 -0.148000
336
+ "H11" "SI" 0 1 131072 2 1 0.090000
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+ "H12" "SI" 0 1 131072 3 1 0.090000
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+ "H13" "SI" 0 1 131072 4 1 0.090000
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+ "S2" "SD" 0 1 131072 5 16 0.312000
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+ "O3" "S0" 0 1 131072 6 8 -0.556000
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+ "C4" "SK" 0 1 131072 7 6 -0.148000
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+ "H41" "SI" 0 1 131072 8 1 0.090000
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+ "H42" "SI" 0 1 131072 9 1 0.090000
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+ "H43" "SI" 0 1 131072 10 1 0.090000
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+ !entry.DMS.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
346
+ "C1" "SK" 0 -1 0.0
347
+ "H11" "SI" 0 -1 0.0
348
+ "H12" "SI" 0 -1 0.0
349
+ "H13" "SI" 0 -1 0.0
350
+ "S2" "SD" 0 -1 0.0
351
+ "O3" "S0" 0 -1 0.0
352
+ "C4" "SK" 0 -1 0.0
353
+ "H41" "SI" 0 -1 0.0
354
+ "H42" "SI" 0 -1 0.0
355
+ "H43" "SI" 0 -1 0.0
356
+ !entry.DMS.unit.boundbox array dbl
357
+ -1.000000
358
+ 0.0
359
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360
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361
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362
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363
+ 2
364
+ !entry.DMS.unit.connect array int
365
+ 0
366
+ 0
367
+ !entry.DMS.unit.connectivity table int atom1x int atom2x int flags
368
+ 1 2 1
369
+ 1 3 1
370
+ 1 4 1
371
+ 1 5 1
372
+ 5 6 1
373
+ 5 7 1
374
+ 7 8 1
375
+ 7 9 1
376
+ 7 10 1
377
+ !entry.DMS.unit.hierarchy table str abovetype int abovex str belowtype int belowx
378
+ "U" 0 "R" 1
379
+ "R" 1 "A" 1
380
+ "R" 1 "A" 2
381
+ "R" 1 "A" 3
382
+ "R" 1 "A" 4
383
+ "R" 1 "A" 5
384
+ "R" 1 "A" 6
385
+ "R" 1 "A" 7
386
+ "R" 1 "A" 8
387
+ "R" 1 "A" 9
388
+ "R" 1 "A" 10
389
+ !entry.DMS.unit.name single str
390
+ "DMS"
391
+ !entry.DMS.unit.positions table dbl x dbl y dbl z
392
+ 1.352215 -0.788524 0.179722
393
+ 1.336198 -1.762516 -0.294359
394
+ 1.276922 -0.884449 1.255734
395
+ 2.275129 -0.280936 -0.067490
396
+ -1.000000E-06 0.222543 -0.433160
397
+ -6.000000E-06 1.469687 0.373265
398
+ -1.352208 -0.788533 0.179722
399
+ -2.275126 -0.280954 -0.067488
400
+ -1.336184 -1.762525 -0.294360
401
+ -1.276914 -0.884460 1.255734
402
+ !entry.DMS.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
403
+ 0 0 0 0 0 0
404
+ !entry.DMS.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
405
+ "DMS" 1 11 1 "w" 0
406
+ !entry.DMS.unit.residuesPdbSequenceNumber array int
407
+ 0
408
+ !entry.DMS.unit.solventcap array dbl
409
+ -1.000000
410
+ 0.0
411
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412
+ 0.0
413
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414
+ !entry.DMS.unit.velocities table dbl x dbl y dbl z
415
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416
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417
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418
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419
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420
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421
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422
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423
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424
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425
+ !entry.IPH.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
426
+ "C1" "PB" 0 1 131072 1 6 0.150000
427
+ "O1" "PO" 0 1 131072 2 8 -0.585000
428
+ "C2" "PA" 0 1 131072 3 6 -0.115000
429
+ "H2" "PI" 0 1 131072 4 1 0.115000
430
+ "C3" "PA" 0 1 131072 5 6 -0.115000
