LAMMPS topo types and mol template format support

include/chemfiles/Connectivity.hpp

@@ -7,6 +7,7 @@
 #include <array>
 #include <vector>
 #include <algorithm> // IWYU pragma: keep
+#include <string>
 
 #include "chemfiles/sorted_set.hpp"
 #include "chemfiles/exports.h"
@@ -317,7 +318,17 @@ class Connectivity final {
     const sorted_set<Improper>& impropers() const;
 
     /// Add a bond between the atoms `i` and `j`
-    void add_bond(size_t i, size_t j, Bond::BondOrder bond_order = Bond::UNKNOWN);
+    void add_bond(size_t i, size_t j, Bond::BondOrder bond_order = Bond::UNKNOWN, std::string bond_type = "");
+
+    /// Add an angle between the atoms `i`, `j` and `k`
+    void add_angle(size_t i, size_t j, size_t k, std::string angle_type = "");
+
+    /// Add a dihedral angle between the atoms `i`, `j`, `k` and `l`
+    void add_dihedral(size_t i, size_t j, size_t k, size_t l, std::string dihedral_type = "");
+
+    /// Add an improper dihedral angle between the atoms `i`, `j`, `k` and `l`
+    void add_improper(size_t i, size_t j, size_t k, size_t l, std::string improper_type = "");
+
 
     /// Remove any bond between the atoms `i` and `j`
     void remove_bond(size_t i, size_t j);
@@ -330,6 +341,18 @@ class Connectivity final {
 
     /// Get the bond order of the bond between i and j
     Bond::BondOrder bond_order(size_t i, size_t j) const;
+
+    /// Get the bond type of the bond between i and j
+    const std::string& bond_type(size_t i, size_t j) const;
+
+    /// Get the angle type of the angle between i, j and k
+    const std::string& angle_type(size_t i, size_t j, size_t k) const;
+
+    /// Get the dihedral type of the dihedral between i, j, k and l
+    const std::string& dihedral_type(size_t i, size_t j, size_t k, size_t l) const;
+
+    /// Get the improper type of the improper between i, j, k and l
+    const std::string& improper_type(size_t i, size_t j, size_t k, size_t l) const;
 private:
     /// Recalculate the angles and the dihedrals from the bond list
     void recalculate() const;
@@ -349,6 +372,14 @@ class Connectivity final {
     mutable bool uptodate_ = false;
     /// Store the bond orders
     std::vector<Bond::BondOrder> bond_orders_;
+    /// Store the bond types
+    mutable std::vector<std::string> bond_types_;
+    /// Store the angle types
+    mutable std::vector<std::string> angle_types_;
+    /// Store the dihedral types
+    mutable std::vector<std::string> dihedral_types_;
+    /// Store the improper types
+    mutable std::vector<std::string> improper_types_;
 };
 
