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docking
ocladock
Commits
80fdbf01
Commit
80fdbf01
authored
Oct 10, 2017
by
Leonardo Solis
Browse files
fixed #2, added license preamble to sources
parent
6f3216ca
Changes
44
Hide whitespace changes
Inline
Side-by-side
common/calcenergy_basic.h
View file @
80fdbf01
/*
OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm
Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.
AutoDock is a Trade Mark of the Scripps Research Institute.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#ifndef CALCENERGY_BASIC_H_
#define CALCENERGY_BASIC_H_
...
...
common/defines.h
View file @
80fdbf01
/*
OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm
Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.
AutoDock is a Trade Mark of the Scripps Research Institute.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#ifndef DEFINES_H_
#define DEFINES_H_
...
...
device/auxiliary_genetic.cl
View file @
80fdbf01
/*
OCLADock,
an
OpenCL
implementation
of
AutoDock
4.2
running
a
Lamarckian
Genetic
Algorithm
Copyright
(
C
)
2017
TU
Darmstadt,
Embedded
Systems
and
Applications
Group,
Germany.
All
rights
reserved.
AutoDock
is
a
Trade
Mark
of
the
Scripps
Research
Institute.
This
program
is
free
software
; you can redistribute it and/or
modify
it
under
the
terms
of
the
GNU
General
Public
License
as
published
by
the
Free
Software
Foundation
; either version 2
of
the
License,
or
(
at
your
option
)
any
later
version.
This
program
is
distributed
in
the
hope
that
it
will
be
useful,
but
WITHOUT
ANY
WARRANTY
; without even the implied warranty of
MERCHANTABILITY
or
FITNESS
FOR
A
PARTICULAR
PURPOSE.
See
the
GNU
General
Public
License
for
more
details.
You
should
have
received
a
copy
of
the
GNU
General
Public
License
along
with
this
program
; if not, write to the Free Software
Foundation,
Inc.,
51
Franklin
Street,
Fifth
Floor,
Boston,
MA
02110-1301,
USA.
*/
//
-------------------------------------------------------
//
//
-------------------------------------------------------
...
...
device/calcenergy.cl
View file @
80fdbf01
/*
OCLADock,
an
OpenCL
implementation
of
AutoDock
4.2
running
a
Lamarckian
Genetic
Algorithm
Copyright
(
C
)
2017
TU
Darmstadt,
Embedded
Systems
and
Applications
Group,
Germany.
All
rights
reserved.
AutoDock
is
a
Trade
Mark
of
the
Scripps
Research
Institute.
This
program
is
free
software
; you can redistribute it and/or
modify
it
under
the
terms
of
the
GNU
General
Public
License
as
published
by
the
Free
Software
Foundation
; either version 2
of
the
License,
or
(
at
your
option
)
any
later
version.
This
program
is
distributed
in
the
hope
that
it
will
be
useful,
but
WITHOUT
ANY
WARRANTY
; without even the implied warranty of
MERCHANTABILITY
or
FITNESS
FOR
A
PARTICULAR
PURPOSE.
See
the
GNU
General
Public
License
for
more
details.
You
should
have
received
a
copy
of
the
GNU
General
Public
License
along
with
this
program
; if not, write to the Free Software
Foundation,
Inc.,
51
Franklin
Street,
Fifth
Floor,
Boston,
MA
02110-1301,
USA.
*/
#
include
"calcenergy_basic.h"
//
All
related
pragmas
are
in
defines.h
(
accesible
by
host
and
device
code
)
...
...
device/kernel1.cl
View file @
80fdbf01
/*
OCLADock,
an
OpenCL
implementation
of
AutoDock
4.2
running
a
Lamarckian
Genetic
Algorithm
Copyright
(
C
)
2017
TU
Darmstadt,
Embedded
Systems
and
Applications
Group,
Germany.
All
rights
reserved.
AutoDock
is
a
Trade
Mark
of
the
Scripps
Research
Institute.
This
program
is
free
software
; you can redistribute it and/or
modify
it
under
the
terms
of
the
GNU
General
Public
License
as
published
by
the
Free
Software
Foundation
; either version 2
of
the
License,
or
(
at
your
option
)
any
later
version.
