SDA (SDA flex)  7.2
Simulation of Diffusional Association
Functions/Subroutines
trajectory2dcd.f90 File Reference

Functions/Subroutines

program trajectory2dcd
 Program trajectory2dcdRead record (complexes or trajectory file ) and convert to pdb / dcd files
Support sda_2proteins / sdamm with flexible solutes. More...
 
subroutine open_dcd_file (filename, ioutf, nb_atoms, nb_frames)
 Open file and write the header. More...
 
subroutine write_dcd (tab_prot, ioutf, nat, cm)
 Write data into the dcd file. More...
 
subroutine write_dcd_all_conf (tab_prot, ioutf, nat, cm, conf_number)
 Version to call if change of conformation with variable number of atoms. More...
 
subroutine generate_pdb (tab_prot, filename, all_filename_pdb, cm, force_all_conf)
 Write pdb files. More...
 
subroutine copy_pdb (prot, filename_pdb, pdb_out_int, cm, max_size, bool_extend)
 Copy one pdb file into an other. More...
 
subroutine copy_all_pdbs (prot, all_filename_pdb, pdb_out_int)
 Copy pdb files for every conformations. 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


Convert record into pdb or dcd file

Function/Subroutine Documentation

◆ copy_all_pdbs()

subroutine copy_all_pdbs ( type ( protein prot,
character*64, dimension(:,:)  all_filename_pdb,
integer  pdb_out_int 
)

Copy pdb files for every conformations.

Copy lines by lines into pdb_out

Parameters
prot: instance of protein
all_filename_pdb: name of all conformations
pdb_out_int: file descriptor of the target pdb file
Here is the caller graph for this function:

◆ copy_pdb()

subroutine copy_pdb ( type ( protein prot,
character*64  filename_pdb,
integer  pdb_out_int,
real ( kind = 8 ), dimension ( 3 )  cm,
integer  max_size,
logical  bool_extend 
)

Copy one pdb file into an other.

Copy lines by lines
Used if gen_conf, will read lines from pdb_in and copy to pdb_out

Parameters
prot: instance of protein
filename_pdb: name of the pdb file
pdb_out_int: file descriptor of the target pdb file
cm: center of geometry of the second solute ( only sda_2proteins )
max_size: maximum number of atoms
bool_extend: if true, all output will have the maximum size
Here is the caller graph for this function:

◆ generate_pdb()

subroutine generate_pdb ( type ( array_protein_type tab_prot,
character*64  filename,
character*64, dimension(:,:)  all_filename_pdb,
real ( kind = 8 ), dimension ( 3 )  cm,
logical  force_all_conf 
)

Write pdb files.

Parameters
tab_prot: instance of array_protein_type
filename: name of the pdb file to write
all_filename_pdb:
cm: center of geometry, only needed for sda_2proteins. send (0,0,0) otherwise
force_all_conf: force to write all conformations
Here is the call graph for this function:
Here is the caller graph for this function:

◆ open_dcd_file()

subroutine open_dcd_file ( character*40, intent(in)  filename,
integer  ioutf,
integer  nb_atoms,
integer  nb_frames 
)

Open file and write the header.

try to separate dcd format, may be a module if used more

Parameters
filename: file to create
ioutf: file descriptor of the file to open
nb_atoms: total number of atoms
nb_frames: number of frames
Here is the caller graph for this function:

◆ write_dcd()

subroutine write_dcd ( type ( array_protein_type tab_prot,
integer  ioutf,
integer  nat,
real ( kind = 8 ), dimension ( 3 )  cm 
)

Write data into the dcd file.

Parameters
tab_prot: instance of array_protein_type
ioutf: file descriptor of the dcd file
nat: number of atoms
cm: center of geometry, only needed for sda_2proteins. send (0,0,0) otherwise
Here is the caller graph for this function:

◆ write_dcd_all_conf()

subroutine write_dcd_all_conf ( type ( array_protein_type tab_prot,
integer  ioutf,
integer  nat,
real ( kind = 8 ), dimension ( 3 )  cm,
integer  conf_number 
)

Version to call if change of conformation with variable number of atoms.

Experimental : write all conformation at once
need to print all x first, then all y and all z, need to test all size inside

Parameters
tab_prot: instance of array_protein_type
ioutf: file descriptor of the dcd file
nat: number of atoms
cm: center of geometry, only needed for sda_2proteins. send (0,0,0) otherwise
conf_number: the conformation to print, all other will be at the exact same position
Here is the caller graph for this function:
Imprint/Privacy