Namespaces
namespace	cif

Classes
struct	Addends

struct	AlignmentResult

struct	AlignmentScoring

struct	Assembly

struct	AsuBrick

struct	AsuData

struct	Atom
	Represents atom site in macromolecular structure (~100 bytes). More...

struct	AtomAddress

struct	AtomGroup_

struct	AtomNameElement

class	BasicInput

struct	BasicRefinementInfo

struct	BesselTables_

struct	BidirIterator

struct	Binner

struct	Blob

struct	BlobCriteria

struct	BondIndex

struct	Box

struct	C4322

struct	Ccp4

struct	Ccp4Base

struct	CenterOfMass

struct	Chain

struct	ChainNameGenerator

class	CharArray

struct	ChemComp

struct	ChemLink

struct	ChemMod

struct	CifToMtz

struct	CisPep

struct	ComplexCorrelation

struct	Connection

struct	const_CRA

struct	ConstFilterProxy

struct	ConstResidueGroup

struct	ConstResidueSpan

struct	ConstUniqProxy

struct	ContactSearch

struct	Correlation

struct	Covariance

struct	CRA

class	CraIterPolicy

struct	CraProxy_

struct	CrystalInfo

struct	DataStats

struct	DensityCalculator

struct	DiffractionInfo

class	DirWalk

struct	Element

struct	EnerLib

struct	Entity

struct	ExpAnisoSum

struct	ExpAnisoSum< N, float >

struct	ExperimentInfo

struct	ExpSum

struct	ExpSum< N, float >

struct	FastaSeq

struct	FileStream

class	FilterIterPolicy

struct	FilterProxy

struct	FloodFill

struct	FPhiProxy

struct	Fractional
	Fractional coordinates. More...

struct	FTransform
	Like Transform, but apply() arg is Fractional (not Vec3 - for type safety). More...

struct	GaussianCoef

struct	GlobWalk

struct	Grid
	Real-space grid. More...

struct	GridBase
	A common subset of Grid and ReciprocalGrid. More...

struct	GridMeta
	The base of Grid classes that does not depend on stored data type. More...

struct	GridOp

class	GroupingIterPolicy

struct	GroupOps

struct	GruberVector

struct	GzStream

struct	Helix

struct	HklMatch

struct	HklValue

struct	Ifstream

class	IndirectIterPolicy

struct	Intensities

struct	IT92

struct	ItemGroup

struct	LevMar

class	LineReader

class	LineReaderBase
	type-erased line-based reader More...

struct	LinkHunt

struct	Logger
	Passes messages (including warnings/errors) to a callback function. More...

struct	MaskedGrid

struct	Mat33

class	MaybeGzipped

struct	MemoryStream

struct	Metadata

struct	MillerHash

struct	MmcifOutputGroups

struct	Model

struct	ModRes

struct	MonLib

struct	Mtz

struct	MtzDataProxy

struct	MtzExternalDataProxy

class	MtzToCif

struct	MutableVectorSpan

struct	NcsOp
	Non-crystallographic symmetry operation (such as in the MTRIXn record) More...

struct	NearestImage
	Result of find_nearest_image. More...

struct	needs_fclose
	deleter for fileptr_t More...

struct	NeighborSearch

struct	Neutron92

struct	NodeInfo

struct	Ofstream

struct	Op

struct	OptionalInt

struct	PdbReadOptions
	options affecting how pdb file is read More...

struct	PdbWriteOptions

struct	Position
	Coordinates in Angstroms - orthogonal (Cartesian) coordinates. More...

struct	ReciprocalAsu

struct	ReciprocalGrid

struct	RefinementInfo

struct	ReflectionsInfo

struct	ReflnBlock

struct	ReflnDataProxy

struct	Residue

struct	ResidueGroup

struct	ResidueId

struct	ResidueInfo

struct	ResidueSpan

struct	Restraints

struct	Scaling

struct	Selection

struct	SellingVector

struct	SeqId

struct	Sheet

struct	SiftsUnpResidue
	Reference to UniProt residue, based on _pdbx_sifts_xref_db. More...

struct	SmallStructure

struct	SMat33

struct	SoftwareItem

struct	SolventMasker

struct	SpaceGroup

struct	SpaceGroupAltName

struct	Span

class	StrideIterPolicy

struct	Structure

class	StructureFactorCalculator

struct	SupResult

struct	TlsGroup

struct	Topo

struct	Transform

class	UniqIterPolicy

struct	UniqProxy

struct	UnitCell
	Unit cell. More...

struct	UnitCellParameters

struct	UnmergedHklMover

struct	UpperTriangularMat33

struct	ValueSigma

struct	Variance

struct	Vec3_

struct	XdsAscii

Typedefs
using	CifWalk = DirWalk< true, impl::IsCifFile >

using	MmCifWalk = DirWalk< true, impl::IsMmCifFile >

using	PdbWalk = DirWalk< true, impl::IsPdbFile >

using	CoorFileWalk = DirWalk< true, impl::IsCoordinateFile >

typedef const char	elname_t[3]

typedef std::unique_ptr< std::FILE, needs_fclose >	fileptr_t

template<typename Value >
using	StrideIter = BidirIterator< StrideIterPolicy< Value > >

template<typename Redirect , typename Value >
using	IndirectIter = BidirIterator< IndirectIterPolicy< Redirect, Value > >

template<typename Vector , typename Value >
using	UniqIter = BidirIterator< UniqIterPolicy< Vector, Value > >

template<typename Vector , typename Value >
using	GroupingIter = BidirIterator< GroupingIterPolicy< Vector, Value > >

template<typename Filter , typename Vector , typename Value >
using	FilterIter = BidirIterator< FilterIterPolicy< Filter, Vector, Value > >

using	Vec3 = Vec3_< double >

using	Vec3f = Vec3_< float >

using	AtomGroup = AtomGroup_< Atom >

using	ConstAtomGroup = AtomGroup_< const Atom >

using	CraProxy = CraProxy_< CRA, std::vector< Chain > & >

using	ConstCraProxy = CraProxy_< const_CRA, const std::vector< Chain > & >

template<typename T >
using	FPhiGrid = ReciprocalGrid< std::complex< T > >

using	Vec6 = std::array< double, 6 >

using	spacegroup_tables = impl::Tables_< void >

using	OpObliquity = std::pair< Op, double >

using	Miller = std::array< int, 3 >
	A synonym for convenient passing of hkl.

Enumerations
enum class	SupSelect { CaP , MainChain , All }

enum class	HowToNameCopiedChain { Short , AddNumber , Dup }

enum class	MapSetup { Full , NoSymmetry , ReorderOnly }

enum class	BondType { Unspec , Single , Double , Triple , Aromatic , Deloc , Metal }

enum class	ChiralityType { Positive , Negative , Both }

enum class	El : unsigned char { X =0 , H , He , Li , Be , B , C , N , O , F , Ne , Na , Mg , Al , Si , P , S , Cl , Ar , K , Ca , Sc , Ti , V , Cr , Mn , Fe , Co , Ni , Cu , Zn , Ga , Ge , As , Se , Br , Kr , Rb , Sr , Y , Zr , Nb , Mo , Tc , Ru , Rh , Pd , Ag , Cd , In , Sn , Sb , Te , I , Xe , Cs , Ba , La , Ce , Pr , Nd , Pm , Sm , Eu , Gd , Tb , Dy , Ho , Er , Tm , Yb , Lu , Hf , Ta , W , Re , Os , Ir , Pt , Au , Hg , Tl , Pb , Bi , Po , At , Rn , Fr , Ra , Ac , Th , Pa , U , Np , Pu , Am , Cm , Bk , Cf , Es , Fm , Md , No , Lr , Rf , Db , Sg , Bh , Hs , Mt , Ds , Rg , Cn , Nh , Fl , Mc , Lv , Ts , Og , D , END }

enum class	AxisOrder : unsigned char { Unknown , XYZ , ZYX }
	Order of grid axis. More...

enum class	GridSizeRounding { Nearest , Up , Down }

enum class	EntityType : unsigned char { Unknown , Polymer , NonPolymer , Branched , Water }

enum class	PolymerType : unsigned char { Unknown , PeptideL , PeptideD , Dna , Rna , DnaRnaHybrid , SaccharideD , SaccharideL , Pna , CyclicPseudoPeptide , Other }

enum class	ChemCompModel { Xyz = 1 , Example = 2 , Ideal = 4 }

enum class	CoorFormat : unsigned char { Unknown , Detect , Pdb , Mmcif , Mmjson , ChemComp }
	File format of a macromolecular model. More...

enum class	CalcFlag : signed char { NotSet =0 , NoHydrogen , Determined , Calculated , Dummy }
	corresponds to _atom_site.calc_flag in mmCIF More...

enum class	DataType { Unknown , Unmerged , Mean , Anomalous }

enum class	ResidueKind : unsigned char { UNKNOWN =0 , AA , AAD , PAA , MAA , RNA , DNA , BUF , HOH , PYR , KET , ELS }

enum class	AtomicRadiiSet { VanDerWaals , Cctbx , Refmac , Constant }

enum class	CrystalSystem : unsigned char { Triclinic =0 , Monoclinic , Orthorhombic , Tetragonal , Trigonal , Hexagonal , Cubic }

enum class	PointGroup : unsigned char { C1 =0 , Ci , C2 , Cs , C2h , D2 , C2v , D2h , C4 , S4 , C4h , D4 , C4v , D2d , D4h , C3 , C3i , D3 , C3v , D3d , C6 , C3h , C6h , D6 , C6v , D3h , D6h , T , Th , O , Td , Oh }

enum class	Laue : unsigned char { L1 =0 , L2m , Lmmm , L4m , L4mmm , L3 , L3m , L6m , L6mmm , Lm3 , Lm3m }

enum class	HydrogenChange { NoChange , Shift , Remove , ReAdd , ReAddButWater , ReAddKnown }

enum class	Asu : unsigned char { Same , Different , Any }

Functions
std::vector< int >	prepare_target_gapo (const ConstResidueSpan &polymer, PolymerType polymer_type, const AlignmentScoring *scoring=nullptr)

AlignmentResult	align_sequence_to_polymer (const std::vector< std::string > &full_seq, const ConstResidueSpan &polymer, PolymerType polymer_type, const AlignmentScoring *scoring=nullptr)

bool	seqid_matches_seqres (const ConstResidueSpan &polymer, const Entity &ent)

void	clear_sequences (Structure &st)

GEMMI_DLL void	assign_best_sequences (Structure &st, const std::vector< std::string > &fasta_sequences)

void	assign_label_seq_to_polymer (ResidueSpan &polymer, const Entity *ent, bool force)

void	clear_label_seq_id (Structure &st)

void	assign_label_seq_id (Structure &st, bool force)

void	prepare_positions_for_superposition (std::vector< Position > &pos1, std::vector< Position > &pos2, ConstResidueSpan fixed, ConstResidueSpan movable, PolymerType ptype, SupSelect sel, char altloc='\0', std::vector< int > *ca_offsets=nullptr)

SupResult	calculate_current_rmsd (ConstResidueSpan fixed, ConstResidueSpan movable, PolymerType ptype, SupSelect sel, char altloc='\0')

SupResult	calculate_superposition (ConstResidueSpan fixed, ConstResidueSpan movable, PolymerType ptype, SupSelect sel, int trim_cycles=0, double trim_cutoff=2.0, char altloc='\0')

std::vector< SupResult >	calculate_superpositions_in_moving_window (ConstResidueSpan fixed, ConstResidueSpan movable, PolymerType ptype, double radius=10.0)

void	ensure_unique_chain_name (const Model &model, Chain &chain)

GEMMI_DLL Model	make_assembly (const Assembly &assembly, const Model &model, HowToNameCopiedChain how, const Logger &logging)

Assembly	pseudo_assembly_for_unit_cell (const UnitCell &cell)

GEMMI_DLL void	transform_to_assembly (Structure &st, const std::string &assembly_name, HowToNameCopiedChain how, const Logger &logging, bool keep_spacegroup=false, double merge_dist=0.2)
	If called with assembly_name="unit_cell" changes structure to unit cell (P1).

GEMMI_DLL Model	expand_ncs_model (const Model &model, const std::vector< NcsOp > &ncs, HowToNameCopiedChain how)

GEMMI_DLL void	merge_atoms_in_expanded_model (Model &model, const UnitCell &cell, double max_dist=0.2, bool compare_serial=true)
	Searches and merges overlapping equivalent atoms from different chains.

GEMMI_DLL void	shorten_chain_names (Structure &st)

GEMMI_DLL void	expand_ncs (Structure &st, HowToNameCopiedChain how, double merge_dist=0.2)

GEMMI_DLL void	split_chains_by_segments (Model &model, HowToNameCopiedChain how)
	HowToNameCopiedChain::Dup adds segment name to chain name.

template<typename Func , typename T >
void	for_matching_reflections (const std::vector< T > &a, const std::vector< T > &b, const Func &func)

template<typename T >
Correlation	calculate_hkl_value_correlation (const std::vector< T > &a, const std::vector< T > &b)

template<typename T >
ComplexCorrelation	calculate_hkl_complex_correlation (const std::vector< T > &a, const std::vector< T > &b)

template<typename T >
int	count_equal_values (const std::vector< T > &a, const std::vector< T > &b)

template<typename T , int N, typename Data >
AsuData< T >	make_asu_data (const Data &data, const std::array< std::string, N > &labels, bool as_is=false)

template<typename T , typename Data >
AsuData< T >	make_asu_data (const Data &data, const std::string &label, bool as_is)

template<typename T >
void	discard_by_sigma_ratio (AsuData< ValueSigma< T > > &asu_data, double cutoff)
	retains only points with positive SIGF and F/SIGF > cutoff

AsuBrick	find_asu_brick (const SpaceGroup *sg)

template<typename V = std::int8_t>
std::vector< V >	get_asu_mask (const GridMeta &grid)

template<typename T >
MaskedGrid< T >	masked_asu (Grid< T > &grid)

template<typename T >
Box< Fractional >	get_nonzero_extent (const GridBase< T > &grid)

from_chars_result	fast_from_chars (const char start, const char end, double &d)

from_chars_result	fast_from_chars (const char *start, double &d)

double	fast_atof (const char p, const char *endptr=nullptr)

bool	is_space (char c)

bool	is_blank (char c)

bool	is_digit (char c)

const char *	skip_blank (const char *p)

const char *	skip_word (const char *p)

std::string	read_word (const char *line)

std::string	read_word (const char line, const char *endptr)

int	string_to_int (const char *p, bool checked, size_t length=0)

int	string_to_int (const std::string &str, bool checked)

int	simple_atoi (const char p, const char *endptr=nullptr)

int	no_sign_atoi (const char p, const char *endptr=nullptr)

template<int N>
double	evaluate_polynomial (const double(&poly)[N], double x)

double	bessel_i1_over_i0 (double x)

double	bessel_i0 (double x)

double	log_bessel_i0 (double x)

Correlation	combine_two_correlations (const Correlation &a, const Correlation &b)

Correlation	combine_correlations (const std::vector< Correlation > &cors)

std::vector< Blob >	find_blobs_by_flood_fill (const gemmi::Grid< float > &grid, const BlobCriteria &criteria, bool negate=false)

template<class T >
bool	has_hydrogen (const T &obj)

template<>
bool	has_hydrogen (const Atom &atom)

template<class T >
size_t	count_atom_sites (const T &obj, const Selection *sel=nullptr)

template<>
size_t	count_atom_sites (const Atom &atom, const Selection *sel)

template<class T >
double	count_occupancies (const T &obj, const Selection *sel=nullptr)

template<>
double	count_occupancies (const Atom &atom, const Selection *sel)

template<class T >
double	calculate_mass (const T &obj)

template<>
double	calculate_mass (const Atom &atom)

template<class T >
CenterOfMass	calculate_center_of_mass (const T &obj)

template<>
CenterOfMass	calculate_center_of_mass (const Atom &atom)

template<class T >
std::pair< float, float >	calculate_b_iso_range (const T &obj)

template<>
std::pair< float, float >	calculate_b_iso_range (const Atom &atom)

std::pair< double, double >	calculate_b_aniso_range (const Model &model)
	uses min/max eigenvalues of Baniso, or Biso if B-factor is isotropic

template<class T >
void	expand_box (const T &obj, Box< Position > &box)

template<>
void	expand_box (const Atom &atom, Box< Position > &box)

Box< Position >	calculate_box (const Structure &st, double margin=0.)

Box< Fractional >	calculate_fractional_box (const Structure &st, double margin=0.)

double	calculate_b_est (const Atom &atom)

double	calculate_angle (const Position &p0, const Position &p1, const Position &p2)

double	calculate_dihedral (const Position &p0, const Position &p1, const Position &p2, const Position &p3)

double	calculate_dihedral_from_atoms (const Atom a, const Atom b, const Atom c, const Atom d)
	the return value is in the same range as that of atan2(), i.e. [-pi, pi]

double	calculate_omega (const Residue &res, const Residue &next)

bool	is_peptide_bond_cis (const Atom ca1, const Atom c, const Atom n, const Atom ca2, double tolerance_deg)

double	calculate_chiral_volume (const Position &actr, const Position &a1, const Position &a2, const Position &a3)

std::array< double, 2 >	calculate_phi_psi (const Residue prev, const Residue &res, const Residue next)

GEMMI_DLL std::array< double, 4 >	find_best_plane (const std::vector< Atom * > &atoms)

double	get_distance_from_plane (const Position &pos, const std::array< double, 4 > &coeff)

GEMMI_DLL FTransform	parse_triplet_as_ftransform (const std::string &s)

template<typename Restr >
double	angle_z (double value_rad, const Restr &restr, double full=360.)

double	chiral_abs_volume (double bond1, double bond2, double bond3, double angle1, double angle2, double angle3)

BondType	bond_type_from_string (const std::string &s)

const char *	bond_type_to_string (BondType btype)

float	order_of_bond_type (BondType btype)

ChiralityType	chirality_from_string (const std::string &s)

ChiralityType	chirality_from_flag_and_volume (const std::string &s, double volume)

const char *	chirality_to_string (ChiralityType chir_type)

ChemComp	make_chemcomp_from_block (const cif::Block &block_)

template<typename DataProxy >
std::pair< DataType, size_t >	check_data_type_under_symmetry (const DataProxy &proxy)

bool	possible_old_style (const ReflnBlock &rb, DataType data_type)

cif::Loop	transcript_old_anomalous_to_standard (const cif::Loop &loop, const SpaceGroup *sg)
	Before _refln.pdbx_F_plus/minus was introduced, anomalous data was stored as two F_meas_au reflections, say (1,1,3) and (-1,-1,-3).

