contacts_sdamm.f90 File Reference

Functions/Subroutines
program	contacts_sdamm
	Program contacts_sdammFinding contacts between protein pairs or protein and a surface. Used with SDAMM-type of trajectory. More...
subroutine	transform_surf_atom_coords (prot, cur_prot)
subroutine	open_contact_output (file_p, file_core_name, type1, type2)
subroutine	open_contact_time_output (file_p, file_core_name, pair1, pair2)
subroutine	open_contact_matrix_output (file_p, file_core_name, pair1, pair2)
subroutine	write_pdb_bfact (prot, pdb_file, out_filep, bfact, occup, map_2CA)
	Write a pdb to the file, with specific values put in the b-factor and/or occupancy columns. 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

---

compute, and print contacts from sdamm trajectory

Function/Subroutine Documentation

open_contact_matrix_output()

subroutine open_contact_matrix_output	(	integer, intent(in)	file_p,
		character (128), intent(in)	file_core_name,
		integer, intent(in)	pair1,
		integer, intent(in)	pair2
	)

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open_contact_output()

subroutine open_contact_output	(	integer, intent(in)	file_p,
		character (128), intent(in)	file_core_name,
		integer, intent(in)	type1,
		integer, intent(in)	type2
	)

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open_contact_time_output()

subroutine open_contact_time_output	(	integer, intent(in)	file_p,
		character (128), intent(in)	file_core_name,
		integer, intent(in)	pair1,
		integer, intent(in)	pair2
	)

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transform_surf_atom_coords()

subroutine transform_surf_atom_coords	(	type ( protein ), intent(inout)	prot,
		type ( one_complexe ), intent(in)	cur_prot
	)

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write_pdb_bfact()

subroutine write_pdb_bfact	(	type( protein ), intent(in)	prot,
		character(128), intent(in)	pdb_file,
		integer, intent(in)	out_filep,
		real( kind = 8 ), dimension(:), intent(in), optional	bfact,
		real( kind = 8 ), dimension(:), intent(in), optional	occup,
		logical, optional	map_2CA
	)

Write a pdb to the file, with specific values put in the b-factor and/or occupancy columns.

Parameters

prot	: input, the protein
pdb_file	: input, filename of the original PDB file with all the atoms of the protein
out_filep	: input, pointer to the open output file
bfact	: input, optional, values to put in the b-factor column (or null)
occup	: input, optional, values to put in the occupancy column (or null)
map_2CA	: input, optional, logical value whether to map the bfactor values to CAlpha atoms (default: .true.)

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