 } // namespace chemfiles

include/chemfiles/Frame.hpp

@@ -4,6 +4,7 @@
 #ifndef CHEMFILES_FRAME_HPP
 #define CHEMFILES_FRAME_HPP
 
+#include <cstddef>
 #include <string>
 #include <vector>
 
@@ -246,8 +247,58 @@ class CHFL_EXPORT Frame final {
     /// @param bond_order the bond order of the new bond
     /// @throws OutOfBounds if `atom_i` or `atom_j` are greater than `size()`
     /// @throws Error if `atom_i == atom_j`, as this is an invalid bond
-    void add_bond(size_t atom_i, size_t atom_j, Bond::BondOrder bond_order = Bond::UNKNOWN) {
-        topology_.add_bond(atom_i, atom_j, bond_order);
+    void add_bond(size_t atom_i, size_t atom_j, Bond::BondOrder bond_order = Bond::UNKNOWN, std::string bond_type = "") {
+        topology_.add_bond(atom_i, atom_j, bond_order, bond_type);
+    }
+
+    /// Add an angle in the system, between the atoms at index `atom_i`,
+    /// `atom_j` and `atom_k`.
+    ///
+    /// @example{frame/add_angle.cpp}
+    ///
+    /// @param atom_i the index of the first atom in the angle
+    /// @param atom_j the index of the second atom in the angle
+    /// @param atom_k the index of the third atom in the angle
+    /// @param angle_type the angle order of the new angle
+    /// @throws OutOfBounds if `atom_i`, `atom_j` and `atom_k` are 
+    /// greater than `size()`
+    /// @throws Error if any two indices are equal as this is an invalid angle
+    void add_angle(size_t atom_i, size_t atom_j, size_t atom_k, std::string angle_type = "") {
+        topology_.add_angle(atom_i, atom_j, atom_k, angle_type);
+    }
+
+    /// Add a dihedral in the system, between the atoms at index `atom_i`,
+    /// `atom_j`, `atom_k`, and `atom_l`.
+    ///
+    /// @example{frame/add_dihedral.cpp}
+    ///
+    /// @param atom_i the index of the first atom in the dihedral
+    /// @param atom_j the index of the second atom in the dihedral
+    /// @param atom_k the index of the third atom in the dihedral
+    /// @param atom_l the index of the forth atom in the dihedral
+    /// @param dihedral_type the dihedral order of the new dihedral
+    /// @throws OutOfBounds if `atom_i`, `atom_j` and `atom_k` are 
+    /// greater than `size()`
+    /// @throws Error if any two indices are equal as this is an invalid dihedral
+    void add_dihedral(size_t atom_i, size_t atom_j, size_t atom_k, size_t atom_l, std::string dihedral_type = "") {
+        topology_.add_dihedral(atom_i, atom_j, atom_k, atom_l, dihedral_type);
+    }
+
+    /// Add a improper in the system, between the atoms at index `atom_i`,
+    /// `atom_j` and `atom_k`.
+    ///
+    /// @example{frame/add_improper.cpp}
+    ///
+    /// @param atom_i the index of the first atom in the improper
+    /// @param atom_j the index of the second atom in the improper
+    /// @param atom_k the index of the third atom in the improper
+    /// @param atom_l the index of the forth atom in the improper
+    /// @param improper_type the improper order of the new improper
+    /// @throws OutOfBounds if `atom_i`, `atom_j` and `atom_k` are 
+    /// greater than `size()`
+    /// @throws Error if any two indices are equal as this is an invalid improper
+    void add_improper(size_t atom_i, size_t atom_j, size_t atom_k, size_t atom_l, std::string improper_type = "") {
+        topology_.add_improper(atom_i, atom_j, atom_k, atom_l, improper_type);
     }
 
