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...	...	@@ -43,48 +43,6 @@
43	43
44	44	{{{ python3 distance_fluctuation.py -h}}}
45	45
46		-
47		-{{{optional arguments:
48		- -h, --help show this help message and exit
49		-
50		-Required arguments:
51		- -ext {pdb,xyz}, --file_ext {pdb,xyz}
52		- Input trajectory file iformat (options: .pdb or .xyz)
53		- -n N_AA, --n_aa N_AA Number of aminoacids in each frame of the .pdb
54		- trajectory
55		-
56		-Optional arguments:
57		- -i IN_NAME, --in_name IN_NAME
58		- Name of the trajectory file (default: trj)
59		- -s S_FRAME, --s_frame S_FRAME
60		- Index of the initial frame (default = 0)
61		- -e E_FRAME, --e_frame E_FRAME
62		- Index of the last frame (default = end)
63		- -c CUTOFF, --cutoff CUTOFF
64		- Cutoff for the distance fluctuation analysis (default = 5)
65		- -t TOLERANCE, --tolerance TOLERANCE
66		- Tolerance for the distance fluctuation analysis (default = 0)
67		- -p {all,c-a}, --pdb_type {all,c-a}
68		- Type of pdb file submitted (only C-alpha, all protein atoms)
69		- -l {s,seq,v,volume}, --local {s,seq,v,volume}
70		- Type of local cutoff used, sequence or volume (default = seq)
71		- -r RADIUS, --radius RADIUS
72		- Radius of the area cutoff (default = 7A)
73		- -rs RES_START, --res_start RES_START
74		- Starting residue if the PDB does not start with res.num. 1
75		- -ro RMS_OUT, --rms_out RMS_OUT
76		- RMS distance output filename (without extension)
77		- -ao AVG_OUT, --avg_out AVG_OUT
78		- Average distance output filename (without extension)
79		- -so SEQ_OUT, --seq_out SEQ_OUT
80		- Profile sequence output filename (without extension)
81		- -da DIST_AN, --dist_an DIST_AN
82		- Distance analysis output filename (without extension)
83		- --blocks BLOCKS File with domains borders
84		-
85		- -rb RMS_B_OUT, --rms_b_out RMS_B_OUT
86		- RMS distance blocks output filename}}}
87		-
88	88
89	89	)))
90	90