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Merged
atillack merged 3 commits into from
Jan 24, 2024
Merged

Automatically dock entire directory contents #250

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846dc2b
Allow to specify a directory with pdbqt files to create a file list t…
atillack Jan 2, 2024
5b80405
Added directory functionality to xml conversion as well.
atillack Jan 4, 2024
b4a2ede
Fix erroneous directory detection.
atillack Jan 24, 2024
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4 changes: 2 additions & 2 deletions Makefile.Cuda
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Original file line number Diff line number Diff line change
Expand Up @@ -40,8 +40,8 @@ TOOL_TARGET := adgpu_analysis

IFLAGS=-I$(COMMON_DIR) -I$(HOST_INC_DIR) -I$(GPU_INCLUDE_PATH) -I$(KRNL_DIR)
LFLAGS=-L$(GPU_LIBRARY_PATH) -Wl,-rpath=$(GPU_LIBRARY_PATH):$(CPU_LIBRARY_PATH)
CFLAGS=-std=c++11 $(IFLAGS) $(LFLAGS)
TOOL_CFLAGS=-std=c++11 -I$(COMMON_DIR) -I$(HOST_INC_DIR)
CFLAGS=-std=c++17 $(IFLAGS) $(LFLAGS)
TOOL_CFLAGS=-std=c++17 -I$(COMMON_DIR) -I$(HOST_INC_DIR)

ifeq ($(DEVICE), CPU)
TARGET:=$(TARGET)_cpu
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4 changes: 2 additions & 2 deletions Makefile.OpenCL
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Expand Up @@ -61,8 +61,8 @@ TOOL_TARGET := adgpu_analysis

IFLAGS=-I$(COMMON_DIR) -I$(OCL_INC_DIR) -I$(HOST_INC_DIR) -I$(KRNL_DIR) -I$(OCLA_INC_PATH)
LFLAGS=-L$(OCLA_LIB_PATH)
CFLAGS=-std=c++11 $(IFLAGS) $(LFLAGS)
TOOL_CFLAGS=-std=c++11 -I$(COMMON_DIR) -I$(HOST_INC_DIR)
CFLAGS=-std=c++17 $(IFLAGS) $(LFLAGS)
TOOL_CFLAGS=-std=c++17 -I$(COMMON_DIR) -I$(HOST_INC_DIR)

# Host sources
OCL_SRC=$(wildcard $(OCL_SRC_DIR)/*.cpp)
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60 changes: 50 additions & 10 deletions host/src/getparameters.cpp
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Expand Up @@ -25,6 +25,7 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA

#include <cstdint>
#include <fstream>
#include <filesystem>
#include <algorithm>
#include <cctype>
#include <locale>
Expand Down Expand Up @@ -738,7 +739,22 @@ int initial_commandpars(
if(specified_dpf){
if((error=parse_dpf(mypars,mygrid,filelist))) return error;
}

