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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
View
@@ -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
```
View
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@@ -1,71 +0,0 @@
-import numpy as np
-import sys
-import os
-#from math import exp
-#from Bio.PDB import *
-
-
-'''
-For each FNM file -- add 0-vectors to so that 10 modes are avail
-
-USAGE:
-python add_zeros_to_fnm.py
-stdin/stdout
-
-'''
-
-
-
-def check_if_list_has_only_floats(list_to_check):
- status = True
- list_of_float_like_chars = ("-", ".", "0", "1", "2", "3", "4", "5", "6", "7", "8", "9")
- for element in list_to_check:
- for charact in element:
- if charact not in list_of_float_like_chars:
- return False
- return status
-
-
-num_modes = 0
-avail_fnm_file_lines = list()
-fnm_file_to_rd = sys.stdin
-mode___2___num_vectors = {}
-number_of_vectors_in_mode = 0 ## re-setting the counter
-for line in fnm_file_to_rd:
- avail_fnm_file_lines.append(line)
- if line[0] is not "#": ## ie, if we're not at file header
- ln_elmnts = list()
- ln_elmnts = line.split()
- if "BEGIN MODE" in line:
- num_modes += 1
- mode_indx = int(ln_elmnts[2])
- number_of_vectors_in_mode = 0 ## re-setting the counter
- if (len(ln_elmnts) == 3) and (check_if_list_has_only_floats(ln_elmnts)):
- number_of_vectors_in_mode += 1
- if line[0:3] == "END":
- mode___2___num_vectors[mode_indx] = number_of_vectors_in_mode
-fnm_file_to_rd.close()
- #for mode in mode___2___num_vectors:
- # print fnm_file + " mode: " + str(mode) + " num_modes: " + str(num_modes)
-
-out_file_name_to_wrt = sys.stdout
-for avail_line in avail_fnm_file_lines:
- out_file_name_to_wrt.write(avail_line)
-
-
-num_remaining_modes_to_print = 10 - num_modes
-starting_mode = 17 - num_remaining_modes_to_print
-mode_to_print = starting_mode
-while mode_to_print <= 16:
- out_file_name_to_wrt.write("BEGIN MODE " + str(mode_to_print) + "\n")
- vect = 0
- while vect < number_of_vectors_in_mode:
- out_file_name_to_wrt.write("0.0000000000 0.0000000000 0.0000000000\n")
- vect += 1
- out_file_name_to_wrt.write("END\n\n")
- mode_to_print += 1
-out_file_name_to_wrt.close()
-
-
-#print "\n\n --- run complete -- \n\n"
-
@@ -1,106 +0,0 @@
-#!python
-
-# This example shows how to calculate approximate low-frequency
-# modes for big proteins. For a description of the techniques,
-# see
-#
-# K. Hinsen
-# Analysis of domain motions by approximate normal mode calculations
-# Proteins 33, 417 (1998)
-#
-# and
-#
-# K. Hinsen, A.J. Petrescu, S. Dellerue, M.C. Bellissent-Funel, G.R. Kneller
-# Harmonicity in slow protein dynamics
-# Chem. Phys. 261, 25 (2000)
-#
-##
-#
-# Adaptation by Simon Mitternacht 2010-2011.
-#
-
-import sys
-from MMTK import *
-from MMTK.Proteins import Protein
-from MMTK.Proteins import PeptideChain
-from MMTK.ForceFields import CalphaForceField
-from MMTK.FourierBasis import FourierBasis, estimateCutoff
-from MMTK.NormalModes import NormalModes, VibrationalModes, SparseMatrixSubspaceNormalModes
-from numpy import *
-import re
-
-
-# top_nm.pl only reads the first 20 modes before exiting. This results in a broken pipe error.
-# Prevent calpha_modes.py from crashing by ignoring SIGPIPE signal.
