headers.rst

gemmi/addends.hpp

Addends to scattering form factors used in DensityCalculator and StructureFactorCalculator.

gemmi/align.hpp

Sequence alignment, label_seq_id assignment, structure superposition.

gemmi/assembly.hpp

Generating biological assemblies by applying operations from struct Assembly to a Model. Includes chain (re)naming utilities.

gemmi/asudata.hpp

AsuData for storing reflection data.

gemmi/asumask.hpp

AsuBrick and MaskedGrid that is used primarily as direct-space asu mask.

gemmi/atof.hpp

Functions that convert strings to floating-point numbers ignoring locale. Simple wrappers around fastfloat::from_chars().

gemmi/atox.hpp

Locale-independent functions that convert strings to integers, equivalents of standard isspace and isdigit, and a few helper functions.

gemmi/bessel.hpp

Functions derived from modified Bessel functions I1(x) and I0(x).

gemmi/binner.hpp

Binning - resolution shells for reflections.

gemmi/blob.hpp

Finding maxima or "blobs" in a Grid (map). Similar to CCP4 PEAKMAX and COOT's "Unmodelled blobs".

gemmi/bond_idx.hpp

BondIndex: for checking which atoms are bonded, calculating graph distance.

gemmi/c4322.hpp

Electron scattering factor coefficients from the International Tables.

gemmi/calculate.hpp

Calculate various properties of the model.

gemmi/ccp4.hpp

CCP4 format for maps and masks.

gemmi/cellred.hpp

Unit cell reductions: Buerger, Niggli, Selling-Delaunay.

gemmi/chemcomp.hpp

ChemComp - chemical component that represents a monomer from Refmac monomer library, or from PDB CCD.

gemmi/cif.hpp

CIF parser (based on PEGTL) with pluggable actions, and a set of actions that prepare Document. To just read the CIF format, include read_cif.hpp instead.

gemmi/cif2mtz.hpp

A class for converting SF-mmCIF to MTZ (merged or unmerged).

gemmi/cifdoc.hpp

struct Document that represents the CIF file (but can also be read from a different representation, such as CIF-JSON or mmJSON).

gemmi/contact.hpp

Contact search, based on NeighborSearch from neighbor.hpp.

gemmi/crd.hpp

Generate Refmac intermediate (prepared) files crd and rst

gemmi/ddl.hpp

Using DDL1/DDL2 dictionaries to validate CIF/mmCIF files.

gemmi/dencalc.hpp

Tools to prepare a grid with values of electron density of a model.

gemmi/dirwalk.hpp

Classes for iterating over files in a directory tree, top-down, in alphabetical order. Wraps the tinydir library (as we cannot yet depend on C++17 <filesystem>).

gemmi/ecalc.hpp

Normalization of amplitudes F->E ("Karle" approach, similar to CCP4 ECALC).

gemmi/eig3.hpp

Eigen decomposition code for symmetric 3x3 matrices.

gemmi/elem.hpp

Elements from the periodic table.

gemmi/enumstr.hpp

Converts between enums (EntityType, PolymerType, Connection::Type, SoftwareItem::Classification) and mmCIF strings.

gemmi/fail.hpp

fail(), unreachable() and __declspec/__attribute__ macros

gemmi/fileutil.hpp

File-related utilities.

gemmi/floodfill.hpp

The flood fill (scanline fill) algorithm for Grid. Assumes periodic boundary conditions in the grid and 6-way connectivity.

gemmi/formfact.hpp

Calculation of atomic form factors approximated by a sum of Gaussians. Tables with numerical coefficients are in it92.hpp and c4322.hpp.

gemmi/fourier.hpp

Fourier transform applied to map coefficients.

gemmi/fprime.hpp

Cromer-Liberman calculation of anomalous scattering factors, with corrections from Kissel & Pratt.

gemmi/fstream.hpp

Ofstream and Ifstream: wrappers around std::ofstream and std::ifstream.

gemmi/grid.hpp

3d grids used by CCP4 maps, cell-method search and hkl data.

gemmi/gz.hpp

Functions for transparent reading of gzipped files. Uses zlib.

gemmi/input.hpp

Input abstraction. Used to decouple file reading and decompression.

gemmi/intensit.hpp

Class Intensities that reads multi-record data from MTZ, mmCIF or XDS_ASCII and merges it into mean or anomalous intensities. It can also read merged data.

gemmi/interop.hpp

Interoperability between Model (MX) and SmallStructure (SX).

gemmi/it92.hpp

X-ray scattering factor coefficients from International Tables for Crystallography Volume C, edition from 1992 or later.

gemmi/iterator.hpp

Bidirectional iterators (over elements of any container) that can filter, uniquify, group, or iterate with a stride.

gemmi/json.hpp

Reading CIF-JSON (COMCIFS) and mmJSON (PDBj) formats into cif::Document.

gemmi/levmar.hpp

Least-squares fitting - Levenberg-Marquardt method.

gemmi/linkhunt.hpp

Searching for links based on the _chem_link table from monomer dictionary.

