abmptools 1.15.0__py3-none-any.whl

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Files changed (75) hide show
  1. abmptools/__init__.py +24 -0
  2. abmptools/abinit_io.py +2025 -0
  3. abmptools/addsolvfrag.py +328 -0
  4. abmptools/ajf2config.py +50 -0
  5. abmptools/ajfserial.py +75 -0
  6. abmptools/amorphous/__init__.py +26 -0
  7. abmptools/amorphous/__main__.py +5 -0
  8. abmptools/amorphous/builder.py +232 -0
  9. abmptools/amorphous/cli.py +154 -0
  10. abmptools/amorphous/density.py +90 -0
  11. abmptools/amorphous/mdp_protocol.py +258 -0
  12. abmptools/amorphous/models.py +72 -0
  13. abmptools/amorphous/molecule_prep.py +131 -0
  14. abmptools/amorphous/ndx_writer.py +67 -0
  15. abmptools/amorphous/packing.py +157 -0
  16. abmptools/amorphous/parameterizer.py +130 -0
  17. abmptools/anlfmo.py +3760 -0
  18. abmptools/convertcpf.py +68 -0
  19. abmptools/core/__init__.py +6 -0
  20. abmptools/core/system_model.py +302 -0
  21. abmptools/cpf2ifielist.py +96 -0
  22. abmptools/cpfmanager.py +1164 -0
  23. abmptools/f90/bin/readifiepiedalib.so +0 -0
  24. abmptools/generate_difie.py +293 -0
  25. abmptools/generateajf.py +291 -0
  26. abmptools/geomopt/__init__.py +37 -0
  27. abmptools/geomopt/mace_optimizer.py +331 -0
  28. abmptools/geomopt/openff_openmm_minimizer.py +651 -0
  29. abmptools/geomopt/pyscf_optimizer.py +679 -0
  30. abmptools/getcharge.py +81 -0
  31. abmptools/getifiepieda.py +328 -0
  32. abmptools/gro2udf/__init__.py +34 -0
  33. abmptools/gro2udf/__main__.py +13 -0
  34. abmptools/gro2udf/cli.py +123 -0
  35. abmptools/gro2udf/default_template.udf +202 -0
  36. abmptools/gro2udf/exporter.py +112 -0
  37. abmptools/gro2udf/gro_adapter.py +140 -0
  38. abmptools/gro2udf/gro_parser.py +159 -0
  39. abmptools/gro2udf/mdp_parser.py +101 -0
  40. abmptools/gro2udf/top_adapter.py +395 -0
  41. abmptools/gro2udf/top_exporter.py +465 -0
  42. abmptools/gro2udf/top_model.py +223 -0
  43. abmptools/gro2udf/top_parser.py +647 -0
  44. abmptools/gro2udf/udf_writer.py +94 -0
  45. abmptools/log2config.py +84 -0
  46. abmptools/log2cpf.py +127 -0
  47. abmptools/logmanager.py +1427 -0
  48. abmptools/mol_io.py +230 -0
  49. abmptools/molcalc.py +1631 -0
  50. abmptools/pdb2fmo.py +121 -0
  51. abmptools/pdb_io.py +1041 -0
  52. abmptools/pdbmodify.py +337 -0
  53. abmptools/readcif.py +982 -0
  54. abmptools/setfmo.py +640 -0
  55. abmptools/udf2fmo.py +113 -0
  56. abmptools/udf2gro/__init__.py +19 -0
  57. abmptools/udf2gro/__main__.py +11 -0
  58. abmptools/udf2gro/cli.py +46 -0
  59. abmptools/udf2gro/exporter.py +99 -0
  60. abmptools/udf2gro/gromacs/__init__.py +1 -0
  61. abmptools/udf2gro/gromacs/writers/__init__.py +7 -0
  62. abmptools/udf2gro/gromacs/writers/gro_writer.py +76 -0
  63. abmptools/udf2gro/gromacs/writers/itp_writer.py +22 -0
  64. abmptools/udf2gro/gromacs/writers/mdp_writer.py +150 -0
  65. abmptools/udf2gro/gromacs/writers/top_writer.py +307 -0
  66. abmptools/udf2gro/udf_adapter.py +1274 -0
  67. abmptools/udf_io.py +903 -0
  68. abmptools/udfcreate.py +1455 -0
  69. abmptools/udfrm_io.py +173 -0
  70. abmptools-1.15.0.dist-info/METADATA +166 -0
  71. abmptools-1.15.0.dist-info/RECORD +75 -0
  72. abmptools-1.15.0.dist-info/WHEEL +5 -0
  73. abmptools-1.15.0.dist-info/entry_points.txt +15 -0
  74. abmptools-1.15.0.dist-info/licenses/LICENSE +21 -0
  75. abmptools-1.15.0.dist-info/top_level.txt +1 -0
abmptools/__init__.py ADDED
@@ -0,0 +1,24 @@
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+ from .pdb_io import pdb_io
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+ from .abinit_io import abinit_io
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+ from .setfmo import setfmo
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+ from .mol_io import mol_io
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+ from .molcalc import molcalc
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+ from .udfrm_io import udfrm_io
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+ from .udf_io import udf_io
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+ from .udfcreate import udfcreate
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+ from .anlfmo import anlfmo
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+ from .cpfmanager import CPFManager
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+ from .logmanager import LOGManager
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+ # udf2gro and gro2udf are imported lazily because they require UDFManager (optional dep)
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+ try:
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+ from .udf2gro import Exporter as Udf2groExporter
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+ except ImportError:
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+ pass
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+ try:
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+ from .gro2udf import Exporter as Gro2udfExporter
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+ except ImportError:
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+ pass
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+ try:
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+ from .amorphous import AmorphousBuilder
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+ except ImportError:
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+ pass