GEMMI_DLL void	setup_for_crd (Structure &st)

GEMMI_DLL void	add_automatic_links (Model &model, Structure &st, const MonLib &monlib)

GEMMI_DLL void	add_dictionary_blocks (cif::Document &doc, const std::vector< std::string > &resnames, const Topo &topo, const MonLib &monlib)

GEMMI_DLL cif::Document	prepare_refmac_crd (Structure &st, const Topo &topo, const MonLib &monlib, HydrogenChange h_change)

template<int N, typename Real >
Real	determine_cutoff_radius (Real x1, const ExpSum< N, Real > &precal, Real cutoff_level)

template<typename Real >
Real	it92_radius_approx (Real b)

std::string	as_utf8 (const _tinydir_char_t *path)

bool	glob_match (const std::string &pattern, const std::string &str)

template<typename DataProxy >
std::vector< double >	calculate_amplitude_normalizers (const DataProxy &data, int fcol_idx, const Binner &binner)

GEMMI_DLL Mat33	eigen_decomposition (const SMat33< double > &A, double(&d)[3])

bool	is_hydrogen (El el)

bool &	is_metal_value (El el)

bool	is_metal (El el)

void	set_is_metal (El el, bool v)

constexpr bool	ce_almost_eq (double x, double y)

double	molecular_weight (El el)

float	covalent_radius (El el)

float	vdw_radius (El el)

const char *	element_name (El el)

elname_t &	element_uppercase_name (El el)

El	find_element (const char *symbol)

const char *	entity_type_to_string (EntityType entity_type)

EntityType	entity_type_from_string (const std::string &t)

const char *	polymer_type_to_string (PolymerType polymer_type)

PolymerType	polymer_type_from_string (const std::string &t)

const char *	connection_type_to_string (Connection::Type t)

Connection::Type	connection_type_from_string (const std::string &t)

std::string	software_classification_to_string (SoftwareItem::Classification c)

SoftwareItem::Classification	software_classification_from_string (const std::string &str)

void	fail (const std::string &msg)

template<typename T , typename... Args>
void	fail (std::string &&str, T &&arg1, Args &&... args)

GEMMI_COLD void	fail (const char *msg)

GEMMI_COLD void	sys_fail (const std::string &msg)

GEMMI_COLD void	sys_fail (const char *msg)

void	unreachable ()

std::string	path_basename (const std::string &path, std::initializer_list< const char * > exts)

fileptr_t	file_open (const char path, const char mode)

fileptr_t	file_open_or (const char path, const char mode, std::FILE *dash_stream)

std::size_t	file_size (std::FILE *f, const std::string &path)

bool	is_little_endian ()

void	swap_two_bytes (void *start)

void	swap_four_bytes (void *start)

void	swap_eight_bytes (void *start)

CharArray	read_file_into_buffer (const std::string &path)

CharArray	read_stdin_into_buffer ()

template<typename T >
CharArray	read_into_buffer (T &&input)

void	mask_nodes_above_threshold (Grid< std::int8_t > &mask, const Grid< float > &grid, double threshold, bool negate=false)

Grid< std::int8_t >	flood_fill_above (const Grid< float > &grid, const std::vector< Position > &seeds, double threshold, bool negate=false)

float	unsafe_expapprox (float x)

template<typename Real >
Real	pow15 (Real x)

template<typename T >
double	phase_in_angles (const std::complex< T > &v, double eps=2e-5)

void	add_asu_f_phi_to_float_vector (std::vector< float > &float_data, const AsuData< std::complex< float > > &asu_data)

template<typename DataProxy >
std::array< int, 3 >	get_size_for_hkl (const DataProxy &data, std::array< int, 3 > min_size, double sample_rate)

template<typename DataProxy >
bool	data_fits_into (const DataProxy &data, std::array< int, 3 > size)

template<typename T >
void	add_friedel_mates (ReciprocalGrid< T > &grid)

template<typename T , typename DataProxy >
void	initialize_hkl_grid (ReciprocalGrid< T > &grid, const DataProxy &data, std::array< int, 3 > size, bool half_l, AxisOrder axis_order)

template<typename T , typename FPhi >
FPhiGrid< T >	get_f_phi_on_grid (const FPhi &fphi, std::array< int, 3 > size, bool half_l, AxisOrder axis_order=AxisOrder::XYZ)

template<typename T , typename DataProxy >
ReciprocalGrid< T >	get_value_on_grid (const DataProxy &data, size_t column, std::array< int, 3 > size, bool half_l, AxisOrder axis_order=AxisOrder::XYZ)

template<typename T >
Grid< T >	transform_f_phi_grid_to_map (FPhiGrid< T > &&hkl)

template<typename T , typename FPhi >
Grid< T >	transform_f_phi_to_map (const FPhi &fphi, std::array< int, 3 > size, double sample_rate, bool exact_size=false, AxisOrder order=AxisOrder::XYZ)

template<typename T , typename FPhi >
Grid< T >	transform_f_phi_to_map2 (const FPhi &fphi, std::array< int, 3 > min_size, double sample_rate, std::array< int, 3 > exact_size, AxisOrder order=AxisOrder::XYZ)

template<typename T >
FPhiGrid< T >	transform_map_to_f_phi (const Grid< T > &map, bool half_l, bool use_scale=true)

GEMMI_DLL void	cromer_liberman_for_array (int z, int npts, const double energy, double fp, double *fpp)
	Cromer-Liberman calculation of anomalous scattering factors.

double	cromer_liberman (int z, double energy, double *fpp)
	returns fp, fpp is returned through the last argument.

template<typename T >
void	open_stream_from_utf8_path (T &ptr, const std::string &filename)

int	modulo (int a, int n)

bool	has_small_factorization (int n)

int	round_with_small_factorization (double exact, GridSizeRounding rounding)

std::array< int, 3 >	good_grid_size (std::array< double, 3 > limit, GridSizeRounding rounding, const SpaceGroup *sg)

void	check_grid_factors (const SpaceGroup *sg, std::array< int, 3 > size)

double	cubic_interpolation (double u, double a, double b, double c, double d)
	Catmull–Rom spline interpolation.

double	cubic_interpolation_der (double u, double a, double b, double c, double d)
	df/du (from Wolfram Alpha)

template<typename T >
void	interpolate_grid (Grid< T > &dest, const Grid< T > &src, const Transform &tr, int order=1)

template<typename T >
Correlation	calculate_correlation (const GridBase< T > &a, const GridBase< T > &b)

GEMMI_DLL size_t	estimate_uncompressed_size (const std::string &path)

std::string	miller_str (const Miller &hkl)

GEMMI_DLL std::string	read_staraniso_b_from_mtz (const Mtz &mtz, SMat33< double > &output)
	Returns STARANISO version or empty string.

SmallStructure::Site	atom_to_site (const Atom &atom, const UnitCell &cell)

SmallStructure	mx_to_sx_structure (const Structure &st, int n=0)

void	jordan_solve (double a, double b, int n)
	This function solves a set of linear algebraic equations using Gauss-Jordan elimination with partial pivoting.

void	jordan_solve (std::vector< double > &a, std::vector< double > &b)

void	print_parameters (const std::string &name, std::vector< double > &a)

template<typename Target >
double	compute_wssr (const Target &target)

template<typename Target >
double	compute_gradients (const Target &target, unsigned n, double *grad)

template<typename Target >
double	compute_lm_matrices (const Target &target, std::vector< double > &alpha, std::vector< double > &beta)

constexpr double	pi ()

constexpr double	hc ()

constexpr double	bohrradius ()

constexpr double	mott_bethe_const ()

constexpr double	u_to_b ()

constexpr double	deg (double angle)

constexpr double	rad (double angle)

constexpr float	sq (float x)

constexpr double	sq (double x)

double	log_cosh (double x)

int	iround (double d)

double	angle_abs_diff (double a, double b, double full=360.0)

Vec3	operator* (double d, const Vec3 &v)

Vec3	rotate_about_axis (const Vec3 &v, const Vec3 &axis, double theta)
	Rodrigues' rotation formula: rotate vector v about given axis of rotation (which must be a unit vector) by given angle (in radians).

bool	is_polypeptide (PolymerType pt)

bool	is_polynucleotide (PolymerType pt)

GEMMI_DLL Structure	make_structure_from_block (const cif::Block &block)
	structure from a coordinate mmCIF block

Structure	make_structure (cif::Document &&doc, cif::Document *save_doc=nullptr)
	structure from a coordinate mmCIF document

constexpr int	operator\| (ChemCompModel a, ChemCompModel b)

GEMMI_DLL Residue	make_residue_from_chemcomp_block (const cif::Block &block, ChemCompModel kind)
	make_residue_from_chemcomp_block

Model	make_model_from_chemcomp_block (const cif::Block &block, ChemCompModel kind)

Structure	make_structure_from_chemcomp_block (const cif::Block &block, int which=7)

int	check_chemcomp_block_number (const cif::Document &doc)

Structure	make_structure_from_chemcomp_doc (const cif::Document &doc, cif::Document *save_doc=nullptr, int which=7)

void	copy_transform_to_mmdb (const Transform &tr, mmdb::mat33 &mat, mmdb::vect3 &vec)

template<int N>
void	strcpy_to_mmdb (char(&dest)[N], const std::string &src)

void	set_seqid_in_mmdb (int *seqnum, mmdb::InsCode &icode, SeqId seqid)

SeqId	seqid_from_mmdb (int seqnum, const mmdb::InsCode &inscode)

mmdb::CisPep *	cispep_to_mmdb (const CisPep &g, int ser_num, int model_num)

CisPep	cispep_from_mmdb (const mmdb::CisPep &m, int model_num)

void	transfer_links_to_mmdb (const Structure &st, mmdb::Manager *mol)

void	transfer_links_from_mmdb (mmdb::LinkContainer &mmdb_links, Structure &st)

void	copy_to_mmdb (const Structure &st, mmdb::Manager *manager)

Atom	copy_atom_from_mmdb (mmdb::Atom &m_atom)

Residue	copy_residue_from_mmdb (mmdb::Residue &m_res)

Chain	copy_chain_from_mmdb (mmdb::Chain &m_chain)

Model	copy_model_from_mmdb (mmdb::Model &m_model)

Structure	copy_from_mmdb (mmdb::Manager *manager)

CoorFormat	coor_format_from_ext (const std::string &path)

CoorFormat	coor_format_from_content (const char buf, const char end)

Structure	make_structure_from_doc (cif::Document &&doc, bool possible_chemcomp, cif::Document *save_doc=nullptr)

Structure	read_structure_from_memory (char data, size_t size, const std::string &path, CoorFormat format=CoorFormat::Unknown, cif::Document save_doc=nullptr)

Structure	read_structure_from_char_array (char data, size_t size, const std::string &path, cif::Document save_doc=nullptr)

template<typename T >
Structure	read_structure (T &&input, CoorFormat format=CoorFormat::Unknown, cif::Document *save_doc=nullptr)

Structure	read_structure_file (const std::string &path, CoorFormat format=CoorFormat::Unknown)

GEMMI_DLL Structure	read_structure_gz (const std::string &path, CoorFormat format=CoorFormat::Unknown, cif::Document *save_doc=nullptr)

GEMMI_DLL Structure	read_pdb_gz (const std::string &path, PdbReadOptions options=PdbReadOptions())

GEMMI_DLL Structure	read_structure_from_chemcomp_gz (const std::string &path, cif::Document *save_doc=nullptr, int which=7)

GEMMI_DLL CoorFormat	coor_format_from_ext_gz (const std::string &path)

template<class T >
void	remove_empty_children (T &obj)

bool	is_same_conformer (char altloc1, char altloc2)

std::string	atom_str (const Chain &chain, const ResidueId &res_id, const Atom &atom)

std::string	atom_str (const const_CRA &cra)

bool	atom_matches (const const_CRA &cra, const AtomAddress &addr, bool ignore_segment=false)

AtomAddress	make_address (const Chain &ch, const Residue &res, const Atom &at)

Entity *	find_entity_of_subchain (const std::string &subchain_id, std::vector< Entity > &entities)

const Entity *	find_entity_of_subchain (const std::string &subchain_id, const std::vector< Entity > &entities)

template<class T >
void	remove_alternative_conformations (T &obj)
	Remove alternative conformations.

template<>
void	remove_alternative_conformations (Chain &chain)

template<class T >
void	remove_hydrogens (T &obj)
	Remove hydrogens.

template<>
void	remove_hydrogens (Residue &res)

template<class T >
void	assign_b_iso (T &obj, float b_min, float b_max)
	Set isotropic ADP to the range (b_min, b_max).

template<>
void	assign_b_iso (Atom &atom, float b_min, float b_max)

template<class T >
void	remove_anisou (T &obj)
	Remove anisotropic ADP.

template<>
void	remove_anisou (Atom &atom)

template<class T >
void	ensure_anisou (T &obj)
	Set absent ANISOU to value from B_iso.

template<>
void	ensure_anisou (Atom &atom)

template<class T >
void	transform_pos_and_adp (T &obj, const Transform &tr)
	apply Transform to both atom's position and ADP

template<>
void	transform_pos_and_adp (Atom &atom, const Transform &tr)

void	assign_serial_numbers (Model &model, bool numbered_ter=false)
	set atom site serial numbers to 1, 2, ..., optionally leaving gaps for TERs

void	assign_serial_numbers (Structure &st, bool numbered_ter=false)

template<typename Func >
void	process_addresses (Structure &st, Func func)
	Helper function for processing (usually: changing) names and numbers in AtomAddress instances in metadata: Connection, CisPep, Helix, Sheet::Strand.

template<typename Func >
void	process_sequence_ids (Structure &st, Func func)
	Takes func(const std::string& chain_name, gemmi::SeqId& seqid).

void	rename_chain (Structure &st, const std::string &old_name, const std::string &new_name)

void	rename_residues (Structure &st, const std::string &old_name, const std::string &new_name)

void	rename_atom_names (Structure &st, const std::string &res_name, const std::map< std::string, std::string > &old_new)

void	replace_d_fraction_with_altlocs (Residue &res)

bool	replace_deuterium_with_fraction (Residue &res)

void	store_deuterium_as_fraction (Structure &st, bool store_fraction)
	Hydrogens modelled as H/D mixture (altlocs H and D with the same position and ADP, but with refined fraction of D), it can be stored in mmCIF either as two atoms (H and D) or, using CCP4/Refmac extension, as H atoms with the ccp4_deuterium_fraction parameter.

void	standardize_crystal_frame (Structure &st)
	Convert coordinates to the standard coordinate system for the unit cell.

void	add_distinct_altlocs (const Residue &res, std::string &altlocs)

bool	atom_match_with_alias (const std::string &atom_id, const std::string &atom, const ChemComp::Aliasing *aliasing)

MonLib	read_monomer_lib (const std::string &monomer_dir, const std::vector< std::string > &resnames, const std::string &libin="", bool ignore_missing=false)

template<typename T , typename FP = typename std::iterator_traits<T>::value_type>
std::array< FP, 2 >	calculate_min_max_disregarding_nans (T begin, T end)

Mtz	read_mtz_file (const std::string &path)

template<typename Input >
Mtz	read_mtz (Input &&input, bool with_data)

MtzDataProxy	data_proxy (const Mtz &mtz)

GEMMI_DLL void	write_staraniso_b_in_mmcif (const SMat33< double > &b, const std::string &entry_id, char *buf, std::ostream &os)

GEMMI_DLL void	remove_appendix_from_column_names (Mtz &mtz, std::ostream &out)
	remove '_dataset_name' that can be appended to column names in ccp4i

GEMMI_DLL bool	validate_merged_mtz_deposition_columns (const Mtz &mtz, std::ostream &out)

GEMMI_DLL bool	validate_merged_intensities (Intensities &mi, Intensities &ui, bool relaxed_check, std::ostream &out)

bool	is_record_type4 (const char s, const char record)
	Compare the first 4 letters of s, ignoring case, with uppercase record.

bool	is_record_type3 (const char s, const char record)
	for record "TER": "TER ", TER , TER\r, TER\t match, TERE, TER1 don't

GEMMI_DLL std::vector< Op >	read_remark_290 (const std::vector< std::string > &raw_remarks)
	Returns operations corresponding to 1555, 2555, ... N555.

GEMMI_DLL Structure	read_pdb_from_stream (LineReaderBase &&line_reader, const std::string &source, PdbReadOptions options)

Structure	read_pdb_file (const std::string &path, PdbReadOptions options=PdbReadOptions())

Structure	read_pdb_from_memory (const char *data, size_t size, const std::string &name, PdbReadOptions options=PdbReadOptions())

Structure	read_pdb_string (const std::string &str, const std::string &name, PdbReadOptions options=PdbReadOptions())

template<typename T >
Structure	read_pdb (T &&input, PdbReadOptions options=PdbReadOptions())

bool	all_alnums (const char *p)

bool	is_pdb_code (const std::string &str)

std::string	expand_pdb_code_to_path (const std::string &code, char type, bool throw_if_unset=false)
	Call it after checking the code with gemmi::is_pdb_code(code).

std::string	expand_if_pdb_code (const std::string &input, char type='M')

bool	is_pir_format (const std::string &s)

std::vector< FastaSeq >	read_pir_or_fasta (const std::string &str)

GEMMI_DLL PolymerType	check_polymer_type (const ConstResidueSpan &span, bool ignore_entity_type=false)

PolymerType	get_or_check_polymer_type (const Entity *ent, const ConstResidueSpan &polymer)

std::vector< AtomNameElement >	get_mainchain_atoms (PolymerType ptype)

bool	in_peptide_bond_distance (const Atom a1, const Atom a2)
	distance-based check for peptide bond

bool	have_peptide_bond (const Residue &r1, const Residue &r2)

bool	in_nucleotide_bond_distance (const Atom a1, const Atom a2)
	distance-based check for phosphodiester bond between nucleotide

bool	have_nucleotide_bond (const Residue &r1, const Residue &r2)

bool	are_connected (const Residue &r1, const Residue &r2, PolymerType ptype)
	check C-N or O3'-P distance

bool	are_connected2 (const Residue &r1, const Residue &r2, PolymerType ptype)
	are_connected2() is less exact, but requires only CA (or P) atoms.

bool	are_connected3 (const Residue &r1, const Residue &r2, PolymerType ptype)
	are_connected3() = are_connected() + fallback to are_connected2()

GEMMI_DLL std::string	make_one_letter_sequence (const ConstResidueSpan &polymer)

GEMMI_DLL void	add_entity_types (Chain &chain, bool overwrite)
	Assigns entity_type=Polymer\|NonPolymer\|Water for each Residue (only for residues with entity_type==Unknown, unless overwrite=true).

GEMMI_DLL void	add_entity_types (Structure &st, bool overwrite)

GEMMI_DLL void	remove_entity_types (Structure &st)
	Assigns entity_type=Unknown for all residues.

GEMMI_DLL void	add_entity_ids (Structure &st, bool overwrite)
	Assigns Residue::entity_id based on Residue::subchain and Entity::subchains.

GEMMI_DLL void	assign_subchain_names (Chain &chain, int &nonpolymer_counter)
	The subchain field in the residue is where we store_atom_site.label_asym_id from mmCIF files.

GEMMI_DLL void	assign_subchains (Structure &st, bool force, bool fail_if_unknown=true)

GEMMI_DLL void	ensure_entities (Structure &st)

GEMMI_DLL void	deduplicate_entities (Structure &st)

void	setup_entities (Structure &st)

GEMMI_DLL char	recommended_het_flag (const Residue &res)
	Determine ATOM/HETATM record type, based on Residue::entity_type.

template<class T >
void	assign_het_flags (T &obj, char flag='R')
	R = recommended_het_flag(), other valid values are A, H and '\0'.

template<>
void	assign_het_flags (Residue &res, char flag)

template<class T >
void	remove_waters (T &obj)

template<>
void	remove_waters (Chain &ch)

template<class T >
void	remove_ligands_and_waters (T &obj)

template<>
void	remove_ligands_and_waters (Chain &ch)

GEMMI_DLL bool	trim_to_alanine (Residue &res)

void	trim_to_alanine (Chain &chain)

GEMMI_DLL void	shorten_ccd_codes (Structure &st)

GEMMI_DLL void	restore_full_ccd_codes (Structure &st)

GEMMI_DLL void	add_microhetero_to_sequences (Structure &st, bool overwrite=false)
	Modifies Entity::full_sequence. Uses only the first chain for each Entity.

double	qcp_inner_product (Mat33 &mat, const Position pos1, const Position &ctr1, const Position pos2, const Position &ctr2, size_t len, const double *weight)

int	fast_calc_rmsd_and_rotation (Mat33 rot, const Mat33 &A, double rmsd, double E0, double len, double min_score)

Position	qcp_calculate_center (const Position pos, size_t len, const double weight)

SupResult	superpose_positions (const Position pos1, const Position pos2, size_t len, const double *weight)

double	calculate_rmsd_of_superposed_positions (const Position pos1, const Position pos2, size_t len, const double *weight)

GEMMI_DLL cif::Document	read_cif_gz (const std::string &path)

GEMMI_DLL cif::Document	read_mmjson_gz (const std::string &path)

GEMMI_DLL CharArray	read_into_buffer_gz (const std::string &path)

GEMMI_DLL cif::Document	read_cif_from_memory (const char data, size_t size, const char name)

GEMMI_DLL cif::Document	read_first_block_gz (const std::string &path, size_t limit)

cif::Document	read_cif_or_mmjson_gz (const std::string &path)

cif::Document	read_cif_from_buffer (const CharArray &buffer, const char *name)

GEMMI_DLL Ccp4< float >	read_ccp4_map (const std::string &path, bool setup)

GEMMI_DLL Ccp4< int8_t >	read_ccp4_mask (const std::string &path, bool setup)

template<typename T >
T	friedel_mate_value (T v)

template<typename T >
std::complex< T >	friedel_mate_value (const std::complex< T > &v)

template<typename Func >
void	for_all_reflections (Func func, const UnitCell &cell, const SpaceGroup *spacegroup, double dmin, double dmax=0., bool unique=true)

int	count_reflections (const UnitCell &cell, const SpaceGroup *spacegroup, double dmin, double dmax=0., bool unique=true)

std::vector< Miller >	make_miller_vector (const UnitCell &cell, const SpaceGroup *spacegroup, double dmin, double dmax=0., bool unique=true)

std::vector< ReflnBlock >	as_refln_blocks (std::vector< cif::Block > &&blocks)

ReflnBlock	get_refln_block (std::vector< cif::Block > &&blocks, const std::vector< std::string > &labels, const char *block_name=nullptr)

ReflnBlock	hkl_cif_as_refln_block (cif::Block &block)

ReflnDataProxy	data_proxy (const ReflnBlock &rb)

GEMMI_DLL ResidueInfo	find_tabulated_residue (const std::string &name)

const char *	expand_one_letter (char c, ResidueKind kind)
	kind can be AA, RNA or DNA

GEMMI_DLL std::vector< std::string >	expand_one_letter_sequence (const std::string &seq, ResidueKind kind)
	kind can be AA, RNA or DNA

const char *	expand_protein_one_letter (char c)

std::vector< std::string >	expand_protein_one_letter_string (const std::string &s)

GEMMI_DLL void	place_hydrogens_on_all_atoms (Topo &topo)

void	adjust_hydrogen_distances (Topo &topo, Restraints::DistanceOf of, double default_scale=1.)

double	vec6_dot (const Vec6 &a, const SMat33< double > &s)

std::vector< Vec6 >	adp_symmetry_constraints (const SpaceGroup *sg)
	Symmetry constraints of ADP.

