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Commit 0fcf9ed5 by Maarten L. Hekkelman
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documenting more

parent c99de817
Showing with 181 additions and 227 deletions
.gitignore
...@@ -8,5 +8,6 @@ msvc/ ...@@ -8,5 +8,6 @@ msvc/
src/revision.hpp src/revision.hpp
test/test-create_sugar_?.cif test/test-create_sugar_?.cif
Testing/ Testing/
include/cif++/exports.hpp
docs/api docs/api
docs/conf.py
\ No newline at end of file
docs/conf.py deleted 100644 → 0
project = 'libmcfp'
copyright = '2023, Maarten L. Hekkelman'
author = 'Maarten L. Hekkelman'
release = '5.1.3'
# -- General configuration ---------------------------------------------------
extensions = [
"breathe",
"exhale",
"myst_parser"
]
breathe_projects = {
"libcifpp": "../build/docs/xml"
}
myst_enable_extensions = [ "colon_fence" ]
breathe_default_project = "libcifpp"
# Setup the exhale extension
exhale_args = {
# These arguments are required
"containmentFolder": "./api",
"rootFileName": "library_root.rst",
"doxygenStripFromPath": "../include/",
# Heavily encouraged optional argument (see docs)
"rootFileTitle": "API Reference",
# Suggested optional arguments
# "createTreeView": True,
# TIP: if using the sphinx-bootstrap-theme, you need
# "treeViewIsBootstrap": True,
"exhaleExecutesDoxygen": False,
"contentsDirectives" : False,
"verboseBuild": False
}
# Tell sphinx what the primary language being documented is.
primary_domain = 'cpp'
# Tell sphinx what the pygments highlight language should be.
highlight_language = 'cpp'
templates_path = ['_templates']
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
# -- Options for HTML output -------------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#
html_theme = 'sphinx_rtd_theme'
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']
html_theme_options = {
}
cpp_index_common_prefix = [
'cif::'
]
docs/conf.py.in
project = 'libmcfp' project = '@PROJECT_NAME@'
copyright = '2023, Maarten L. Hekkelman' copyright = '2023, Maarten L. Hekkelman'
author = 'Maarten L. Hekkelman' author = 'Maarten L. Hekkelman'
release = '@PROJECT_VERSION@' release = '@PROJECT_VERSION@'
......
include/cif++/atom_type.hpp
...@@ -33,6 +33,7 @@ ...@@ -33,6 +33,7 @@
#include "cif++/exports.hpp" #include "cif++/exports.hpp"
#include <cstdint> #include <cstdint>
#include <limits>
#include <stdexcept> #include <stdexcept>
#include <string> #include <string>
...@@ -43,166 +44,175 @@ namespace cif ...@@ -43,166 +44,175 @@ namespace cif
enum atom_type : uint8_t enum atom_type : uint8_t
{ {
Nn = 0, //< Unknown Nn = 0, ///< Unknown
H = 1, //< Hydro­gen H = 1, ///< Hydro­gen
He = 2, //< He­lium He = 2, ///< He­lium
Li = 3, //< Lith­ium Li = 3, ///< Lith­ium
Be = 4, //< Beryl­lium Be = 4, ///< Beryl­lium
