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libcifpp
Commit 5476eef0 by Maarten L. Hekkelman
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some extensions for sugar tree building

parent 33c1eea9
Showing with 61 additions and 14 deletions
include/cif++/compound.hpp
...@@ -36,6 +36,7 @@ ...@@ -36,6 +36,7 @@
#include <cif++.hpp> #include <cif++.hpp>
#include <cif++/atom_type.hpp> #include <cif++/atom_type.hpp>
#include <cif++/point.hpp>
namespace cif namespace cif
{ {
...@@ -75,6 +76,11 @@ struct compound_atom ...@@ -75,6 +76,11 @@ struct compound_atom
bool leaving_atom = false; bool leaving_atom = false;
bool stereo_config = false; bool stereo_config = false;
float x, y, z; float x, y, z;
point get_location() const
{
return { x, y, z };
}
}; };
/// -------------------------------------------------------------------- /// --------------------------------------------------------------------
...@@ -114,6 +120,7 @@ class compound ...@@ -114,6 +120,7 @@ class compound
compound_atom get_atom_by_atom_id(const std::string &atom_id) const; compound_atom get_atom_by_atom_id(const std::string &atom_id) const;
bool atoms_bonded(const std::string &atomId_1, const std::string &atomId_2) const; bool atoms_bonded(const std::string &atomId_1, const std::string &atomId_2) const;
float bond_length(const std::string &atomId_1, const std::string &atomId_2) const;
bool is_water() const bool is_water() const
{ {
......
include/cif++/model.hpp
...@@ -394,7 +394,7 @@ class residue ...@@ -394,7 +394,7 @@ class residue
friend class structure; friend class structure;
// constructor // constructor
residue(const structure &structure, const std::string &compoundID, residue(structure &structure, const std::string &compoundID,
const std::string &asymID, int seqID, const std::string &asymID, int seqID,
const std::string &authAsymID, const std::string &authSeqID, const std::string &authAsymID, const std::string &authSeqID,
const std::string &pdbInsCode) const std::string &pdbInsCode)
...@@ -408,7 +408,7 @@ class residue ...@@ -408,7 +408,7 @@ class residue
{ {
} }
residue(const structure &structure, const std::vector<atom> &atoms); residue(structure &structure, const std::vector<atom> &atoms);
residue(const residue &rhs) = delete; residue(const residue &rhs) = delete;
residue &operator=(const residue &rhs) = delete; residue &operator=(const residue &rhs) = delete;
...@@ -432,7 +432,7 @@ class residue ...@@ -432,7 +432,7 @@ class residue
const std::string &get_compound_id() const { return m_compound_id; } const std::string &get_compound_id() const { return m_compound_id; }
void set_compound_id(const std::string &id) { m_compound_id = id; } void set_compound_id(const std::string &id) { m_compound_id = id; }
const structure *get_structure() const { return m_structure; } structure *get_structure() const { return m_structure; }
// const compound &compound() const; // const compound &compound() const;
...@@ -489,7 +489,7 @@ class residue ...@@ -489,7 +489,7 @@ class residue
protected: protected:
residue() {} residue() {}
const structure *m_structure = nullptr; structure *m_structure = nullptr;
std::string m_compound_id, m_asym_id; std::string m_compound_id, m_asym_id;
int m_seq_id = 0; int m_seq_id = 0;
std::string m_auth_asym_id, m_auth_seq_id, m_pdb_ins_code; std::string m_auth_asym_id, m_auth_seq_id, m_pdb_ins_code;
...@@ -573,7 +573,7 @@ class monomer : public residue ...@@ -573,7 +573,7 @@ class monomer : public residue
class polymer : public std::vector<monomer> class polymer : public std::vector<monomer>
{ {
public: public:
polymer(const structure &s, const std::string &entityID, const std::string &asymID, const std::string &auth_asym_id); polymer(structure &s, const std::string &entityID, const std::string &asymID, const std::string &auth_asym_id);
polymer(const polymer &) = delete; polymer(const polymer &) = delete;
polymer &operator=(const polymer &) = delete; polymer &operator=(const polymer &) = delete;
...@@ -581,7 +581,7 @@ class polymer : public std::vector<monomer> ...@@ -581,7 +581,7 @@ class polymer : public std::vector<monomer>
// monomer &getBySeqID(int seqID); // monomer &getBySeqID(int seqID);
// const monomer &getBySeqID(int seqID) const; // const monomer &getBySeqID(int seqID) const;
const structure *get_structure() const { return m_structure; } structure *get_structure() const { return m_structure; }
std::string get_asym_id() const { return m_asym_id; } std::string get_asym_id() const { return m_asym_id; }
std::string get_auth_asym_id() const { return m_auth_asym_id; } // The PDB chain ID, actually std::string get_auth_asym_id() const { return m_auth_asym_id; } // The PDB chain ID, actually
