compute_distance.f90 File Reference

Functions/Subroutines
subroutine	compute_dist_pbc (geom, prot1, prot2, dist, r_corrected)
	Compute distance and relative position between 2 solutes. Always r2-r1. More...
subroutine	compute_distance (prot1, prot2, dist)
	Compute the distance between two proteins Take into if a surface is present, but not for pbc ( call compute_dist_pbc instead ) More...
subroutine	compute_distance_test (geom, rtry, prot1_pos, dist)
	Version used by make_bd_2prot to update dist. . More...
subroutine	compute_distance_criteria_v2 (prot1, prot2, pos_relat, n1, n2, dist)
	Compute the distance need by reaction criteria . More...
integer function, dimension(:,:), allocatable	get_atoms_min_dist (prot1, prot2, max_contact_dist, min_contact_dist)
	Compute the minimum distance between the surface atoms (i.e., solvent accessible atoms) of the two given proteins (prot1 and prot2). More...

Detailed Description

Version

{version 7.2.3 (2019)}

Copyright (c) 2009, 2010, 2015, 2016, 2019 Heidelberg Institute of Theoretical Studies (HITS, www.h-its.org) Schloss-Wolfsbrunnenweg 35 69118 Heidelberg, Germany

Please send your contact address to get information on updates and new features to "mcmsoft@h-its.org". Questions will be answered as soon as possible.

References: see also http://mcm.h-its.org/sda7/do:c/doc_sda7/references.html:

Brownian dynamics simulation of protein-protein diffusional encounter. (1998) Methods, 14, 329-341.

SDA 7: A modular and parallel implementation of the simulation of diffusional association software. Journal of computational chemistry 36.21 (2015): 1631-1645.

Authors: M.Martinez, N.J.Bruce, J.Romanowska, D.B.Kokh, P.Mereghetti, X. Yu, M. Ozboyaci, M. Reinhardt, P. Friedrich, R.R.Gabdoulline, S.Richter and R.C.Wade

---

General functions to compute the distance between 2 proteins

Function/Subroutine Documentation

compute_dist_pbc()

subroutine compute_dist_pbc	(	type ( geometry )	geom,
		type ( protein ), intent(in)	prot1,
		type ( protein ), intent(in)	prot2,
		real ( kind=4 ), intent(out)	dist,
		real ( kind=8 ), dimension ( 3 ), intent(out)	r_corrected
	)

Compute distance and relative position between 2 solutes.
Always r2-r1.

Applied with sdamm (should work with sda_2prot). Take into account sphere/box, PBC, surface

It returns the correct relative position (after PBC)
but the distance (dist) is only along the z-axis if one of the solute is a surface.
So sqrt( dot(r_corrected,r_corrected) ) is not always equal to dist.

This function should always be called in force or energy calculation in the case of sdamm. With sda_2proteins, pos_relat is always = prot2 % position, and dist is setup correctly by compute_distance_test

Parameters

geom	: instance of mod_geometry
prot1	: solute 1, instance of protein
prot2	: solute 2, instance of protein
dist	: return distance between the 2 solutes
r_corrected	: return corrected relative position

Here is the caller graph for this function:

compute_distance()

subroutine compute_distance	(	type ( protein ), intent(in)	prot1,
		type ( protein ), intent(in)	prot2,
		real ( kind=4 ), intent(out)	dist
	)

Compute the distance between two proteins
Take into if a surface is present, but not for pbc ( call compute_dist_pbc instead )

Todo:

See if some function should be moved into mod_geometry.

Parameters

prot1	: solute 1, instance of protein
prot2	: solute 2, instance of protein
dist	: return distance between the 2 solutes

Here is the caller graph for this function:

compute_distance_criteria_v2()

subroutine compute_distance_criteria_v2	(	type ( protein )	prot1,
		type ( protein )	prot2,
		real ( kind = 4 ), dimension( 3 ), intent(in)	pos_relat,
		integer, intent(in)	n1,
		integer, intent(in)	n2,
		real ( kind=4 ), dimension ( n2-n1+1 )	dist
	)

Compute the distance need by reaction criteria
.

version changed because the movable atoms belong to protein now. checked if prot1 is a surface - then, taking only the z-distance

Parameters

prot1	: solute 1
prot2	: solute 2
pos_relat	: relative position
n1	: which reaction criterium to start from
n2	: which reaction criterium to end on
dist	: array with values of squared distance for each reaction criterium

Here is the caller graph for this function:

compute_distance_test()

subroutine compute_distance_test	(	type ( geometry )	geom,
		real ( kind = 8 ), dimension ( 3 )	rtry,
		real ( kind = 8 ), dimension ( 3 )	prot1_pos,
		real ( kind=4 )	dist
	)

Version used by make_bd_2prot to update dist.
.

Used only by sda_2proteins, check if one of the solute is a surface

Here tricky, because move not yet accepted before test escape
Particular to sda_2proteins, rtry is the potential new position

Todo:

prot_pos1, always 0 (only call by 2proteins) ?? prot1_pos to delete ?

Parameters

geom	: instance of mod_geometry
rtry	: potential new position of the solute
prot1_pos	: position of the solute 1
dist	: return the new distance if the move rtry is accepted

Here is the caller graph for this function:

get_atoms_min_dist()

integer function, dimension ( :,: ), allocatable get_atoms_min_dist	(	type ( protein ), intent(in)	prot1,
		type ( protein ), intent(in)	prot2,
		real ( kind = 8 ), intent(in)	max_contact_dist,
		real ( kind = 8 ), intent(in)	min_contact_dist
	)

Compute the minimum distance between the surface atoms (i.e., solvent accessible atoms) of the two given proteins (prot1 and prot2).

Parameters

prot1	: input, solute 1
prot2	: input, solute 2
max_contact_dist	: input, the maximum distance between two atoms from the two proteins that is required to define a contact
min_contact_dist	: input, the minimum ditance between atoms on the same proteins to define two different contacts

Returns

contact_atoms : output, array of pairs of numbers, pointing to the accessible atoms lists of prot1 and prot2, respectively

Here is the caller graph for this function: