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libcifpp
Commit 24ca1017 by Maarten L. Hekkelman
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Fix mm::polymer to have its own auth_asym_id

parent 85c21aeb
Showing with 28 additions and 30 deletions
include/cif++/model.hpp
...@@ -403,12 +403,16 @@ class residue ...@@ -403,12 +403,16 @@ class residue
// constructor // constructor
residue(const structure &structure, const std::string &compoundID, residue(const structure &structure, const std::string &compoundID,
const std::string &asymID, int seqID, const std::string &authSeqID) const std::string &asymID, int seqID,
const std::string &authAsymID, const std::string &authSeqID,
const std::string &pdbInsCode)
: m_structure(&structure) : m_structure(&structure)
, m_compound_id(compoundID) , m_compound_id(compoundID)
, m_asym_id(asymID) , m_asym_id(asymID)
, m_seq_id(seqID) , m_seq_id(seqID)
, m_auth_asym_id(authAsymID)
, m_auth_seq_id(authSeqID) , m_auth_seq_id(authSeqID)
, m_pdb_ins_code(pdbInsCode)
{ {
} }
...@@ -427,16 +431,9 @@ class residue ...@@ -427,16 +431,9 @@ class residue
const std::string &get_asym_id() const { return m_asym_id; } const std::string &get_asym_id() const { return m_asym_id; }
int get_seq_id() const { return m_seq_id; } int get_seq_id() const { return m_seq_id; }
const std::string get_auth_asym_id() const const std::string get_auth_asym_id() const { return m_auth_asym_id; }
{
return m_atoms.empty() ? m_asym_id : m_atoms.front().get_auth_asym_id();
}
const std::string get_auth_seq_id() const { return m_auth_seq_id; } const std::string get_auth_seq_id() const { return m_auth_seq_id; }
std::string get_pdb_ins_code() const { return m_pdb_ins_code; }
std::string get_pdb_ins_code() const
{
return m_atoms.empty() ? "" : m_atoms.front().get_pdb_ins_code();
}
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; }
...@@ -501,7 +498,7 @@ class residue ...@@ -501,7 +498,7 @@ class residue
const structure *m_structure = nullptr; const 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_seq_id; std::string m_auth_asym_id, m_auth_seq_id, m_pdb_ins_code;
std::vector<atom> m_atoms; std::vector<atom> m_atoms;
}; };
...@@ -519,7 +516,7 @@ class monomer : public residue ...@@ -519,7 +516,7 @@ class monomer : public residue
monomer &operator=(monomer &&rhs); monomer &operator=(monomer &&rhs);
monomer(const polymer &polymer, size_t index, int seqID, const std::string &authSeqID, monomer(const polymer &polymer, size_t index, int seqID, const std::string &authSeqID,
const std::string &compoundID); const std::string &pdbInsCode, const std::string &compoundID);
bool is_first_in_chain() const; bool is_first_in_chain() const;
bool is_last_in_chain() const; bool is_last_in_chain() const;
...@@ -582,7 +579,7 @@ class monomer : public residue ...@@ -582,7 +579,7 @@ 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); polymer(const 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;
...@@ -593,16 +590,16 @@ class polymer : public std::vector<monomer> ...@@ -593,16 +590,16 @@ class polymer : public std::vector<monomer>
const structure *get_structure() const { return m_structure; } const 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_entity_id() const { return m_entity_id; } std::string get_entity_id() const { return m_entity_id; }
// std::string chainID() const;
// int Distance(const monomer &a, const monomer &b) const; // int Distance(const monomer &a, const monomer &b) const;
private: private:
const structure *m_structure; const 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;
}; };
// -------------------------------------------------------------------- // --------------------------------------------------------------------
......
