Gemmi C++ API
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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 | Helix |
struct | HklMatch |
struct | HklValue |
struct | Ifstream |
class | IndirectIterPolicy |
struct | Intensities |
struct | IT92 |
struct | ItemGroup |
struct | LevMar |
struct | LinkHunt |
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 | NeighborSearch |
struct | Neutron92 |
struct | NodeInfo |
struct | Ofstream |
struct | OldToNew |
helper type used for Structure::shortened_ccd_codes More... | |
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 | UnmergedHklMover |
struct | UpperTriangularMat33 |
struct | ValueSigma |
struct | Variance |
struct | Vec3_ |
struct | XdsAscii |
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 | ChemCompModel { Xyz , Example , Ideal } |
enum class | El : unsigned char { X =0 , H =1 , 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 | CoorFormat { 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 } |
using gemmi::CifWalk = typedef DirWalk<true, impl::IsCifFile> |
Definition at line 247 of file dirwalk.hpp.
using gemmi::MmCifWalk = typedef DirWalk<true, impl::IsMmCifFile> |
Definition at line 248 of file dirwalk.hpp.
using gemmi::PdbWalk = typedef DirWalk<true, impl::IsPdbFile> |
Definition at line 249 of file dirwalk.hpp.
using gemmi::CoorFileWalk = typedef DirWalk<true, impl::IsCoordinateFile> |
Definition at line 250 of file dirwalk.hpp.
typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> gemmi::fileptr_t |
Definition at line 37 of file fileutil.hpp.
Definition at line 71 of file iterator.hpp.
Definition at line 94 of file iterator.hpp.
Definition at line 126 of file iterator.hpp.
Definition at line 177 of file iterator.hpp.
Definition at line 204 of file iterator.hpp.
using gemmi::ConstAtomGroup = typedef AtomGroup_<const Atom> |
using gemmi::CraProxy = typedef CraProxy_<CRA, std::vector<Chain>&> |
typedef cif::Document(* gemmi::read_cif_func) (const std::string &) |
Definition at line 21 of file monlib.hpp.
using gemmi::FPhiGrid = typedef ReciprocalGrid<std::complex<T> > |
Definition at line 170 of file recgrid.hpp.
using gemmi::Vec6 = typedef std::array<double, 6> |
Definition at line 13 of file scaling.hpp.
using gemmi::spacegroup_tables = typedef impl::Tables_<void> |
Definition at line 1876 of file symmetry.hpp.
using gemmi::Miller = typedef std::array<int, 3> |
A synonym for convenient passing of hkl.
Definition at line 128 of file unitcell.hpp.
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Short | |
AddNumber | |
Dup |
Definition at line 16 of file assembly.hpp.
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Enumerator | |
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Unspec | |
Single | |
Double | |
Triple | |
Aromatic | |
Deloc | |
Metal |
Definition at line 20 of file chemcomp.hpp.
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Enumerator | |
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Positive | |
Negative | |
Both |
Definition at line 23 of file chemcomp.hpp.
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Enumerator | |
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Xyz | |
Example | |
Ideal |
Definition at line 17 of file chemcomp_xyz.hpp.
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Enumerator | |
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Unknown | |
Polymer | |
NonPolymer | |
Branched | |
Water |
Definition at line 186 of file metadata.hpp.
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Enumerator | |
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Unknown | |
PeptideL | |
PeptideD | |
Dna | |
Rna | |
DnaRnaHybrid | |
SaccharideD | |
SaccharideL | |
Pna | |
CyclicPseudoPeptide | |
Other |
Definition at line 197 of file metadata.hpp.
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File format of a macromolecular model.
When passed to read_structure(): Unknown = guess format from the extension, Detect = guess format from the content.
Enumerator | |
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Unknown | |
Detect | |
Pdb | |
Mmcif | |
Mmjson | |
ChemComp |
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Enumerator | |
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UNKNOWN | |
AA | |
AAD | |
PAA | |
MAA | |
RNA | |
DNA | |
BUF | |
HOH | |
PYR | |
KET | |
ELS |
Definition at line 26 of file resinfo.hpp.
