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/*
* Copyright (c) Schrodinger, LLC.
*
* Datastructure for `bond_dict`, parsed from CIF files with
* `chem_comp_bond` records.
*
* This file includes a generic reference implementation (1), and an
* optimized fast and memory efficient implementation (2) with key
* string length limitations.
*/
#ifndef CIFBONDDICT_H
#define CIFBONDDICT_H
#include <map>
#include <algorithm>
#include <string>
#include "os_std.h"
#include "PyMOLGlobals.h"
#if 1
// (2)
// Optimized implementation, tuned on speed and memory usage.
// Only supports resn length <= 8 and atom name length <= 4.
// Working with this limitation is currently reasonable in PyMOL,
// since cResnLen=5 and cAtomNameLen=4 (see AtomInfo.h).
#include <cstdint>
#include <unordered_map>
#include <string.h>
// mapped type of bond_dict_t
class res_bond_dict_t {
using key_type = std::int_fast64_t;
using halfkey_t = std::int32_t;
using mapped_type = signed char;
static halfkey_t make_halfkey(const char* name) {
union { halfkey_t i; char s[sizeof(halfkey_t)]; };
strncpy(s, name, sizeof(halfkey_t));
return i;
}
static key_type make_key(const char * name1, const char * name2) {
auto i1 = make_halfkey(name1);
auto i2 = make_halfkey(name2);
if (i1 > i2)
std::swap(i1, i2);
// construct 8-byte key from the two 4-byte names
return (((key_type)i1) << 32) | i2;
}
std::unordered_map<key_type, mapped_type> m_map;
std::unordered_map<halfkey_t, std::string> m_alt_names;
const char* get_standard_name(const char* name) const {
auto it = m_alt_names.find(make_halfkey(name));
if (it != m_alt_names.end()) {
return it->second.c_str();
}
return name;
}
public:
void add_alt_name(const char* name, const char* alt) {
m_alt_names[make_halfkey(alt)] = name;
}
void set(const char * name1, const char * name2, mapped_type order) {
m_map[make_key(name1, name2)] = order;
}
mapped_type get(const char * name1, const char * name2) const {
name1 = get_standard_name(name1);
name2 = get_standard_name(name2);
auto it = m_map.find(make_key(name1, name2));
if (it == m_map.end())
return -1;
return it->second;
}
};
// type for mapping: resn -> ((name1, name2) -> bond order)
class bond_dict_t {
using key_type = std::int_fast64_t;
using mapped_type = res_bond_dict_t;
static key_type make_key(const char * s_) {
union { key_type i; char s[sizeof(key_type)]; };
strncpy(s, s_, sizeof(s));
return i;
}
std::map<key_type, mapped_type> m_map;
std::set<key_type> unknown_resn;
public:
bool empty() const { return m_map.empty(); }
mapped_type& operator[](const char* resn) { return m_map[make_key(resn)]; }
void set_unknown(const char * resn) {
unknown_resn.insert(make_key(resn));
}
const mapped_type * get(PyMOLGlobals *, const char * resn, bool try_download=true);
};
#else
// (1)
// Generic reference implementation. Supports arbitrary key lengths,
// but is slower and less memory efficient. Equivalent to:
//
// typedef std::map<std::string,
// std::map<std::string,
// std::map<std::string, int> > > bond_dict_t;
//
// with added get/set methods.
#include <string>
class res_bond_dict_t {
std::map<std::string, std::map<std::string, int> > m_data;
public:
void set(const char * name1, const char * name2, int order) {
if (strcmp(name1, name2) < 0)
std::swap(name1, name2);
m_data[name1][name2] = order;
}
int get(const char * name1, const char * name2) const {
if (strcmp(name1, name2) < 0)
std::swap(name1, name2);
try {
return m_data.at(name1).at(name2);
} catch (const std::out_of_range& e) {
return -1;
}
}
};
class bond_dict_t {
std::map<std::string, res_bond_dict_t> m_data;
public:
void set(const char * resn, const char * name1, const char * name2, int order) {
m_data[resn].set(name1, name2, order);
}
const res_bond_dict_t * get(const char * resn) const {
auto it = m_data.find(resn);
if (it == m_data.end())
return NULL;
return &it->second;
}
bool empty() const {
return m_data.empty();
}
};
#endif
#endif
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