src/model.cpp
...@@ -566,8 +566,8 @@ std::ostream &operator<<(std::ostream &os, const residue &res) ...@@ -566,8 +566,8 @@ std::ostream &operator<<(std::ostream &os, const residue &res)
// -------------------------------------------------------------------- // --------------------------------------------------------------------
// monomer // monomer
monomer::monomer(const polymer &polymer, size_t index, int seqID, const std::string &authSeqID, const std::string &compoundID) monomer::monomer(const polymer &polymer, size_t index, int seqID, const std::string &authSeqID, const std::string &pdbInsCode, const std::string &compoundID)
: residue(*polymer.get_structure(), compoundID, polymer.get_asym_id(), seqID, authSeqID) : residue(*polymer.get_structure(), compoundID, polymer.get_asym_id(), seqID, polymer.get_auth_asym_id(), authSeqID, pdbInsCode)
, m_polymer(&polymer) , m_polymer(&polymer)
, m_index(index) , m_index(index)
{ {
...@@ -955,11 +955,11 @@ bool monomer::is_cis(const monomer &a, const monomer &b) ...@@ -955,11 +955,11 @@ bool monomer::is_cis(const monomer &a, const monomer &b)
// -------------------------------------------------------------------- // --------------------------------------------------------------------
// polymer // polymer
polymer::polymer(const structure &s, const std::string &entityID, const std::string &asym_id) polymer::polymer(const structure &s, const std::string &entityID, const std::string &asym_id, const std::string &auth_asym_id)
: m_structure(const_cast<structure *>(&s)) : m_structure(const_cast<structure *>(&s))
, m_entity_id(entityID) , m_entity_id(entityID)
, m_asym_id(asym_id) , m_asym_id(asym_id)
// , mPolySeq(s.m_db["pdbx_poly_seq_scheme"), key("asym_id") == m_asym_id and key("entity_id") == m_entity_i]) , m_auth_asym_id(auth_asym_id)
{ {
using namespace cif::literals; using namespace cif::literals;
...@@ -971,8 +971,8 @@ polymer::polymer(const structure &s, const std::string &entityID, const std::str ...@@ -971,8 +971,8 @@ polymer::polymer(const structure &s, const std::string &entityID, const std::str
for (auto r : poly_seq_scheme.find("asym_id"_key == asym_id)) for (auto r : poly_seq_scheme.find("asym_id"_key == asym_id))
{ {
int seqID; int seqID;
std::string compoundID, authSeqID; std::string compoundID, authSeqID, pdbInsCode;
cif::tie(seqID, authSeqID, compoundID) = r.get("seq_id", "auth_seq_num", "mon_id"); cif::tie(seqID, authSeqID, compoundID, pdbInsCode) = r.get("seq_id", "auth_seq_num", "mon_id", "pdb_ins_code");
size_t index = size(); size_t index = size();
...@@ -980,11 +980,11 @@ polymer::polymer(const structure &s, const std::string &entityID, const std::str ...@@ -980,11 +980,11 @@ polymer::polymer(const structure &s, const std::string &entityID, const std::str
if (not ix.count(seqID)) if (not ix.count(seqID))
{ {
ix[seqID] = index; ix[seqID] = index;
emplace_back(*this, index, seqID, authSeqID, compoundID); emplace_back(*this, index, seqID, authSeqID, pdbInsCode, compoundID);
} }
else if (VERBOSE > 0) else if (VERBOSE > 0)
{ {
monomer m{*this, index, seqID, authSeqID, compoundID}; monomer m{*this, index, seqID, authSeqID, pdbInsCode, compoundID};
std::cerr << "Dropping alternate residue " << m << std::endl; std::cerr << "Dropping alternate residue " << m << std::endl;
} }
} }
