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... | |
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.
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
subroutine mod_pdb_type::access_pdb_object | ( | type (type_pdb_file), intent(inout) | this, |
real (kind=4), intent(in) | probe | ||
) |
subroutine mod_pdb_type::allocate_pdb_object | ( | type(type_pdb_file), intent(inout) | this, |
integer, intent(in) | nlines | ||
) |
Create a new histogram instance.
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) |
subroutine mod_pdb_type::fill_pdb_object | ( | type(type_pdb_file), intent(inout) | this, |
integer, intent(in) | pdb_file | ||
) |
integer function mod_pdb_type::size_pdb | ( | integer | pdb_file | ) |
subroutine mod_pdb_type::vdw_pdb_object | ( | type (type_pdb_file), intent(inout) | this | ) |
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.
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). |