This
program
is
distributed
in
the
hope
that
it
will
be
useful,
but
WITHOUT
ANY
WARRANTY
; without even the implied warranty of
MERCHANTABILITY
or
FITNESS
FOR
A
PARTICULAR
PURPOSE.
See
the
GNU
General
Public
License
for
more
details.
You
should
have
received
a
copy
of
the
GNU
General
Public
License
along
with
this
program
; if not, write to the Free Software
Foundation,
Inc.,
51
Franklin
Street,
Fifth
Floor,
Boston,
MA
02110-1301,
USA.
*/
__kernel
void
__attribute__
((
reqd_work_group_size
(
NUM_OF_THREADS_PER_BLOCK,1,1
)))
gpu_calc_initpop
(
char
dockpars_num_of_atoms,
char
dockpars_num_of_atypes,
...
...
device/kernel2.cl
View file @
80fdbf01
/*
OCLADock,
an
OpenCL
implementation
of
AutoDock
4.2
running
a
Lamarckian
Genetic
Algorithm
Copyright
(
C
)
2017
TU
Darmstadt,
Embedded
Systems
and
Applications
Group,
Germany.
All
rights
reserved.
AutoDock
is
a
Trade
Mark
of
the
Scripps
Research
Institute.
This
program
is
free
software
; you can redistribute it and/or
modify
it
under
the
terms
of
the
GNU
General
Public
License
as
published
by
the
Free
Software
Foundation
; either version 2
of
the
License,
or
(
at
your
option
)
any
later
version.
This
program
is
distributed
in
the
hope
that
it
will
be
useful,
but
WITHOUT
ANY
WARRANTY
; without even the implied warranty of
MERCHANTABILITY
or
FITNESS
FOR
A
PARTICULAR
PURPOSE.
See
the
GNU
General
Public
License
for
more
details.
You
should
have
received
a
copy
of
the
GNU
General
Public
License
along
with
this
program
; if not, write to the Free Software
Foundation,
Inc.,
51
Franklin
Street,
Fifth
Floor,
Boston,
MA
02110-1301,
USA.
*/
__kernel
void
__attribute__
((
reqd_work_group_size
(
NUM_OF_THREADS_PER_BLOCK,1,1
)))
gpu_sum_evals
(
/*unsigned
long
pop_size,*/
unsigned
int
pop_size,
...
...
device/kernel3.cl
View file @
80fdbf01
/*
OCLADock,
an
OpenCL
implementation
of
AutoDock
4.2
running
a
Lamarckian
Genetic
Algorithm
Copyright
(
C
)
2017
TU
Darmstadt,
Embedded
Systems
and
Applications
Group,
Germany.
All
rights
reserved.
AutoDock
is
a
Trade
Mark
of
the
Scripps
Research
Institute.
This
program
is
free
software
; you can redistribute it and/or
modify
it
under
the
terms
of
the
GNU
General
Public
License
as
published
by
the
Free
Software
Foundation
; either version 2
of
the
License,
or
(
at
your
option
)
any
later
version.
This
program
is
distributed
in
the
hope
that
it
will
be
useful,
but
WITHOUT
ANY
WARRANTY
; without even the implied warranty of
MERCHANTABILITY
or
FITNESS
FOR
A
PARTICULAR
PURPOSE.
See
the
GNU
General
Public
License
for
more
details.
You
should
have
received
a
copy
of
the
GNU
General
Public
License
along
with
this
program
; if not, write to the Free Software
Foundation,
Inc.,
51
Franklin
Street,
Fifth
Floor,
Boston,
MA
02110-1301,
USA.
*/
__kernel
void
__attribute__
((
reqd_work_group_size
(
NUM_OF_THREADS_PER_BLOCK,1,1
)))
perform_LS
(
char
dockpars_num_of_atoms,
char
dockpars_num_of_atypes,
...
...
device/kernel4.cl
View file @
80fdbf01
/*
OCLADock,
an
OpenCL
implementation
of
AutoDock
4.2
running
a
Lamarckian
Genetic
Algorithm
Copyright
(
C
)
2017
TU
Darmstadt,
Embedded
Systems
and
Applications
Group,
Germany.
All
rights
reserved.
AutoDock
is
a
Trade
Mark
of
the
Scripps
Research
Institute.