431
+ "H3" "PI" 0 1 131072 6 1 0.115000
432
+ "C4" "PA" 0 1 131072 7 6 -0.115000
433
+ "H4" "PI" 0 1 131072 8 1 0.115000
434
+ "C5" "PA" 0 1 131072 9 6 -0.115000
435
+ "H5" "PI" 0 1 131072 10 1 0.115000
436
+ "C6" "PA" 0 1 131072 11 6 -0.115000
437
+ "H6" "PI" 0 1 131072 12 1 0.115000
438
+ "H11" "PJ" 0 1 131072 13 1 0.435000
439
+ !entry.IPH.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
440
+ "C1" "PB" 0 -1 0.0
441
+ "O1" "PO" 0 -1 0.0
442
+ "C2" "PA" 0 -1 0.0
443
+ "H2" "PI" 0 -1 0.0
444
+ "C3" "PA" 0 -1 0.0
445
+ "H3" "PI" 0 -1 0.0
446
+ "C4" "PA" 0 -1 0.0
447
+ "H4" "PI" 0 -1 0.0
448
+ "C5" "PA" 0 -1 0.0
449
+ "H5" "PI" 0 -1 0.0
450
+ "C6" "PA" 0 -1 0.0
451
+ "H6" "PI" 0 -1 0.0
452
+ "H11" "PJ" 0 -1 0.0
453
+ !entry.IPH.unit.boundbox array dbl
454
+ -1.000000
455
+ 0.0
456
+ 0.0
457
+ 0.0
458
+ 0.0
459
+ !entry.IPH.unit.childsequence single int
460
+ 2
461
+ !entry.IPH.unit.connect array int
462
+ 0
463
+ 0
464
+ !entry.IPH.unit.connectivity table int atom1x int atom2x int flags
465
+ 1 2 1
466
+ 1 3 1
467
+ 1 11 1
468
+ 2 13 1
469
+ 3 4 1
470
+ 3 5 1
471
+ 5 6 1
472
+ 5 7 1
473
+ 7 8 1
474
+ 7 9 1
475
+ 9 10 1
476
+ 9 11 1
477
+ 11 12 1
478
+ !entry.IPH.unit.hierarchy table str abovetype int abovex str belowtype int belowx
479
+ "U" 0 "R" 1
480
+ "R" 1 "A" 1
481
+ "R" 1 "A" 2
482
+ "R" 1 "A" 3
483
+ "R" 1 "A" 4
484
+ "R" 1 "A" 5
485
+ "R" 1 "A" 6
486
+ "R" 1 "A" 7
487
+ "R" 1 "A" 8
488
+ "R" 1 "A" 9
489
+ "R" 1 "A" 10
490
+ "R" 1 "A" 11
491
+ "R" 1 "A" 12
492
+ "R" 1 "A" 13
493
+ !entry.IPH.unit.name single str
494
+ "IPH"
495
+ !entry.IPH.unit.positions table dbl x dbl y dbl z
496
+ 0.562381 1.214422 0.361091
497
+ 0.998762 2.156756 0.641280
498
+ -0.779445 1.146099 0.020041
499
+ -1.384257 2.035418 0.035592
500
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501
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502
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503
+ -0.998762 -2.156756 -0.641280
504
+ 0.779445 -1.146099 -0.020041
505
+ 1.384257 -2.035417 -0.035592
506
+ 1.341826 0.068323 0.341049
507
+ 2.383019 0.121338 0.605688
508
+ 1.498762 3.056756 0.941280
509
+ !entry.IPH.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
510
+ 0 0 0 0 0 0
511
+ !entry.IPH.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
512
+ "IPH" 1 14 1 "w" 0
513
+ !entry.IPH.unit.residuesPdbSequenceNumber array int
514
+ 0
515
+ !entry.IPH.unit.solventcap array dbl
516
+ -1.000000
517
+ 0.0
518
+ 0.0
519
+ 0.0
520
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521
+ !entry.IPH.unit.velocities table dbl x dbl y dbl z
522
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523
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524
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525
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526
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527
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528
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529
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530
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531
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532
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533
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534
+ 0.0 0.0 0.0
535
+ !entry.MOH.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
536
+ "H11" "H1" 0 1 131072 1 1 -0.009600
537
+ "C1" "CT" 0 1 131072 2 6 0.282400
538
+ "H12" "H1" 0 1 131072 3 1 -0.009600
539
+ "H13" "H1" 0 1 131072 4 1 -0.009600
540
+ "O2" "OH" 0 1 131072 5 8 -0.633700
541
+ "H2" "HO" 0 1 131072 6 1 0.380100
542
+ !entry.MOH.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
543
+ "H11" "H1" 0 -1 0.0
544
+ "C1" "CT" 0 -1 0.0
545
+ "H12" "H1" 0 -1 0.0
546
+ "H13" "H1" 0 -1 0.0
547