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Enumerator | |
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VanDerWaals | |
Cctbx | |
Refmac | |
Constant |
Definition at line 14 of file solmask.hpp.
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Enumerator | |
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Triclinic | |
Monoclinic | |
Orthorhombic | |
Tetragonal | |
Trigonal | |
Hexagonal | |
Cubic |
Definition at line 908 of file symmetry.hpp.
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Enumerator | |
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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 920 of file symmetry.hpp.
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Enumerator | |
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L1 | |
L2m | |
Lmmm | |
L4m | |
L4mmm | |
L3 | |
L3m | |
L6m | |
L6mmm | |
Lm3 | |
Lm3m |
Definition at line 936 of file symmetry.hpp.
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Enumerator | |
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Same | |
Different | |
Any |
Definition at line 76 of file unitcell.hpp.
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GEMMI_DLL void gemmi::assign_best_sequences | ( | Structure & | st, |
const std::vector< std::string > & | fasta_sequences | ||
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Definition at line 85 of file assembly.hpp.
GEMMI_DLL Model gemmi::make_assembly | ( | const Assembly & | assembly, |
const Model & | model, | ||
HowToNameCopiedChain | how, | ||
std::ostream * | out | ||
) |
Definition at line 96 of file assembly.hpp.
GEMMI_DLL void gemmi::transform_to_assembly | ( | Structure & | st, |
const std::string & | assembly_name, | ||
HowToNameCopiedChain | how, | ||
std::ostream * | out, | ||
bool | keep_spacegroup = false , |
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double | merge_dist = 0.2 |
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If called with assembly_name="unit_cell" changes structure to unit cell (P1).
GEMMI_DLL Model gemmi::expand_ncs_model | ( | const Model & | model, |
const std::vector< NcsOp > & | ncs, | ||
HowToNameCopiedChain | how | ||
) |
GEMMI_DLL void gemmi::merge_atoms_in_expanded_model | ( | Model & | model, |
const UnitCell & | cell, | ||
double | max_dist = 0.2 , |
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bool | compare_serial = true |
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Searches and merges overlapping equivalent atoms from different chains.
To be used after expand_ncs() and make_assembly().
GEMMI_DLL void gemmi::expand_ncs | ( | Structure & | st, |
HowToNameCopiedChain | how, | ||
double | merge_dist = 0.2 |
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GEMMI_DLL void gemmi::split_chains_by_segments | ( | Model & | model, |
HowToNameCopiedChain | how | ||
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HowToNameCopiedChain::Dup adds segment name to chain name.
void gemmi::for_matching_reflections | ( | const std::vector< T > & | a, |
const std::vector< T > & | b, | ||
const Func & | func | ||
) |
Definition at line 45 of file asudata.hpp.
Correlation gemmi::calculate_hkl_value_correlation | ( | const std::vector< T > & | a, |
const std::vector< T > & | b | ||
) |
Definition at line 65 of file asudata.hpp.
ComplexCorrelation gemmi::calculate_hkl_complex_correlation | ( | const std::vector< T > & | a, |
const std::vector< T > & | b | ||
) |
Definition at line 76 of file asudata.hpp.
Definition at line 87 of file asudata.hpp.
AsuData< T > gemmi::make_asu_data | ( | const Data & | data, |
const std::array< std::string, N > & | labels, | ||
bool | as_is = false |
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) |
Definition at line 230 of file asudata.hpp.
Definition at line 237 of file asudata.hpp.
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Definition at line 67 of file asumask.hpp.
Definition at line 255 of file asumask.hpp.
Definition at line 280 of file asumask.hpp.
Definition at line 331 of file asumask.hpp.
Definition at line 22 of file bessel.hpp.
Definition at line 81 of file bessel.hpp.
Definition at line 101 of file bessel.hpp.
Definition at line 115 of file bessel.hpp.
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Definition at line 176 of file binner.hpp.
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Definition at line 190 of file binner.hpp.