gemmi/logger.hpp

Logger - a tiny utility for passing messages through a callback.

gemmi/math.hpp

Math utilities. 3D linear algebra.

gemmi/metadata.hpp

Metadata from coordinate files.

gemmi/mmcif.hpp

Read mmCIF (PDBx/mmCIF) file into a Structure from model.hpp.

gemmi/mmcif_impl.hpp

Functions used in both mmcif.hpp and refln.hpp (for coordinate and reflection mmCIF files).

gemmi/mmdb.hpp

Converts between gemmi::Structure and mmdb::Manager.

gemmi/mmread.hpp

Read any supported coordinate file. Usually, mmread_gz.hpp is preferred.

gemmi/mmread_gz.hpp

Functions for reading possibly gzipped coordinate files.

gemmi/model.hpp

Data structures to store macromolecular structure models.

gemmi/modify.hpp

Modify various properties of the model.

gemmi/monlib.hpp

Monomer library - (Refmac) restraints dictionary, which consists of monomers (chemical components), links, and modifications.

gemmi/mtz.hpp

MTZ reflection file format.

gemmi/mtz2cif.hpp

A class for converting MTZ (merged or unmerged) to SF-mmCIF

gemmi/neighbor.hpp

Cell-linked lists method for atom searching (a.k.a. grid search, binning, bucketing, cell technique for neighbor search, etc).

gemmi/neutron92.hpp

Neutron coherent scattering lengths of the elements, from Neutron News, Vol. 3, No. 3, 1992.

gemmi/numb.hpp

Utilities for parsing CIF numbers (the CIF spec calls them 'numb').

gemmi/pdb.hpp

Read the PDB file format and store it in Structure.

gemmi/pdb_id.hpp

Handling PDB ID and $PDB_DIR: is_pdb_code(), expand_pdb_code_to_path(), ...

gemmi/pirfasta.hpp

Read sequences from PIR or (multi-)FASTA formats.

gemmi/polyheur.hpp

Heuristic methods for working with chains and polymers. Also includes a few well-defined functions, such as removal of waters.

gemmi/qcp.hpp

Structural superposition, the QCP method.

gemmi/read_cif.hpp

Functions for reading possibly gzipped CIF files.

gemmi/recgrid.hpp

ReciprocalGrid -- grid for reciprocal space data.

gemmi/reciproc.hpp

Reciprocal space helper functions.

gemmi/refln.hpp

Reads reflection data from the mmCIF format.

gemmi/resinfo.hpp

List of common residues with basic data.

gemmi/riding_h.hpp

Place hydrogens according to bond lengths and angles from monomer library.

gemmi/scaling.hpp

Anisotropic scaling of data (includes scaling of bulk solvent parameters).

gemmi/select.hpp

Selections.

gemmi/seqalign.hpp

Simple pairwise sequence alignment.

gemmi/seqid.hpp

SeqId -- residue number and insertion code together.

gemmi/seqtools.hpp

Functions for working with sequences (other than alignment).

gemmi/serialize.hpp

Binary serialization for Structure (as well as Model, UnitCell, etc).

gemmi/sfcalc.hpp

Direct calculation of structure factors.

gemmi/small.hpp

Representation of a small molecule or inorganic crystal. Flat list of atom sites. Minimal functionality.

gemmi/smcif.hpp

Read small molecule CIF file into SmallStructure (from small.hpp).

gemmi/solmask.hpp

Flat bulk solvent mask. With helper tools that modify data on grid.

gemmi/span.hpp

Span - span of array or std::vector. MutableVectorSpan - span of std::vector with insert() and erase()

gemmi/sprintf.hpp

interface to stb_sprintf: snprintf_z, to_str(float|double)

gemmi/stats.hpp

Statistics utilities: classes Covariance, Correlation, DataStats

gemmi/symmetry.hpp

Crystallographic Symmetry. Space Groups. Coordinate Triplets.

gemmi/to_chemcomp.hpp

Create cif::Block with monomer library _chem_comp* categories from struct ChemComp.

gemmi/to_cif.hpp

Writing cif::Document or its parts to std::ostream.

gemmi/to_json.hpp

Writing cif::Document or its parts as JSON (mmJSON, CIF-JSON, etc).

gemmi/to_mmcif.hpp

Create cif::Document (for PDBx/mmCIF file) from Structure.

gemmi/to_pdb.hpp

Writing PDB file format (Structure -> pdb file).

gemmi/topo.hpp

Topo(logy) - restraints (from a monomer library) applied to a model.

gemmi/twin.hpp

Twinning laws.

gemmi/unitcell.hpp

Unit cell.

gemmi/utf.hpp

Conversion between UTF-8 and wchar. Used only for file names on Windows.

gemmi/util.hpp

Utilities. Mostly for working with strings and vectors.

gemmi/version.hpp

Version number.

gemmi/xds2mtz.hpp

Convert XDS_ASCII to MTZ.

gemmi/xds_ascii.hpp

Read XDS files: XDS_ASCII.HKL and INTEGRATE.HKL.