B = 5, //< Boron B = 5, ///< Boron
C = 6, //< Carbon C = 6, ///< Carbon
N = 7, //< Nitro­gen N = 7, ///< Nitro­gen
O = 8, //< Oxy­gen O = 8, ///< Oxy­gen
F = 9, //< Fluor­ine F = 9, ///< Fluor­ine
Ne = 10, //< Neon Ne = 10, ///< Neon
Na = 11, //< So­dium Na = 11, ///< So­dium
Mg = 12, //< Magne­sium Mg = 12, ///< Magne­sium
Al = 13, //< Alumin­ium Al = 13, ///< Alumin­ium
Si = 14, //< Sili­con Si = 14, ///< Sili­con
P = 15, //< Phos­phorus P = 15, ///< Phos­phorus
S = 16, //< Sulfur S = 16, ///< Sulfur
Cl = 17, //< Chlor­ine Cl = 17, ///< Chlor­ine
Ar = 18, //< Argon Ar = 18, ///< Argon
K = 19, //< Potas­sium K = 19, ///< Potas­sium
Ca = 20, //< Cal­cium Ca = 20, ///< Cal­cium
Sc = 21, //< Scan­dium Sc = 21, ///< Scan­dium
Ti = 22, //< Tita­nium Ti = 22, ///< Tita­nium
V = 23, //< Vana­dium V = 23, ///< Vana­dium
Cr = 24, //< Chrom­ium Cr = 24, ///< Chrom­ium
Mn = 25, //< Manga­nese Mn = 25, ///< Manga­nese
Fe = 26, //< Iron Fe = 26, ///< Iron
Co = 27, //< Cobalt Co = 27, ///< Cobalt
Ni = 28, //< Nickel Ni = 28, ///< Nickel
Cu = 29, //< Copper Cu = 29, ///< Copper
Zn = 30, //< Zinc Zn = 30, ///< Zinc
Ga = 31, //< Gallium Ga = 31, ///< Gallium
Ge = 32, //< Germa­nium Ge = 32, ///< Germa­nium
As = 33, //< Arsenic As = 33, ///< Arsenic
Se = 34, //< Sele­nium Se = 34, ///< Sele­nium
Br = 35, //< Bromine Br = 35, ///< Bromine
Kr = 36, //< Kryp­ton Kr = 36, ///< Kryp­ton
Rb = 37, //< Rubid­ium Rb = 37, ///< Rubid­ium
Sr = 38, //< Stront­ium Sr = 38, ///< Stront­ium
Y = 39, //< Yttrium Y = 39, ///< Yttrium
Zr = 40, //< Zirco­nium Zr = 40, ///< Zirco­nium
Nb = 41, //< Nio­bium Nb = 41, ///< Nio­bium
Mo = 42, //< Molyb­denum Mo = 42, ///< Molyb­denum
Tc = 43, //< Tech­netium Tc = 43, ///< Tech­netium
Ru = 44, //< Ruthe­nium Ru = 44, ///< Ruthe­nium
Rh = 45, //< Rho­dium Rh = 45, ///< Rho­dium
Pd = 46, //< Pallad­ium Pd = 46, ///< Pallad­ium
Ag = 47, //< Silver Ag = 47, ///< Silver
Cd = 48, //< Cad­mium Cd = 48, ///< Cad­mium
In = 49, //< Indium In = 49, ///< Indium
Sn = 50, //< Tin Sn = 50, ///< Tin
Sb = 51, //< Anti­mony Sb = 51, ///< Anti­mony
Te = 52, //< Tellurium Te = 52, ///< Tellurium
I = 53, //< Iodine I = 53, ///< Iodine
Xe = 54, //< Xenon Xe = 54, ///< Xenon
Cs = 55, //< Cae­sium Cs = 55, ///< Cae­sium
Ba = 56, //< Ba­rium Ba = 56, ///< Ba­rium
La = 57, //< Lan­thanum La = 57, ///< Lan­thanum
Hf = 72, //< Haf­nium Hf = 72, ///< Haf­nium
Ta = 73, //< Tanta­lum Ta = 73, ///< Tanta­lum
W = 74, //< Tung­sten W = 74, ///< Tung­sten
Re = 75, //< Rhe­nium Re = 75, ///< Rhe­nium
Os = 76, //< Os­mium Os = 76, ///< Os­mium
Ir = 77, //< Iridium Ir = 77, ///< Iridium
Pt = 78, //< Plat­inum Pt = 78, ///< Plat­inum
Au = 79, //< Gold Au = 79, ///< Gold
Hg = 80, //< Mer­cury Hg = 80, ///< Mer­cury
Tl = 81, //< Thallium Tl = 81, ///< Thallium