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Definition at line 13 of file calculate.hpp.
Definition at line 19 of file calculate.hpp.
deprecated, use has_hydrogen() or count_atom_sites(..., Selection("[H,D]")
Definition at line 24 of file calculate.hpp.
Definition at line 30 of file calculate.hpp.
Definition at line 34 of file calculate.hpp.
Definition at line 40 of file calculate.hpp.
CenterOfMass gemmi::calculate_center_of_mass | ( | const T & | obj | ) |
Definition at line 50 of file calculate.hpp.
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Definition at line 58 of file calculate.hpp.
Definition at line 63 of file calculate.hpp.
Definition at line 67 of file calculate.hpp.
Definition at line 72 of file calculate.hpp.
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Definition at line 80 of file calculate.hpp.
Definition at line 96 of file calculate.hpp.
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Definition at line 102 of file calculate.hpp.
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Definition at line 108 of file calculate.hpp.
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the return value is in the same range as that of atan2(), i.e. [-pi, pi]
Definition at line 121 of file calculate.hpp.
Definition at line 128 of file calculate.hpp.
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Definition at line 133 of file calculate.hpp.
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Definition at line 139 of file calculate.hpp.
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Definition at line 144 of file calculate.hpp.
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Definition at line 162 of file calculate.hpp.
double gemmi::angle_z | ( | double | value_rad, |
const Restr & | restr, | ||
double | full = 360. |
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Definition at line 300 of file chemcomp.hpp.
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Definition at line 304 of file chemcomp.hpp.
Definition at line 509 of file chemcomp.hpp.
Definition at line 527 of file chemcomp.hpp.
Definition at line 540 of file chemcomp.hpp.
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Definition at line 554 of file chemcomp.hpp.
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Definition at line 564 of file chemcomp.hpp.
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Definition at line 574 of file chemcomp.hpp.
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Definition at line 583 of file chemcomp.hpp.
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Definition at line 23 of file chemcomp_xyz.hpp.
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Definition at line 67 of file chemcomp_xyz.hpp.
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Definition at line 86 of file chemcomp_xyz.hpp.
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Definition at line 107 of file chemcomp_xyz.hpp.
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Definition at line 124 of file chemcomp_xyz.hpp.
std::pair< DataType, size_t > gemmi::check_data_type_under_symmetry | ( | const DataProxy & | proxy | ) |
Definition at line 23 of file cif2mtz.hpp.
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Definition at line 49 of file cif2mtz.hpp.
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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.
GEMMI_DLL cif::Document gemmi::prepare_refmac_crd | ( | const Structure & | st, |
const Topo & | topo, | ||
const MonLib & | monlib, | ||
HydrogenChange | h_change | ||
) |
Real gemmi::determine_cutoff_radius | ( | Real | x1, |
const ExpSum< N, Real > & | precal, | ||
Real | cutoff_level | ||
) |
Definition at line 17 of file dencalc.hpp.
Definition at line 65 of file dencalc.hpp.
Definition at line 69 of file dencalc.hpp.
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Definition at line 43 of file dirwalk.hpp.
Definition at line 52 of file dirwalk.hpp.
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Definition at line 14 of file enumstr.hpp.
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Definition at line 24 of file enumstr.hpp.
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Definition at line 33 of file enumstr.hpp.
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Definition at line 50 of file enumstr.hpp.
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Definition at line 66 of file enumstr.hpp.
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Definition at line 73 of file enumstr.hpp.
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Definition at line 81 of file enumstr.hpp.
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Definition at line 97 of file enumstr.hpp.
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Definition at line 23 of file fileutil.hpp.
Definition at line 39 of file fileutil.hpp.
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Definition at line 54 of file fileutil.hpp.
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Definition at line 61 of file fileutil.hpp.
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Definition at line 73 of file fileutil.hpp.
Definition at line 78 of file fileutil.hpp.
Definition at line 83 of file fileutil.hpp.
Definition at line 89 of file fileutil.hpp.
Definition at line 98 of file fileutil.hpp.