-import signal
-signal.signal(signal.SIGPIPE, signal.SIG_DFL)
-
-
-
-
-def modes_in_sequential_order(protein,modes):
- modes_inseq = []
- for mode in modes: #[modes.rawMode(i) for i in xrange(len(modes))]:
- tmp_mode = []
- for chain in protein:
- for residue in chain.residues():
- tmp = mode[residue.peptide.C_alpha]
- norm = 1#math.sqrt(residue.mass())
- tmp_vec = [tmp.x()/norm, tmp.y()/norm, tmp.z()/norm]
- tmp_mode.append(tmp_vec)
- modes_inseq.append(tmp_mode)
- return modes_inseq
-
-
-
-if (len(sys.argv) != 2 and len(sys.argv) != 3):
- print "Usage: %s pdb [v|f]" % sys.argv[0]
- print "Outputs the 10 % lowest frequency normal modes,to stdout. "
- print "Second optional argument specifies if VibrationalModes or FourierBasis should be used."
- exit()
-
-
-# Check CL arguments
-pdb_file = sys.argv[1]
-type = "auto"
-if (len(sys.argv) > 2):
- arg = sys.argv[2]
- if (arg != 'v' and arg != 'f'):
- sys.stderr.write("Argument \'%s\' invalid" % arg)
- exit()
- type = arg
-
-# Construct system
-universe = InfiniteUniverse(CalphaForceField(2.5))
-universe.protein = Protein(pdb_file, model='calpha')
-
-# Find a reasonable basis set size and cutoff
-cutoff = None
-if (type == "auto") or (type == "f"):
- nbasis = max(10, universe.numberOfAtoms()/10)
- cutoff, nbasis = estimateCutoff(universe, nbasis)
-
-# calculate modes for first system
-if (cutoff is None):
- # Do full normal mode calculation
- print "# VibrationalModes"
- modes = VibrationalModes(universe)
- print "# %d" % len(modes)
-else:
- # Do subspace mode calculation with Fourier basis for large proteins
- print "# FourierBasis: cutoff = %d, nbasis = %d" % (cutoff, nbasis)
- subspace = FourierBasis(universe, cutoff)
- subspace.may_modify = 1
- modes = SparseMatrixSubspaceNormalModes(universe, subspace)
-
-modes_seq = modes_in_sequential_order(universe.protein, modes)
-N = min(len(modes_seq),3*universe.numberOfAtoms()/10+6)
-
-for i in range(6,N):
- print "BEGIN MODE %d" % ((i+1))
- for d in modes_seq[i]:
- print "%.10f %.10f %.10f" % (d[0], d[1], d[2])
- print "END"
- print ""
-
-
@@ -1,35 +0,0 @@
-CC = gcc -std=c99
-OBJS = pdbFile.o modes.o transformations.o network.o surfaceProbe.o bindingSiteMeasures.o bindingSites.o
-
-OPTIONS = -c -O3 -Wall -ggdb
-
-LIBS = -lm
-
-all: bindingSites
-
-bindingSites: $(OBJS)
- $(CC) -o bindingSites $(OBJS) $(LIBS)
-
-bindingSites.o: bindingSites.c
- $(CC) $(OPTIONS) bindingSites.c $(LIBS)
-
-pdbFile.o: pdbFile.c pdbFile.h
- $(CC) $(OPTIONS) pdbFile.c $(LIBS)
-
-surfaceProbe.o: surfaceProbe.c surfaceProbe.h
- $(CC) $(OPTIONS) surfaceProbe.c $(LIBS)
-
-network.o: network.c network.h
- $(CC) $(OPTIONS) network.c $(LIBS)
-
-transformations.o: transformations.c transformations.h
- $(CC) $(OPTIONS) transformations.c $(LIBS)
-
-modes.o: modes.c modes.h
- $(CC) $(OPTIONS) modes.c $(LIBS)
-
-bindingSiteMeasures.o: bindingSiteMeasures.c bindingSiteMeasures.h
- $(CC) $(OPTIONS) bindingSiteMeasures.c $(LIBS)
-
-clean:
- rm -f *.o core
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