     /// Remove a bond in the system, between the atoms at index `atom_i` and

include/chemfiles/Topology.hpp

@@ -4,6 +4,7 @@
 #ifndef CHEMFILES_TOPOLOGY_HPP
 #define CHEMFILES_TOPOLOGY_HPP
 
+#include <cstddef>
 #include <string>
 #include <vector>
 #include <unordered_map>
@@ -113,9 +114,54 @@ class CHFL_EXPORT Topology final {
     /// @param atom_i the index of the first atom in the bond
     /// @param atom_j the index of the second atom in the bond
     /// @param bond_order the bond order for the bond added
+    /// @param bond_type the bond type for the bond added
     /// @throws OutOfBounds if `atom_i` or `atom_j` are greater than `size()`
     /// @throws Error if `atom_i == atom_j`, as this is an invalid bond
-    void add_bond(size_t atom_i, size_t atom_j, Bond::BondOrder bond_order = Bond::UNKNOWN);
+    void add_bond(size_t atom_i, size_t atom_j, Bond::BondOrder bond_order = Bond::UNKNOWN, std::string bond_type = "");
+
+    /// Add an angle in the system, between the atoms at index `atom_i`,
+    /// `atom_j` and `atom_k`
+    ///
+    /// @example{topology/add_angle.cpp}
+    ///
+    /// @param atom_i the index of the first atom in the angle
+    /// @param atom_j the index of the second atom in the angle
+    /// @param atom_k the index of the third atom in the angle
+    /// @param angle_type the angle type for the angle added
+    /// @throws OutOfBounds if any index is greater than `size()`
+    /// @throws Error if any atom index is duplicate, 
+    ///         as this is an invalid angle
+    void add_angle(size_t atom_i, size_t atom_j, size_t atom_k, std::string angle_type = "");
+
+    /// Add a dihedral in the system, between the atoms at index `atom_i`,
+    /// `atom_j` and `atom_k`
+    ///
+    /// @example{topology/add_dihedral.cpp}
+    ///
+    /// @param atom_i the index of the first atom in the dihedral
+    /// @param atom_j the index of the second atom in the dihedral
+    /// @param atom_k the index of the third atom in the dihedral
+    /// @param atom_l the index of the forth atom in the dihedral
+    /// @param dihedral_type the dihedral type for the dihedral added
+    /// @throws OutOfBounds if any index is greater than `size()`
+    /// @throws Error if any atom index is duplicate, 
+    ///         as this is an invalid dihedral
+    void add_dihedral(size_t atom_i, size_t atom_j, size_t atom_k, size_t atom_l, std::string dihedral_type = "");
+
+    /// Add an improper in the system, between the atoms at index `atom_i`,
+    /// `atom_j` and `atom_k`
+    ///
+    /// @example{topology/add_improper.cpp}
+    ///
+    /// @param atom_i the index of the first atom in the improper
+    /// @param atom_j the index of the second atom in the improper
+    /// @param atom_k the index of the third atom in the improper
+    /// @param atom_l the index of the forth atom in the improper
+    /// @param improper_type the improper type for the improper added
+    /// @throws OutOfBounds if any index is greater than `size()`
+    /// @throws Error if any atom index is duplicate, 
+    ///         as this is an invalid improper
+    void add_improper(size_t atom_i, size_t atom_j, size_t atom_k, size_t atom_l, std::string improper_type = "");
 
     /// Remove a bond in the system, between the atoms at index `atom_i` and
     /// `atom_j`.
@@ -141,6 +187,57 @@ class CHFL_EXPORT Topology final {
     /// @throws Error if no bond between `atom_i` and `atom_j` exists.
     Bond::BondOrder bond_order(size_t atom_i, size_t atom_j) const;
 
+    /// Get the bond type for the given bond
+    ///
+    /// If the bond does not exist, this will thrown an Error.
+    ///
+    /// @example{topology/bond_type.cpp}
+    ///
+    /// @param atom_i the index of the first atom in the bond
+    /// @param atom_j the index of the second atom in the bond
+    /// @throws OutOfBounds if `atom_i` or `atom_j` are greater than `size()`
+    /// @throws Error if no bond between `atom_i` and `atom_j` exists.
+    const std::string& bond_type(size_t atom_i, size_t atom_j) const;
+
+    /// Get the angle type for the given angle
+    ///
+    /// If the angle does not exist, this will thrown an Error.
+    ///
+    /// @example{topology/angle_type.cpp}
+    ///
+    /// @param atom_i the index of the first atom in the angle
+    /// @param atom_j the index of the second atom in the angle
+    /// @param atom_k the index of the third atom in the angle
+    /// @throws OutOfBounds if any index is greater than `size()`
+    /// @throws Error if no angle exists.
+    const std::string& angle_type(size_t atom_i, size_t atom_j, size_t atom_k) const;
+
+    /// Get the dihedral type for the given dihedral
+    ///
+    /// If the dihedral does not exist, this will thrown an Error.
+    ///
+    /// @example{topology/dihedral_type.cpp}
+    ///
+    /// @param atom_i the index of the first atom in the dihedral
+    /// @param atom_j the index of the second atom in the dihedral
+    /// @param atom_k the index of the third atom in the dihedral
+    /// @throws OutOfBounds if any index is greater than `size()`
+    /// @throws Error if no dihedral exists.
+    const std::string& dihedral_type(size_t atom_i, size_t atom_j, size_t atom_k, size_t atom_l) const;
+
+    /// Get the improper type for the given improper
+    ///
+    /// If the improper does not exist, this will thrown an Error.
+    ///
+    /// @example{topology/angle_type.cpp}
+    ///
+    /// @param atom_i the index of the first atom in the improper
+    /// @param atom_j the index of the second atom in the improper
+    /// @param atom_k the index of the third atom in the improper
+    /// @throws OutOfBounds if any index is greater than `size()`
+    /// @throws Error if no improper exists.
+    const std::string& improper_type(size_t atom_i, size_t atom_j, size_t atom_k, size_t atom_l) const;
+
     /// Get the number of atoms in the topology
     ///
     /// @example{topology/size.cpp}