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Definition at line 107 of file fileutil.hpp.
Definition at line 122 of file fileutil.hpp.
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Definition at line 134 of file floodfill.hpp.
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Definition at line 143 of file floodfill.hpp.
Definition at line 21 of file formfact.hpp.
Definition at line 24 of file fourier.hpp.
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Definition at line 34 of file fourier.hpp.
std::array< int, 3 > gemmi::get_size_for_hkl | ( | const DataProxy & | data, |
std::array< int, 3 > | min_size, | ||
double | sample_rate | ||
) |
Definition at line 46 of file fourier.hpp.
bool gemmi::data_fits_into | ( | const DataProxy & | data, |
std::array< int, 3 > | size | ||
) |
Definition at line 75 of file fourier.hpp.
void gemmi::add_friedel_mates | ( | ReciprocalGrid< T > & | grid | ) |
Definition at line 86 of file fourier.hpp.
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 130 of file fourier.hpp.
FPhiGrid< T > gemmi::get_f_phi_on_grid | ( | const FPhi & | fphi, |
std::array< int, 3 > | size, | ||
bool | half_l, | ||
AxisOrder | axis_order = AxisOrder::XYZ |
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Definition at line 166 of file fourier.hpp.
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 |
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) |
Definition at line 200 of file fourier.hpp.
Definition at line 282 of file fourier.hpp.
Grid< T > gemmi::transform_f_phi_to_map | ( | const FPhi & | fphi, |
std::array< int, 3 > | size, | ||
double | sample_rate, | ||
bool | exact_size = false , |
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AxisOrder | order = AxisOrder::XYZ |
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Definition at line 289 of file fourier.hpp.
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 |
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) |
Definition at line 303 of file fourier.hpp.
FPhiGrid< T > gemmi::transform_map_to_f_phi | ( | const Grid< T > & | map, |
bool | half_l, | ||
bool | use_scale = true |
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Definition at line 314 of file fourier.hpp.
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Definition at line 2946 of file fprime.hpp.
Definition at line 2961 of file fprime.hpp.
Definition at line 2971 of file fprime.hpp.
Definition at line 27 of file fstream.hpp.
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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/
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Definition at line 13 of file interop.hpp.
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Definition at line 45 of file interop.hpp.
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 28 of file levmar.hpp.
Definition at line 82 of file levmar.hpp.
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Definition at line 211 of file metadata.hpp.
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Definition at line 215 of file metadata.hpp.
GEMMI_DLL Structure gemmi::make_structure_from_block | ( | const cif::Block & | block | ) |
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Definition at line 20 of file mmread.hpp.
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Definition at line 31 of file mmread.hpp.
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Definition at line 49 of file mmread.hpp.
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Definition at line 60 of file mmread.hpp.
Structure gemmi::read_structure | ( | T && | input, |
CoorFormat | format = CoorFormat::Unknown , |
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cif::Document * | save_doc = nullptr |
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Definition at line 77 of file mmread.hpp.
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Definition at line 104 of file mmread.hpp.
GEMMI_DLL Structure gemmi::read_structure_gz | ( | const std::string & | path, |
CoorFormat | format = CoorFormat::Unknown , |
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cif::Document * | save_doc = nullptr |
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) |
GEMMI_DLL Structure gemmi::read_pdb_gz | ( | const std::string & | path, |
PdbReadOptions | options = PdbReadOptions() |
||
) |
GEMMI_DLL CoorFormat gemmi::coor_format_from_ext_gz | ( | const std::string & | path | ) |
Remove alternative conformations.
Definition at line 17 of file modify.hpp.
Definition at line 21 of file modify.hpp.
Remove hydrogens.
Definition at line 43 of file modify.hpp.
Definition at line 47 of file modify.hpp.
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.
Definition at line 60 of file modify.hpp.
Remove anisotropic ADP.
Definition at line 65 of file modify.hpp.
Definition at line 69 of file modify.hpp.
Set absent ANISOU to value from B_iso.