Pb = 82, //< Lead Pb = 82, ///< Lead
Bi = 83, //< Bis­muth Bi = 83, ///< Bis­muth
Po = 84, //< Polo­nium Po = 84, ///< Polo­nium
At = 85, //< Asta­tine At = 85, ///< Asta­tine
Rn = 86, //< Radon Rn = 86, ///< Radon
Fr = 87, //< Fran­cium Fr = 87, ///< Fran­cium
Ra = 88, //< Ra­dium Ra = 88, ///< Ra­dium
Ac = 89, //< Actin­ium Ac = 89, ///< Actin­ium
Rf = 104, //< Ruther­fordium Rf = 104, ///< Ruther­fordium
Db = 105, //< Dub­nium Db = 105, ///< Dub­nium
Sg = 106, //< Sea­borgium Sg = 106, ///< Sea­borgium
Bh = 107, //< Bohr­ium Bh = 107, ///< Bohr­ium
Hs = 108, //< Has­sium Hs = 108, ///< Has­sium
Mt = 109, //< Meit­nerium Mt = 109, ///< Meit­nerium
Ds = 110, //< Darm­stadtium Ds = 110, ///< Darm­stadtium
Rg = 111, //< Roent­genium Rg = 111, ///< Roent­genium
Cn = 112, //< Coper­nicium Cn = 112, ///< Coper­nicium
Nh = 113, //< Nihon­ium Nh = 113, ///< Nihon­ium
Fl = 114, //< Flerov­ium Fl = 114, ///< Flerov­ium
Mc = 115, //< Moscov­ium Mc = 115, ///< Moscov­ium
Lv = 116, //< Liver­morium Lv = 116, ///< Liver­morium
Ts = 117, //< Tenness­ine Ts = 117, ///< Tenness­ine
Og = 118, //< Oga­nesson Og = 118, ///< Oga­nesson
Ce = 58, //< Cerium Ce = 58, ///< Cerium
Pr = 59, //< Praseo­dymium Pr = 59, ///< Praseo­dymium
Nd = 60, //< Neo­dymium Nd = 60, ///< Neo­dymium
Pm = 61, //< Prome­thium Pm = 61, ///< Prome­thium
Sm = 62, //< Sama­rium Sm = 62, ///< Sama­rium
Eu = 63, //< Europ­ium Eu = 63, ///< Europ­ium
Gd = 64, //< Gadolin­ium Gd = 64, ///< Gadolin­ium
Tb = 65, //< Ter­bium Tb = 65, ///< Ter­bium
Dy = 66, //< Dyspro­sium Dy = 66, ///< Dyspro­sium
Ho = 67, //< Hol­mium Ho = 67, ///< Hol­mium
Er = 68, //< Erbium Er = 68, ///< Erbium
Tm = 69, //< Thulium Tm = 69, ///< Thulium
Yb = 70, //< Ytter­bium Yb = 70, ///< Ytter­bium
Lu = 71, //< Lute­tium Lu = 71, ///< Lute­tium
Th = 90, //< Thor­ium Th = 90, ///< Thor­ium
Pa = 91, //< Protac­tinium Pa = 91, ///< Protac­tinium
U = 92, //< Ura­nium U = 92, ///< Ura­nium
Np = 93, //< Neptu­nium Np = 93, ///< Neptu­nium
Pu = 94, //< Pluto­nium Pu = 94, ///< Pluto­nium
Am = 95, //< Ameri­cium Am = 95, ///< Ameri­cium
Cm = 96, //< Curium Cm = 96, ///< Curium
Bk = 97, //< Berkel­ium Bk = 97, ///< Berkel­ium
Cf = 98, //< Califor­nium Cf = 98, ///< Califor­nium
Es = 99, //< Einstei­nium Es = 99, ///< Einstei­nium
Fm = 100, //< Fer­mium Fm = 100, ///< Fer­mium
Md = 101, //< Mende­levium Md = 101, ///< Mende­levium
No = 102, //< Nobel­ium No = 102, ///< Nobel­ium
Lr = 103, //< Lawren­cium Lr = 103, ///< Lawren­cium
D = 119, //< Deuterium D = 119, ///< Deuterium
}; };
// -------------------------------------------------------------------- // --------------------------------------------------------------------
/// An enum used to select the desired radius for an atom /// An enum used to select the desired radius for an atom.
