updated preamble and changed name to AutoDock-GPU

ccsb-scripps · Jul 12, 2019 · 89c9a2e · 89c9a2e
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diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,4 @@
-# OCLADock specific files
+# AutoDock-GPU specific files
 initpop.txt
 *.dlg
 *.xml

diff --git a/LICENSE b/LICENSE
@@ -290,8 +290,12 @@ to attach them to the start of each source file to most effectively
 convey the exclusion of warranty; and each file should have at least
 the "copyright" line and a pointer to where the full notice is found.
 
-    ocladock
-    Copyright (C) 2017  docking
+    AutoDock-GPU, 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.
+    For some of the code, Copyright (C) 2019 Computational Structural Biology Center, the Scripps Research Institute.
+
+    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

diff --git a/Makefile b/Makefile
@@ -57,7 +57,7 @@ K_NAMES=-DK1=$(K1_NAME) -DK2=$(K2_NAME) -DK3=$(K3_NAME) -DK4=$(K4_NAME) -DK5=$(K
 # Kernel flags
 KFLAGS=-DKRNL_SOURCE=$(KRNL_DIR)/$(KRNL_MAIN) -DKRNL_DIRECTORY=$(KRNL_DIR) -DKCMN_DIRECTORY=$(KCMN_DIR) $(K_NAMES)
 
-TARGET := ocladock
+TARGET := autodock
 ifeq ($(DEVICE), CPU)
 	TARGET:=$(TARGET)_cpu
 else ifeq ($(DEVICE), GPU)

diff --git a/README.md b/README.md
@@ -30,7 +30,7 @@ make DEVICE=<TYPE> NUMWI=<NWI>
 | `<NWI>`    | OpenCL work-group size | `16`, `32`, `64`, `128`, `256` |
 
 
-After successful compilation, the host binary **ocladock_&lt;type&gt;_&lt;N&gt;wi** is placed under [bin](./bin).
+After successful compilation, the host binary **autodock_&lt;type&gt;_&lt;N&gt;wi** is placed under [bin](./bin).
 
 | Binary-name portion | Description            | Values                         |
 |:-------------------:|:----------------------:|:------------------------------:|
@@ -41,7 +41,7 @@ After successful compilation, the host binary **ocladock_&lt;type&gt;_&lt;N&gt;w
 
 ## Basic command
 ```zsh
-./bin/ocladock_<type>_<N>wi \
+./bin/autodock_<type>_<N>wi \
 -ffile <protein>.maps.fld \
 -lfile <ligand>.pdbqt \
 -nrun <nruns>
@@ -54,7 +54,7 @@ After successful compilation, the host binary **ocladock_&lt;type&gt;_&lt;N&gt;w
 
 ## Example
 ```zsh
-./bin/ocladock_gpu_64wi \
+./bin/autodock_gpu_64wi \
 -ffile ./input/1stp/derived/1stp_protein.maps.fld \
 -lfile ./input/1stp/derived/1stp_ligand.pdbqt \
 -nrun 10

diff --git a/common/calcenergy_basic.h b/common/calcenergy_basic.h
@@ -1,25 +1,3 @@
-/*
-
-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_

diff --git a/common/defines.h b/common/defines.h
@@ -1,25 +1,3 @@
-/*
-
-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_

diff --git a/device/auxiliary_genetic.cl b/device/auxiliary_genetic.cl
@@ -1,25 +1,3 @@
-/*
-
-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.
-
-*/
 
 
 // -------------------------------------------------------

diff --git a/device/calcMergedEneGra.cl b/device/calcMergedEneGra.cl
@@ -1,25 +1,3 @@
-/*
-
-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.
-
-*/
 
 // IMPORTANT: The following block contains definitions
 // already made either in energy or gradient calculation files.
@@ -508,7 +486,7 @@ partial_interE[get_local_id(0)] += TRILININTERPOL(cube, weights);
 
 			// -------------------------------------------------------------------
 			// Deltas dx, dy, dz are already normalized 
-			// (by host/src/getparameters.cpp) in OCLaDock.
+			// (by host/src/getparameters.cpp) in AutoDock-GPU.
 			// The correspondance between vertices in xyz axes is:
 			// 0, 1, 2, 3, 4, 5, 6, 7  and  000, 100, 010, 001, 101, 110, 011, 111
 			// -------------------------------------------------------------------
@@ -1039,7 +1017,7 @@ barrier(CLK_LOCAL_MEM_FENCE);
 		// Scaling gradient for translational genes as 
 		// their corresponding gradients were calculated in the space 
 		// where these genes are in Angstrom,
-		// but OCLaDock translational genes are within in grids
+		// but AutoDock-GPU translational genes are within in grids
 		gradient_genotype[0] *= dockpars_grid_spacing;
 		gradient_genotype[1] *= dockpars_grid_spacing;
 		gradient_genotype[2] *= dockpars_grid_spacing;

diff --git a/device/calcenergy.cl b/device/calcenergy.cl
@@ -1,25 +1,3 @@
-/*
-
-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.
-
-*/
 
