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folder name change and README minor format

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ShantaoL committed Sep 16, 2015
1 parent ebc77da commit feb882e4e156427da7bc50bb3d260ad76f0705ab
Showing with 9 additions and 21,320 deletions.
  1. +7 −2 README.md
  2. BIN code_bundle_BL/.DS_Store
  3. +0 −71 code_bundle_BL/add_zeros_to_fnm.py
  4. +0 −106 code_bundle_BL/calpha_modes.py
  5. +0 −35 code_bundle_BL/code_pack/Makefile
  6. +0 −281 code_bundle_BL/code_pack/bindingSiteMeasures.c
  7. +0 −29 code_bundle_BL/code_pack/bindingSiteMeasures.h
  8. BIN code_bundle_BL/code_pack/bindingSiteMeasures.o
  9. BIN code_bundle_BL/code_pack/bindingSites
  10. +0 −608 code_bundle_BL/code_pack/bindingSites.c
  11. BIN code_bundle_BL/code_pack/bindingSites.o
  12. +0 −147 code_bundle_BL/code_pack/modes.c
  13. +0 −28 code_bundle_BL/code_pack/modes.h
  14. BIN code_bundle_BL/code_pack/modes.o
  15. +0 −207 code_bundle_BL/code_pack/network.c
  16. +0 −58 code_bundle_BL/code_pack/network.h
  17. BIN code_bundle_BL/code_pack/network.o
  18. +0 −85 code_bundle_BL/code_pack/pdbFile.c
  19. +0 −37 code_bundle_BL/code_pack/pdbFile.h
  20. BIN code_bundle_BL/code_pack/pdbFile.o
  21. +0 −1,650 code_bundle_BL/code_pack/surfaceProbe.c
  22. +0 −149 code_bundle_BL/code_pack/surfaceProbe.h
  23. BIN code_bundle_BL/code_pack/surfaceProbe.o
  24. +0 −1,654 code_bundle_BL/code_pack/surfaceProbe2.c
  25. +0 −1,649 code_bundle_BL/code_pack/surfaceProbe_ORIG.c
  26. +0 −466 code_bundle_BL/code_pack/transformations.c
  27. +0 −70 code_bundle_BL/code_pack/transformations.h
  28. BIN code_bundle_BL/code_pack/transformations.o
  29. +0 −153 code_bundle_BL/gap_theory_calculations.py
  30. +0 −201 code_bundle_BL/get_box_size_to_det_num_MC_steps.py
  31. +0 −222 code_bundle_BL/identify_high_confidence_BL_sites.py
  32. +0 −136 code_bundle_BL/just_make_simplified_pdb__CA_LINES_ONLY.py
  33. +0 −132 code_bundle_BL/just_make_simplified_pdb_and_rm_HETATM.py
  34. +0 −282 code_bundle_BL/map_raw_sites__to__BL_sites.py
  35. +0 −22 code_bundle_BL/top_nm.pl
  36. BIN code_bundle_GN/.DS_Store
  37. +0 −71 code_bundle_GN/add_zeros_to_fnm.py
  38. +0 −106 code_bundle_GN/calpha_modes.py
  39. +0 −268 code_bundle_GN/correlate_motions_ver2.py
  40. +0 −113 code_bundle_GN/get_highest_btwnss_edges_frm_gn_output.py
  41. +0 −136 code_bundle_GN/just_make_simplified_pdb__CA_LINES_ONLY.py
  42. +0 −132 code_bundle_GN/just_make_simplified_pdb_and_rm_HETATM.py
  43. +0 −271 code_bundle_GN/make_contact_map.py
  44. +0 −29 code_bundle_GN/mod_cont_map_for_gn.py
  45. +0 −27 code_bundle_GN/networkTools/Community.h
  46. +0 −84 code_bundle_GN/networkTools/Flow.c
  47. +0 −91 code_bundle_GN/networkTools/Flow.h
  48. BIN code_bundle_GN/networkTools/Flow.o
  49. +0 −197 code_bundle_GN/networkTools/GNCommunities.c
  50. BIN code_bundle_GN/networkTools/GNCommunities.o
  51. +0 −121 code_bundle_GN/networkTools/GNCommunities_ORIG.c
  52. +0 −2,132 code_bundle_GN/networkTools/Graph.c
  53. +0 −301 code_bundle_GN/networkTools/Graph.h
  54. BIN code_bundle_GN/networkTools/Graph.o
  55. +0 −84 code_bundle_GN/networkTools/GraphNetwork.c
  56. +0 −2,105 code_bundle_GN/networkTools/Graph_ORIG.c
  57. +0 −2,120 code_bundle_GN/networkTools/Graph_mem_freed.c
  58. +0 −2,132 code_bundle_GN/networkTools/Graph_prv.c
  59. +0 −306 code_bundle_GN/networkTools/List.c
  60. +0 −212 code_bundle_GN/networkTools/List.h
  61. BIN code_bundle_GN/networkTools/List.o
  62. +0 −60 code_bundle_GN/networkTools/Makefile
  63. +0 −163 code_bundle_GN/networkTools/SuboptimalPaths.c
  64. BIN code_bundle_GN/networkTools/SuboptimalPaths.o
  65. +0 −168 code_bundle_GN/networkTools/Tree.c
  66. +0 −119 code_bundle_GN/networkTools/Tree.h
  67. BIN code_bundle_GN/networkTools/Tree.o
  68. +0 −271 code_bundle_GN/networkTools/alignment.c
  69. +0 −122 code_bundle_GN/networkTools/alignment.h
  70. BIN code_bundle_GN/networkTools/gncommunities
  71. +0 −393 code_bundle_GN/networkTools/networkComparison.c
  72. +0 −107 code_bundle_GN/networkTools/networkComparison.h
  73. +0 −140 code_bundle_GN/networkTools/networkEvolution.c
  74. BIN code_bundle_GN/networkTools/subopt
  75. +0 −122 code_bundle_GN/residues__2__resids_types_chains.py
  76. +0 −113 code_bundle_GN/residues__2__resids_types_chains_wo_VMD.py
  77. +0 −22 code_bundle_GN/top_nm.pl
  78. +2 −2 stress.sh
@@ -11,11 +11,16 @@ Python, Perl, C compiler, MMTK

Before running the code, you need to compile the C package, type:
```
cd code_bundle_BL/code_pack
cd INSTALLFOLDER/surface_residues/code_pack
make clean
make
cd ../../code_bundle_GN/networkTools
cd INSTALLFOLDER/interior_residues/networkTools
make clean
make
```

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