+ "O2" "OH" 0 -1 0.0
548
+ "H2" "HO" 0 -1 0.0
549
+ !entry.MOH.unit.boundbox array dbl
550
+ -1.000000
551
+ 0.0
552
+ 0.0
553
+ 0.0
554
+ 0.0
555
+ !entry.MOH.unit.childsequence single int
556
+ 2
557
+ !entry.MOH.unit.connect array int
558
+ 0
559
+ 0
560
+ !entry.MOH.unit.connectivity table int atom1x int atom2x int flags
561
+ 1 2 1
562
+ 2 3 1
563
+ 2 4 1
564
+ 2 5 1
565
+ 5 6 1
566
+ !entry.MOH.unit.hierarchy table str abovetype int abovex str belowtype int belowx
567
+ "U" 0 "R" 1
568
+ "R" 1 "A" 1
569
+ "R" 1 "A" 2
570
+ "R" 1 "A" 3
571
+ "R" 1 "A" 4
572
+ "R" 1 "A" 5
573
+ "R" 1 "A" 6
574
+ !entry.MOH.unit.name single str
575
+ "MOH"
576
+ !entry.MOH.unit.positions table dbl x dbl y dbl z
577
+ -1.076631 0.975959 0.0
578
+ -0.655546 -0.019723 0.0
579
+ -1.012856 -0.543375 -0.883547
580
+ -1.012855 -0.543375 0.883547
581
+ 0.736965 0.120595 0.0
582
+ 1.139896 -0.735629 0.0
583
+ !entry.MOH.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
584
+ 0 0 0 0 0 0
585
+ !entry.MOH.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
586
+ "MOH" 1 7 1 "w" 0
587
+ !entry.MOH.unit.residuesPdbSequenceNumber array int
588
+ 0
589
+ !entry.MOH.unit.solventcap array dbl
590
+ -1.000000
591
+ 0.0
592
+ 0.0
593
+ 0.0
594
+ 0.0
595
+ !entry.MOH.unit.velocities table dbl x dbl y dbl z
596
+ 0.0 0.0 0.0
597
+ 0.0 0.0 0.0
598
+ 0.0 0.0 0.0
599
+ 0.0 0.0 0.0
600
+ 0.0 0.0 0.0
601
+ 0.0 0.0 0.0
602
+ !entry.NMA.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
603
+ "H1" "HC" 0 1 131072 1 1 0.017300
604
+ "C1" "CT" 0 1 131072 2 6 -0.041100
605
+ "H2" "HC" 0 1 131072 3 1 0.017300
606
+ "H3" "HC" 0 1 131072 4 1 0.017300
607
+ "C" "C" 0 1 131072 5 6 0.586900
608
+ "O" "MO" 0 1 131072 6 8 -0.591100
609
+ "N" "N" 0 1 131072 7 7 -0.419200
610
+ "HN" "H" 0 1 131072 8 1 0.282300
611
+ "C2" "CT" 0 1 131072 9 6 -0.207800
612
+ "H4" "H1" 0 1 131072 10 1 0.112700
613
+ "H5" "H1" 0 1 131072 11 1 0.112700
614
+ "H6" "H1" 0 1 131072 12 1 0.112700
615
+ !entry.NMA.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
616
+ "H1" "HC" 0 -1 0.0
617
+ "C1" "CT" 0 -1 0.0
618
+ "H2" "HC" 0 -1 0.0
619
+ "H3" "HC" 0 -1 0.0
620
+ "C" "C" 0 -1 0.0
621
+ "O" "MO" 0 -1 0.0
622
+ "N" "N" 0 -1 0.0
623
+ "HN" "H" 0 -1 0.0
624
+ "C2" "CT" 0 -1 0.0
625
+ "H4" "H1" 0 -1 0.0
626
+ "H5" "H1" 0 -1 0.0
627
+ "H6" "H1" 0 -1 0.0
628
+ !entry.NMA.unit.boundbox array dbl
629
+ -1.000000
630
+ 0.0
631
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632
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633
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634
+ !entry.NMA.unit.childsequence single int
635
+ 2
636
+ !entry.NMA.unit.connect array int
637
+ 0
638
+ 0
639
+ !entry.NMA.unit.connectivity table int atom1x int atom2x int flags
640
+ 1 2 1
641
+ 2 5 1
642
+ 2 3 1
643
+ 2 4 1
644
+ 5 6 1
645
+ 5 7 1
646
+ 7 9 1
647
+ 7 8 1
648
+ 9 10 1
649
+ 9 11 1
650
+ 9 12 1
651
+ !entry.NMA.unit.hierarchy table str abovetype int abovex str belowtype int belowx
652
+ "U" 0 "R" 1
653
+ "R" 1 "A" 1
654
+ "R" 1 "A" 2
655
+ "R" 1 "A" 3
656
+ "R" 1 "A" 4
657
+ "R" 1 "A" 5
658
+ "R" 1 "A" 6
659
+ "R" 1 "A" 7
660
+ "R" 1 "A" 8
661
+ "R" 1 "A" 9
662
+ "R" 1 "A" 10
663
+ "R" 1 "A" 11
664
+ "R" 1 "A" 12
665
+ !entry.NMA.unit.name single str
666
+ "NMA"
667
+ !entry.NMA.unit.positions table dbl x dbl y dbl z
668
+ 15.821200 21.442700 9.323500
669
+ 16.374200 22.338700 9.041500
670
+ 16.131200 22.709700 8.045500
671
+ 17.423200 22.119700 8.842500
672
+ 16.079200 23.456700 10.116500
673
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674
+ 17.061200 23.688700 10.988500
675
+ 17.809200 23.016700 10.889500
676
+ 17.419200 25.060700 11.269500
677
+ 18.369200 25.024700 11.802500
678
+ 17.466200 25.672700 10.369500
679
+ 16.702200 25.482700 11.974500
680