/// All values are collected from the wikipedia pages on atom radii
enum class radius_type enum class radius_type
{ {
calculated, calculated, ///< Calculated radius from theoretical models
empirical, empirical, ///< Empirically measured covalent radii
/// @deprecated It is a bit unclear where these values came from. So, better not use them
covalent_empirical, covalent_empirical,
single_bond, single_bond, ///< Bond length for a single covalent bond calculated using statistically analysis
double_bond, double_bond, ///< Bond length for a double covalent bond calculated using statistically analysis
triple_bond, triple_bond, ///< Bond length for a triple covalent bond calculated using statistically analysis
van_der_waals, van_der_waals, ///< Radius of an imaginary hard sphere representing the distance of closest approach for another atom
type_count type_count ///< Number of radii
}; };
/// @brief The number of radii per element which can be requested from @ref atom_type_info
constexpr size_t kRadiusTypeCount = static_cast<size_t>(radius_type::type_count); constexpr size_t kRadiusTypeCount = static_cast<size_t>(radius_type::type_count);
/// An enum used to select either the effective or the crystal radius of an ion /// An enum used to select either the effective or the crystal radius of an ion.
/// See explanation on Wikipedia: https://en.wikipedia.org/wiki/Ionic_radius
enum class ionic_radius_type enum class ionic_radius_type
{ {
effective, crystal effective, ///< Based on distance between ions in a crystal structure as determined by X-ray crystallography
crystal ///< Calculated ion radius based on a function of ionic charge and spin
}; };
/// Requests for an unknown radius value return kNA
constexpr float kNA = std::numeric_limits<float>::quiet_NaN();
/// A struct holding the known information for all elements defined in @ref atom_type /// A struct holding the known information for all elements defined in @ref atom_type
struct atom_type_info struct atom_type_info
...@@ -222,7 +232,7 @@ struct atom_type_info ...@@ -222,7 +232,7 @@ struct atom_type_info
/// A flag indicating whether the element is a metal /// A flag indicating whether the element is a metal
bool metal; bool metal;
/// Array containing all known radii for this element. A value of std::nanf("1") is /// Array containing all known radii for this element. A value of @ref cif::kNA is
/// stored for unknown values /// stored for unknown values
float radii[kRadiusTypeCount]; float radii[kRadiusTypeCount];
}; };
...@@ -234,7 +244,7 @@ extern CIFPP_EXPORT const atom_type_info kKnownAtoms[]; ...@@ -234,7 +244,7 @@ extern CIFPP_EXPORT const atom_type_info kKnownAtoms[];
// -------------------------------------------------------------------- // --------------------------------------------------------------------
// AtomTypeTraits // AtomTypeTraits
/// A traits class to access information on known elements /// A traits class to access information for known elements
class atom_type_traits class atom_type_traits
{ {
...@@ -245,12 +255,12 @@ class atom_type_traits ...@@ -245,12 +255,12 @@ class atom_type_traits
/// Constructor based on the element as a string in \a symbol /// Constructor based on the element as a string in \a symbol
atom_type_traits(const std::string &symbol); atom_type_traits(const std::string &symbol);
atom_type type() const { return m_info->type; } atom_type type() const { return m_info->type; } ///< Returns the @ref atom_type
std::string name() const { return m_info->name; } std::string name() const { return m_info->name; } ///< Returns the name of the element
std::string symbol() const { return m_info->symbol; } std::string symbol() const { return m_info->symbol; } ///< Returns the symbol of the element
float weight() const { return m_info->weight; } float weight() const { return m_info->weight; } ///< Returns the average weight of the element
bool is_metal() const { return m_info->metal; } bool is_metal() const { return m_info->metal; } ///< Returns true if the element is a metal