include/chemfiles/config.h

@@ -0,0 +1,36 @@
+// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) Guillaume Fraux and contributors -- BSD license
+
+// clang-format off
+#ifndef CHEMFILES_CONFIG_HPP
+#define CHEMFILES_CONFIG_HPP
+
+/// An integer containing the major (x.0.0) version number
+#define CHEMFILES_VERSION_MAJOR 0
+/// An integer containing the minor (0.y.0) version number
+#define CHEMFILES_VERSION_MINOR 11
+/// An integer containing the patch (0.0.z) version number
+#define CHEMFILES_VERSION_PATCH 0
+/// The full version of chemfiles ("x.y.z"), as a string
+#define CHEMFILES_VERSION "0.11.0-dev"
+
+#define CHEMFILES_SIZEOF_VOID_P 8
+
+/// Are we building code on Windows?
+/* #undef CHEMFILES_WINDOWS */
+
+// Should we include GEMMI code?
+/* #undef CHFL_DISABLE_GEMMI */
+
+/// thread_local implementation
+#ifdef __cplusplus
+    #if 1
+        #define CHFL_THREAD_LOCAL thread_local
+    #else
+        #define CHFL_THREAD_LOCAL
+    #endif
+#endif
+
+// clang-format on
+
+#endif

include/chemfiles/exports.h

@@ -0,0 +1,42 @@
+
+#ifndef CHFL_EXPORT_H
+#define CHFL_EXPORT_H
+
+#ifdef CHFL_STATIC_DEFINE
+#  define CHFL_EXPORT
+#  define CHFL_NO_EXPORT
+#else
+#  ifndef CHFL_EXPORT
+#    ifdef chemfiles_EXPORTS
+        /* We are building this library */
+#      define CHFL_EXPORT 
+#    else
+        /* We are using this library */
+#      define CHFL_EXPORT 
+#    endif
+#  endif
+
+#  ifndef CHFL_NO_EXPORT
+#    define CHFL_NO_EXPORT 
+#  endif
+#endif
+
+#ifndef CHFL_DEPRECATED
+#  define CHFL_DEPRECATED __attribute__ ((__deprecated__))
+#endif
+
+#ifndef CHFL_DEPRECATED_EXPORT
+#  define CHFL_DEPRECATED_EXPORT CHFL_EXPORT CHFL_DEPRECATED
+#endif
+
+#ifndef CHFL_DEPRECATED_NO_EXPORT
+#  define CHFL_DEPRECATED_NO_EXPORT CHFL_NO_EXPORT CHFL_DEPRECATED
+#endif
+
+#if 0 /* DEFINE_NO_DEPRECATED */
+#  ifndef CHFL_NO_DEPRECATED
+#    define CHFL_NO_DEPRECATED
+#  endif
+#endif
+
+#endif /* CHFL_EXPORT_H */