AlignmentResult	align_sequences (const std::vector< std::uint8_t > &query, const std::vector< std::uint8_t > &target, const std::vector< int > &target_gapo, std::uint8_t m, const AlignmentScoring &scoring)
	All values in query and target must be less then m.

AlignmentResult	align_string_sequences (const std::vector< std::string > &query, const std::vector< std::string > &target, const std::vector< int > &target_gapo, const AlignmentScoring *scoring)

std::string	atom_str (const std::string &chain_name, const ResidueId &res_id, const std::string &atom_name, char altloc)

constexpr double	h2o_weight ()

double	calculate_sequence_weight (const std::vector< std::string > &seq, double unknown=0.)

std::string	one_letter_code (const std::vector< std::string > &seq)

std::string	pdbx_one_letter_code (const std::vector< std::string > &seq, ResidueKind kind)
	Returns the format used in _entity_poly.pdbx_seq_one_letter_code, in which non-standard amino acids/nucleotides are represented by CCD codes in parenthesis, e.g.

ResidueKind	sequence_kind (PolymerType ptype)
	used with expand_one_letter_sequence()

std::complex< double >	calculate_sf_part (const Fractional &fpos, const Miller &hkl)

bool	is_complete (const GroupOps &gops)

std::vector< Op >	triplets_to_ops (const std::vector< std::string > &symops)

template<typename T >
void	split_element_and_charge (const std::string &label, T *dest)

SmallStructure	make_small_structure_from_block (const cif::Block &block_)

cif::Block	make_cif_block_from_small_structure (const SmallStructure &st)

float	cctbx_vdw_radius (El el)

float	refmac_radius_for_bulk_solvent (El el)

template<typename T >
void	mask_points_in_constant_radius (Grid< T > &mask, const Model &model, double radius, T value, bool ignore_hydrogen, bool ignore_zero_occupancy_atoms)

template<typename T >
void	mask_points_in_varied_radius (Grid< T > &mask, const Model &model, AtomicRadiiSet atomic_radii_set, double r_probe, T value, bool ignore_hydrogen, bool ignore_zero_occupancy_atoms)

template<typename T >
void	set_margin_around (Grid< T > &mask, double r, T value, T margin_value)

void	mask_with_node_info (Grid< NodeInfo > &mask, const Model &model, double radius)
	Populate NodeInfo grid for nodes near the model.

void	unmask_symmetry_mates (Grid< NodeInfo > &mask)
	Skip nodes that are closer to a symmetry mate of the model than to the original model.

template<typename T >
void	interpolate_grid_of_aligned_model2 (Grid< T > &dest, const Grid< T > &src, const Transform &tr, const Model &dest_model, double radius, int order=1)

template<typename T >
void	add_soft_edge_to_mask (Grid< T > &grid, double width)

GEMMI_DLL int	snprintf_z (char buf, int count, char const fmt,...) GEMMI_ATTRIBUTE_FORMAT(3
	stb_snprintf in gemmi namespace - like snprintf, but ignores locale and is always zero-terminated (hence _z).

GEMMI_DLL int GEMMI_DLL int	sprintf_z (char buf, char const fmt,...) GEMMI_ATTRIBUTE_FORMAT(2
	stb_sprintf in gemmi namespace

GEMMI_DLL int GEMMI_DLL int std::string	to_str (double d)

std::string	to_str (float d)

template<int Prec>
std::string	to_str_prec (double d)

char *	to_chars_z (char first, char last, int value)
	zero-terminated to_chars()

char *	to_chars_z (char first, char last, size_t value)

template<typename T >
DataStats	calculate_data_statistics (const std::vector< T > &data)

bool	operator== (const Op &a, const Op &b)

bool	operator!= (const Op &a, const Op &b)

Op	operator* (const Op &a, const Op &b)

Op &	operator*= (Op &a, const Op &b)

Op	seitz_to_op (const std::array< std::array< double, 4 >, 4 > &t)

int	interpret_miller_character (char c, const std::string &s)

std::array< int, 4 >	parse_triplet_part (const std::string &s, double *decimal_fract=nullptr)

Op	parse_triplet (const std::string &s)

std::string	make_triplet_part (const std::array< int, 3 > &xyz, int w, char style='x')

std::vector< Op::Tran >	centring_vectors (char centring_type)

GroupOps	split_centering_vectors (const std::vector< Op > &ops)

Op::Rot	hall_rotation_z (int N)

Op::Tran	hall_translation_from_symbol (char symbol)

Op	hall_matrix_symbol (const char start, const char end, int pos, int &prev)

Op	parse_hall_change_of_basis (const char start, const char end)

GroupOps	generators_from_hall (const char *hall)

GroupOps	symops_from_hall (const char *hall)

const char *	crystal_system_str (CrystalSystem system)

const char *	point_group_hm (PointGroup pg)

Laue	pointgroup_to_laue (PointGroup pg)

PointGroup	laue_to_pointgroup (Laue laue)

const char *	laue_class_str (Laue laue)

CrystalSystem	crystal_system (Laue laue)

CrystalSystem	crystal_system (PointGroup pg)

unsigned char	point_group_index_and_category (int space_group_number)

PointGroup	point_group (int space_group_number)

bool	is_sohncke (int space_group_number)

bool	is_enantiomorphic (int space_group_number)

bool	is_symmorphic (int space_group_number)

Op::Tran	nonzero_inversion_center (int space_group_number)
	Inversion center of the Euclidean normalizer that is not at the origin of reference settings.

const char *	get_basisop (int basisop_idx)

Op::Rot	centred_to_primitive (char centring_type)

const SpaceGroup *	find_spacegroup_by_number (int ccp4) noexcept

const SpaceGroup &	get_spacegroup_by_number (int ccp4)

const SpaceGroup &	get_spacegroup_reference_setting (int number)

const SpaceGroup *	find_spacegroup_by_name (std::string name, double alpha=0., double gamma=0., const char *prefer=nullptr)
	If angles alpha and gamma are provided, they are used to distinguish hexagonal and rhombohedral settings (e.g.

const SpaceGroup &	get_spacegroup_by_name (const std::string &name)

const SpaceGroup &	get_spacegroup_p1 ()

const SpaceGroup *	find_spacegroup_by_ops (const GroupOps &gops)

void	add_chemcomp_to_block (const ChemComp &cc, cif::Block &block)

GEMMI_DLL void	update_mmcif_block (const Structure &st, cif::Block &block, MmcifOutputGroups groups=MmcifOutputGroups(true))

GEMMI_DLL cif::Document	make_mmcif_document (const Structure &st, MmcifOutputGroups groups=MmcifOutputGroups(true))

GEMMI_DLL cif::Block	make_mmcif_block (const Structure &st, MmcifOutputGroups groups=MmcifOutputGroups(true))

GEMMI_DLL cif::Block	make_mmcif_headers (const Structure &st)

GEMMI_DLL void	add_minimal_mmcif_data (const Structure &st, cif::Block &block)

GEMMI_DLL void	write_ncs_oper (const Structure &st, cif::Block &block)

GEMMI_DLL void	write_struct_conn (const Structure &st, cif::Block &block)

GEMMI_DLL void	write_cispeps (const Structure &st, cif::Block &block)

GEMMI_DLL bool	use_hetatm (const Residue &res)
	record type ATOM/HETATM to use for writing given residue

GEMMI_DLL void	write_pdb (const Structure &st, std::ostream &os, PdbWriteOptions opt=PdbWriteOptions())

GEMMI_DLL std::string	make_pdb_string (const Structure &st, PdbWriteOptions opt=PdbWriteOptions())

void	write_minimal_pdb (const Structure &st, std::ostream &os)

std::string	make_pdb_headers (const Structure &st)

GEMMI_DLL std::unique_ptr< Topo >	prepare_topology (Structure &st, MonLib &monlib, size_t model_index, HydrogenChange h_change, bool reorder, const Logger &logger={}, bool ignore_unknown_links=false, bool use_cispeps=false)

GEMMI_DLL std::unique_ptr< ChemComp >	make_chemcomp_with_restraints (const Residue &res)

GEMMI_DLL std::vector< AtomAddress >	find_missing_atoms (const Topo &topo, bool including_hydrogen=false)

double	calculate_cos_obliquity (const UnitCell &reduced_cell, const Vec3 &d_axis, const Vec3 &r_axis)

std::vector< OpObliquity >	find_lattice_2fold_ops (const UnitCell &reduced_cell, double max_obliq)

GroupOps	find_lattice_symmetry_r (const UnitCell &reduced_cell, double max_obliq)

GroupOps	find_lattice_symmetry (const UnitCell &cell, char centring, double max_obliq)

std::vector< Op >	find_twin_laws (const UnitCell &cell, const SpaceGroup *sg, double max_obliq, bool all_ops)

Mat33	rot_as_mat33 (const Op::Rot &rot)

Mat33	rot_as_mat33 (const Op &op)

Vec3	tran_as_vec3 (const Op &op)

Position	operator* (double d, const Position &v)

std::wstring	UTF8_to_wchar (const char *in)

std::string	wchar_to_UTF8 (const wchar_t *in)

void	append_to_str (std::string &out, int v)

void	append_to_str (std::string &out, size_t v)

template<typename T >
void	append_to_str (std::string &out, const T &v)

void	cat_to (std::string &)

template<typename T , typename... Args>
void	cat_to (std::string &out, const T &value, Args const &... args)

template<class... Args>
std::string	cat (Args const &... args)

bool	starts_with (const std::string &str, const std::string &prefix)

template<size_t N>
bool	starts_with (const char *a, const char(&b)[N])

bool	ends_with (const std::string &str, const std::string &suffix)

char	lower (char c)

char	alpha_up (char c)

std::string	to_lower (std::string str)

std::string	to_upper (std::string str)

bool	isame (char a, char b)

bool	iequal_from (const std::string &str, size_t offset, const std::string &low)

bool	iequal (const std::string &str, const std::string &low)

bool	istarts_with (const std::string &str, const std::string &prefix)

bool	iends_with (const std::string &str, const std::string &suffix)

bool	giends_with (const std::string &str, const std::string &suffix)

std::string	trim_str (const std::string &str)

std::string	rtrim_str (const std::string &str)

const char *	rtrim_cstr (const char start, const char end=nullptr)

template<typename S >
void	split_str_into (const std::string &str, S sep, std::vector< std::string > &result)

template<typename S >
std::vector< std::string >	split_str (const std::string &str, S sep)

void	split_str_into_multi (const std::string &str, const char *seps, std::vector< std::string > &result)

std::vector< std::string >	split_str_multi (const std::string &str, const char *seps=" \t")

template<typename T , typename S , typename F >
std::string	join_str (T begin, T end, const S &sep, const F &getter)

template<typename T , typename S >
std::string	join_str (T begin, T end, const S &sep)

template<typename T , typename S , typename F >
std::string	join_str (const T &iterable, const S &sep, const F &getter)

template<typename T , typename S >
std::string	join_str (const T &iterable, const S &sep)

template<typename T , typename S >
void	string_append_sep (std::string &str, S sep, const T &item)

void	replace_all (std::string &s, const std::string &old, const std::string &new_)

bool	is_in_list (const std::string &name, const std::string &list, char sep=',')

template<class T >
bool	in_vector (const T &x, const std::vector< T > &v)

template<typename F , typename T >
bool	in_vector_f (F f, const std::vector< T > &v)

template<class T >
T *	vector_end_ptr (std::vector< T > &v)

template<class T >
const T *	vector_end_ptr (const std::vector< T > &v)

template<class T >
void	vector_move_extend (std::vector< T > &dst, std::vector< T > &&src)

template<class T , typename F >
void	vector_remove_if (std::vector< T > &v, F &&condition)

template<class T >
void	vector_insert_columns (std::vector< T > &data, size_t old_width, size_t length, size_t n, size_t pos, const T &new_value)

template<class T >
void	vector_remove_column (std::vector< T > &data, size_t new_width, size_t pos)

constexpr int	ialpha4_id (const char *s)

constexpr int	ialpha3_id (const char *s)

bool	likely_in_house_source (double wavelength)

XdsAscii	read_xds_ascii_file (const std::string &path)

Variables
GEMMI_DLL const char *const	zlib_description

Typedef Documentation

◆ CifWalk

using gemmi::CifWalk = typedef DirWalk<true, impl::IsCifFile>

Definition at line 248 of file dirwalk.hpp.

◆ MmCifWalk

using gemmi::MmCifWalk = typedef DirWalk<true, impl::IsMmCifFile>

Definition at line 249 of file dirwalk.hpp.

◆ PdbWalk

using gemmi::PdbWalk = typedef DirWalk<true, impl::IsPdbFile>

Definition at line 250 of file dirwalk.hpp.

◆ CoorFileWalk

using gemmi::CoorFileWalk = typedef DirWalk<true, impl::IsCoordinateFile>

Definition at line 251 of file dirwalk.hpp.

◆ elname_t

typedef const char gemmi::elname_t[3]

Definition at line 200 of file elem.hpp.

◆ fileptr_t

typedef std::unique_ptr<std::FILE, needs_fclose> gemmi::fileptr_t

Definition at line 47 of file fileutil.hpp.

◆ StrideIter

template<typename Value >

using gemmi::StrideIter = typedef BidirIterator<StrideIterPolicy<Value> >

Definition at line 71 of file iterator.hpp.

◆ IndirectIter

template<typename Redirect , typename Value >

using gemmi::IndirectIter = typedef BidirIterator<IndirectIterPolicy<Redirect, Value> >

Definition at line 94 of file iterator.hpp.

◆ UniqIter

template<typename Vector , typename Value >

using gemmi::UniqIter = typedef BidirIterator<UniqIterPolicy<Vector, Value> >

Definition at line 126 of file iterator.hpp.

◆ GroupingIter

template<typename Vector , typename Value >

using gemmi::GroupingIter = typedef BidirIterator<GroupingIterPolicy<Vector, Value> >

Definition at line 177 of file iterator.hpp.

◆ FilterIter

template<typename Filter , typename Vector , typename Value >

using gemmi::FilterIter = typedef BidirIterator<FilterIterPolicy<Filter, Vector, Value> >

Definition at line 204 of file iterator.hpp.

◆ Vec3

using gemmi::Vec3 = typedef Vec3_<double>

Definition at line 108 of file math.hpp.

◆ Vec3f

using gemmi::Vec3f = typedef Vec3_<float>

Definition at line 109 of file math.hpp.

◆ AtomGroup

using gemmi::AtomGroup = typedef AtomGroup_<Atom>

Definition at line 180 of file model.hpp.

◆ ConstAtomGroup

using gemmi::ConstAtomGroup = typedef AtomGroup_<const Atom>

Definition at line 181 of file model.hpp.

◆ CraProxy

using gemmi::CraProxy = typedef CraProxy_<CRA, std::vector<Chain>&>

Definition at line 709 of file model.hpp.

◆ ConstCraProxy

using gemmi::ConstCraProxy = typedef CraProxy_<const_CRA, const std::vector<Chain>&>

Definition at line 710 of file model.hpp.

◆ FPhiGrid

template<typename T >

using gemmi::FPhiGrid = typedef ReciprocalGrid<std::complex<T> >

Definition at line 172 of file recgrid.hpp.

◆ Vec6

using gemmi::Vec6 = typedef std::array<double, 6>

Definition at line 16 of file scaling.hpp.

◆ spacegroup_tables

using gemmi::spacegroup_tables = typedef impl::Tables_<void>

Definition at line 1854 of file symmetry.hpp.

◆ OpObliquity

using gemmi::OpObliquity = typedef std::pair<Op, double>

Definition at line 128 of file twin.hpp.

◆ Miller

using gemmi::Miller = typedef std::array<int, 3>

A synonym for convenient passing of hkl.

Definition at line 129 of file unitcell.hpp.

Enumeration Type Documentation

◆ SupSelect

enum class gemmi::SupSelect

strong

Enumerator
CaP
MainChain
All

Definition at line 165 of file align.hpp.

◆ HowToNameCopiedChain

enum class gemmi::HowToNameCopiedChain

strong

Enumerator
Short
AddNumber
Dup

Definition at line 16 of file assembly.hpp.

◆ MapSetup

enum class gemmi::MapSetup

strong

Enumerator
Full
NoSymmetry
ReorderOnly

Definition at line 29 of file ccp4.hpp.

◆ BondType

enum class gemmi::BondType

strong

Enumerator
Unspec
Single
Double
Triple
Aromatic
Deloc
Metal

Definition at line 20 of file chemcomp.hpp.

◆ ChiralityType

enum class gemmi::ChiralityType

strong

Enumerator
Positive
Negative
Both

Definition at line 23 of file chemcomp.hpp.

◆ El

enum class gemmi::El : unsigned char

strong

Enumerator
X
H
He
Li
Be
B
C
N
O
F
Ne
Na
Mg
Al
Si
P
S
Cl
Ar
K
Ca
Sc
Ti
V
Cr
Mn
Fe
Co
Ni
Cu
Zn
Ga
Ge
As
Se
Br
Kr
Rb
Sr
Y
Zr
Nb
Mo
Tc
Ru
Rh
Pd
Ag
Cd
In
Sn
Sb
Te
I
Xe
Cs
Ba
La
Ce
Pr
Nd
Pm
Sm
Eu
Gd
Tb
Dy
Ho
Er
Tm
Yb
Lu
Hf
Ta
W
Re
Os
Ir
Pt
Au
Hg
Tl
Pb
Bi
Po
At
Rn
Fr
Ra
Ac
Th
Pa
U
Np
Pu
Am
Cm
Bk
Cf
Es
Fm
Md
No
Lr
Rf
Db
Sg
Bh
Hs
Mt
Ds
Rg
Cn
Nh
Fl
Mc
Lv
Ts
Og
D
END

Definition at line 13 of file elem.hpp.

◆ AxisOrder

enum class gemmi::AxisOrder : unsigned char

strong

Order of grid axis.

Some Grid functionality works only with the XYZ order. The values XYZ and ZYX are used only when the grid covers whole unit cell.

Enumerator
Unknown
XYZ
ZYX

Definition at line 24 of file grid.hpp.

◆ GridSizeRounding

enum class gemmi::GridSizeRounding

strong

Enumerator
Nearest
Up
Down

Definition at line 31 of file grid.hpp.

◆ EntityType

enum class gemmi::EntityType : unsigned char

strong

Enumerator
Unknown
Polymer
NonPolymer
Branched
Water

Definition at line 196 of file metadata.hpp.

◆ PolymerType

enum class gemmi::PolymerType : unsigned char

strong

Enumerator
Unknown
PeptideL
PeptideD
Dna
Rna
DnaRnaHybrid
SaccharideD
SaccharideL
Pna
CyclicPseudoPeptide
Other

Definition at line 207 of file metadata.hpp.

◆ ChemCompModel

enum class gemmi::ChemCompModel

strong

Enumerator
Xyz
Example
Ideal

Definition at line 33 of file mmcif.hpp.

◆ CoorFormat

enum class gemmi::CoorFormat : unsigned char

strong

File format of a macromolecular model.

When passed to read_structure(): Unknown = guess format from the extension, Detect = guess format from the content.

Enumerator
Unknown
Detect
Pdb
Mmcif
Mmjson
ChemComp

Definition at line 88 of file model.hpp.

◆ CalcFlag

enum class gemmi::CalcFlag : signed char

strong

corresponds to _atom_site.calc_flag in mmCIF

Enumerator
NotSet
NoHydrogen
Determined
Calculated
Dummy

Definition at line 93 of file model.hpp.

◆ DataType

enum class gemmi::DataType

strong

Enumerator
Unknown
Unmerged
Mean
Anomalous

Definition at line 18 of file refln.hpp.

◆ ResidueKind

enum class gemmi::ResidueKind : unsigned char

strong

Enumerator
UNKNOWN
AA
AAD
PAA
MAA
RNA
DNA
BUF
HOH
PYR
KET
ELS

Definition at line 26 of file resinfo.hpp.

◆ AtomicRadiiSet

enum class gemmi::AtomicRadiiSet

strong

Enumerator
VanDerWaals
Cctbx
Refmac
Constant

Definition at line 14 of file solmask.hpp.

◆ CrystalSystem

enum class gemmi::CrystalSystem : unsigned char

strong

Enumerator
Triclinic
Monoclinic
Orthorhombic
Tetragonal
Trigonal
Hexagonal
Cubic

Definition at line 935 of file symmetry.hpp.

◆ PointGroup

enum class gemmi::PointGroup : unsigned char

strong

Enumerator
C1
Ci
C2
Cs
C2h
D2
C2v
D2h
C4
S4
C4h
D4
C4v
D2d
D4h
C3
C3i
D3
C3v
D3d
C6
C3h
C6h
D6
C6v
D3h
D6h
T
Th
O
Td
Oh

Definition at line 947 of file symmetry.hpp.

◆ Laue

enum class gemmi::Laue : unsigned char

strong

Enumerator
L1
L2m
Lmmm
L4m
L4mmm
L3
L3m
L6m
L6mmm
Lm3
Lm3m

Definition at line 963 of file symmetry.hpp.