+ !entry.NMA.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
681
+ 0 0 0 0 0 0
682
+ !entry.NMA.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
683
+ "NMA" 1 13 1 "w" 0
684
+ !entry.NMA.unit.residuesPdbSequenceNumber array int
685
+ 0
686
+ !entry.NMA.unit.solventcap array dbl
687
+ -1.000000
688
+ 0.0
689
+ 0.0
690
+ 0.0
691
+ 0.0
692
+ !entry.NMA.unit.velocities table dbl x dbl y dbl z
693
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694
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695
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696
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697
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698
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699
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700
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701
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702
+ 0.0 0.0 0.0
703
+ 0.0 0.0 0.0
704
+ 0.0 0.0 0.0
705
+ !entry.TFE.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
706
+ "C1" "TC" 0 1 131072 1 6 0.906650
707
+ "F11" "TF" 0 1 131072 2 9 -0.321850
708
+ "F12" "TF" 0 1 131072 3 9 -0.321850
709
+ "F13" "TF" 0 1 131072 4 9 -0.321850
710
+ "C2" "TC" 0 1 131072 5 6 0.047600
711
+ "H21" "H1" 0 1 131072 6 1 0.084100
712
+ "H22" "H1" 0 1 131072 7 1 0.084100
713
+ "O3" "TO" 0 1 131072 8 8 -0.651900
714
+ "H3" "HO" 0 1 131072 9 1 0.495000
715
+ !entry.TFE.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
716
+ "C1" "TC" 0 -1 0.0
717
+ "F11" "TF" 0 -1 0.0
718
+ "F12" "TF" 0 -1 0.0
719
+ "F13" "TF" 0 -1 0.0
720
+ "C2" "TC" 0 -1 0.0
721
+ "H21" "H1" 0 -1 0.0
722
+ "H22" "H1" 0 -1 0.0
723
+ "O3" "TO" 0 -1 0.0
724
+ "H3" "HO" 0 -1 0.0
725
+ !entry.TFE.unit.boundbox array dbl
726
+ -1.000000
727
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728
+ 0.0
729
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730
+ 0.0
731
+ !entry.TFE.unit.childsequence single int
732
+ 2
733
+ !entry.TFE.unit.connect array int
734
+ 0
735
+ 0
736
+ !entry.TFE.unit.connectivity table int atom1x int atom2x int flags
737
+ 1 2 1
738
+ 1 3 1
739
+ 1 4 1
740
+ 1 5 1
741
+ 5 6 1
742
+ 5 7 1
743
+ 5 8 1
744
+ 8 9 1
745
+ !entry.TFE.unit.hierarchy table str abovetype int abovex str belowtype int belowx
746
+ "U" 0 "R" 1
747
+ "R" 1 "A" 1
748
+ "R" 1 "A" 2
749
+ "R" 1 "A" 3
750
+ "R" 1 "A" 4
751
+ "R" 1 "A" 5
752
+ "R" 1 "A" 6
753
+ "R" 1 "A" 7
754
+ "R" 1 "A" 8
755
+ "R" 1 "A" 9
756
+ !entry.TFE.unit.name single str
757
+ "TFE"
758
+ !entry.TFE.unit.positions table dbl x dbl y dbl z
759
+ -0.418911 0.006161 -1.000000E-06
760
+ -1.405454 0.892984 -8.000000E-06
761
+ -0.564976 -0.755627 -1.065998
762
+ -0.564979 -0.755614 1.066006
763
+ 0.903062 0.731787 -3.000000E-06
764
+ 0.928153 1.362287 -0.882733
765
+ 0.928150 1.362298 0.882720
766
+ 1.912325 -0.223499 4.000000E-06
767
+ 2.758872 0.200033 8.000000E-06
768
+ !entry.TFE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
769
+ 0 0 0 0 0 0
770
+ !entry.TFE.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
771
+ "TFE" 1 10 1 "w" 0
772
+ !entry.TFE.unit.residuesPdbSequenceNumber array int
773
+ 0
774
+ !entry.TFE.unit.solventcap array dbl
775
+ -1.000000
776
+ 0.0
777
+ 0.0
778
+ 0.0
779
+ 0.0
780
+ !entry.TFE.unit.velocities table dbl x dbl y dbl z
781
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782
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783
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784
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785
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786
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787
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788
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789
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