/// Return true if the symbol in \a symbol actually exists in the list of known elements in @ref atom_type /// Return true if the symbol in \a symbol actually exists in the list of known elements in @ref atom_type
static bool is_element(const std::string &symbol); static bool is_element(const std::string &symbol);
...@@ -258,6 +268,9 @@ class atom_type_traits ...@@ -258,6 +268,9 @@ class atom_type_traits
/// Return true if the symbol in \a symbol exists and is a metal /// Return true if the symbol in \a symbol exists and is a metal
static bool is_metal(const std::string &symbol); static bool is_metal(const std::string &symbol);
/// @brief Return the radius for the element, use \a type to select which radius to return
/// @param type The selector for which radius to return
/// @return The requested radius or @ref cif::kNA if not known (or applicable)
float radius(radius_type type = radius_type::single_bond) const float radius(radius_type type = radius_type::single_bond) const
{ {
if (type >= radius_type::type_count) if (type >= radius_type::type_count)
...@@ -294,21 +307,28 @@ class atom_type_traits ...@@ -294,21 +307,28 @@ class atom_type_traits
double a[6], b[6]; double a[6], b[6];
}; };
// to get the Cval and Siva values, use this constant as charge: // to get the Cval and Siva scattering factor values, use this constant as charge:
enum static constexpr int kWKSFVal = -99;
{
kWKSFVal = -99
};
/// @brief Return the Waasmaier & Kirfel scattering factor values for the element
///
/// The coefficients from Waasmaier & Kirfel (1995), Acta Cryst. A51, 416-431.
///
/// @param charge The charge for which the structure values should be returned, use @ref kWSKFVal to return the Cval and Siva values
/// @return The scattering factors as a @ref SFData struct
const SFData &wksf(int charge = 0) const; const SFData &wksf(int charge = 0) const;
/// @brief Return the electron scattering factor values for the element
///
/// @return The scattering factors as a @ref SFData struct
const SFData &elsf() const; const SFData &elsf() const;
// Clipper doesn't like atoms with charges that do not have a scattering factor. And /// Clipper doesn't like atoms with charges that do not have a scattering factor. And
// rightly so, but we need to know in advance if this is the case /// rightly so, but we need to know in advance if this is the case
bool has_sf(int charge) const; bool has_sf(int charge) const;
private: private:
const struct atom_type_info *m_info; const struct atom_type_info *m_info;
}; };
} // namespace pdbx } // namespace cif
src/atom_type.cpp
...@@ -34,8 +34,6 @@ namespace cif ...@@ -34,8 +34,6 @@ namespace cif
namespace data namespace data
{ {
const float kNA = std::nanf("1");
const atom_type_info kKnownAtoms[] = const atom_type_info kKnownAtoms[] =
{ {
{ Nn, "Unknown", "Nn", 0, false, { kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // 0 Nn Unknown { Nn, "Unknown", "Nn", 0, false, { kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // 0 Nn Unknown
...@@ -1145,7 +1143,7 @@ auto atom_type_traits::elsf() const -> const SFData& ...@@ -1145,7 +1143,7 @@ auto atom_type_traits::elsf() const -> const SFData&
float atom_type_traits::crystal_ionic_radius(int charge) const float atom_type_traits::crystal_ionic_radius(int charge) const
{ {
float result = data::kNA; float result = kNA;
if (charge >= -3 and charge <= 8) if (charge >= -3 and charge <= 8)
{ {
...@@ -1164,7 +1162,7 @@ float atom_type_traits::crystal_ionic_radius(int charge) const ...@@ -1164,7 +1162,7 @@ float atom_type_traits::crystal_ionic_radius(int charge) const
float atom_type_traits::effective_ionic_radius(int charge) const float atom_type_traits::effective_ionic_radius(int charge) const
{ {
float result = data::kNA; float result = kNA;
if (charge >= -3 and charge <= 8) if (charge >= -3 and charge <= 8)
{ {
......
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