Definition at line 74 of file modify.hpp.
Definition at line 78 of file modify.hpp.
apply Transform to both atom's position and ADP
Definition at line 86 of file modify.hpp.
Definition at line 90 of file modify.hpp.
set atom site serial numbers to 1, 2, ..., optionally leaving gaps for TERs
Definition at line 97 of file modify.hpp.
Definition at line 108 of file modify.hpp.
Definition at line 115 of file modify.hpp.
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Definition at line 138 of file modify.hpp.
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Definition at line 155 of file modify.hpp.
Definition at line 176 of file modify.hpp.
Definition at line 207 of file modify.hpp.
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 243 of file modify.hpp.
Convert coordinates to the standard coordinate system for the unit cell.
Definition at line 259 of file modify.hpp.
Definition at line 23 of file monlib.hpp.
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Definition at line 29 of file monlib.hpp.
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Definition at line 315 of file monlib.hpp.
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GEMMI_DLL void gemmi::write_staraniso_b_in_mmcif | ( | const SMat33< double > & | b, |
const std::string & | entry_id, | ||
char * | buf, | ||
std::ostream & | os | ||
) |
remove '_dataset_name' that can be appended to column names in ccp4i
GEMMI_DLL bool gemmi::validate_merged_mtz_deposition_columns | ( | const Mtz & | mtz, |
std::ostream & | out | ||
) |
GEMMI_DLL bool gemmi::validate_merged_intensities | ( | Intensities & | mi, |
Intensities & | ui, | ||
bool | relaxed_check, | ||
std::ostream & | out | ||
) |
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Definition at line 16 of file pdb_id.hpp.
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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.
Definition at line 26 of file pdb_id.hpp.
Definition at line 55 of file pdb_id.hpp.
Definition at line 21 of file pirfasta.hpp.
Definition at line 28 of file pirfasta.hpp.
GEMMI_DLL PolymerType gemmi::check_polymer_type | ( | const ConstResidueSpan & | span, |
bool | ignore_entity_type = false |
||
) |
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Definition at line 22 of file polyheur.hpp.
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Definition at line 31 of file polyheur.hpp.
distance-based check for peptide bond
Definition at line 40 of file polyheur.hpp.
Definition at line 43 of file polyheur.hpp.
distance-based check for phosphodiester bond between nucleotide
Definition at line 48 of file polyheur.hpp.
Definition at line 51 of file polyheur.hpp.
check C-N or O3'-P distance
Definition at line 56 of file polyheur.hpp.
are_connected2() is less exact, but requires only CA (or P) atoms.
Definition at line 65 of file polyheur.hpp.
are_connected3() = are_connected() + fallback to are_connected2()
Definition at line 87 of file polyheur.hpp.
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Definition at line 106 of file polyheur.hpp.
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.
Assigns entity_type=Unknown for all residues.
Assigns Residue::entity_id based on Residue::subchain and Entity::subchains.
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:
Here we use naming and rules different from both wwPDB and makecif. Note: call add_entity_types() first.
Definition at line 153 of file polyheur.hpp.
Definition at line 161 of file polyheur.hpp.
Definition at line 165 of file polyheur.hpp.
Definition at line 171 of file polyheur.hpp.
Definition at line 175 of file polyheur.hpp.
Definition at line 184 of file polyheur.hpp.
Definition at line 200 of file polyheur.hpp.
GEMMI_DLL void gemmi::change_ccd_code | ( | Structure & | st, |
const std::string & | old, | ||
const std::string & | new_ | ||
) |
Definition at line 212 of file polyheur.hpp.
GEMMI_DLL cif::Document gemmi::read_cif_gz | ( | const std::string & | path | ) |
GEMMI_DLL cif::Document gemmi::read_mmjson_gz | ( | const std::string & | path | ) |
GEMMI_DLL cif::Document gemmi::read_first_block_gz | ( | const std::string & | path, |
size_t | limit | ||
) |
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Definition at line 21 of file read_cif.hpp.
Definition at line 13 of file recgrid.hpp.
