SDA (SDA flex)  7.2
Simulation of Diffusional Association
Data Types | Functions/Subroutines
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


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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