...@@ -590,7 +590,7 @@ class polymer : public std::vector<monomer> ...@@ -590,7 +590,7 @@ class polymer : public std::vector<monomer>
// int Distance(const monomer &a, const monomer &b) const; // int Distance(const monomer &a, const monomer &b) const;
private: private:
const structure *m_structure; structure *m_structure;
std::string m_entity_id; std::string m_entity_id;
std::string m_asym_id; std::string m_asym_id;
std::string m_auth_asym_id; std::string m_auth_asym_id;
...@@ -604,7 +604,7 @@ class branch; ...@@ -604,7 +604,7 @@ class branch;
class sugar : public residue class sugar : public residue
{ {
public: public:
sugar(const branch &branch, const std::string &compoundID, sugar(branch &branch, const std::string &compoundID,
const std::string &asymID, int authSeqID); const std::string &asymID, int authSeqID);
sugar(sugar &&rhs); sugar(sugar &&rhs);
...@@ -631,27 +631,42 @@ class sugar : public residue ...@@ -631,27 +631,42 @@ class sugar : public residue
return result; return result;
} }
cif::mm::atom add_atom(row_initializer atom_info);
private: private:
const branch *m_branch; branch *m_branch;
atom m_link; atom m_link;
}; };
class branch : public std::vector<sugar> class branch : public std::vector<sugar>
{ {
public: public:
branch(structure &structure, const std::string &asymID); branch(structure &structure, const std::string &asym_id, const std::string &entity_id);
branch(const branch &) = delete;
branch &operator=(const branch &) = delete;
branch(branch &&) = default;
branch &operator=(branch &&) = default;
void link_atoms(); void link_atoms();
std::string name() const; std::string name() const;
float weight() const; float weight() const;
std::string get_asym_id() const { return m_asym_id; } std::string get_asym_id() const { return m_asym_id; }
std::string get_entity_id() const { return m_entity_id; }
structure &get_structure() { return *m_structure; } structure &get_structure() { return *m_structure; }
const structure &get_structure() const { return *m_structure; } structure &get_structure() const { return *m_structure; }
sugar &getSugarByNum(int nr); sugar &get_sugar_by_num(int nr);
const sugar &getSugarByNum(int nr) const;
const sugar &get_sugar_by_num(int nr) const
{
return const_cast<branch *>(this)->get_sugar_by_num(nr);
}
sugar &construct_sugar(const std::string &compound_id);
private: private:
friend sugar; friend sugar;
...@@ -659,7 +674,7 @@ class branch : public std::vector<sugar> ...@@ -659,7 +674,7 @@ class branch : public std::vector<sugar>
std::string name(const sugar &s) const; std::string name(const sugar &s) const;
structure *m_structure; structure *m_structure;
std::string m_asym_id; std::string m_asym_id, m_entity_id;
}; };
// // -------------------------------------------------------------------- // // --------------------------------------------------------------------
...@@ -851,6 +866,9 @@ class structure ...@@ -851,6 +866,9 @@ class structure
/// \return The newly create asym ID /// \return The newly create asym ID
std::string create_non_poly(const std::string &entity_id, std::vector<row_initializer> atoms); std::string create_non_poly(const std::string &entity_id, std::vector<row_initializer> atoms);
/// \brief Create a new and empty (sugar) branch
branch &create_branch();
/// \brief Create a new (sugar) branch with one first NAG containing atoms constructed from \a atoms /// \brief Create a new (sugar) branch with one first NAG containing atoms constructed from \a atoms
branch &create_branch(std::vector<row_initializer> atoms); branch &create_branch(std::vector<row_initializer> atoms);
......
src/compound.cpp
...@@ -223,6 +223,28 @@ bool compound::atoms_bonded(const std::string &atomId_1, const std::string &atom ...@@ -223,6 +223,28 @@ bool compound::atoms_bonded(const std::string &atomId_1, const std::string &atom
return i != m_bonds.end(); return i != m_bonds.end();
} }
float compound::bond_length(const std::string &atomId_1, const std::string &atomId_2) const
{
auto i = find_if(m_bonds.begin(), m_bonds.end(),
[&](const compound_bond &b)
{
return (b.atom_id[0] == atomId_1 and b.atom_id[1] == atomId_2) or (b.atom_id[0] == atomId_2 and b.atom_id[1] == atomId_1);
});
float result = std::numeric_limits<float>::max();
if (i != m_bonds.end())
{
auto a = get_atom_by_atom_id(atomId_1);
auto b = get_atom_by_atom_id(atomId_2);
result = distance(point{a.x, a.y, a.z}, point{b.x, b.y, b.z});
}
return result;
}
// -------------------------------------------------------------------- // --------------------------------------------------------------------
// known amino acids and bases // known amino acids and bases
......
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