Definition at line 14 of file recgrid.hpp.
Definition at line 15 of file recgrid.hpp.
Definition at line 18 of file recgrid.hpp.
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.
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Definition at line 38 of file reciproc.hpp.
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Definition at line 47 of file reciproc.hpp.
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Definition at line 527 of file remarks.hpp.
Definition at line 533 of file remarks.hpp.
Definition at line 560 of file remarks.hpp.
GEMMI_DLL ResidueInfo gemmi::find_tabulated_residue | ( | const std::string & | name | ) |
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kind can be AA, RNA or DNA
Definition at line 64 of file resinfo.hpp.
GEMMI_DLL std::vector< std::string > gemmi::expand_one_letter_sequence | ( | const std::string & | seq, |
ResidueKind | kind | ||
) |
kind can be AA, RNA or DNA
Definition at line 94 of file resinfo.hpp.
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Definition at line 98 of file resinfo.hpp.
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Definition at line 15 of file riding_h.hpp.
Definition at line 15 of file scaling.hpp.
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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 24 of file scaling.hpp.
Definition at line 543 of file select.hpp.
Definition at line 550 of file select.hpp.
Definition at line 554 of file select.hpp.
Definition at line 561 of file select.hpp.
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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 194 of file seqalign.hpp.
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Definition at line 295 of file seqalign.hpp.
Definition at line 13 of file seqtools.hpp.
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Definition at line 15 of file seqtools.hpp.
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Definition at line 25 of file seqtools.hpp.
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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.
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used with expand_one_letter_sequence()
Definition at line 50 of file seqtools.hpp.
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Definition at line 21 of file sfcalc.hpp.
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Definition at line 17 of file solmask.hpp.
Definition at line 57 of file solmask.hpp.
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.
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.
Definition at line 147 of file solmask.hpp.
void gemmi::interpolate_grid | ( | Grid< T > & | dest, |
const Grid< T > & | src, | ||
const Transform & | tr, | ||
int | order = 2 |
||
) |
Definition at line 336 of file solmask.hpp.
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Populate NodeInfo grid for nodes near the model.
Definition at line 356 of file solmask.hpp.
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 389 of file solmask.hpp.
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 = 2 |
||
) |
Definition at line 409 of file solmask.hpp.
Definition at line 432 of file solmask.hpp.
stb_snprintf in gemmi namespace - like snprintf, but ignores locale and is always zero-terminated (hence _z).
stb_sprintf in gemmi namespace
Definition at line 36 of file sprintf.hpp.
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Definition at line 42 of file sprintf.hpp.
Definition at line 49 of file sprintf.hpp.
zero-terminated to_chars()
Definition at line 58 of file sprintf.hpp.
Definition at line 68 of file sprintf.hpp.
Definition at line 188 of file symmetry.hpp.
Definition at line 191 of file symmetry.hpp.
Definition at line 193 of file symmetry.hpp.
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Definition at line 194 of file symmetry.hpp.
Definition at line 219 of file symmetry.hpp.
Definition at line 242 of file symmetry.hpp.
Definition at line 252 of file symmetry.hpp.
Definition at line 302 of file symmetry.hpp.
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Definition at line 366 of file symmetry.hpp.
Definition at line 415 of file symmetry.hpp.
Definition at line 728 of file symmetry.hpp.
Definition at line 749 of file symmetry.hpp.
Definition at line 763 of file symmetry.hpp.
Definition at line 779 of file symmetry.hpp.
Definition at line 841 of file symmetry.hpp.
Definition at line 856 of file symmetry.hpp.
Definition at line 900 of file symmetry.hpp.
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Definition at line 912 of file symmetry.hpp.
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Definition at line 925 of file symmetry.hpp.
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Definition at line 940 of file symmetry.hpp.
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Definition at line 958 of file symmetry.hpp.
Definition at line 967 of file symmetry.hpp.
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Definition at line 971 of file symmetry.hpp.
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Definition at line 984 of file symmetry.hpp.
Definition at line 988 of file symmetry.hpp.
