replace popt in rbdock

.github/docker/Dockerfile.centos-stream9

@@ -1,4 +1,4 @@
 FROM quay.io/centos/centos:stream9 AS base
 
 # Install dependencies
-RUN yum install -y popt-devel gcc-c++ make diffutils
+RUN yum install -y gcc-c++ make diffutils

.github/docker/Dockerfile.debian-10

@@ -1,4 +1,4 @@
 FROM debian:10 AS base
 
 # Install dependencies
-RUN apt-get update && apt-get install -y --no-install-recommends make g++ libpopt-dev libpopt0
+RUN apt-get update && apt-get install -y --no-install-recommends make g++

.github/docker/Dockerfile.debian-11

@@ -1,4 +1,4 @@
 FROM debian:11 AS base
 
 # Install dependencies
-RUN apt-get update && apt-get install -y --no-install-recommends make g++ libpopt-dev libpopt0
+RUN apt-get update && apt-get install -y --no-install-recommends make g++

.github/docker/Dockerfile.debian-12

@@ -1,4 +1,4 @@
 FROM debian:12 AS base
 
 # Install dependencies
-RUN apt-get update && apt-get install -y --no-install-recommends make g++ libpopt-dev libpopt0
+RUN apt-get update && apt-get install -y --no-install-recommends make g++

.github/docker/Dockerfile.ubuntu-20.04

@@ -1,4 +1,4 @@
 FROM ubuntu:20.04 AS base
 
 # Install dependencies
-RUN apt-get update && apt-get install -y --no-install-recommends make g++ libpopt-dev libpopt0
+RUN apt-get update && apt-get install -y --no-install-recommends make g++

.github/docker/Dockerfile.ubuntu-22.04

@@ -1,4 +1,4 @@
 FROM ubuntu:24.04 AS base
 
 # Install dependencies
-RUN apt-get update && apt-get install -y --no-install-recommends make g++ libpopt-dev libpopt0
+RUN apt-get update && apt-get install -y --no-install-recommends make g++

.github/docker/Dockerfile.ubuntu-22.04-clang

@@ -1,4 +1,4 @@
 FROM ubuntu:22.04 AS base
 
 # Install dependencies
-RUN apt-get update && apt-get install -y --no-install-recommends make clang libpopt-dev libpopt0
+RUN apt-get update && apt-get install -y --no-install-recommends make clang

.github/docker/Dockerfile.ubuntu-24.04

@@ -1,4 +1,4 @@
 FROM ubuntu:22.04 AS base
 
 # Install dependencies
-RUN apt-get update && apt-get install -y --no-install-recommends make g++ libpopt-dev libpopt0
+RUN apt-get update && apt-get install -y --no-install-recommends make g++

Makefile

@@ -95,11 +95,11 @@ endif
 DEFINES                     += -DRBT_VERSION=\"$(RBT_VERSION)\"
 CXX_FLAGS                   := $(CXX_BASE_FLAGS) $(CXX_CONFIG_FLAGS) $(CXX_WARNING_FLAGS) $(CXX_EXTRA_FLAGS) $(DEFINES)
 LINK_FLAGS                  := -shared
-LIB_DEPENDENCIES            = -lm -lpopt
+LIB_DEPENDENCIES            += -lm
 
 # Modify library dependencies for macOS
 ifeq ($(shell uname),Darwin)
-    LIB_DEPENDENCIES = -L$(BREW_PREFIX)/lib -lpopt -lm
+    LIB_DEPENDENCIES = -L$(BREW_PREFIX)/lib -lm
 endif
 
 LIBS                        += $(LIB_DEPENDENCIES) -lRbt

README.md

@@ -22,13 +22,12 @@ make sure the following requirements are installed and available:
 