◆ HydrogenChange

enum class gemmi::HydrogenChange

strong

Enumerator
NoChange
Shift
Remove
ReAdd
ReAddButWater
ReAddKnown

Definition at line 19 of file topo.hpp.

◆ Asu

enum class gemmi::Asu : unsigned char

strong

Enumerator
Same
Different
Any

Definition at line 76 of file unitcell.hpp.

Function Documentation

◆ prepare_target_gapo()

std::vector< int > gemmi::prepare_target_gapo	(	const ConstResidueSpan &	polymer,
		PolymerType	polymer_type,
		const AlignmentScoring *	scoring = `nullptr`
	)

inline

Definition at line 18 of file align.hpp.

◆ align_sequence_to_polymer()

AlignmentResult gemmi::align_sequence_to_polymer	(	const std::vector< std::string > &	full_seq,
		const ConstResidueSpan &	polymer,
		PolymerType	polymer_type,
		const AlignmentScoring *	scoring = `nullptr`
	)

inline

Definition at line 38 of file align.hpp.

◆ seqid_matches_seqres()

bool gemmi::seqid_matches_seqres	(	const ConstResidueSpan &	polymer,
		const Entity &	ent
	)

inline

Definition at line 72 of file align.hpp.

◆ clear_sequences()

void gemmi::clear_sequences ( Structure & st )

inline

Definition at line 85 of file align.hpp.

◆ assign_best_sequences()

GEMMI_DLL void gemmi::assign_best_sequences	(	Structure &	st,
		const std::vector< std::string > &	fasta_sequences
	)

◆ assign_label_seq_to_polymer()

void gemmi::assign_label_seq_to_polymer	(	ResidueSpan &	polymer,
		const Entity *	ent,
		bool	force
	)

inline

Definition at line 98 of file align.hpp.

◆ clear_label_seq_id()

void gemmi::clear_label_seq_id ( Structure & st )

inline

Definition at line 145 of file align.hpp.

◆ assign_label_seq_id()

void gemmi::assign_label_seq_id	(	Structure &	st,
		bool	force
	)

inline

Definition at line 152 of file align.hpp.

◆ prepare_positions_for_superposition()

void gemmi::prepare_positions_for_superposition	(	std::vector< Position > &	pos1,
		std::vector< Position > &	pos2,
		ConstResidueSpan	fixed,
		ConstResidueSpan	movable,
		PolymerType	ptype,
		SupSelect	sel,
		char	altloc = `'\0'`,
		std::vector< int > *	ca_offsets = `nullptr`
	)

inline

Definition at line 171 of file align.hpp.

◆ calculate_current_rmsd()

SupResult gemmi::calculate_current_rmsd	(	ConstResidueSpan	fixed,
		ConstResidueSpan	movable,
		PolymerType	ptype,
		SupSelect	sel,
		char	altloc = `'\0'`
	)

inline

Definition at line 229 of file align.hpp.

◆ calculate_superposition()

SupResult gemmi::calculate_superposition	(	ConstResidueSpan	fixed,
		ConstResidueSpan	movable,
		PolymerType	ptype,
		SupSelect	sel,
		int	trim_cycles = `0`,
		double	trim_cutoff = `2.0`,
		char	altloc = `'\0'`
	)

inline

Definition at line 245 of file align.hpp.

◆ calculate_superpositions_in_moving_window()

std::vector< SupResult > gemmi::calculate_superpositions_in_moving_window	(	ConstResidueSpan	fixed,
		ConstResidueSpan	movable,
		PolymerType	ptype,
		double	radius = `10.0`
	)

inline

Definition at line 285 of file align.hpp.

◆ ensure_unique_chain_name()

void gemmi::ensure_unique_chain_name	(	const Model &	model,
		Chain &	chain
	)

inline

Definition at line 82 of file assembly.hpp.

◆ make_assembly()

GEMMI_DLL Model gemmi::make_assembly	(	const Assembly &	assembly,
		const Model &	model,
		HowToNameCopiedChain	how,
		const Logger &	logging
	)

◆ pseudo_assembly_for_unit_cell()

Assembly gemmi::pseudo_assembly_for_unit_cell ( const UnitCell & cell )

inline

Definition at line 93 of file assembly.hpp.

◆ transform_to_assembly()

GEMMI_DLL void gemmi::transform_to_assembly	(	Structure &	st,
		const std::string &	assembly_name,
		HowToNameCopiedChain	how,
		const Logger &	logging,
		bool	keep_spacegroup = `false`,
		double	merge_dist = `0.2`
	)

If called with assembly_name="unit_cell" changes structure to unit cell (P1).

keep_spacegroup preserves space group and unit cell - is it needed?

◆ expand_ncs_model()

GEMMI_DLL Model gemmi::expand_ncs_model	(	const Model &	model,
		const std::vector< NcsOp > &	ncs,
		HowToNameCopiedChain	how
	)

◆ merge_atoms_in_expanded_model()

GEMMI_DLL void gemmi::merge_atoms_in_expanded_model	(	Model &	model,
		const UnitCell &	cell,
		double	max_dist = `0.2`,
		bool	compare_serial = `true`
	)

Searches and merges overlapping equivalent atoms from different chains.

To be used after expand_ncs() and make_assembly().

◆ shorten_chain_names()

GEMMI_DLL void gemmi::shorten_chain_names ( Structure & st )

◆ expand_ncs()

GEMMI_DLL void gemmi::expand_ncs	(	Structure &	st,
		HowToNameCopiedChain	how,
		double	merge_dist = `0.2`
	)

◆ split_chains_by_segments()

GEMMI_DLL void gemmi::split_chains_by_segments	(	Model &	model,
		HowToNameCopiedChain	how
	)

HowToNameCopiedChain::Dup adds segment name to chain name.

◆ for_matching_reflections()

template<typename Func , typename T >

void gemmi::for_matching_reflections	(	const std::vector< T > &	a,
		const std::vector< T > &	b,
		const Func &	func
	)

Precondition: a and b are sorted

Definition at line 46 of file asudata.hpp.

◆ calculate_hkl_value_correlation()

template<typename T >

Correlation gemmi::calculate_hkl_value_correlation	(	const std::vector< T > &	a,
		const std::vector< T > &	b
	)

Precondition: a and b are sorted

Definition at line 66 of file asudata.hpp.

◆ calculate_hkl_complex_correlation()

template<typename T >

ComplexCorrelation gemmi::calculate_hkl_complex_correlation	(	const std::vector< T > &	a,
		const std::vector< T > &	b
	)

Precondition: a and b are sorted

Definition at line 77 of file asudata.hpp.

◆ count_equal_values()

template<typename T >

int gemmi::count_equal_values	(	const std::vector< T > &	a,
		const std::vector< T > &	b
	)

Precondition: a and b are sorted

Definition at line 88 of file asudata.hpp.

◆ make_asu_data() [1/2]

template<typename T , int N, typename Data >

AsuData< T > gemmi::make_asu_data	(	const Data &	data,
		const std::array< std::string, N > &	labels,
		bool	as_is = `false`
	)

Definition at line 231 of file asudata.hpp.

◆ make_asu_data() [2/2]

template<typename T , typename Data >

AsuData< T > gemmi::make_asu_data	(	const Data &	data,
		const std::string &	label,
		bool	as_is
	)

Definition at line 238 of file asudata.hpp.

◆ discard_by_sigma_ratio()

template<typename T >

void gemmi::discard_by_sigma_ratio	(	AsuData< ValueSigma< T > > &	asu_data,
		double	cutoff
	)

retains only points with positive SIGF and F/SIGF > cutoff

Definition at line 246 of file asudata.hpp.

◆ find_asu_brick()

AsuBrick gemmi::find_asu_brick ( const SpaceGroup * sg )

inline

Definition at line 65 of file asumask.hpp.

◆ get_asu_mask()

template<typename V = std::int8_t>

std::vector< V > gemmi::get_asu_mask ( const GridMeta & grid )

Definition at line 240 of file asumask.hpp.

◆ masked_asu()

template<typename T >

MaskedGrid< T > gemmi::masked_asu ( Grid< T > & grid )

Definition at line 265 of file asumask.hpp.

◆ get_nonzero_extent()

template<typename T >

Box< Fractional > gemmi::get_nonzero_extent ( const GridBase< T > & grid )

Definition at line 316 of file asumask.hpp.

◆ fast_from_chars() [1/2]

from_chars_result gemmi::fast_from_chars	(	const char *	start,
		const char *	end,
		double &	d
	)

inline

Definition at line 16 of file atof.hpp.

◆ fast_from_chars() [2/2]

from_chars_result gemmi::fast_from_chars	(	const char *	start,
		double &	d
	)

inline

Definition at line 24 of file atof.hpp.

◆ fast_atof()

double gemmi::fast_atof	(	const char *	p,
		const char **	endptr = `nullptr`
	)

inline

Definition at line 32 of file atof.hpp.

◆ is_space()

bool gemmi::is_space ( char c )

inline

Definition at line 23 of file atox.hpp.

◆ is_blank()

bool gemmi::is_blank ( char c )

inline

Definition at line 38 of file atox.hpp.

◆ is_digit()

bool gemmi::is_digit ( char c )

inline

Definition at line 43 of file atox.hpp.

◆ skip_blank()

const char * gemmi::skip_blank ( const char * p )

inline

Definition at line 47 of file atox.hpp.

◆ skip_word()

const char * gemmi::skip_word ( const char * p )

inline

Definition at line 54 of file atox.hpp.

◆ read_word() [1/2]

std::string gemmi::read_word ( const char * line )

inline

Definition at line 61 of file atox.hpp.

◆ read_word() [2/2]

std::string gemmi::read_word	(	const char *	line,
		const char **	endptr
	)

inline

Definition at line 66 of file atox.hpp.

◆ string_to_int() [1/2]

int gemmi::string_to_int	(	const char *	p,
		bool	checked,
		size_t	length = `0`
	)

inline

Definition at line 73 of file atox.hpp.

◆ string_to_int() [2/2]

int gemmi::string_to_int	(	const std::string &	str,
		bool	checked
	)

inline

Definition at line 101 of file atox.hpp.

◆ simple_atoi()

int gemmi::simple_atoi	(	const char *	p,
		const char **	endptr = `nullptr`
	)

inline

Definition at line 105 of file atox.hpp.

◆ no_sign_atoi()

int gemmi::no_sign_atoi	(	const char *	p,
		const char **	endptr = `nullptr`
	)

inline

Definition at line 123 of file atox.hpp.

◆ evaluate_polynomial()

template<int N>

double gemmi::evaluate_polynomial	(	const double(&)	poly[N],
		double	x
	)

inline

Definition at line 22 of file bessel.hpp.

◆ bessel_i1_over_i0()

double gemmi::bessel_i1_over_i0 ( double x )

inline

Definition at line 81 of file bessel.hpp.

◆ bessel_i0()

double gemmi::bessel_i0 ( double x )

inline

Definition at line 101 of file bessel.hpp.

◆ log_bessel_i0()

double gemmi::log_bessel_i0 ( double x )

inline

Definition at line 115 of file bessel.hpp.

◆ combine_two_correlations()

Correlation gemmi::combine_two_correlations	(	const Correlation &	a,
		const Correlation &	b
	)

inline

Definition at line 180 of file binner.hpp.

◆ combine_correlations()

Correlation gemmi::combine_correlations ( const std::vector< Correlation > & cors )

inline

Definition at line 194 of file binner.hpp.

◆ find_blobs_by_flood_fill()

std::vector< Blob > gemmi::find_blobs_by_flood_fill	(	const gemmi::Grid< float > &	grid,
		const BlobCriteria &	criteria,
		bool	negate = `false`
	)

inline

Definition at line 82 of file blob.hpp.

◆ has_hydrogen() [1/2]

template<class T >

bool gemmi::has_hydrogen ( const T & obj )

Definition at line 15 of file calculate.hpp.

◆ has_hydrogen() [2/2]

template<>

bool gemmi::has_hydrogen ( const Atom & atom )

inline

Definition at line 21 of file calculate.hpp.

◆ count_atom_sites() [1/2]

template<class T >

size_t gemmi::count_atom_sites	(	const T &	obj,
		const Selection *	sel = `nullptr`
	)

Definition at line 25 of file calculate.hpp.

◆ count_atom_sites() [2/2]

template<>

size_t gemmi::count_atom_sites	(	const Atom &	atom,
		const Selection *	sel
	)

inline

Definition at line 32 of file calculate.hpp.

◆ count_occupancies() [1/2]

template<class T >

double gemmi::count_occupancies	(	const T &	obj,
		const Selection *	sel = `nullptr`
	)

Definition at line 36 of file calculate.hpp.

◆ count_occupancies() [2/2]

template<>

double gemmi::count_occupancies	(	const Atom &	atom,
		const Selection *	sel
	)

inline

Definition at line 43 of file calculate.hpp.

◆ calculate_mass() [1/2]

template<class T >

double gemmi::calculate_mass ( const T & obj )

Definition at line 48 of file calculate.hpp.

◆ calculate_mass() [2/2]

template<>

double gemmi::calculate_mass ( const Atom & atom )

inline

Definition at line 54 of file calculate.hpp.

◆ calculate_center_of_mass() [1/2]

template<class T >

CenterOfMass gemmi::calculate_center_of_mass ( const T & obj )

Definition at line 64 of file calculate.hpp.

◆ calculate_center_of_mass() [2/2]

template<>

CenterOfMass gemmi::calculate_center_of_mass ( const Atom & atom )

inline

Definition at line 72 of file calculate.hpp.

◆ calculate_b_iso_range() [1/2]

template<class T >

std::pair< float, float > gemmi::calculate_b_iso_range ( const T & obj )

Definition at line 77 of file calculate.hpp.

◆ calculate_b_iso_range() [2/2]

template<>

std::pair< float, float > gemmi::calculate_b_iso_range ( const Atom & atom )

inline

Definition at line 86 of file calculate.hpp.

◆ calculate_b_aniso_range()

std::pair< double, double > gemmi::calculate_b_aniso_range ( const Model & model )

inline

uses min/max eigenvalues of Baniso, or Biso if B-factor is isotropic

Definition at line 91 of file calculate.hpp.

◆ expand_box() [1/2]

template<class T >

void gemmi::expand_box	(	const T &	obj,
		Box< Position > &	box
	)

Definition at line 112 of file calculate.hpp.

◆ expand_box() [2/2]

template<>

void gemmi::expand_box	(	const Atom &	atom,
		Box< Position > &	box
	)

inline

Definition at line 116 of file calculate.hpp.

◆ calculate_box()

Box< Position > gemmi::calculate_box	(	const Structure &	st,
		double	margin = `0.`
	)

inline

Definition at line 121 of file calculate.hpp.

◆ calculate_fractional_box()

Box< Fractional > gemmi::calculate_fractional_box	(	const Structure &	st,
		double	margin = `0.`
	)

inline

Definition at line 129 of file calculate.hpp.

◆ calculate_b_est()

double gemmi::calculate_b_est ( const Atom & atom )

inline

Definition at line 147 of file calculate.hpp.

◆ calculate_angle()

double gemmi::calculate_angle	(	const Position &	p0,
		const Position &	p1,
		const Position &	p2
	)

inline

Definition at line 153 of file calculate.hpp.

◆ calculate_dihedral()

double gemmi::calculate_dihedral	(	const Position &	p0,
		const Position &	p1,
		const Position &	p2,
		const Position &	p3
	)

inline

Definition at line 159 of file calculate.hpp.

◆ calculate_dihedral_from_atoms()

double gemmi::calculate_dihedral_from_atoms	(	const Atom *	a,
		const Atom *	b,
		const Atom *	c,
		const Atom *	d
	)

inline

the return value is in the same range as that of atan2(), i.e. [-pi, pi]

Definition at line 172 of file calculate.hpp.

◆ calculate_omega()

double gemmi::calculate_omega	(	const Residue &	res,
		const Residue &	next
	)

inline

Definition at line 179 of file calculate.hpp.

◆ is_peptide_bond_cis()

bool gemmi::is_peptide_bond_cis	(	const Atom *	ca1,
		const Atom *	c,
		const Atom *	n,
		const Atom *	ca2,
		double	tolerance_deg
	)

inline

Definition at line 184 of file calculate.hpp.

◆ calculate_chiral_volume()

double gemmi::calculate_chiral_volume	(	const Position &	actr,
		const Position &	a1,
		const Position &	a2,
		const Position &	a3
	)

inline

Definition at line 191 of file calculate.hpp.

◆ calculate_phi_psi()

std::array< double, 2 > gemmi::calculate_phi_psi	(	const Residue *	prev,
		const Residue &	res,
		const Residue *	next
	)

inline

Definition at line 196 of file calculate.hpp.

◆ find_best_plane()

GEMMI_DLL std::array< double, 4 > gemmi::find_best_plane ( const std::vector< Atom * > & atoms )

◆ get_distance_from_plane()

double gemmi::get_distance_from_plane	(	const Position &	pos,
		const std::array< double, 4 > &	coeff
	)

inline

Definition at line 214 of file calculate.hpp.

◆ parse_triplet_as_ftransform()

GEMMI_DLL FTransform gemmi::parse_triplet_as_ftransform ( const std::string & s )

◆ angle_z()

template<typename Restr >

double gemmi::angle_z	(	double	value_rad,
		const Restr &	restr,
		double	full = `360.`
	)

Definition at line 300 of file chemcomp.hpp.

◆ chiral_abs_volume()

double gemmi::chiral_abs_volume	(	double	bond1,
		double	bond2,
		double	bond3,
		double	angle1,
		double	angle2,
		double	angle3
	)

inline

Definition at line 304 of file chemcomp.hpp.

◆ bond_type_from_string()

BondType gemmi::bond_type_from_string ( const std::string & s )

inline

Definition at line 509 of file chemcomp.hpp.

◆ bond_type_to_string()

const char * gemmi::bond_type_to_string ( BondType btype )

inline

Definition at line 527 of file chemcomp.hpp.

◆ order_of_bond_type()

float gemmi::order_of_bond_type ( BondType btype )

inline

Definition at line 540 of file chemcomp.hpp.

◆ chirality_from_string()

ChiralityType gemmi::chirality_from_string ( const std::string & s )

inline

Definition at line 554 of file chemcomp.hpp.

◆ chirality_from_flag_and_volume()

ChiralityType gemmi::chirality_from_flag_and_volume	(	const std::string &	s,
		double	volume
	)

inline

Definition at line 564 of file chemcomp.hpp.

◆ chirality_to_string()

const char * gemmi::chirality_to_string ( ChiralityType chir_type )

inline

Definition at line 574 of file chemcomp.hpp.

◆ make_chemcomp_from_block()

ChemComp gemmi::make_chemcomp_from_block ( const cif::Block & block_ )

inline

Definition at line 583 of file chemcomp.hpp.

◆ check_data_type_under_symmetry()

template<typename DataProxy >

std::pair< DataType, size_t > gemmi::check_data_type_under_symmetry ( const DataProxy & proxy )

Definition at line 23 of file cif2mtz.hpp.

◆ possible_old_style()

bool gemmi::possible_old_style	(	const ReflnBlock &	rb,
		DataType	data_type
	)

inline

Definition at line 49 of file cif2mtz.hpp.

◆ transcript_old_anomalous_to_standard()

cif::Loop gemmi::transcript_old_anomalous_to_standard	(	const cif::Loop &	loop,
		const SpaceGroup *	sg
	)

inline

Before _refln.pdbx_F_plus/minus was introduced, anomalous data was stored as two F_meas_au reflections, say (1,1,3) and (-1,-1,-3).

This function transcribes it to how the anomalous data is stored in PDBx/mmCIF nowadays: _refln.F_meas_au -> pdbx_F_plus / pdbx_F_minus, _refln.F_meas_sigma_au -> pdbx_F_plus_sigma / pdbx_F_minus_sigma. _refln.intensity_{meas,sigma} -> _refln.pdbx_F_plus{,_sigma} / ...

Definition at line 78 of file cif2mtz.hpp.

◆ setup_for_crd()

GEMMI_DLL void gemmi::setup_for_crd ( Structure & st )

◆ add_automatic_links()

GEMMI_DLL void gemmi::add_automatic_links	(	Model &	model,
		Structure &	st,
		const MonLib &	monlib
	)

◆ add_dictionary_blocks()

GEMMI_DLL void gemmi::add_dictionary_blocks	(	cif::Document &	doc,
		const std::vector< std::string > &	resnames,
		const Topo &	topo,
		const MonLib &	monlib
	)

◆ prepare_refmac_crd()

GEMMI_DLL cif::Document gemmi::prepare_refmac_crd	(	Structure &	st,
		const Topo &	topo,
		const MonLib &	monlib,
		HydrogenChange	h_change
	)

◆ determine_cutoff_radius()

template<int N, typename Real >

Real gemmi::determine_cutoff_radius	(	Real	x1,
		const ExpSum< N, Real > &	precal,
		Real	cutoff_level
	)

Definition at line 18 of file dencalc.hpp.

