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## Spatial distribution functions: sdf.f

This utility computes spatial distribution functions and creates a file which can be visualized using gOpenMol package (http://.www.csc.fi/gopenmol/).

Compilation:

`f77 -O3 -o sdf sdf.f tranal_base.f`

The input into `sdf` utility consists of a NAMELIST section `SDFIN` and subsequent lines defining sites which will be displayed for visualization of the molecule around which SDF is calculated

The NAMELIST section

     $SDFIN
     parameter=value(s),
     ...
     $END

contains the following parameters

- `FILORI = <filename>`

  The name of the output file with SDF written as ``formatted'' plt-file for gOpenMol package. Before visualization, it must be converted to the binary using ``pltfile'' utility of gOpenMol (available also from gOpenMol menu).

- `FILCRD = <filename>` The name of file into which average coordinates of molecule, defining the local basis, are written. These coordinates are computed using the basis of the molecule itself, and they in fact used for visualization of the local basis. This file is written in ``XMOL'' format. The last column shows the variance (average deviations) of atoms around their average positions in the local coordinate system, which may serve also for evaluation of molecular flexibility.

- `NOI = <int.value>` Defines the number of equivalent local coordinate systems on the molecule (for example, for DNA SDFs can be defined around each of phosphate group used as a local basis)

-     IO1 = <n1_1>,<n1_2>,...,<n1_NOI>
      IO2 = <n2_1>,<n2_2>,...,<n2_NOI>
      IO3 = <n3_1>,<n3_2>,...,<n3_NOI>

  `NOI` values in each of these three lines. They define `NOI` local basises. Each basis is defined by three sites (for example, `<n1_1>,<n2_1>,<n3_1>`. The center of local coordinate system is set at the first site, the X-axis goes as a mediana of 2-1-3 angle, and the Z-axis is perpendicular to the plane defined by these three sites.

- `NSOR = <int.value>`

  Number of sites for calculation of SDF.

- `ISOR = <n1>,<n2> ...`

  `NSOR` integer values. They define SDF of which sites to compute, and then take an average over them.

-     RXMAX = <value>
      RYMAX = <value>
      RZMAX = <value>

  These parameters define the box inside which SDF is calculated (for example, from `-RXMAX` to `RXMAX` in X-direction)

-     NOMX = <value>
      NOMY = <value>
      NOMZ = <value>

  resolution (number of bins) in each direction

After the NAMELIST section, there is a section in the input file which describes which atoms are displayed in the center of SDF as a structure defining the local basis. The first line of this section may be either an integer number or the word ```ALL`''.

If an integer number is specified, it defines the number of atoms displayed in the central structure. Then this number of lines follows, each line per atom, each consisting of `NOI + 1` values.

The first position in each line is one of numbers 1,2,3. Positions from 2 to `NOI + 1` define sites which are to be displayed, for each of `NOI` equivalent local coordinate system.

The number in the first position of each line means the following:

1 - coordinates of this atom are averaged independently of the next atom

2 - average coordinates of this atom are calculated taking into account the next atom also (for example, if these are two hydrogens of water)

3 - average coordinates of this atom are calculated taking into account the next two atoms (for instance, treating hydrogens in CH3 group)

Example of these lines for water:

    1 1
    2 2
    1 3

and for methanol (see the order of atoms in CH3OH.mmol file)

    1  1
    1  2
    1  3
    3  4
    2  5
    1  6

If parameter `ALL` is specified in the first (and the only) line of this section, then all the atoms of the molecule defining the local basis are displayed, without any special treatment of averaging coordinates of equivalent atoms.

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