mod_pdb_type Module Reference

Module to define a pdb type and pdb reading and writing routine for tools. prepare_atom_protein routine has poor modularity making use in tools difficult. – could be merged later – need to add into protein object structure. More...

Data Types
type	type_pdb_file
	Data type for storing binned data (eg. Radial distribution functions) More...

Functions/Subroutines
subroutine	allocate_pdb_object (this, nlines)
	Create a new histogram instance. More...
integer function	size_pdb (pdb_file)
	Function that runs through lines of a PDB file and calculates the number of ATOM or HETATM records which is returned. More...
subroutine	fill_pdb_object (this, pdb_file)
subroutine	vdw_pdb_object (this)
subroutine	access_pdb_object (this, probe)
subroutine	write_pdb_file_object (this, irecord)
	Subroutine to write a pdb file. The format of the file created matches standard PDB columns, except that occupancy and b factor columns are widened. More...

Detailed Description

Module to define a pdb type and pdb reading and writing routine for tools. prepare_atom_protein routine has poor modularity making use in tools difficult. – could be merged later – need to add into protein object structure.

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

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Author

Neil Bruce

Function/Subroutine Documentation

access_pdb_object()

subroutine mod_pdb_type::access_pdb_object	(	type (type_pdb_file), intent(inout)	this,
		real (kind=4), intent(in)	probe
	)

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allocate_pdb_object()

subroutine mod_pdb_type::allocate_pdb_object	(	type(type_pdb_file), intent(inout)	this,
		integer, intent(in)	nlines
	)

Create a new histogram instance.

Parameters

this	: histogram instance to be created
length	: number of elements in histogram array
unit_width	: unit value of one bin width
opt_initial_value	: unit value of beginning of first bin (zero if not set)

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fill_pdb_object()

subroutine mod_pdb_type::fill_pdb_object	(	type(type_pdb_file), intent(inout)	this,
		integer, intent(in)	pdb_file
	)

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size_pdb()

integer function mod_pdb_type::size_pdb

(

integer

pdb_file

)

Function that runs through lines of a PDB file and calculates the number of ATOM or HETATM records which is returned.

Parameters

pdb_file

: record number for PDB file. Should already be opened in calling routine

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vdw_pdb_object()

subroutine mod_pdb_type::vdw_pdb_object

(

type (type_pdb_file), intent(inout)

this

)

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write_pdb_file_object()

subroutine mod_pdb_type::write_pdb_file_object	(	type (type_pdb_file)	this,
		integer	irecord
	)

Subroutine to write a pdb file. The format of the file created matches standard PDB columns, except that occupancy and b factor columns are widened.

Parameters

this	: object of type mod_pdb_type::type_pdb_file that stores information to write.
irecord	: file record number to write to (should already be open and writable).

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