◆ it92_radius_approx()

template<typename Real >

Real gemmi::it92_radius_approx ( Real b )

Definition at line 66 of file dencalc.hpp.

◆ as_utf8()

std::string gemmi::as_utf8 ( const _tinydir_char_t * path )

inline

Definition at line 43 of file dirwalk.hpp.

◆ glob_match()

bool gemmi::glob_match	(	const std::string &	pattern,
		const std::string &	str
	)

inline

Definition at line 52 of file dirwalk.hpp.

◆ calculate_amplitude_normalizers()

template<typename DataProxy >

std::vector< double > gemmi::calculate_amplitude_normalizers	(	const DataProxy &	data,
		int	fcol_idx,
		const Binner &	binner
	)

Definition at line 14 of file ecalc.hpp.

◆ eigen_decomposition()

GEMMI_DLL Mat33 gemmi::eigen_decomposition	(	const SMat33< double > &	A,
		double(&)	d[3]
	)

◆ is_hydrogen()

bool gemmi::is_hydrogen ( El el )

inline

Definition at line 26 of file elem.hpp.

◆ is_metal_value()

bool & gemmi::is_metal_value ( El el )

inline

Definition at line 29 of file elem.hpp.

◆ is_metal()

bool gemmi::is_metal ( El el )

inline

Definition at line 64 of file elem.hpp.

◆ set_is_metal()

void gemmi::set_is_metal	(	El	el,
		bool	v
	)

inline

Definition at line 65 of file elem.hpp.

◆ ce_almost_eq()

constexpr bool gemmi::ce_almost_eq	(	double	x,
		double	y
	)

constexpr

Definition at line 70 of file elem.hpp.

◆ molecular_weight()

double gemmi::molecular_weight ( El el )

inline

Definition at line 74 of file elem.hpp.

◆ covalent_radius()

float gemmi::covalent_radius ( El el )

inline

Definition at line 116 of file elem.hpp.

◆ vdw_radius()

float gemmi::vdw_radius ( El el )

inline

Definition at line 161 of file elem.hpp.

◆ element_name()

const char * gemmi::element_name ( El el )

inline

Definition at line 202 of file elem.hpp.

◆ element_uppercase_name()

elname_t & gemmi::element_uppercase_name ( El el )

inline

Definition at line 227 of file elem.hpp.

◆ find_element()

El gemmi::find_element ( const char * symbol )

inline

Definition at line 274 of file elem.hpp.

◆ entity_type_to_string()

const char * gemmi::entity_type_to_string ( EntityType entity_type )

inline

Definition at line 14 of file enumstr.hpp.

◆ entity_type_from_string()

EntityType gemmi::entity_type_from_string ( const std::string & t )

inline

Definition at line 24 of file enumstr.hpp.

◆ polymer_type_to_string()

const char * gemmi::polymer_type_to_string ( PolymerType polymer_type )

inline

Definition at line 33 of file enumstr.hpp.

◆ polymer_type_from_string()

PolymerType gemmi::polymer_type_from_string ( const std::string & t )

inline

Definition at line 50 of file enumstr.hpp.

◆ connection_type_to_string()

const char * gemmi::connection_type_to_string ( Connection::Type t )

inline

Definition at line 66 of file enumstr.hpp.

◆ connection_type_from_string()

Connection::Type gemmi::connection_type_from_string ( const std::string & t )

inline

Definition at line 73 of file enumstr.hpp.

◆ software_classification_to_string()

std::string gemmi::software_classification_to_string ( SoftwareItem::Classification c )

inline

Definition at line 81 of file enumstr.hpp.

◆ software_classification_from_string()

SoftwareItem::Classification gemmi::software_classification_from_string ( const std::string & str )

inline

Definition at line 97 of file enumstr.hpp.

◆ fail() [1/3]

void gemmi::fail ( const std::string & msg )

inline

Definition at line 59 of file fail.hpp.

◆ fail() [2/3]

template<typename T , typename... Args>

void gemmi::fail	(	std::string &&	str,
		T &&	arg1,
		Args &&...	args
	)

Definition at line 62 of file fail.hpp.

◆ fail() [3/3]

GEMMI_COLD void gemmi::fail ( const char * msg )

inline

Definition at line 68 of file fail.hpp.

◆ sys_fail() [1/2]

GEMMI_COLD void gemmi::sys_fail ( const std::string & msg )

inline

Definition at line 71 of file fail.hpp.

◆ sys_fail() [2/2]

GEMMI_COLD void gemmi::sys_fail ( const char * msg )

inline

Definition at line 75 of file fail.hpp.

◆ unreachable()

void gemmi::unreachable ( )

inline

Definition at line 80 of file fail.hpp.

◆ path_basename()

std::string gemmi::path_basename	(	const std::string &	path,
		std::initializer_list< const char * >	exts
	)

inline

Definition at line 23 of file fileutil.hpp.

◆ file_open()

fileptr_t gemmi::file_open	(	const char *	path,
		const char *	mode
	)

inline

Definition at line 49 of file fileutil.hpp.

◆ file_open_or()

fileptr_t gemmi::file_open_or	(	const char *	path,
		const char *	mode,
		std::FILE *	dash_stream
	)

inline

Definition at line 64 of file fileutil.hpp.

◆ file_size()

std::size_t gemmi::file_size	(	std::FILE *	f,
		const std::string &	path
	)

inline

Definition at line 71 of file fileutil.hpp.

◆ is_little_endian()

bool gemmi::is_little_endian ( )

inline

Definition at line 83 of file fileutil.hpp.

◆ swap_two_bytes()

void gemmi::swap_two_bytes ( void * start )

inline

Definition at line 88 of file fileutil.hpp.

◆ swap_four_bytes()

void gemmi::swap_four_bytes ( void * start )

inline

Definition at line 93 of file fileutil.hpp.

◆ swap_eight_bytes()

void gemmi::swap_eight_bytes ( void * start )

inline

Definition at line 99 of file fileutil.hpp.

◆ read_file_into_buffer()

CharArray gemmi::read_file_into_buffer ( const std::string & path )

inline

Definition at line 108 of file fileutil.hpp.

◆ read_stdin_into_buffer()

CharArray gemmi::read_stdin_into_buffer ( )

inline

Definition at line 117 of file fileutil.hpp.

◆ read_into_buffer()

template<typename T >

CharArray gemmi::read_into_buffer ( T && input )

inline

Definition at line 132 of file fileutil.hpp.

◆ mask_nodes_above_threshold()

void gemmi::mask_nodes_above_threshold	(	Grid< std::int8_t > &	mask,
		const Grid< float > &	grid,
		double	threshold,
		bool	negate = `false`
	)

inline

Definition at line 134 of file floodfill.hpp.

◆ flood_fill_above()

Grid< std::int8_t > gemmi::flood_fill_above	(	const Grid< float > &	grid,
		const std::vector< Position > &	seeds,
		double	threshold,
		bool	negate = `false`
	)

inline

Definition at line 143 of file floodfill.hpp.

◆ unsafe_expapprox()

float gemmi::unsafe_expapprox ( float x )

inline

Definition at line 22 of file formfact.hpp.

◆ pow15()

template<typename Real >

Real gemmi::pow15 ( Real x )

Definition at line 121 of file formfact.hpp.

◆ phase_in_angles()

template<typename T >

double gemmi::phase_in_angles	(	const std::complex< T > &	v,
		double	eps = `2e-5`
	)

Definition at line 28 of file fourier.hpp.

◆ add_asu_f_phi_to_float_vector()

void gemmi::add_asu_f_phi_to_float_vector	(	std::vector< float > &	float_data,
		const AsuData< std::complex< float > > &	asu_data
	)

inline

Definition at line 36 of file fourier.hpp.

◆ get_size_for_hkl()

template<typename DataProxy >

std::array< int, 3 > gemmi::get_size_for_hkl	(	const DataProxy &	data,
		std::array< int, 3 >	min_size,
		double	sample_rate
	)

Definition at line 48 of file fourier.hpp.

◆ data_fits_into()

template<typename DataProxy >

bool gemmi::data_fits_into	(	const DataProxy &	data,
		std::array< int, 3 >	size
	)

Definition at line 77 of file fourier.hpp.

◆ add_friedel_mates()

template<typename T >

void gemmi::add_friedel_mates ( ReciprocalGrid< T > & grid )

Definition at line 88 of file fourier.hpp.

◆ initialize_hkl_grid()

template<typename T , typename DataProxy >

void gemmi::initialize_hkl_grid	(	ReciprocalGrid< T > &	grid,
		const DataProxy &	data,
		std::array< int, 3 >	size,
		bool	half_l,
		AxisOrder	axis_order
	)

Definition at line 132 of file fourier.hpp.

◆ get_f_phi_on_grid()

template<typename T , typename FPhi >

FPhiGrid< T > gemmi::get_f_phi_on_grid	(	const FPhi &	fphi,
		std::array< int, 3 >	size,
		bool	half_l,
		AxisOrder	axis_order = `AxisOrder::XYZ`
	)

Definition at line 168 of file fourier.hpp.

◆ get_value_on_grid()

template<typename T , typename DataProxy >

ReciprocalGrid< T > gemmi::get_value_on_grid	(	const DataProxy &	data,
		size_t	column,
		std::array< int, 3 >	size,
		bool	half_l,
		AxisOrder	axis_order = `AxisOrder::XYZ`
	)

Definition at line 202 of file fourier.hpp.

◆ transform_f_phi_grid_to_map()

template<typename T >

Grid< T > gemmi::transform_f_phi_grid_to_map ( FPhiGrid< T > && hkl )

Definition at line 284 of file fourier.hpp.

◆ transform_f_phi_to_map()

template<typename T , typename FPhi >

Grid< T > gemmi::transform_f_phi_to_map	(	const FPhi &	fphi,
		std::array< int, 3 >	size,
		double	sample_rate,
		bool	exact_size = `false`,
		AxisOrder	order = `AxisOrder::XYZ`
	)

Definition at line 291 of file fourier.hpp.

◆ transform_f_phi_to_map2()

template<typename T , typename FPhi >

Grid< T > gemmi::transform_f_phi_to_map2	(	const FPhi &	fphi,
		std::array< int, 3 >	min_size,
		double	sample_rate,
		std::array< int, 3 >	exact_size,
		AxisOrder	order = `AxisOrder::XYZ`
	)

Definition at line 305 of file fourier.hpp.

◆ transform_map_to_f_phi()

template<typename T >

FPhiGrid< T > gemmi::transform_map_to_f_phi	(	const Grid< T > &	map,
		bool	half_l,
		bool	use_scale = `true`
	)

Definition at line 316 of file fourier.hpp.

◆ cromer_liberman_for_array()

GEMMI_DLL void gemmi::cromer_liberman_for_array	(	int	z,
		int	npts,
		const double *	energy,
		double *	fp,
		double *	fpp
	)

Cromer-Liberman calculation of anomalous scattering factors.

input: z - atomic number npts - array length energy - energies in eV output: fp - f' (real part of anomalous scattering) fpp - f" (imaginary part of anomalous scattering)

◆ cromer_liberman()

double gemmi::cromer_liberman	(	int	z,
		double	energy,
		double *	fpp
	)

inline

returns fp, fpp is returned through the last argument.

Definition at line 25 of file fprime.hpp.

◆ open_stream_from_utf8_path()

template<typename T >

void gemmi::open_stream_from_utf8_path	(	T &	ptr,
		const std::string &	filename
	)

inline

Definition at line 27 of file fstream.hpp.

◆ modulo()

int gemmi::modulo	(	int	a,
		int	n
	)

inline

Definition at line 37 of file grid.hpp.

◆ has_small_factorization()

bool gemmi::has_small_factorization ( int n )

inline

Definition at line 45 of file grid.hpp.

◆ round_with_small_factorization()

int gemmi::round_with_small_factorization	(	double	exact,
		GridSizeRounding	rounding
	)

inline

Definition at line 54 of file grid.hpp.

◆ good_grid_size()

std::array< int, 3 > gemmi::good_grid_size	(	std::array< double, 3 >	limit,
		GridSizeRounding	rounding,
		const SpaceGroup *	sg
	)

inline

Definition at line 78 of file grid.hpp.

◆ check_grid_factors()

void gemmi::check_grid_factors	(	const SpaceGroup *	sg,
		std::array< int, 3 >	size
	)

inline

Definition at line 128 of file grid.hpp.

◆ cubic_interpolation()

double gemmi::cubic_interpolation	(	double	u,
		double	a,
		double	b,
		double	c,
		double	d
	)

inline

Catmull–Rom spline interpolation.

CINT_u from: https://en.wikipedia.org/wiki/Cubic_Hermite_spline The same as (24) in https://journals.iucr.org/d/issues/2018/06/00/ic5103/

Definition at line 153 of file grid.hpp.

◆ cubic_interpolation_der()

double gemmi::cubic_interpolation_der	(	double	u,
		double	a,
		double	b,
		double	c,
		double	d
	)

inline

df/du (from Wolfram Alpha)

Definition at line 161 of file grid.hpp.

◆ interpolate_grid()

template<typename T >

void gemmi::interpolate_grid	(	Grid< T > &	dest,
		const Grid< T > &	src,
		const Transform &	tr,
		int	order = `1`
	)

Definition at line 794 of file grid.hpp.

◆ calculate_correlation()

template<typename T >

Correlation gemmi::calculate_correlation	(	const GridBase< T > &	a,
		const GridBase< T > &	b
	)

Definition at line 807 of file grid.hpp.

◆ estimate_uncompressed_size()

GEMMI_DLL size_t gemmi::estimate_uncompressed_size ( const std::string & path )

◆ miller_str()

std::string gemmi::miller_str ( const Miller & hkl )

inline

Definition at line 21 of file intensit.hpp.

◆ read_staraniso_b_from_mtz()

GEMMI_DLL std::string gemmi::read_staraniso_b_from_mtz	(	const Mtz &	mtz,
		SMat33< double > &	output
	)

Returns STARANISO version or empty string.

◆ atom_to_site()

SmallStructure::Site gemmi::atom_to_site	(	const Atom &	atom,
		const UnitCell &	cell
	)

inline

Definition at line 13 of file interop.hpp.

◆ mx_to_sx_structure()

SmallStructure gemmi::mx_to_sx_structure	(	const Structure &	st,
		int	n = `0`
	)

inline

Definition at line 45 of file interop.hpp.

◆ jordan_solve() [1/2]

void gemmi::jordan_solve	(	double *	a,
		double *	b,
		int	n
	)

inline

This function solves a set of linear algebraic equations using Gauss-Jordan elimination with partial pivoting.

A * x = b

a is n x n matrix (in vector) b is vector of length n, This function returns vector x[] in b[], and 1-matrix in a[].

Definition at line 29 of file levmar.hpp.

◆ jordan_solve() [2/2]

void gemmi::jordan_solve	(	std::vector< double > &	a,
		std::vector< double > &	b
	)

inline

Definition at line 72 of file levmar.hpp.

◆ print_parameters()

void gemmi::print_parameters	(	const std::string &	name,
		std::vector< double > &	a
	)

inline

Definition at line 77 of file levmar.hpp.

◆ compute_wssr()

template<typename Target >

double gemmi::compute_wssr ( const Target & target )

Definition at line 85 of file levmar.hpp.

◆ compute_gradients()

template<typename Target >

double gemmi::compute_gradients	(	const Target &	target,
		unsigned	n,
		double *	grad
	)

Definition at line 93 of file levmar.hpp.

◆ compute_lm_matrices()

template<typename Target >

double gemmi::compute_lm_matrices	(	const Target &	target,
		std::vector< double > &	alpha,
		std::vector< double > &	beta
	)

Definition at line 135 of file levmar.hpp.

◆ pi()

constexpr double gemmi::pi ( )

constexpr

Definition at line 16 of file math.hpp.

◆ hc()

constexpr double gemmi::hc ( )

constexpr

Definition at line 20 of file math.hpp.

◆ bohrradius()

constexpr double gemmi::bohrradius ( )

constexpr

Definition at line 23 of file math.hpp.

◆ mott_bethe_const()

constexpr double gemmi::mott_bethe_const ( )

constexpr

Definition at line 26 of file math.hpp.

◆ u_to_b()

constexpr double gemmi::u_to_b ( )

constexpr

Definition at line 29 of file math.hpp.

◆ deg()

constexpr double gemmi::deg ( double angle )

constexpr

Definition at line 31 of file math.hpp.

◆ rad()

constexpr double gemmi::rad ( double angle )

constexpr

Definition at line 32 of file math.hpp.

◆ sq() [1/2]

constexpr float gemmi::sq ( float x )

constexpr

Definition at line 34 of file math.hpp.

◆ sq() [2/2]

constexpr double gemmi::sq ( double x )

constexpr

Definition at line 35 of file math.hpp.

◆ log_cosh()

double gemmi::log_cosh ( double x )

inline

Definition at line 37 of file math.hpp.

◆ iround()

int gemmi::iround ( double d )

inline

Definition at line 44 of file math.hpp.

◆ angle_abs_diff()

double gemmi::angle_abs_diff	(	double	a,
		double	b,
		double	full = `360.0`
	)

inline

Definition at line 46 of file math.hpp.

◆ operator*() [1/3]

Vec3 gemmi::operator*	(	double	d,
		const Vec3 &	v
	)

inline

Definition at line 111 of file math.hpp.

◆ rotate_about_axis()

Vec3 gemmi::rotate_about_axis	(	const Vec3 &	v,
		const Vec3 &	axis,
		double	theta
	)

inline

Rodrigues' rotation formula: rotate vector v about given axis of rotation (which must be a unit vector) by given angle (in radians).

Definition at line 115 of file math.hpp.

◆ is_polypeptide()

bool gemmi::is_polypeptide ( PolymerType pt )

inline

Definition at line 221 of file metadata.hpp.

◆ is_polynucleotide()

bool gemmi::is_polynucleotide ( PolymerType pt )

inline

Definition at line 225 of file metadata.hpp.

◆ make_structure_from_block()

GEMMI_DLL Structure gemmi::make_structure_from_block ( const cif::Block & block )

structure from a coordinate mmCIF block

◆ make_structure()

Structure gemmi::make_structure	(	cif::Document &&	doc,
		cif::Document *	save_doc = `nullptr`
	)

inline

structure from a coordinate mmCIF document

Definition at line 19 of file mmcif.hpp.

◆ operator|()

constexpr int gemmi::operator\|	(	ChemCompModel	a,
		ChemCompModel	b
	)

constexpr

Definition at line 39 of file mmcif.hpp.

◆ make_residue_from_chemcomp_block()

GEMMI_DLL Residue gemmi::make_residue_from_chemcomp_block	(	const cif::Block &	block,
		ChemCompModel	kind
	)

make_residue_from_chemcomp_block

◆ make_model_from_chemcomp_block()

Model gemmi::make_model_from_chemcomp_block	(	const cif::Block &	block,
		ChemCompModel	kind
	)

inline

Definition at line 44 of file mmcif.hpp.

◆ make_structure_from_chemcomp_block()

Structure gemmi::make_structure_from_chemcomp_block	(	const cif::Block &	block,
		int	which = `7`
	)

inline

Definition at line 55 of file mmcif.hpp.

◆ check_chemcomp_block_number()

int gemmi::check_chemcomp_block_number ( const cif::Document & doc )

inline

Definition at line 75 of file mmcif.hpp.

◆ make_structure_from_chemcomp_doc()

Structure gemmi::make_structure_from_chemcomp_doc	(	const cif::Document &	doc,
		cif::Document *	save_doc = `nullptr`,
		int	which = `7`
	)

inline

Definition at line 92 of file mmcif.hpp.

◆ copy_transform_to_mmdb()

void gemmi::copy_transform_to_mmdb	(	const Transform &	tr,
		mmdb::mat33 &	mat,
		mmdb::vect3 &	vec
	)

inline

Definition at line 16 of file mmdb.hpp.

◆ strcpy_to_mmdb()

template<int N>

void gemmi::strcpy_to_mmdb	(	char(&)	dest[N],
		const std::string &	src
	)

Definition at line 26 of file mmdb.hpp.

◆ set_seqid_in_mmdb()

void gemmi::set_seqid_in_mmdb	(	int *	seqnum,
		mmdb::InsCode &	icode,
		SeqId	seqid
	)

inline

Definition at line 32 of file mmdb.hpp.

◆ seqid_from_mmdb()

SeqId gemmi::seqid_from_mmdb	(	int	seqnum,
		const mmdb::InsCode &	inscode
	)

inline

Definition at line 39 of file mmdb.hpp.

◆ cispep_to_mmdb()

mmdb::CisPep * gemmi::cispep_to_mmdb	(	const CisPep &	g,
		int	ser_num,
		int	model_num
	)

inline

Definition at line 43 of file mmdb.hpp.

◆ cispep_from_mmdb()

CisPep gemmi::cispep_from_mmdb	(	const mmdb::CisPep &	m,
		int	model_num
	)

inline

Definition at line 57 of file mmdb.hpp.

◆ transfer_links_to_mmdb()

void gemmi::transfer_links_to_mmdb	(	const Structure &	st,
		mmdb::Manager *	mol
	)

inline

Definition at line 70 of file mmdb.hpp.