...@@ -1043,7 +1043,7 @@ polymer::polymer(const structure &s, const std::string &entityID, const std::str ...@@ -1043,7 +1043,7 @@ polymer::polymer(const structure &s, const std::string &entityID, const std::str
sugar::sugar(const branch &branch, const std::string &compoundID, sugar::sugar(const branch &branch, const std::string &compoundID,
const std::string &asym_id, int authSeqID) const std::string &asym_id, int authSeqID)
: residue(branch.get_structure(), compoundID, asym_id, 0, std::to_string(authSeqID)) : residue(branch.get_structure(), compoundID, asym_id, 0, asym_id, std::to_string(authSeqID), "")
, m_branch(&branch) , m_branch(&branch)
{ {
} }
...@@ -1318,10 +1318,10 @@ void structure::load_data() ...@@ -1318,10 +1318,10 @@ void structure::load_data()
{ {
auto &polySeqScheme = m_db["pdbx_poly_seq_scheme"]; auto &polySeqScheme = m_db["pdbx_poly_seq_scheme"];
for (const auto &[asym_id, entityID] : polySeqScheme.rows<std::string,std::string>("asym_id", "entity_id")) for (const auto &[asym_id, auth_asym_id, entityID] : polySeqScheme.rows<std::string,std::string,std::string>("asym_id", "pdb_strand_id", "entity_id"))
{ {
if (m_polymers.empty() or m_polymers.back().get_asym_id() != asym_id or m_polymers.back().get_entity_id() != entityID) if (m_polymers.empty() or m_polymers.back().get_asym_id() != asym_id or m_polymers.back().get_entity_id() != entityID)
m_polymers.emplace_back(*this, entityID, asym_id); m_polymers.emplace_back(*this, entityID, asym_id, auth_asym_id);
} }
auto &branchScheme = m_db["pdbx_branch_scheme"]; auto &branchScheme = m_db["pdbx_branch_scheme"];
...@@ -1334,8 +1334,9 @@ void structure::load_data() ...@@ -1334,8 +1334,9 @@ void structure::load_data()
auto &nonPolyScheme = m_db["pdbx_nonpoly_scheme"]; auto &nonPolyScheme = m_db["pdbx_nonpoly_scheme"];
for (const auto&[asym_id, monID, pdbSeqNum] : nonPolyScheme.rows<std::string,std::string,std::string>("asym_id", "mon_id", "pdb_seq_num")) for (const auto&[asym_id, monID, pdbStrandID, pdbSeqNum, pdbInsCode] :
m_non_polymers.emplace_back(*this, monID, asym_id, 0, pdbSeqNum); nonPolyScheme.rows<std::string,std::string,std::string,std::string,std::string>("asym_id", "mon_id", "pdb_strand_id", "pdb_seq_num", "pdb_ins_code"))
m_non_polymers.emplace_back(*this, monID, asym_id, 0, pdbStrandID, pdbSeqNum, pdbInsCode);
// place atoms in residues // place atoms in residues
...@@ -2110,7 +2111,7 @@ std::string structure::create_non_poly(const std::string &entity_id, const std:: ...@@ -2110,7 +2111,7 @@ std::string structure::create_non_poly(const std::string &entity_id, const std::
auto &atom_site = m_db["atom_site"]; auto &atom_site = m_db["atom_site"];
auto &res = m_non_polymers.emplace_back(*this, comp_id, asym_id, 0, "1"); auto &res = m_non_polymers.emplace_back(*this, comp_id, asym_id, 0, asym_id, "1", "");
for (auto &atom : atoms) for (auto &atom : atoms)
{ {
...@@ -2181,7 +2182,7 @@ std::string structure::create_non_poly(const std::string &entity_id, std::vector ...@@ -2181,7 +2182,7 @@ std::string structure::create_non_poly(const std::string &entity_id, std::vector
auto &atom_site = m_db["atom_site"]; auto &atom_site = m_db["atom_site"];
auto &res = m_non_polymers.emplace_back(*this, comp_id, asym_id, 0, "1"); auto &res = m_non_polymers.emplace_back(*this, comp_id, asym_id, 0, asym_id, "1", "");
for (auto &atom : atoms) for (auto &atom : atoms)
{ {
......
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