 //#define DEBUG_ENERGY_KERNEL
 

diff --git a/device/calcgradient.cl b/device/calcgradient.cl
@@ -1,25 +1,3 @@
-/*
-
-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"
@@ -434,7 +412,7 @@ void gpu_calc_gradient(
 
 			// -------------------------------------------------------------------
 			// Deltas dx, dy, dz are already normalized 
-			// (by host/src/getparameters.cpp) in OCLaDock.
+			// (by host/src/getparameters.cpp) in AutoDock-GPU.
 			// The correspondance between vertices in xyz axes is:
 			// 0, 1, 2, 3, 4, 5, 6, 7  and  000, 100, 010, 001, 101, 110, 011, 111
 			// -------------------------------------------------------------------
@@ -851,7 +829,7 @@ void gpu_calc_gradient(
 		// Scaling gradient for translational genes as 
 		// their corresponding gradients were calculated in the space 
 		// where these genes are in Angstrom,
-		// but OCLaDock translational genes are within in grids
+		// but AutoDock-GPU translational genes are within in grids
 		gradient_genotype[0] *= dockpars_grid_spacing;
 		gradient_genotype[1] *= dockpars_grid_spacing;
 		gradient_genotype[2] *= dockpars_grid_spacing;

diff --git a/device/kernel1.cl b/device/kernel1.cl
@@ -1,25 +1,3 @@
-/*
-
-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.
-
-*/
 
 //#define DEBUG_ENERGY_KERNEL1
 

diff --git a/device/kernel2.cl b/device/kernel2.cl
@@ -1,25 +1,3 @@
-/*
-
-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)))

diff --git a/device/kernel3.cl b/device/kernel3.cl
@@ -1,25 +1,3 @@
-/*
-
-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)))

diff --git a/device/kernel4.cl b/device/kernel4.cl
@@ -1,25 +1,3 @@
-/*
-
-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.
-
-*/
 
 //#define DEBUG_ENERGY_KERNEL4
 

diff --git a/device/kernel_sd.cl b/device/kernel_sd.cl
@@ -291,7 +291,7 @@ gradient_minSD(
 	do {
 		#if 0
 		// Specific input genotypes for a ligand with no rotatable bonds (1ac8).
-		// Translation genes must be expressed in grids in OCLADock (genotype [0|1|2]).
+		// Translation genes must be expressed in grids in AutoDock-GPU (genotype [0|1|2]).
 		// However, for testing purposes, 
 		// we start using translation values in real space (Angstrom): {31.79575, 93.743875, 47.699875}
 		// Rotation genes are expresed in the Shoemake space: genotype [3|4|5]

diff --git a/doc/readme/readme_users.md b/doc/readme/readme_users.md
@@ -37,7 +37,7 @@ For more details, go to the [developers section](readme_developers.md#to-keep-in
 
 ## Basic
 ```zsh
-./bin/ocladock_<type>_<N>wi -ffile <protein>.maps.fld -lfile <ligand>.pdbqt -nrun <nruns>
+./bin/autodock_<type>_<N>wi -ffile <protein>.maps.fld -lfile <ligand>.pdbqt -nrun <nruns>
 ```
 | Mandatory options | Description   | Value                     |
 |:-----------------:|:-------------:|:-------------------------:|
@@ -46,7 +46,7 @@ For more details, go to the [developers section](readme_developers.md#to-keep-in
 
 ## Example
 ```zsh
-./bin/ocladock_gpu_64wi -ffile ./input/1stp/derived/1stp_protein.maps.fld -lfile ./input/1stp/derived/1stp_ligand.pdbqt -nrun 10
+./bin/autodock_gpu_64wi -ffile ./input/1stp/derived/1stp_protein.maps.fld -lfile ./input/1stp/derived/1stp_ligand.pdbqt -nrun 10
 
 Kernel source file:                      ./device/calcenergy.cl                  
 Kernel compilation flags:                 -I ./device -I ./common -DN64WI