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Definition at line 1019 of file symmetry.hpp.
Definition at line 1025 of file symmetry.hpp.
Definition at line 1030 of file symmetry.hpp.
Definition at line 1035 of file symmetry.hpp.
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 1043 of file symmetry.hpp.
Definition at line 1058 of file symmetry.hpp.
Definition at line 1115 of file symmetry.hpp.
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Definition at line 1878 of file symmetry.hpp.
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Definition at line 1887 of file symmetry.hpp.
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Definition at line 1895 of file symmetry.hpp.
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Definition at line 1905 of file symmetry.hpp.
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Definition at line 1987 of file symmetry.hpp.
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Definition at line 1994 of file symmetry.hpp.
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Definition at line 1998 of file symmetry.hpp.
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Definition at line 14 of file to_chemcomp.hpp.
Definition at line 293 of file to_json.hpp.
GEMMI_DLL void gemmi::update_mmcif_block | ( | const Structure & | st, |
cif::Block & | block, | ||
MmcifOutputGroups | groups = MmcifOutputGroups(true) |
||
) |
GEMMI_DLL cif::Document gemmi::make_mmcif_document | ( | const Structure & | st, |
MmcifOutputGroups | groups = MmcifOutputGroups(true) |
||
) |
GEMMI_DLL cif::Block gemmi::make_mmcif_block | ( | const Structure & | st, |
MmcifOutputGroups | groups = MmcifOutputGroups(true) |
||
) |
GEMMI_DLL cif::Block gemmi::make_mmcif_headers | ( | const Structure & | st | ) |
GEMMI_DLL void gemmi::add_minimal_mmcif_data | ( | const Structure & | st, |
cif::Block & | block | ||
) |
GEMMI_DLL void gemmi::write_struct_conn | ( | const Structure & | st, |
cif::Block & | block | ||
) |
GEMMI_DLL void gemmi::write_cispeps | ( | const Structure & | st, |
cif::Block & | block | ||
) |
GEMMI_DLL void gemmi::write_pdb | ( | const Structure & | st, |
std::ostream & | os, | ||
PdbWriteOptions | opt = PdbWriteOptions() |
||
) |
GEMMI_DLL std::string gemmi::make_pdb_string | ( | const Structure & | st, |
PdbWriteOptions | opt = PdbWriteOptions() |
||
) |
Definition at line 54 of file to_pdb.hpp.
Definition at line 58 of file to_pdb.hpp.
GEMMI_DLL std::unique_ptr< Topo > gemmi::prepare_topology | ( | Structure & | st, |
MonLib & | monlib, | ||
size_t | model_index, | ||
HydrogenChange | h_change, | ||
bool | reorder, | ||
std::ostream * | warnings = nullptr , |
||
bool | ignore_unknown_links = false , |
||
bool | use_cispeps = false |
||
) |
GEMMI_DLL std::vector< AtomAddress > gemmi::find_missing_atoms | ( | const Topo & | topo, |
bool | including_hydrogen = false |
||
) |
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Definition at line 17 of file unitcell.hpp.
Definition at line 23 of file unitcell.hpp.
Definition at line 26 of file unitcell.hpp.
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Definition at line 47 of file unitcell.hpp.
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Definition at line 20 of file xds_ascii.hpp.
bool gemmi::starts_with_ptr | ( | const char * | a, |
const char(&) | b[N], | ||
const char ** | endptr | ||
) |
Definition at line 197 of file xds_ascii.hpp.
bool gemmi::starts_with_ptr_b | ( | const char * | a, |
const char(&) | b[N], | ||
const char ** | endptr | ||
) |
Definition at line 205 of file xds_ascii.hpp.
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Definition at line 209 of file xds_ascii.hpp.
void gemmi::parse_numbers_into_array | ( | const char * | start, |
const char * | end, | ||
double(&) | arr[N], | ||
const char * | line | ||
) |
Definition at line 218 of file xds_ascii.hpp.
Definition at line 386 of file xds_ascii.hpp.