BONDLA : Bond lengths and angles

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`BONDLA` : Bond lengths and angles

atrad	atomic radii by atom type
addpek	add peak site to atom list from `pek`file
bond	calculate a specific bond distance
angle	calculate a specific bond angle
dihed	calculate a specific dihedral angle
nviron	calculate distances to a specific atom site
site	enter temporary atom sites needed for geometry

BONDLA	Option	Code	Arg		Def
	bond distances	`bond`		list all bond distances
		`nbon`		no bond distances
	bond angles	`angl`		list all bond angles
		`nang`		no angles
	contact distances	`ncon`		no contact distances
		`cont`		list all contact distances
	dihedral angles	`ndih`		no dihedral angles
		`dihe`		list all dihedral angles
	bond check	`chek`		for Acta Cryst CIF bond checking
	sort bond & contact distances	`nsor`		do not sort distances
		`sort`		sort distances
	optimally connect input sites	`clus`		recluster input sites
		`nclu`		use input sites
	use full symmetry to searches	`symm`		apply full symmetry
		`nsym`		no symmetry
	do not output geom data to bdf	`nbdf`			output tobdf
	use brackets in `pch` output file	`brac`			no brackets
	number of cells searched	`cell`	`n`	`1`for 1 unit cell	`3`
				`2`for 27 cells
				`3`for 125 cells

atrad	1	atom-type symbol to which the radii apply(max 8 chars)
	2	maximum radius to be used in identifying contacts	`1.25`
	3	maximum radius to be used in identifying bonds	`0.9`
	4	minimum radius to be used in identifying bonds	`0.015`

addpek	1	atom-type symbol assigned to selected peak sites (max 8 chars)
	2	number of peaks assigned to atom-type	`1`
	3	maximum radius to be used in identifying contacts	`1.25`
	4	maximum radius to be used in identifying bonds	`0.9`
	5	minimum radius to be used in identifying bonds	`0.015`
	6	thermal displacement parameter assigned to output site	`0.035`

bond	1-2	atom labels of sites 1 and 2 (max 24 chars)
	3-4	numbers ^[a]of symops applied to sites 1 and 2	`1`
	5-6	codes of cell translations applied to sites 1 and 2	`555`
^[a]Symmetry matrix number as entered into STARTX.

angle	1-3	atom labels of sites 1, 2 and 3 (max 24 chars)
	4-6	numbers ^[a]of symops applied to sites 1, 2 and 3	`1`
	7-9	codes of cell translations applied to sites 1, 2 and 3	`555`
^[a]Symmetry matrix number as entered into STARTX.

dihed	1-4	atom labels of sites 1, 2, 3 and 4 (max 24 chars)
	5-8	numbers ^[a]of symops applied to sites 1, 2, 3 and 4	`1`
	9-12	codes of cell translations applied to sites 1, 2, 3 and 4	`555`
^[a]Symmetry matrix number as entered into STARTX.

nviron	1	atom label of central site (max 24 chars)
	2	number ^[a]of symop applied to sites	`1`
	3	code of cell translations applied to site	`555`
	4	radius of sphere to be searched for other sites	`3`
^[a]Symmetry matrix number as entered into STARTX.

site	1	atom label of site ^[a](max 24 chars)
	2-4	fractional coordinates x, y, z
	5	U	`0.035`
	6	population	`1`
	7-9	$\sigma x, \sigma y, \sigma z$	`0.0`
^[a]If label matches site on the bdf, these coordinates will be substituted for the calculation. Otherwise a new site will be added to the atom list. This site will not be added to the bdf.

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