◆ transfer_links_from_mmdb()

void gemmi::transfer_links_from_mmdb	(	mmdb::LinkContainer &	mmdb_links,
		Structure &	st
	)

inline

Definition at line 104 of file mmdb.hpp.

◆ copy_to_mmdb()

void gemmi::copy_to_mmdb	(	const Structure &	st,
		mmdb::Manager *	manager
	)

inline

Definition at line 137 of file mmdb.hpp.

◆ copy_atom_from_mmdb()

Atom gemmi::copy_atom_from_mmdb ( mmdb::Atom & m_atom )

inline

Definition at line 238 of file mmdb.hpp.

◆ copy_residue_from_mmdb()

Residue gemmi::copy_residue_from_mmdb ( mmdb::Residue & m_res )

inline

Definition at line 259 of file mmdb.hpp.

◆ copy_chain_from_mmdb()

Chain gemmi::copy_chain_from_mmdb ( mmdb::Chain & m_chain )

inline

Definition at line 282 of file mmdb.hpp.

◆ copy_model_from_mmdb()

Model gemmi::copy_model_from_mmdb ( mmdb::Model & m_model )

inline

Definition at line 302 of file mmdb.hpp.

◆ copy_from_mmdb()

Structure gemmi::copy_from_mmdb ( mmdb::Manager * manager )

inline

Definition at line 312 of file mmdb.hpp.

◆ coor_format_from_ext()

CoorFormat gemmi::coor_format_from_ext ( const std::string & path )

inline

Definition at line 19 of file mmread.hpp.

◆ coor_format_from_content()

CoorFormat gemmi::coor_format_from_content	(	const char *	buf,
		const char *	end
	)

inline

Definition at line 30 of file mmread.hpp.

◆ make_structure_from_doc()

Structure gemmi::make_structure_from_doc	(	cif::Document &&	doc,
		bool	possible_chemcomp,
		cif::Document *	save_doc = `nullptr`
	)

inline

Definition at line 48 of file mmread.hpp.

◆ read_structure_from_memory()

Structure gemmi::read_structure_from_memory	(	char *	data,
		size_t	size,
		const std::string &	path,
		CoorFormat	format = `CoorFormat::Unknown`,
		cif::Document *	save_doc = `nullptr`
	)

inline

Definition at line 60 of file mmread.hpp.

◆ read_structure_from_char_array()

Structure gemmi::read_structure_from_char_array	(	char *	data,
		size_t	size,
		const std::string &	path,
		cif::Document *	save_doc = `nullptr`
	)

inline

Definition at line 79 of file mmread.hpp.

◆ read_structure()

template<typename T >

Structure gemmi::read_structure	(	T &&	input,
		CoorFormat	format = `CoorFormat::Unknown`,
		cif::Document *	save_doc = `nullptr`
	)

Definition at line 86 of file mmread.hpp.

◆ read_structure_file()

Structure gemmi::read_structure_file	(	const std::string &	path,
		CoorFormat	format = `CoorFormat::Unknown`
	)

inline

Definition at line 116 of file mmread.hpp.

◆ read_structure_gz()

GEMMI_DLL Structure gemmi::read_structure_gz	(	const std::string &	path,
		CoorFormat	format = `CoorFormat::Unknown`,
		cif::Document *	save_doc = `nullptr`
	)

◆ read_pdb_gz()

GEMMI_DLL Structure gemmi::read_pdb_gz	(	const std::string &	path,
		PdbReadOptions	options = `PdbReadOptions()`
	)

◆ read_structure_from_chemcomp_gz()

GEMMI_DLL Structure gemmi::read_structure_from_chemcomp_gz	(	const std::string &	path,
		cif::Document *	save_doc = `nullptr`,
		int	which = `7`
	)

◆ coor_format_from_ext_gz()

GEMMI_DLL CoorFormat gemmi::coor_format_from_ext_gz ( const std::string & path )

◆ remove_empty_children()

template<class T >

void gemmi::remove_empty_children ( T & obj )

Definition at line 109 of file model.hpp.

◆ is_same_conformer()

bool gemmi::is_same_conformer	(	char	altloc1,
		char	altloc2
	)

inline

Definition at line 114 of file model.hpp.

◆ atom_str() [1/3]

std::string gemmi::atom_str	(	const Chain &	chain,
		const ResidueId &	res_id,
		const Atom &	atom
	)

inline

Definition at line 606 of file model.hpp.

◆ atom_str() [2/3]

std::string gemmi::atom_str ( const const_CRA & cra )

inline

Definition at line 625 of file model.hpp.

◆ atom_matches()

bool gemmi::atom_matches	(	const const_CRA &	cra,
		const AtomAddress &	addr,
		bool	ignore_segment = `false`
	)

inline

Definition at line 633 of file model.hpp.

◆ make_address()

AtomAddress gemmi::make_address	(	const Chain &	ch,
		const Residue &	res,
		const Atom &	at
	)

inline

Definition at line 641 of file model.hpp.

◆ find_entity_of_subchain() [1/2]

Entity * gemmi::find_entity_of_subchain	(	const std::string &	subchain_id,
		std::vector< Entity > &	entities
	)

inline

Definition at line 864 of file model.hpp.

◆ find_entity_of_subchain() [2/2]

const Entity * gemmi::find_entity_of_subchain	(	const std::string &	subchain_id,
		const std::vector< Entity > &	entities
	)

inline

Definition at line 872 of file model.hpp.

◆ remove_alternative_conformations() [1/2]

template<class T >

void gemmi::remove_alternative_conformations ( T & obj )

Remove alternative conformations.

Definition at line 17 of file modify.hpp.

◆ remove_alternative_conformations() [2/2]

template<>

void gemmi::remove_alternative_conformations ( Chain & chain )

inline

Definition at line 21 of file modify.hpp.

◆ remove_hydrogens() [1/2]

template<class T >

void gemmi::remove_hydrogens ( T & obj )

Remove hydrogens.

Definition at line 43 of file modify.hpp.

◆ remove_hydrogens() [2/2]

template<>

void gemmi::remove_hydrogens ( Residue & res )

inline

Definition at line 47 of file modify.hpp.

◆ assign_b_iso() [1/2]

template<class T >

void gemmi::assign_b_iso	(	T &	obj,
		float	b_min,
		float	b_max
	)

Set isotropic ADP to the range (b_min, b_max).

Values smaller than b_min are changed to b_min, values larger than b_max to b_max. Anisotropic ADP is left unchanged.

Definition at line 56 of file modify.hpp.

◆ assign_b_iso() [2/2]

template<>

void gemmi::assign_b_iso	(	Atom &	atom,
		float	b_min,
		float	b_max
	)

inline

Definition at line 60 of file modify.hpp.

◆ remove_anisou() [1/2]

template<class T >

void gemmi::remove_anisou ( T & obj )

Remove anisotropic ADP.

Definition at line 65 of file modify.hpp.

◆ remove_anisou() [2/2]

template<>

void gemmi::remove_anisou ( Atom & atom )

inline

Definition at line 69 of file modify.hpp.

◆ ensure_anisou() [1/2]

template<class T >

void gemmi::ensure_anisou ( T & obj )

Set absent ANISOU to value from B_iso.

Definition at line 74 of file modify.hpp.

◆ ensure_anisou() [2/2]

template<>

void gemmi::ensure_anisou ( Atom & atom )

inline

Definition at line 78 of file modify.hpp.

◆ transform_pos_and_adp() [1/2]

template<class T >

void gemmi::transform_pos_and_adp	(	T &	obj,
		const Transform &	tr
	)

apply Transform to both atom's position and ADP

Definition at line 86 of file modify.hpp.

◆ transform_pos_and_adp() [2/2]

template<>

void gemmi::transform_pos_and_adp	(	Atom &	atom,
		const Transform &	tr
	)

inline

Definition at line 90 of file modify.hpp.

◆ assign_serial_numbers() [1/2]

void gemmi::assign_serial_numbers	(	Model &	model,
		bool	numbered_ter = `false`
	)

inline

set atom site serial numbers to 1, 2, ..., optionally leaving gaps for TERs

Definition at line 97 of file modify.hpp.

◆ assign_serial_numbers() [2/2]

void gemmi::assign_serial_numbers	(	Structure &	st,
		bool	numbered_ter = `false`
	)

inline

Definition at line 108 of file modify.hpp.

◆ process_addresses()

template<typename Func >

void gemmi::process_addresses	(	Structure &	st,
		Func	func
	)

Helper function for processing (usually: changing) names and numbers in AtomAddress instances in metadata: Connection, CisPep, Helix, Sheet::Strand.

Other fields are not updated here, in particular: ModRes, Entity::DbRef, Entity::full_sequence, TlsGroup::Selection.

Definition at line 120 of file modify.hpp.

◆ process_sequence_ids()

template<typename Func >

void gemmi::process_sequence_ids	(	Structure &	st,
		Func	func
	)

Takes func(const std::string& chain_name, gemmi::SeqId& seqid).

It doesn't process Entity::DbRef::seq_begin/seq_end (b/c there is no single corresponding chain name).

Definition at line 146 of file modify.hpp.

◆ rename_chain()

void gemmi::rename_chain	(	Structure &	st,
		const std::string &	old_name,
		const std::string &	new_name
	)

inline

Definition at line 158 of file modify.hpp.

◆ rename_residues()

void gemmi::rename_residues	(	Structure &	st,
		const std::string &	old_name,
		const std::string &	new_name
	)

inline

Definition at line 176 of file modify.hpp.

◆ rename_atom_names()

void gemmi::rename_atom_names	(	Structure &	st,
		const std::string &	res_name,
		const std::map< std::string, std::string > &	old_new
	)

inline

Definition at line 205 of file modify.hpp.

◆ replace_d_fraction_with_altlocs()

void gemmi::replace_d_fraction_with_altlocs ( Residue & res )

inline

Definition at line 226 of file modify.hpp.

◆ replace_deuterium_with_fraction()

bool gemmi::replace_deuterium_with_fraction ( Residue & res )

inline

Definition at line 257 of file modify.hpp.

◆ store_deuterium_as_fraction()

void gemmi::store_deuterium_as_fraction	(	Structure &	st,
		bool	store_fraction
	)

inline

Hydrogens modelled as H/D mixture (altlocs H and D with the same position and ADP, but with refined fraction of D), it can be stored in mmCIF either as two atoms (H and D) or, using CCP4/Refmac extension, as H atoms with the ccp4_deuterium_fraction parameter.

This function switches fraction <-> altlocs

Definition at line 293 of file modify.hpp.

◆ standardize_crystal_frame()

void gemmi::standardize_crystal_frame ( Structure & st )

inline

Convert coordinates to the standard coordinate system for the unit cell.

Definition at line 309 of file modify.hpp.

◆ add_distinct_altlocs()

void gemmi::add_distinct_altlocs	(	const Residue &	res,
		std::string &	altlocs
	)

inline

Definition at line 21 of file monlib.hpp.

◆ atom_match_with_alias()

bool gemmi::atom_match_with_alias	(	const std::string &	atom_id,
		const std::string &	atom,
		const ChemComp::Aliasing *	aliasing
	)

inline

Definition at line 27 of file monlib.hpp.

◆ read_monomer_lib()

MonLib gemmi::read_monomer_lib	(	const std::string &	monomer_dir,
		const std::vector< std::string > &	resnames,
		const std::string &	libin = `""`,
		bool	ignore_missing = `false`
	)

inline

Definition at line 242 of file monlib.hpp.

◆ calculate_min_max_disregarding_nans()

template<typename T , typename FP = typename std::iterator_traits<T>::value_type>

std::array< FP, 2 > gemmi::calculate_min_max_disregarding_nans	(	T	begin,
		T	end
	)

Definition at line 32 of file mtz.hpp.

◆ read_mtz_file()

Mtz gemmi::read_mtz_file ( const std::string & path )

inline

Definition at line 902 of file mtz.hpp.

◆ read_mtz()

template<typename Input >

Mtz gemmi::read_mtz	(	Input &&	input,
		bool	with_data
	)

Definition at line 909 of file mtz.hpp.

◆ data_proxy() [1/2]

MtzDataProxy gemmi::data_proxy ( const Mtz & mtz )

inline

Definition at line 947 of file mtz.hpp.

◆ write_staraniso_b_in_mmcif()

GEMMI_DLL void gemmi::write_staraniso_b_in_mmcif	(	const SMat33< double > &	b,
		const std::string &	entry_id,
		char *	buf,
		std::ostream &	os
	)

◆ remove_appendix_from_column_names()

GEMMI_DLL void gemmi::remove_appendix_from_column_names	(	Mtz &	mtz,
		std::ostream &	out
	)

remove '_dataset_name' that can be appended to column names in ccp4i

◆ validate_merged_mtz_deposition_columns()

GEMMI_DLL bool gemmi::validate_merged_mtz_deposition_columns	(	const Mtz &	mtz,
		std::ostream &	out
	)

◆ validate_merged_intensities()

GEMMI_DLL bool gemmi::validate_merged_intensities	(	Intensities &	mi,
		Intensities &	ui,
		bool	relaxed_check,
		std::ostream &	out
	)

◆ is_record_type4()

bool gemmi::is_record_type4	(	const char *	s,
		const char *	record
	)

inline

Compare the first 4 letters of s, ignoring case, with uppercase record.

Both args must have at least 3+1 chars. ' ' and NUL are equivalent in s.

Definition at line 26 of file pdb.hpp.

◆ is_record_type3()

bool gemmi::is_record_type3	(	const char *	s,
		const char *	record
	)

inline

for record "TER": "TER ", TER
, TER\r, TER\t match, TERE, TER1 don't

Definition at line 30 of file pdb.hpp.

◆ read_remark_290()

GEMMI_DLL std::vector< Op > gemmi::read_remark_290 ( const std::vector< std::string > & raw_remarks )

Returns operations corresponding to 1555, 2555, ... N555.

◆ read_pdb_from_stream()

GEMMI_DLL Structure gemmi::read_pdb_from_stream	(	LineReaderBase &&	line_reader,
		const std::string &	source,
		PdbReadOptions	options
	)

◆ read_pdb_file()

Structure gemmi::read_pdb_file	(	const std::string &	path,
		PdbReadOptions	options = `PdbReadOptions()`
	)

inline

Definition at line 41 of file pdb.hpp.

◆ read_pdb_from_memory()

Structure gemmi::read_pdb_from_memory	(	const char *	data,
		size_t	size,
		const std::string &	name,
		PdbReadOptions	options = `PdbReadOptions()`
	)

inline

Definition at line 47 of file pdb.hpp.

◆ read_pdb_string()

Structure gemmi::read_pdb_string	(	const std::string &	str,
		const std::string &	name,
		PdbReadOptions	options = `PdbReadOptions()`
	)

inline

Definition at line 53 of file pdb.hpp.

◆ read_pdb()

template<typename T >

Structure gemmi::read_pdb	(	T &&	input,
		PdbReadOptions	options = `PdbReadOptions()`
	)

inline

Definition at line 61 of file pdb.hpp.

◆ all_alnums()

bool gemmi::all_alnums ( const char * p )

inline

Definition at line 16 of file pdb_id.hpp.

◆ is_pdb_code()

bool gemmi::is_pdb_code ( const std::string & str )

inline

Definition at line 23 of file pdb_id.hpp.

◆ expand_pdb_code_to_path()

std::string gemmi::expand_pdb_code_to_path	(	const std::string &	code,
		char	type,
		bool	throw_if_unset = `false`
	)

inline

Call it after checking the code with gemmi::is_pdb_code(code).

The convention for $PDB_DIR is the same as in BioJava, see the docs.

type is the requested file type: 'M' for mmCIF or 'P' for PDB, 'S' for SF-mmCIF.

Definition at line 32 of file pdb_id.hpp.

◆ expand_if_pdb_code()

std::string gemmi::expand_if_pdb_code	(	const std::string &	input,
		char	type = `'M'`
	)

inline

type is: 'M' for mmCIF or 'P' for PDB, 'S' for SF-mmCIF.

Definition at line 61 of file pdb_id.hpp.

◆ is_pir_format()

bool gemmi::is_pir_format ( const std::string & s )

inline

Definition at line 21 of file pirfasta.hpp.

◆ read_pir_or_fasta()

std::vector< FastaSeq > gemmi::read_pir_or_fasta ( const std::string & str )

inline

Definition at line 28 of file pirfasta.hpp.

◆ check_polymer_type()

GEMMI_DLL PolymerType gemmi::check_polymer_type	(	const ConstResidueSpan &	span,
		bool	ignore_entity_type = `false`
	)

◆ get_or_check_polymer_type()

PolymerType gemmi::get_or_check_polymer_type	(	const Entity *	ent,
		const ConstResidueSpan &	polymer
	)

inline

Definition at line 21 of file polyheur.hpp.

◆ get_mainchain_atoms()

std::vector< AtomNameElement > gemmi::get_mainchain_atoms ( PolymerType ptype )

inline

Definition at line 30 of file polyheur.hpp.

◆ in_peptide_bond_distance()

bool gemmi::in_peptide_bond_distance	(	const Atom *	a1,
		const Atom *	a2
	)

inline

distance-based check for peptide bond

Definition at line 39 of file polyheur.hpp.

◆ have_peptide_bond()

bool gemmi::have_peptide_bond	(	const Residue &	r1,
		const Residue &	r2
	)

inline

Definition at line 42 of file polyheur.hpp.

◆ in_nucleotide_bond_distance()

bool gemmi::in_nucleotide_bond_distance	(	const Atom *	a1,
		const Atom *	a2
	)

inline

distance-based check for phosphodiester bond between nucleotide

Definition at line 47 of file polyheur.hpp.

◆ have_nucleotide_bond()

bool gemmi::have_nucleotide_bond	(	const Residue &	r1,
		const Residue &	r2
	)

inline

Definition at line 50 of file polyheur.hpp.

◆ are_connected()

bool gemmi::are_connected	(	const Residue &	r1,
		const Residue &	r2,
		PolymerType	ptype
	)

inline

check C-N or O3'-P distance

Definition at line 55 of file polyheur.hpp.

◆ are_connected2()

bool gemmi::are_connected2	(	const Residue &	r1,
		const Residue &	r2,
		PolymerType	ptype
	)

inline

are_connected2() is less exact, but requires only CA (or P) atoms.

Definition at line 64 of file polyheur.hpp.

◆ are_connected3()

bool gemmi::are_connected3	(	const Residue &	r1,
		const Residue &	r2,
		PolymerType	ptype
	)

inline

are_connected3() = are_connected() + fallback to are_connected2()

Definition at line 86 of file polyheur.hpp.

◆ make_one_letter_sequence()

GEMMI_DLL std::string gemmi::make_one_letter_sequence ( const ConstResidueSpan & polymer )

◆ add_entity_types() [1/2]

GEMMI_DLL void gemmi::add_entity_types	(	Chain &	chain,
		bool	overwrite
	)

Assigns entity_type=Polymer|NonPolymer|Water for each Residue (only for residues with entity_type==Unknown, unless overwrite=true).

Determining where the polymer ends and ligands start is sometimes arbitrary – there can be a non-standard residue at the end that can be regarded as as either the last residue or a linked ligand.

◆ add_entity_types() [2/2]

GEMMI_DLL void gemmi::add_entity_types	(	Structure &	st,
		bool	overwrite
	)

◆ remove_entity_types()

GEMMI_DLL void gemmi::remove_entity_types ( Structure & st )

Assigns entity_type=Unknown for all residues.

◆ add_entity_ids()

GEMMI_DLL void gemmi::add_entity_ids	(	Structure &	st,
		bool	overwrite
	)

Assigns Residue::entity_id based on Residue::subchain and Entity::subchains.

◆ assign_subchain_names()

GEMMI_DLL void gemmi::assign_subchain_names	(	Chain &	chain,
		int &	nonpolymer_counter
	)

The subchain field in the residue is where we store_atom_site.label_asym_id from mmCIF files.

As of 2018 wwPDB software splits author's chains (auth_asym_id) into label_asym_id units: * linear polymer, * non-polymers (each residue has different separate label_asym_id), * and waters. Refmac/makecif is doing similar thing but using different naming and somewhat different rules (it was written in 1990's before PDBx/mmCIF).

Here we use naming and rules different from both wwPDB and makecif. Note: call add_entity_types() first.

◆ assign_subchains()

GEMMI_DLL void gemmi::assign_subchains	(	Structure &	st,
		bool	force,
		bool	fail_if_unknown = `true`
	)

◆ ensure_entities()

GEMMI_DLL void gemmi::ensure_entities ( Structure & st )

◆ deduplicate_entities()

GEMMI_DLL void gemmi::deduplicate_entities ( Structure & st )

◆ setup_entities()

void gemmi::setup_entities ( Structure & st )

inline

Definition at line 140 of file polyheur.hpp.

◆ recommended_het_flag()

GEMMI_DLL char gemmi::recommended_het_flag ( const Residue & res )

Determine ATOM/HETATM record type, based on Residue::entity_type.