This
program
is
free
software
; you can redistribute it and/or
modify
it
under
the
terms
of
the
GNU
General
Public
License
as
published
by
the
Free
Software
Foundation
; either version 2
of
the
License,
or
(
at
your
option
)
any
later
version.
This
program
is
distributed
in
the
hope
that
it
will
be
useful,
but
WITHOUT
ANY
WARRANTY
; without even the implied warranty of
MERCHANTABILITY
or
FITNESS
FOR
A
PARTICULAR
PURPOSE.
See
the
GNU
General
Public
License
for
more
details.
You
should
have
received
a
copy
of
the
GNU
General
Public
License
along
with
this
program
; if not, write to the Free Software
Foundation,
Inc.,
51
Franklin
Street,
Fifth
Floor,
Boston,
MA
02110-1301,
USA.
*/
__kernel
void
__attribute__
((
reqd_work_group_size
(
NUM_OF_THREADS_PER_BLOCK,1,1
)))
gpu_gen_and_eval_newpops
(
char
dockpars_num_of_atoms,
char
dockpars_num_of_atypes,
...
...
host/inc/calcenergy.h
View file @
80fdbf01
/*
OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm
Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.
AutoDock is a Trade Mark of the Scripps Research Institute.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#ifndef CALCENERGY_H_
#define CALCENERGY_H_
...
...
host/inc/getparameters.h
View file @
80fdbf01
/*
OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm
Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.
AutoDock is a Trade Mark of the Scripps Research Institute.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#ifndef GETPARAMETERS_H_
#define GETPARAMETERS_H_
...
...
host/inc/miscellaneous.h
View file @
80fdbf01
/*
OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm
Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.
AutoDock is a Trade Mark of the Scripps Research Institute.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#ifndef MISCELLANEOUS_H_
#define MISCELLANEOUS_H_
...
...
host/inc/performdocking.h
View file @
80fdbf01
/*
OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm
Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.
AutoDock is a Trade Mark of the Scripps Research Institute.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#ifndef PERFORMDOCKING_H_
#define PERFORMDOCKING_H_
...
...
host/inc/processgrid.h
View file @
80fdbf01
/*
OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm
Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.
AutoDock is a Trade Mark of the Scripps Research Institute.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#ifndef PROCESSGRID_H_
#define PROCESSGRID_H_
...
...
host/inc/processligand.h
View file @
80fdbf01
/*
OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm
Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.
AutoDock is a Trade Mark of the Scripps Research Institute.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#ifndef PROCESSLIGAND_H_
#define PROCESSLIGAND_H_
...
...
host/inc/processresult.h
View file @
80fdbf01
/*
OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm
Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.
AutoDock is a Trade Mark of the Scripps Research Institute.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#ifndef PROCESSRESULT_H_
#define PROCESSRESULT_H_
...
...
host/src/calcenergy.cpp
View file @
80fdbf01
/*
OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm
Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.
AutoDock is a Trade Mark of the Scripps Research Institute.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#include
"calcenergy.h"
int
prepare_const_fields_for_gpu
(
Liganddata
*
myligand_reference
,
...
...
host/src/getparameters.cpp
View file @
80fdbf01
/*
OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm
Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.
AutoDock is a Trade Mark of the Scripps Research Institute.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#include
"getparameters.h"
int
get_filenames_and_ADcoeffs
(
const
int
*
argc
,
...
...
host/src/main.cpp
View file @
80fdbf01
/*
OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm
Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.
AutoDock is a Trade Mark of the Scripps Research Institute.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
//#include <stdio.h>
//#include <stdlib.h>
#include
<time.h>
...
...
host/src/miscellaneous.cpp
View file @
80fdbf01
/*
OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm
Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.
AutoDock is a Trade Mark of the Scripps Research Institute.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#include
"miscellaneous.h"
int
float2fracint
(
double
toconv
,
int
frac
)
...
...
host/src/performdocking.cpp
View file @
80fdbf01
/*
OCLADock, an OpenCL implementation of AutoDock 4.2 running a Lamarckian Genetic Algorithm
Copyright (C) 2017 TU Darmstadt, Embedded Systems and Applications Group, Germany. All rights reserved.
AutoDock is a Trade Mark of the Scripps Research Institute.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#ifndef _WIN32
#define STRINGIZE2(s) #s
#define STRINGIZE(s) STRINGIZE2(s)
...
...
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