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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
// constructor
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_compound_id(compoundID)
, m_asym_id(asymID)
, m_seq_id(seqID)
, m_auth_asym_id(authAsymID)
, m_auth_seq_id(authSeqID)
, m_pdb_ins_code(pdbInsCode)
{
}
......@@ -427,16 +431,9 @@ class residue
const std::string &get_asym_id() const { return m_asym_id; }
int get_seq_id() const { return m_seq_id; }
const std::string get_auth_asym_id() const
{
return m_atoms.empty() ? m_asym_id : m_atoms.front().get_auth_asym_id();
}
const std::string get_auth_asym_id() const { return m_auth_asym_id; }
const std::string get_auth_seq_id() const { return m_auth_seq_id; }
std::string get_pdb_ins_code() const
{
return m_atoms.empty() ? "" : m_atoms.front().get_pdb_ins_code();
}
std::string get_pdb_ins_code() const { return m_pdb_ins_code; }
const std::string &get_compound_id() const { return m_compound_id; }
void set_compound_id(const std::string &id) { m_compound_id = id; }
......@@ -501,7 +498,7 @@ class residue
const structure *m_structure = nullptr;
std::string m_compound_id, m_asym_id;
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;
};
......@@ -519,7 +516,7 @@ class monomer : public residue
monomer &operator=(monomer &&rhs);
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_last_in_chain() const;
......@@ -582,7 +579,7 @@ class monomer : public residue
class polymer : public std::vector<monomer>
{
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 &operator=(const polymer &) = delete;
......@@ -593,16 +590,16 @@ class polymer : public std::vector<monomer>
const structure *get_structure() const { return m_structure; }
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 chainID() const;
// int Distance(const monomer &a, const monomer &b) const;
private:
const structure *m_structure;
std::string m_entity_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)
// --------------------------------------------------------------------
// monomer
monomer::monomer(const polymer &polymer, size_t index, int seqID, const std::string &authSeqID, const std::string &compoundID)
: residue(*polymer.get_structure(), compoundID, polymer.get_asym_id(), seqID, authSeqID)
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, polymer.get_auth_asym_id(), authSeqID, pdbInsCode)
, m_polymer(&polymer)
, m_index(index)
{
......@@ -955,11 +955,11 @@ bool monomer::is_cis(const monomer &a, const monomer &b)
// --------------------------------------------------------------------
// 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_entity_id(entityID)
, 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;
......@@ -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))
{
int seqID;
std::string compoundID, authSeqID;
cif::tie(seqID, authSeqID, compoundID) = r.get("seq_id", "auth_seq_num", "mon_id");
std::string compoundID, authSeqID, pdbInsCode;
cif::tie(seqID, authSeqID, compoundID, pdbInsCode) = r.get("seq_id", "auth_seq_num", "mon_id", "pdb_ins_code");
size_t index = size();
......@@ -980,11 +980,11 @@ polymer::polymer(const structure &s, const std::string &entityID, const std::str
if (not ix.count(seqID))
{
ix[seqID] = index;
emplace_back(*this, index, seqID, authSeqID, compoundID);
emplace_back(*this, index, seqID, authSeqID, pdbInsCode, compoundID);
}
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;
}
}
......@@ -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,
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)
{
}
......@@ -1318,10 +1318,10 @@ void structure::load_data()
{
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)
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"];
......@@ -1334,8 +1334,9 @@ void structure::load_data()
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"))
m_non_polymers.emplace_back(*this, monID, asym_id, 0, pdbSeqNum);
for (const auto&[asym_id, monID, pdbStrandID, pdbSeqNum, pdbInsCode] :
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
......@@ -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 &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)
{
......@@ -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 &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)
{
......
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