◆ assign_het_flags() [1/2]

template<class T >

void gemmi::assign_het_flags	(	T &	obj,
		char	flag = `'R'`
	)

R = recommended_het_flag(), other valid values are A, H and '\0'.

Definition at line 150 of file polyheur.hpp.

◆ assign_het_flags() [2/2]

template<>

void gemmi::assign_het_flags	(	Residue &	res,
		char	flag
	)

inline

Definition at line 154 of file polyheur.hpp.

◆ remove_waters() [1/2]

template<class T >

void gemmi::remove_waters ( T & obj )

Definition at line 162 of file polyheur.hpp.

◆ remove_waters() [2/2]

template<>

void gemmi::remove_waters ( Chain & ch )

inline

Definition at line 166 of file polyheur.hpp.

◆ remove_ligands_and_waters() [1/2]

template<class T >

void gemmi::remove_ligands_and_waters ( T & obj )

Definition at line 172 of file polyheur.hpp.

◆ remove_ligands_and_waters() [2/2]

template<>

void gemmi::remove_ligands_and_waters ( Chain & ch )

inline

Definition at line 176 of file polyheur.hpp.

◆ trim_to_alanine() [1/2]

GEMMI_DLL bool gemmi::trim_to_alanine ( Residue & res )

◆ trim_to_alanine() [2/2]

void gemmi::trim_to_alanine ( Chain & chain )

inline

Definition at line 187 of file polyheur.hpp.

◆ shorten_ccd_codes()

GEMMI_DLL void gemmi::shorten_ccd_codes ( Structure & st )

◆ restore_full_ccd_codes()

GEMMI_DLL void gemmi::restore_full_ccd_codes ( Structure & st )

◆ add_microhetero_to_sequences()

GEMMI_DLL void gemmi::add_microhetero_to_sequences	(	Structure &	st,
		bool	overwrite = `false`
	)

Modifies Entity::full_sequence. Uses only the first chain for each Entity.

◆ qcp_inner_product()

double gemmi::qcp_inner_product	(	Mat33 &	mat,
		const Position *	pos1,
		const Position &	ctr1,
		const Position *	pos2,
		const Position &	ctr2,
		size_t	len,
		const double *	weight
	)

inline

Definition at line 94 of file qcp.hpp.

◆ fast_calc_rmsd_and_rotation()

int gemmi::fast_calc_rmsd_and_rotation	(	Mat33 *	rot,
		const Mat33 &	A,
		double *	rmsd,
		double	E0,
		double	len,
		double	min_score
	)

inline

Definition at line 120 of file qcp.hpp.

◆ qcp_calculate_center()

Position gemmi::qcp_calculate_center	(	const Position *	pos,
		size_t	len,
		const double *	weight
	)

inline

Definition at line 284 of file qcp.hpp.

◆ superpose_positions()

SupResult gemmi::superpose_positions	(	const Position *	pos1,
		const Position *	pos2,
		size_t	len,
		const double *	weight
	)

inline

Definition at line 297 of file qcp.hpp.

◆ calculate_rmsd_of_superposed_positions()

double gemmi::calculate_rmsd_of_superposed_positions	(	const Position *	pos1,
		const Position *	pos2,
		size_t	len,
		const double *	weight
	)

inline

Definition at line 330 of file qcp.hpp.

◆ read_cif_gz()

GEMMI_DLL cif::Document gemmi::read_cif_gz ( const std::string & path )

◆ read_mmjson_gz()

GEMMI_DLL cif::Document gemmi::read_mmjson_gz ( const std::string & path )

◆ read_into_buffer_gz()

GEMMI_DLL CharArray gemmi::read_into_buffer_gz ( const std::string & path )

◆ read_cif_from_memory()

GEMMI_DLL cif::Document gemmi::read_cif_from_memory	(	const char *	data,
		size_t	size,
		const char *	name
	)

◆ read_first_block_gz()

GEMMI_DLL cif::Document gemmi::read_first_block_gz	(	const std::string &	path,
		size_t	limit
	)

◆ read_cif_or_mmjson_gz()

cif::Document gemmi::read_cif_or_mmjson_gz ( const std::string & path )

inline

Definition at line 19 of file read_cif.hpp.

◆ read_cif_from_buffer()

cif::Document gemmi::read_cif_from_buffer	(	const CharArray &	buffer,
		const char *	name
	)

inline

Definition at line 26 of file read_cif.hpp.

◆ read_ccp4_map()

GEMMI_DLL Ccp4< float > gemmi::read_ccp4_map	(	const std::string &	path,
		bool	setup
	)

◆ read_ccp4_mask()

GEMMI_DLL Ccp4< int8_t > gemmi::read_ccp4_mask	(	const std::string &	path,
		bool	setup
	)

◆ friedel_mate_value() [1/2]

template<typename T >

T gemmi::friedel_mate_value ( T v )

Definition at line 14 of file recgrid.hpp.

◆ friedel_mate_value() [2/2]

template<typename T >

std::complex< T > gemmi::friedel_mate_value ( const std::complex< T > & v )

Definition at line 16 of file recgrid.hpp.

◆ for_all_reflections()

template<typename Func >

void gemmi::for_all_reflections	(	Func	func,
		const UnitCell &	cell,
		const SpaceGroup *	spacegroup,
		double	dmin,
		double	dmax = `0.`,
		bool	unique = `true`
	)

Definition at line 15 of file reciproc.hpp.

◆ count_reflections()

int gemmi::count_reflections	(	const UnitCell &	cell,
		const SpaceGroup *	spacegroup,
		double	dmin,
		double	dmax = `0.`,
		bool	unique = `true`
	)

inline

Definition at line 38 of file reciproc.hpp.

◆ make_miller_vector()

std::vector< Miller > gemmi::make_miller_vector	(	const UnitCell &	cell,
		const SpaceGroup *	spacegroup,
		double	dmin,
		double	dmax = `0.`,
		bool	unique = `true`
	)

inline

Definition at line 47 of file reciproc.hpp.

◆ as_refln_blocks()

std::vector< ReflnBlock > gemmi::as_refln_blocks ( std::vector< cif::Block > && blocks )

inline

Definition at line 150 of file refln.hpp.

◆ get_refln_block()

ReflnBlock gemmi::get_refln_block	(	std::vector< cif::Block > &&	blocks,
		const std::vector< std::string > &	labels,
		const char *	block_name = `nullptr`
	)

inline

Definition at line 176 of file refln.hpp.

◆ hkl_cif_as_refln_block()

ReflnBlock gemmi::hkl_cif_as_refln_block ( cif::Block & block )

inline

Definition at line 205 of file refln.hpp.

◆ data_proxy() [2/2]

ReflnDataProxy gemmi::data_proxy ( const ReflnBlock & rb )

inline

Definition at line 243 of file refln.hpp.

◆ find_tabulated_residue()

GEMMI_DLL ResidueInfo gemmi::find_tabulated_residue ( const std::string & name )

◆ expand_one_letter()

const char * gemmi::expand_one_letter	(	char	c,
		ResidueKind	kind
	)

inline

kind can be AA, RNA or DNA

Definition at line 64 of file resinfo.hpp.

◆ expand_one_letter_sequence()

GEMMI_DLL std::vector< std::string > gemmi::expand_one_letter_sequence	(	const std::string &	seq,
		ResidueKind	kind
	)

kind can be AA, RNA or DNA

◆ expand_protein_one_letter()

const char * gemmi::expand_protein_one_letter ( char c )

inline

Definition at line 94 of file resinfo.hpp.

◆ expand_protein_one_letter_string()

std::vector< std::string > gemmi::expand_protein_one_letter_string ( const std::string & s )

inline

Definition at line 98 of file resinfo.hpp.

◆ place_hydrogens_on_all_atoms()

GEMMI_DLL void gemmi::place_hydrogens_on_all_atoms ( Topo & topo )

◆ adjust_hydrogen_distances()

void gemmi::adjust_hydrogen_distances	(	Topo &	topo,
		Restraints::DistanceOf	of,
		double	default_scale = `1.`
	)

inline

Definition at line 15 of file riding_h.hpp.

◆ vec6_dot()

double gemmi::vec6_dot	(	const Vec6 &	a,
		const SMat33< double > &	s
	)

inline

Definition at line 18 of file scaling.hpp.

◆ adp_symmetry_constraints()

std::vector< Vec6 > gemmi::adp_symmetry_constraints ( const SpaceGroup * sg )

inline

Symmetry constraints of ADP.

The number of rows is the number of independent coefficients in U. For example, for tetragonal crystal returns two normalized Vec6 vectors in directions [1 1 0 0 0 0] and [0 0 1 0 0 0].

Definition at line 27 of file scaling.hpp.

◆ align_sequences()

AlignmentResult gemmi::align_sequences	(	const std::vector< std::uint8_t > &	query,
		const std::vector< std::uint8_t > &	target,
		const std::vector< int > &	target_gapo,
		std::uint8_t	m,
		const AlignmentScoring &	scoring
	)

inline

All values in query and target must be less then m.

target_gapo, if set, has gap opening penalties at specific positions in target.

Definition at line 195 of file seqalign.hpp.

◆ align_string_sequences()

AlignmentResult gemmi::align_string_sequences	(	const std::vector< std::string > &	query,
		const std::vector< std::string > &	target,
		const std::vector< int > &	target_gapo,
		const AlignmentScoring *	scoring
	)

inline

Definition at line 298 of file seqalign.hpp.

◆ atom_str() [3/3]

std::string gemmi::atom_str	(	const std::string &	chain_name,
		const ResidueId &	res_id,
		const std::string &	atom_name,
		char	altloc
	)

inline

Definition at line 107 of file seqid.hpp.

◆ h2o_weight()

constexpr double gemmi::h2o_weight ( )

constexpr

Definition at line 13 of file seqtools.hpp.

◆ calculate_sequence_weight()

double gemmi::calculate_sequence_weight	(	const std::vector< std::string > &	seq,
		double	unknown = `0.`
	)

inline

Definition at line 15 of file seqtools.hpp.

◆ one_letter_code()

std::string gemmi::one_letter_code ( const std::vector< std::string > & seq )

inline

Definition at line 25 of file seqtools.hpp.

◆ pdbx_one_letter_code()

std::string gemmi::pdbx_one_letter_code	(	const std::vector< std::string > &	seq,
		ResidueKind	kind
	)

inline

Returns the format used in _entity_poly.pdbx_seq_one_letter_code, in which non-standard amino acids/nucleotides are represented by CCD codes in parenthesis, e.g.

AA(MSE)H.

Definition at line 35 of file seqtools.hpp.

◆ sequence_kind()

ResidueKind gemmi::sequence_kind ( PolymerType ptype )

inline

used with expand_one_letter_sequence()

Definition at line 50 of file seqtools.hpp.

◆ calculate_sf_part()

std::complex< double > gemmi::calculate_sf_part	(	const Fractional &	fpos,
		const Miller &	hkl
	)

inline

Definition at line 21 of file sfcalc.hpp.

◆ is_complete()

bool gemmi::is_complete ( const GroupOps & gops )

inline

Definition at line 22 of file small.hpp.

◆ triplets_to_ops()

std::vector< Op > gemmi::triplets_to_ops ( const std::vector< std::string > & symops )

inline

Definition at line 30 of file small.hpp.

◆ split_element_and_charge()

template<typename T >

void gemmi::split_element_and_charge	(	const std::string &	label,
		T *	dest
	)

inline

Definition at line 214 of file small.hpp.

◆ make_small_structure_from_block()

SmallStructure gemmi::make_small_structure_from_block ( const cif::Block & block_ )

inline

Definition at line 16 of file smcif.hpp.

◆ make_cif_block_from_small_structure()

cif::Block gemmi::make_cif_block_from_small_structure ( const SmallStructure & st )

inline

Definition at line 130 of file smcif.hpp.

◆ cctbx_vdw_radius()

float gemmi::cctbx_vdw_radius ( El el )

inline

Definition at line 17 of file solmask.hpp.

◆ refmac_radius_for_bulk_solvent()

float gemmi::refmac_radius_for_bulk_solvent ( El el )

inline

Definition at line 57 of file solmask.hpp.

◆ mask_points_in_constant_radius()

template<typename T >

void gemmi::mask_points_in_constant_radius	(	Grid< T > &	mask,
		const Model &	model,
		double	radius,
		T	value,
		bool	ignore_hydrogen,
		bool	ignore_zero_occupancy_atoms
	)

Definition at line 107 of file solmask.hpp.

◆ mask_points_in_varied_radius()

template<typename T >

void gemmi::mask_points_in_varied_radius	(	Grid< T > &	mask,
		const Model &	model,
		AtomicRadiiSet	atomic_radii_set,
		double	r_probe,
		T	value,
		bool	ignore_hydrogen,
		bool	ignore_zero_occupancy_atoms
	)

Definition at line 122 of file solmask.hpp.

◆ set_margin_around()

template<typename T >

void gemmi::set_margin_around	(	Grid< T > &	mask,
		double	r,
		T	value,
		T	margin_value
	)

Definition at line 147 of file solmask.hpp.

◆ mask_with_node_info()

void gemmi::mask_with_node_info	(	Grid< NodeInfo > &	mask,
		const Model &	model,
		double	radius
	)

inline

Populate NodeInfo grid for nodes near the model.

Definition at line 343 of file solmask.hpp.

◆ unmask_symmetry_mates()

void gemmi::unmask_symmetry_mates ( Grid< NodeInfo > & mask )

inline

Skip nodes that are closer to a symmetry mate of the model than to the original model.

A node is closer to a symmetry mate when it has a symmetry image that is closer to the original model than the node. We ignore NCS here.

Definition at line 376 of file solmask.hpp.

◆ interpolate_grid_of_aligned_model2()

template<typename T >

void gemmi::interpolate_grid_of_aligned_model2	(	Grid< T > &	dest,
		const Grid< T > &	src,
		const Transform &	tr,
		const Model &	dest_model,
		double	radius,
		int	order = `1`
	)

Definition at line 396 of file solmask.hpp.

◆ add_soft_edge_to_mask()

template<typename T >

void gemmi::add_soft_edge_to_mask	(	Grid< T > &	grid,
		double	width
	)

Definition at line 419 of file solmask.hpp.

◆ snprintf_z()

GEMMI_DLL int gemmi::snprintf_z	(	char *	buf,
		int	count,
		char const *	fmt,
			...
	)

stb_snprintf in gemmi namespace - like snprintf, but ignores locale and is always zero-terminated (hence _z).

◆ sprintf_z()

GEMMI_DLL int GEMMI_DLL int gemmi::sprintf_z	(	char *	buf,
		char const *	fmt,
			...
	)

stb_sprintf in gemmi namespace

◆ to_str() [1/2]

GEMMI_DLL int GEMMI_DLL int std::string gemmi::to_str ( double d )

inline

Definition at line 36 of file sprintf.hpp.

◆ to_str() [2/2]

std::string gemmi::to_str ( float d )

inline

Definition at line 42 of file sprintf.hpp.

◆ to_str_prec()

template<int Prec>

std::string gemmi::to_str_prec ( double d )

Definition at line 49 of file sprintf.hpp.

◆ to_chars_z() [1/2]

char * gemmi::to_chars_z	(	char *	first,
		char *	last,
		int	value
	)

inline

zero-terminated to_chars()

Definition at line 58 of file sprintf.hpp.

◆ to_chars_z() [2/2]

char * gemmi::to_chars_z	(	char *	first,
		char *	last,
		size_t	value
	)

inline

Definition at line 68 of file sprintf.hpp.

◆ calculate_data_statistics()

template<typename T >

DataStats gemmi::calculate_data_statistics ( const std::vector< T > & data )

Definition at line 83 of file stats.hpp.

◆ operator==()

bool gemmi::operator==	(	const Op &	a,
		const Op &	b
	)

inline

Definition at line 194 of file symmetry.hpp.

◆ operator!=()

bool gemmi::operator!=	(	const Op &	a,
		const Op &	b
	)

inline

Definition at line 197 of file symmetry.hpp.

◆ operator*() [2/3]

Op gemmi::operator*	(	const Op &	a,
		const Op &	b
	)

inline

Definition at line 199 of file symmetry.hpp.

◆ operator*=()

Op & gemmi::operator*=	(	Op &	a,
		const Op &	b
	)

inline

Definition at line 200 of file symmetry.hpp.

◆ seitz_to_op()

Op gemmi::seitz_to_op ( const std::array< std::array< double, 4 >, 4 > & t )

inline

Definition at line 225 of file symmetry.hpp.

◆ interpret_miller_character()

int gemmi::interpret_miller_character	(	char	c,
		const std::string &	s
	)

inline

Definition at line 248 of file symmetry.hpp.

◆ parse_triplet_part()

std::array< int, 4 > gemmi::parse_triplet_part	(	const std::string &	s,
		double *	decimal_fract = `nullptr`
	)

inline

Definition at line 259 of file symmetry.hpp.

◆ parse_triplet()

Op gemmi::parse_triplet ( const std::string & s )

inline

Definition at line 328 of file symmetry.hpp.

◆ make_triplet_part()

std::string gemmi::make_triplet_part	(	const std::array< int, 3 > &	xyz,
		int	w,
		char	style = `'x'`
	)

inline

Definition at line 392 of file symmetry.hpp.

◆ centring_vectors()

std::vector< Op::Tran > gemmi::centring_vectors ( char centring_type )

inline

Definition at line 441 of file symmetry.hpp.

◆ split_centering_vectors()

GroupOps gemmi::split_centering_vectors ( const std::vector< Op > & ops )

inline

Definition at line 754 of file symmetry.hpp.

◆ hall_rotation_z()

Op::Rot gemmi::hall_rotation_z ( int N )

inline

Definition at line 776 of file symmetry.hpp.

◆ hall_translation_from_symbol()

Op::Tran gemmi::hall_translation_from_symbol ( char symbol )

inline

Definition at line 790 of file symmetry.hpp.

◆ hall_matrix_symbol()

Op gemmi::hall_matrix_symbol	(	const char *	start,
		const char *	end,
		int	pos,
		int &	prev
	)

inline

Definition at line 806 of file symmetry.hpp.

◆ parse_hall_change_of_basis()

Op gemmi::parse_hall_change_of_basis	(	const char *	start,
		const char *	end
	)

inline

Definition at line 868 of file symmetry.hpp.

◆ generators_from_hall()

GroupOps gemmi::generators_from_hall ( const char * hall )

inline

Definition at line 883 of file symmetry.hpp.

◆ symops_from_hall()

GroupOps gemmi::symops_from_hall ( const char * hall )

inline

Definition at line 927 of file symmetry.hpp.

◆ crystal_system_str()

const char * gemmi::crystal_system_str ( CrystalSystem system )

inline

Definition at line 939 of file symmetry.hpp.

◆ point_group_hm()

const char * gemmi::point_group_hm ( PointGroup pg )

inline

Definition at line 952 of file symmetry.hpp.

◆ pointgroup_to_laue()

Laue gemmi::pointgroup_to_laue ( PointGroup pg )

inline

Definition at line 967 of file symmetry.hpp.

◆ laue_to_pointgroup()

PointGroup gemmi::laue_to_pointgroup ( Laue laue )

inline

Definition at line 985 of file symmetry.hpp.

◆ laue_class_str()

const char * gemmi::laue_class_str ( Laue laue )

inline

Definition at line 994 of file symmetry.hpp.

◆ crystal_system() [1/2]

CrystalSystem gemmi::crystal_system ( Laue laue )

inline

Definition at line 998 of file symmetry.hpp.

◆ crystal_system() [2/2]

CrystalSystem gemmi::crystal_system ( PointGroup pg )

inline

Definition at line 1011 of file symmetry.hpp.

◆ point_group_index_and_category()

unsigned char gemmi::point_group_index_and_category ( int space_group_number )

inline

Definition at line 1015 of file symmetry.hpp.

◆ point_group()

PointGroup gemmi::point_group ( int space_group_number )

inline

Definition at line 1046 of file symmetry.hpp.

◆ is_sohncke()

bool gemmi::is_sohncke ( int space_group_number )

inline

Definition at line 1052 of file symmetry.hpp.

◆ is_enantiomorphic()

bool gemmi::is_enantiomorphic ( int space_group_number )

inline

Definition at line 1057 of file symmetry.hpp.

◆ is_symmorphic()

bool gemmi::is_symmorphic ( int space_group_number )

inline

Definition at line 1062 of file symmetry.hpp.

◆ nonzero_inversion_center()

Op::Tran gemmi::nonzero_inversion_center ( int space_group_number )

inline

Inversion center of the Euclidean normalizer that is not at the origin of reference settings.

Returns (0,0,0) if absent. Based on tables in ch. 3.5 of ITA (2016) doi:10.1107/97809553602060000933 (column "Inversion through a centre at").

Definition at line 1070 of file symmetry.hpp.

◆ get_basisop()

const char * gemmi::get_basisop ( int basisop_idx )

inline

Definition at line 1857 of file symmetry.hpp.

◆ centred_to_primitive()

Op::Rot gemmi::centred_to_primitive ( char centring_type )

inline

Definition at line 1088 of file symmetry.hpp.