 - make
 - a c++ compiler (g++ by default)
-- popt and development headers (libpopt0 and libpopt-dev in ubuntu)
 - git (optional if you download the code directly)
 
 if you're running ubuntu, you can get all of them by running
 
 ```
-sudo apt update && sudo apt install -y make git libpopt0 libpopt-dev g++
+sudo apt update && sudo apt install -y make git g++
 ```
 
 if you're running `macOS`, make sure to use gcc instead of clang. You can install gcc and popt using homebrew

include/RbtArgParser.h

@@ -2,6 +2,7 @@
 #define _RBTARGPARSER_H_
 
 #include <cxxopts.hpp>
+#include <optional>
 #include <string>
 #include <vector>
 
@@ -61,6 +62,12 @@ class RbtOptionValue {
         return *this;
     }
 
+    template <typename T>
+    RbtOptionValue &operator>>(std::optional<T> &v) {
+        v = value.as<T>();
+        return *this;
+    }
+
     inline bool is_present() { return value.count() > 0; }
 };
 

include/rbdock/rbdock_argparser.h

@@ -0,0 +1,16 @@
+#ifndef _RBT_RBDOCK_ARGPARSER_H_
+#define _RBT_RBDOCK_ARGPARSER_H_
+
+#include "rbdock/rbdock_config.h"
+
+#include "RbtArgParser.h"
+
+namespace RBDock {
+
+RbtArgParser::RbtArgParser get_options_parser();
+
+RBDock::RBDockConfig parse_args(int argc, const char *argv[]);
+
+}  // namespace RBDock
+
+#endif  // _RBT_RBDOCK_ARGPARSER_H_