if(xml_files.size() == 1){
if(is_dirname(xml_files[0].c_str())){
struct stat dir_stat;
int dir_int = stat(xml_files[0].c_str(), &dir_stat);
if ((dir_int != 0) || !(dir_stat.st_mode & S_IFDIR)){
printf("\nError: Specified directory \"%s\" for xml conversion does not exist.\n", xml_files[0].c_str());
exit(12);
}
std::string dir(xml_files[0]);
std::string ext(".xml");
xml_files.clear();
for(const std::filesystem::directory_entry& l : std::filesystem::directory_iterator(dir))
if(l.path().extension() == ext)
xml_files.push_back(l.path().string());
}
}
if(xml_files.size()>0){ // use filelist parameter list in case multiple xml files are converted
mypars->xml_files = xml_files.size();
if(mypars->xml_files>100){ // output progress bar
Expand Down Expand Up @@ -882,7 +898,7 @@ int get_filelist(
return 0;
}
bool read_ligands = false;
std::vector<char*> ligands;
std::vector<std::string> ligands;
for (int i=1; i<(*argc)-1+(read_ligands); i+=1+(!read_ligands))
{
// wildcards for -filelist are allowed (or multiple file names)
Expand Down Expand Up @@ -912,7 +928,26 @@ int get_filelist(
}
}
mypars->filelist_files = ligands.size();
if(ligands.size()>1){
bool add_pdbqts = (ligands.size() > 1);
if(ligands.size() == 1){
if(is_dirname(ligands[0].c_str())){
struct stat dir_stat;
int dir_int = stat(ligands[0].c_str(), &dir_stat);
if ((dir_int != 0) || !(dir_stat.st_mode & S_IFDIR)){
printf("\nError: Specified directory \"%s\" for file list with `--filelist` does not exist.\n", ligands[0].c_str());
exit(12);
}
std::string dir(ligands[0]);
std::string ext(".pdbqt");
ligands.clear();
for(const std::filesystem::directory_entry& l : std::filesystem::directory_iterator(dir))
if(l.path().extension() == ext)
ligands.push_back(l.path().string());
// ligands may also contain receptor and/or flexres pdbqt - gets filtered out below
add_pdbqts = true;
} else filelist.filename = strdup(ligands[0].c_str());
}
if(add_pdbqts){
// Need to setup file names from command line in case they weren't set with a dpf
if (get_filenames_and_ADcoeffs(argc, argv, mypars, filelist.used, false) != 0){
return 1;
Expand All @@ -930,9 +965,17 @@ int get_filelist(
printf("Error: get_gridinfo failed with fld file specified in file list.\n");
return 1;
}
std::string receptor_name=mygrid->grid_file_path;
if(mygrid->grid_file_path.size()>0) receptor_name+="/";
receptor_name += mygrid->receptor_name + ".pdbqt";
// Add the grid info
filelist.mygrids.push_back(*mygrid);
for(unsigned int i=0; i<ligands.size(); i++){
bool skip = (receptor_name.compare(ligands[i]) == 0);
if(mypars->flexresfile != NULL){
skip |= (ligands[i].compare(mypars->flexresfile) == 0);
}
if(skip) continue;
// Need new mypars->fldfile char* block to preserve previous one
if(filelist.mypars.size()>0){
if((filelist.mypars.back().fldfile) &&
Expand All @@ -945,11 +988,11 @@ int get_filelist(
(filelist.mypars.back().xrayligandfile==mypars->xrayligandfile))
mypars->xrayligandfile=strdup(mypars->xrayligandfile);
}
mypars->ligandfile = strdup(ligands[i]);
mypars->ligandfile = strdup(ligands[i].c_str());
filelist.ligand_files.push_back(ligands[i]);
mypars->list_nr++;
long long len = strrchr(ligands[i],'.')-ligands[i];
if(len<1) len=strlen(ligands[i]);
long long len = strrchr(mypars->ligandfile,'.')-mypars->ligandfile;
if(len<1) len=strlen(mypars->ligandfile);
filelist.resnames.push_back(filelist.ligand_files[i].substr(0,len));
mypars->resname=strdup(filelist.resnames[i].c_str());
mypars->free_roaming_ligand=true;
Expand All @@ -961,14 +1004,11 @@ int get_filelist(

filelist.preload_maps&=filelist.used;
if(mypars->contact_analysis && filelist.preload_maps){
std::string receptor_name=mygrid->grid_file_path;
if(mygrid->grid_file_path.size()>0) receptor_name+="/";
receptor_name += mygrid->receptor_name + ".pdbqt";
mypars->receptor_atoms = read_receptor(receptor_name.c_str(),mygrid,mypars->receptor_map,mypars->receptor_map_list);
mypars->nr_receptor_atoms = mypars->receptor_atoms.size();
}
return 0;
} else if(ligands.size()==1) filelist.filename = strdup(ligands[0]);
}

if (filelist.filename){ // true when -filelist specifies a filename
// filelist.used may be true when dpf file is specified as it uses the filelist to store runs
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6 changes: 3 additions & 3 deletions host/src/miscellaneous.cpp
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Expand Up @@ -263,9 +263,9 @@ bool is_dirname(const char* filename)
{
if((filename[strlen(filename)-1] == '/') ||
(filename[strlen(filename)-1] == '\\')) return true;
struct stat res_stat;
int res_int = stat(filename, &res_stat);
return (res_stat.st_mode & S_IFDIR);
struct stat f_stat;
int f_int = stat(filename, &f_stat);
return (f_stat.st_mode & S_IFDIR);
}

bool has_absolute_path(const char* filename)
Expand Down