TracedNeighbors

Installation

$ mkdir build
$ cd build
$ cmake -DCMAKE_BUILD_TYPE=release ..
$ make -j4
$ src/TraceHBonds

To cross-compile, use:

$ cmake -DCMAKE_BUILD_TYPE=release -DCMAKE_TOOLCHAIN_FILE=<Toolchain cmake file> ..

Data file format

Lines starting with a '#' are treated as comments and ignored. As an example, a few lines from a data file follows.

# Current Element : 12
# Atoms in Chain : 3
# Molecules : 2
# Unique forcefields : 2
# Times chain switched between Molecules (switching) : 1
# Periodic boundary conditions applied.
  19.4613   24.7503    8.3695 [O]  Molecule46  O12  o2h
  19.1470   25.4855    8.8586 [H]  Molecule46  H46  h1o
  18.4838   26.8268    9.4373 [O]  Molecule11  O2520  o2h
# Chain end-to-end distance: 2.5313


# Current Element : 13
# Atoms in Chain : 9
# Molecules : 2
# Unique forcefields : 3
# Times chain switched between Molecules (switching) : 2
# Periodic boundary conditions applied.
  30.9381   14.5898   12.0551 [O]  Molecule30  O7312  o2h
  30.3610   14.9652   11.4027 [H]  Molecule30  H7440  h1o
  30.2690   15.6199    9.9280 [O]  Molecule30  O7311  o2h
  29.8640   15.9833    9.1749 [H]  Molecule30  H7439  h1o
  29.5535   17.0631    7.5373 [O]  Molecule25  O6072  o2h
  29.9669   17.8535    7.5743 [H]  Molecule25  H6200  h1o
  31.5896   19.0999    6.5789 [O]  Molecule25  O6071  o1=
  32.2751   19.7160    6.1825 [H]  Molecule25  H6199  h1o
  33.0222   21.8475    5.3229 [O]  Molecule30  O7215  o2h
# Chain end-to-end distance: 10.1163

Output format

The output is tab delimited text which includes 3 different tables. The output can be redirected to a text file, and should be easy to import into any spredsheet.

First Table

The first table has a Count, Average, and StdDev column for each file imported, so the table can have many columns if many data files are read. It's not uncommon to read 100, 1000, or more data files. The first table output from the example data is shown below, in table format for easy viewing. Note: Only one (1) data file is read, so this table, and table two, turn out to be the same.

Oxygen neighbor distances. n.n. = Nearest neighbor

Atoms in chain	Nth n.n.	Count	Average	StdDev
3	1	1	2.53131	0
5	1	0	0	0
	2	0	0	0
7	1	0	0	0
	2	0	0	0
	3	0	0	0
9	1	4	2.92945	0.369107
	2	3	5.55041	0.678408
	3	2	7.67215	0.774919
	4	1	10.1163	0

Second Table

The second table combines the data from all the imported files into single Count, Average, StdDev columns. The second table output from the example data is shown below, in table format for easy viewing. Note: Only one (1) data file is read, so this table, and table one above, turn out to be the same.

Combining all files:

Atoms in chain	Nth n.n.	Count	Average	StdDev
3	1	1	2.53131	0
5	1	0	0	0
	2	0	0	0
7	1	0	0	0
	2	0	0	0
	3	0	0	0
9	1	4	2.92945	0.369107
	2	3	5.55041	0.678408
	3	2	7.67215	0.774919
	4	1	10.1163	0

Third Table

The Third table combines all files as in table two, and also all the 'Atoms in chain' column for a complete nearest neighbor table. The third table output from the example data is shown below, in table format for easy viewing.

####Combining all files and Chains:

Nth n.n.	Count	Average	StdDev
1	5	2.84983	0.422505
2	3	5.55041	0.959413
3	2	7.67215	0
4	1	10.1163	0

olsonbg/TracedNeighbors