include/rbdock/rbdock_config.h

@@ -0,0 +1,114 @@
+#ifndef _RBDOCK_CONFIG_H_
+#define _RBDOCK_CONFIG_H_
+
+#include <iostream>
+#include <optional>
+#include <sstream>
+#include <string>
+
+#include "RbtValidationError.h"
+
+namespace RBDock {
+
+struct RBDockConfig {
+    // mandatory parameters
+    std::string strLigandMdlFile;
+    std::string strReceptorPrmFile;
+    std::string strParamFile;
+
+    // optional parameters
+    std::optional<std::string> strOutputPrefix;
+    std::optional<std::string> strFilterFile;
+    std::optional<int> nDockingRuns;
+    std::optional<double> dTargetScore;
+    std::optional<int> nSeed;
+    std::optional<int> iTrace;
+
+    // flags
+    bool bContinue = false;
+    bool bPosIonise = false;
+    bool bNegIonise = false;
+    bool bAllH = false;
+
+    friend std::ostream &operator<<(std::ostream &os, const RBDockConfig &config) {
+        os << "Command line args:" << std::endl;
+        os << " -i " << config.strLigandMdlFile << std::endl;
+        os << " -r " << config.strReceptorPrmFile << std::endl;
+        os << " -p " << config.strParamFile << std::endl;
+        if (config.strOutputPrefix.has_value()) {
+            os << " -o " << config.strOutputPrefix.value() << std::endl;
+        } else {
+            os << "WARNING: output file name is missing." << std::endl;
+        }
+        auto def_aux = config.nDockingRuns.has_value() ? " (default) " : "";
+        os << " -n " << config.nDockingRuns.value_or(1) << def_aux << std::endl;
+        if (config.nSeed.has_value()) os << " -s " << config.nSeed.value() << std::endl;
+        if (config.iTrace.has_value()) os << " -T " << config.iTrace.value() << std::endl;
+        if (config.bPosIonise) os << " --ap " << std::endl;
+        if (config.bNegIonise) os << " --an " << std::endl;
+        if (!config.bAllH) os << " --allH " << std::endl;
+        if (config.dTargetScore.has_value()) os << " -t " << config.dTargetScore.value() << std::endl;
+        if (config.bContinue) os << " --cont " << std::endl;
+        if (config.bPosIonise)
+            os << "Automatically protonating positive ionisable groups (amines, imidazoles, guanidines)" << std::endl;
+        if (config.bNegIonise)
+            os << "Automatically deprotonating negative ionisable groups (carboxylic acids, phosphates, sulphates, "
+                  "sulphonates)"
+               << std::endl;
+        if (!config.bAllH)
+            os << "Reading polar hydrogens only from ligand SD file" << std::endl;
+        else
+            os << "Reading all hydrogens from ligand SD file" << std::endl;
+
+        if (config.dTargetScore.has_value()) {
+            os << std::endl << "Lower target intermolecular score = " << config.dTargetScore.value() << std::endl;
+        }
+        if (config.strFilterFile.has_value()) os << " -f " << config.strFilterFile.value() << std::endl;
+
+        return os;
+    }
+
+    void validate() {
+        if (strLigandMdlFile.empty()) throw Rbt::ValidationError("input ligand SD file is mandatory");
+        if (strReceptorPrmFile.empty()) throw Rbt::ValidationError("receptor parameter file is mandatory");
+        if (nDockingRuns.has_value() && nDockingRuns < 1)
+            throw Rbt::ValidationError("number of runs must be greater than 0");
+    }
+
+    bool operator==(const RBDockConfig &rhs) const {
+        return strLigandMdlFile == rhs.strLigandMdlFile && strOutputPrefix == rhs.strOutputPrefix
+               && strReceptorPrmFile == rhs.strReceptorPrmFile && strParamFile == rhs.strParamFile
+               && strFilterFile == rhs.strFilterFile && nDockingRuns == rhs.nDockingRuns && bContinue == rhs.bContinue
+               && dTargetScore == rhs.dTargetScore && bPosIonise == rhs.bPosIonise && bNegIonise == rhs.bNegIonise
+               && bAllH == rhs.bAllH && nSeed == rhs.nSeed && iTrace == rhs.iTrace;
+    }
+
+    std::string get_filter_string() const {
+        std::ostringstream strAuxFilter;
+        if (strFilterFile.has_value()) return "";
+        if (dTargetScore.has_value()) {       // -t<TS>
+            if (!nDockingRuns.has_value()) {  // -t<TS> only
+                strAuxFilter << "0 1 - SCORE.INTER " << dTargetScore.value() << std::endl;
+            } else  // -t<TS> -n<N> need to check if -cont present
+                    // for all other cases it doesn't matter
+                if (bContinue) {  // -t<TS> -n<N> -cont
+                    strAuxFilter << "1 if - SCORE.NRUNS " << (nDockingRuns.value() - 1)
+                                 << " 0.0 -1.0,\n1 - SCORE.INTER " << dTargetScore.value() << std::endl;
+                } else {  // -t<TS> -n<N>
+                    strAuxFilter << "1 if - " << dTargetScore.value() << " SCORE.INTER 0.0 "
+                                 << "if - SCORE.NRUNS " << (nDockingRuns.value() - 1) << " 0.0 -1.0,\n1 - SCORE.INTER "
+                                 << dTargetScore.value() << std::endl;
+                }
+        }                                     // no target score, no filter
+        else if (nDockingRuns.has_value()) {  // -n<N>
+            strAuxFilter << "1 if - SCORE.NRUNS " << (nDockingRuns.value() - 1) << " 0.0 -1.0,\n0";
+        } else {  // no -t no -n
+            strAuxFilter << "0 0\n";
+        }
+        return strAuxFilter.str();
+    }
+};
+
+}  // namespace RBDock
+
+#endif  // _RBDOCK_CONFIG_H_

include/rbdock/rbdock_main.h

@@ -0,0 +1,12 @@
+#ifndef _RBT_RBDOCK_MAIN_H_
+#define _RBT_RBDOCK_MAIN_H_
+
+#include <string>
+
+#include "rbdock/rbdock_config.h"
+
+namespace RBDock {
+void RBDock(const RBDockConfig &config, const std::string &strExeName);
+}  // namespace RBDock
+
+#endif  // _RBT_RBDOCK_MAIN_H_