◆ find_spacegroup_by_number()

const SpaceGroup * gemmi::find_spacegroup_by_number ( int ccp4 )

inlinenoexcept

Definition at line 1914 of file symmetry.hpp.

◆ get_spacegroup_by_number()

const SpaceGroup & gemmi::get_spacegroup_by_number ( int ccp4 )

inline

Definition at line 1923 of file symmetry.hpp.

◆ get_spacegroup_reference_setting()

const SpaceGroup & gemmi::get_spacegroup_reference_setting ( int number )

inline

Definition at line 1931 of file symmetry.hpp.

◆ find_spacegroup_by_name()

const SpaceGroup * gemmi::find_spacegroup_by_name	(	std::string	name,
		double	alpha = `0.`,
		double	gamma = `0.`,
		const char *	prefer = `nullptr`
	)

inline

If angles alpha and gamma are provided, they are used to distinguish hexagonal and rhombohedral settings (e.g.

for "R 3").

Parameters

prefer can specify preferred H/R settings and 1/2 origin choice. For example, prefer="2H" means the origin choice 2 and hexagonal settings. The default is "1H".

Definition at line 1944 of file symmetry.hpp.

◆ get_spacegroup_by_name()

const SpaceGroup & gemmi::get_spacegroup_by_name ( const std::string & name )

inline

Definition at line 2053 of file symmetry.hpp.

◆ get_spacegroup_p1()

const SpaceGroup & gemmi::get_spacegroup_p1 ( )

inline

Definition at line 2060 of file symmetry.hpp.

◆ find_spacegroup_by_ops()

const SpaceGroup * gemmi::find_spacegroup_by_ops ( const GroupOps & gops )

inline

Definition at line 2064 of file symmetry.hpp.

◆ add_chemcomp_to_block()

void gemmi::add_chemcomp_to_block	(	const ChemComp &	cc,
		cif::Block &	block
	)

inline

Definition at line 14 of file to_chemcomp.hpp.

◆ update_mmcif_block()

GEMMI_DLL void gemmi::update_mmcif_block	(	const Structure &	st,
		cif::Block &	block,
		MmcifOutputGroups	groups = `MmcifOutputGroups(true)`
	)

◆ make_mmcif_document()

GEMMI_DLL cif::Document gemmi::make_mmcif_document	(	const Structure &	st,
		MmcifOutputGroups	groups = `MmcifOutputGroups(true)`
	)

◆ make_mmcif_block()

GEMMI_DLL cif::Block gemmi::make_mmcif_block	(	const Structure &	st,
		MmcifOutputGroups	groups = `MmcifOutputGroups(true)`
	)

◆ make_mmcif_headers()

GEMMI_DLL cif::Block gemmi::make_mmcif_headers ( const Structure & st )

◆ add_minimal_mmcif_data()

GEMMI_DLL void gemmi::add_minimal_mmcif_data	(	const Structure &	st,
		cif::Block &	block
	)

◆ write_ncs_oper()

GEMMI_DLL void gemmi::write_ncs_oper	(	const Structure &	st,
		cif::Block &	block
	)

◆ write_struct_conn()

GEMMI_DLL void gemmi::write_struct_conn	(	const Structure &	st,
		cif::Block &	block
	)

◆ write_cispeps()

GEMMI_DLL void gemmi::write_cispeps	(	const Structure &	st,
		cif::Block &	block
	)

◆ use_hetatm()

GEMMI_DLL bool gemmi::use_hetatm ( const Residue & res )

record type ATOM/HETATM to use for writing given residue

◆ write_pdb()

GEMMI_DLL void gemmi::write_pdb	(	const Structure &	st,
		std::ostream &	os,
		PdbWriteOptions	opt = `PdbWriteOptions()`
	)

◆ make_pdb_string()

GEMMI_DLL std::string gemmi::make_pdb_string	(	const Structure &	st,
		PdbWriteOptions	opt = `PdbWriteOptions()`
	)

◆ write_minimal_pdb()

void gemmi::write_minimal_pdb	(	const Structure &	st,
		std::ostream &	os
	)

inline

Definition at line 57 of file to_pdb.hpp.

◆ make_pdb_headers()

std::string gemmi::make_pdb_headers ( const Structure & st )

inline

Definition at line 61 of file to_pdb.hpp.

◆ prepare_topology()

GEMMI_DLL std::unique_ptr< Topo > gemmi::prepare_topology	(	Structure &	st,
		MonLib &	monlib,
		size_t	model_index,
		HydrogenChange	h_change,
		bool	reorder,
		const Logger &	logger = `{}`,
		bool	ignore_unknown_links = `false`,
		bool	use_cispeps = `false`
	)

◆ make_chemcomp_with_restraints()

GEMMI_DLL std::unique_ptr< ChemComp > gemmi::make_chemcomp_with_restraints ( const Residue & res )

◆ find_missing_atoms()

GEMMI_DLL std::vector< AtomAddress > gemmi::find_missing_atoms	(	const Topo &	topo,
		bool	including_hydrogen = `false`
	)

◆ calculate_cos_obliquity()

double gemmi::calculate_cos_obliquity	(	const UnitCell &	reduced_cell,
		const Vec3 &	d_axis,
		const Vec3 &	r_axis
	)

inline

Definition at line 132 of file twin.hpp.

◆ find_lattice_2fold_ops()

std::vector< OpObliquity > gemmi::find_lattice_2fold_ops	(	const UnitCell &	reduced_cell,
		double	max_obliq
	)

inline

Definition at line 147 of file twin.hpp.

◆ find_lattice_symmetry_r()

GroupOps gemmi::find_lattice_symmetry_r	(	const UnitCell &	reduced_cell,
		double	max_obliq
	)

inline

Definition at line 172 of file twin.hpp.

◆ find_lattice_symmetry()

GroupOps gemmi::find_lattice_symmetry	(	const UnitCell &	cell,
		char	centring,
		double	max_obliq
	)

inline

Definition at line 190 of file twin.hpp.

◆ find_twin_laws()

std::vector< Op > gemmi::find_twin_laws	(	const UnitCell &	cell,
		const SpaceGroup *	sg,
		double	max_obliq,
		bool	all_ops
	)

inline

Definition at line 202 of file twin.hpp.

◆ rot_as_mat33() [1/2]

Mat33 gemmi::rot_as_mat33 ( const Op::Rot & rot )

inline

Definition at line 17 of file unitcell.hpp.

◆ rot_as_mat33() [2/2]

Mat33 gemmi::rot_as_mat33 ( const Op & op )

inline

Definition at line 23 of file unitcell.hpp.

◆ tran_as_vec3()

Vec3 gemmi::tran_as_vec3 ( const Op & op )

inline

Definition at line 26 of file unitcell.hpp.

◆ operator*() [3/3]

Position gemmi::operator*	(	double	d,
		const Position &	v
	)

inline

Definition at line 47 of file unitcell.hpp.

◆ UTF8_to_wchar()

std::wstring gemmi::UTF8_to_wchar ( const char * in )

inline

Definition at line 12 of file utf.hpp.

◆ wchar_to_UTF8()

std::string gemmi::wchar_to_UTF8 ( const wchar_t * in )

inline

Definition at line 42 of file utf.hpp.

◆ append_to_str() [1/3]

void gemmi::append_to_str	(	std::string &	out,
		int	v
	)

inline

Definition at line 20 of file util.hpp.

◆ append_to_str() [2/3]

void gemmi::append_to_str	(	std::string &	out,
		size_t	v
	)

inline

Definition at line 21 of file util.hpp.

◆ append_to_str() [3/3]

template<typename T >

void gemmi::append_to_str	(	std::string &	out,
		const T &	v
	)

Definition at line 23 of file util.hpp.

◆ cat_to() [1/2]

void gemmi::cat_to ( std::string & )

inline

Definition at line 25 of file util.hpp.

◆ cat_to() [2/2]

template<typename T , typename... Args>

void gemmi::cat_to	(	std::string &	out,
		const T &	value,
		Args const &...	args
	)

Definition at line 27 of file util.hpp.

◆ cat()

template<class... Args>

std::string gemmi::cat ( Args const &... args )

Definition at line 32 of file util.hpp.

◆ starts_with() [1/2]

bool gemmi::starts_with	(	const std::string &	str,
		const std::string &	prefix
	)

inline

Definition at line 38 of file util.hpp.

◆ starts_with() [2/2]

template<size_t N>

bool gemmi::starts_with	(	const char *	a,
		const char(&)	b[N]
	)

Definition at line 43 of file util.hpp.

◆ ends_with()

bool gemmi::ends_with	(	const std::string &	str,
		const std::string &	suffix
	)

inline

Definition at line 47 of file util.hpp.

◆ lower()

char gemmi::lower ( char c )

inline

Definition at line 53 of file util.hpp.

◆ alpha_up()

char gemmi::alpha_up ( char c )

inline

Definition at line 60 of file util.hpp.

◆ to_lower()

std::string gemmi::to_lower ( std::string str )

inline

Definition at line 62 of file util.hpp.

◆ to_upper()

std::string gemmi::to_upper ( std::string str )

inline

Definition at line 69 of file util.hpp.

◆ isame()

bool gemmi::isame	(	char	a,
		char	b
	)

inline

Definition at line 77 of file util.hpp.

◆ iequal_from()

bool gemmi::iequal_from	(	const std::string &	str,
		size_t	offset,
		const std::string &	low
	)

inline

Definition at line 83 of file util.hpp.

◆ iequal()

bool gemmi::iequal	(	const std::string &	str,
		const std::string &	low
	)

inline

Definition at line 89 of file util.hpp.

◆ istarts_with()

bool gemmi::istarts_with	(	const std::string &	str,
		const std::string &	prefix
	)

inline

Definition at line 93 of file util.hpp.

◆ iends_with()

bool gemmi::iends_with	(	const std::string &	str,
		const std::string &	suffix
	)

inline

Definition at line 98 of file util.hpp.

◆ giends_with()

bool gemmi::giends_with	(	const std::string &	str,
		const std::string &	suffix
	)

inline

Definition at line 105 of file util.hpp.

◆ trim_str()

std::string gemmi::trim_str ( const std::string & str )

inline

Definition at line 109 of file util.hpp.

◆ rtrim_str()

std::string gemmi::rtrim_str ( const std::string & str )

inline

Definition at line 118 of file util.hpp.

◆ rtrim_cstr()

const char * gemmi::rtrim_cstr	(	const char *	start,
		const char *	end = `nullptr`
	)

inline

Definition at line 124 of file util.hpp.

◆ split_str_into()

template<typename S >

void gemmi::split_str_into	(	const std::string &	str,
		S	sep,
		std::vector< std::string > &	result
	)

Definition at line 145 of file util.hpp.

◆ split_str()

template<typename S >

std::vector< std::string > gemmi::split_str	(	const std::string &	str,
		S	sep
	)

Definition at line 156 of file util.hpp.

◆ split_str_into_multi()

void gemmi::split_str_into_multi	(	const std::string &	str,
		const char *	seps,
		std::vector< std::string > &	result
	)

inline

Definition at line 164 of file util.hpp.

◆ split_str_multi()

std::vector< std::string > gemmi::split_str_multi	(	const std::string &	str,
		const char *	seps = `" \t"`
	)

inline

Definition at line 174 of file util.hpp.

◆ join_str() [1/4]

template<typename T , typename S , typename F >

std::string gemmi::join_str	(	T	begin,
		T	end,
		const S &	sep,
		const F &	getter
	)

Definition at line 182 of file util.hpp.

◆ join_str() [2/4]

template<typename T , typename S >

std::string gemmi::join_str	(	T	begin,
		T	end,
		const S &	sep
	)

Definition at line 195 of file util.hpp.

◆ join_str() [3/4]

template<typename T , typename S , typename F >

std::string gemmi::join_str	(	const T &	iterable,
		const S &	sep,
		const F &	getter
	)

Definition at line 200 of file util.hpp.

◆ join_str() [4/4]

template<typename T , typename S >

std::string gemmi::join_str	(	const T &	iterable,
		const S &	sep
	)

Definition at line 205 of file util.hpp.

◆ string_append_sep()

template<typename T , typename S >

void gemmi::string_append_sep	(	std::string &	str,
		S	sep,
		const T &	item
	)

Definition at line 210 of file util.hpp.

◆ replace_all()

void gemmi::replace_all	(	std::string &	s,
		const std::string &	old,
		const std::string &	new_
	)

inline

Definition at line 216 of file util.hpp.

◆ is_in_list()

bool gemmi::is_in_list	(	const std::string &	name,
		const std::string &	list,
		char	sep = `','`
	)

inline

Definition at line 226 of file util.hpp.

◆ in_vector()

template<class T >

bool gemmi::in_vector	(	const T &	x,
		const std::vector< T > &	v
	)

Definition at line 241 of file util.hpp.

◆ in_vector_f()

template<typename F , typename T >

bool gemmi::in_vector_f	(	F	f,
		const std::vector< T > &	v
	)

Definition at line 246 of file util.hpp.

◆ vector_end_ptr() [1/2]

template<class T >

T * gemmi::vector_end_ptr ( std::vector< T > & v )

Definition at line 251 of file util.hpp.

◆ vector_end_ptr() [2/2]

template<class T >

const T * gemmi::vector_end_ptr ( const std::vector< T > & v )

Definition at line 253 of file util.hpp.

◆ vector_move_extend()

template<class T >

void gemmi::vector_move_extend	(	std::vector< T > &	dst,
		std::vector< T > &&	src
	)

Definition at line 256 of file util.hpp.

◆ vector_remove_if()

template<class T , typename F >

void gemmi::vector_remove_if	(	std::vector< T > &	v,
		F &&	condition
	)

Definition at line 266 of file util.hpp.

◆ vector_insert_columns()

template<class T >

void gemmi::vector_insert_columns	(	std::vector< T > &	data,
		size_t	old_width,
		size_t	length,
		size_t	n,
		size_t	pos,
		const T &	new_value
	)

data - 2d array (old_width x length) in a vector: Insert

n new columns at position pos.

Definition at line 273 of file util.hpp.

◆ vector_remove_column()

template<class T >

void gemmi::vector_remove_column	(	std::vector< T > &	data,
		size_t	new_width,
		size_t	pos
	)

data - 2d array with new_width+1 columns, in a vector: Remove column at position pos.

Definition at line 292 of file util.hpp.

◆ ialpha4_id()

constexpr int gemmi::ialpha4_id ( const char * s )

constexpr

Definition at line 305 of file util.hpp.

◆ ialpha3_id()

constexpr int gemmi::ialpha3_id ( const char * s )

constexpr

Definition at line 309 of file util.hpp.

◆ likely_in_house_source()

bool gemmi::likely_in_house_source ( double wavelength )

inline

Definition at line 20 of file xds_ascii.hpp.

◆ read_xds_ascii_file()

XdsAscii gemmi::read_xds_ascii_file ( const std::string & path )

inline

Definition at line 176 of file xds_ascii.hpp.

Variable Documentation

◆ zlib_description

GEMMI_DLL const char* const gemmi::zlib_description

extern

Enumerator
X
H
He
Li
Be
B
C
N
O
F
Ne
Na
Mg
Al
Si
P
S
Cl
Ar
K
Ca
Sc
Ti
V
Cr
Mn
Fe
Co
Ni
Cu
Zn
Ga
Ge
As
Se
Br
Kr
Rb
Sr
Y
Zr
Nb
Mo
Tc
Ru
Rh
Pd
Ag
Cd
In
Sn
Sb
Te
I
Xe
Cs
Ba
La
Ce
Pr
Nd
Pm
Sm
Eu
Gd
Tb
Dy
Ho
Er
Tm
Yb
Lu
Hf
Ta
W
Re
Os
Ir
Pt
Au
Hg
Tl
Pb
Bi
Po
At
Rn
Fr
Ra
Ac
Th
Pa
U
Np
Pu
Am
Cm
Bk
Cf
Es
Fm
Md
No
Lr
Rf
Db
Sg
Bh
Hs
Mt
Ds
Rg
Cn
Nh
Fl
Mc
Lv
Ts
Og
D
END

Enumerator
C1
Ci
C2
Cs
C2h
D2
C2v
D2h
C4
S4
C4h
D4
C4v
D2d
D4h
C3
C3i
D3
C3v
D3d
C6
C3h
C6h
D6
C6v
D3h
D6h
T
Th
O
Td
Oh

Enumerator
X
H
He
Li
Be
B
C
N
O
F
Ne
Na
Mg
Al
Si
P
S
Cl
Ar
K
Ca
Sc
Ti
V
Cr
Mn
Fe
Co
Ni
Cu
Zn
Ga
Ge
As
Se
Br
Kr
Rb
Sr
Y
Zr
Nb
Mo
Tc
Ru
Rh
Pd
Ag
Cd
In
Sn
Sb
Te
I
Xe
Cs
Ba
La
Ce
Pr
Nd
Pm
Sm
Eu
Gd
Tb
Dy
Ho
Er
Tm
Yb
Lu
Hf
Ta
W
Re
Os
Ir
Pt
Au
Hg
Tl
Pb
Bi
Po
At
Rn
Fr
Ra
Ac
Th
Pa
U
Np
Pu
Am
Cm
Bk
Cf
Es
Fm
Md
No
Lr
Rf
Db
Sg
Bh
Hs
Mt
Ds
Rg
Cn
Nh
Fl
Mc
Lv
Ts
Og
D
END

Enumerator
C1
Ci
C2
Cs
C2h
D2
C2v
D2h
C4
S4
C4h
D4
C4v
D2d
D4h
C3
C3i
D3
C3v
D3d
C6
C3h
C6h
D6
C6v
D3h
D6h
T
Th
O
Td
Oh

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

◆ CifWalk

◆ MmCifWalk

◆ PdbWalk

◆ CoorFileWalk

◆ elname_t

◆ fileptr_t

◆ StrideIter

◆ IndirectIter

◆ UniqIter

◆ GroupingIter

◆ FilterIter

◆ Vec3

◆ Vec3f

◆ AtomGroup

◆ ConstAtomGroup

◆ CraProxy

◆ ConstCraProxy

◆ FPhiGrid

◆ Vec6

◆ spacegroup_tables

◆ OpObliquity

◆ Miller

Enumeration Type Documentation

◆ SupSelect

◆ HowToNameCopiedChain

◆ MapSetup

◆ BondType

◆ ChiralityType

◆ El

◆ AxisOrder

◆ GridSizeRounding

◆ EntityType

◆ PolymerType

◆ ChemCompModel

◆ CoorFormat

◆ CalcFlag

◆ DataType

◆ ResidueKind

◆ AtomicRadiiSet

◆ CrystalSystem

◆ PointGroup

◆ Laue

◆ HydrogenChange

◆ Asu

Function Documentation

◆ prepare_target_gapo()

◆ align_sequence_to_polymer()

◆ seqid_matches_seqres()

◆ clear_sequences()

◆ assign_best_sequences()

◆ assign_label_seq_to_polymer()

◆ clear_label_seq_id()

◆ assign_label_seq_id()

◆ prepare_positions_for_superposition()

◆ calculate_current_rmsd()

◆ calculate_superposition()

◆ calculate_superpositions_in_moving_window()

◆ ensure_unique_chain_name()

◆ make_assembly()

◆ pseudo_assembly_for_unit_cell()

◆ transform_to_assembly()

◆ expand_ncs_model()

◆ merge_atoms_in_expanded_model()

◆ shorten_chain_names()

◆ expand_ncs()

◆ split_chains_by_segments()

◆ for_matching_reflections()

◆ calculate_hkl_value_correlation()

◆ calculate_hkl_complex_correlation()

◆ count_equal_values()

◆ make_asu_data() [1/2]

◆ make_asu_data() [2/2]

◆ discard_by_sigma_ratio()

Enumerator
X
H
He
Li
Be
B
C
N
O
F
Ne
Na
Mg
Al
Si
P
S
Cl
Ar
K
Ca
Sc
Ti
V
Cr
Mn
Fe
Co
Ni
Cu
Zn
Ga
Ge
As
Se
Br
Kr
Rb
Sr
Y
Zr
Nb
Mo
Tc
Ru
Rh
Pd
Ag
Cd
In
Sn
Sb
Te
I
Xe
Cs
Ba
La
Ce
Pr
Nd
Pm
Sm
Eu
Gd
Tb
Dy
Ho
Er
Tm
Yb
Lu
Hf
Ta
W
Re
Os
Ir
Pt
Au
Hg
Tl
Pb
Bi
Po
At
Rn
Fr
Ra
Ac
Th
Pa
U
Np
Pu
Am
Cm
Bk
Cf
Es
Fm
Md
No
Lr
Rf
Db
Sg
Bh
Hs
Mt
Ds
Rg
Cn
Nh
Fl
Mc
Lv
Ts
Og
D
END

Enumerator
C1
Ci
C2
Cs
C2h
D2
C2v
D2h
C4
S4
C4h
D4
C4v
D2d
D4h
C3
C3i
D3
C3v
D3d
C6
C3h
C6h
D6
C6v
D3h
D6h
T
Th
O
Td
Oh