gemmi module
Python bindings to GEMMI - a library used in macromolecular crystallography and related fields
Outdated!!!
Python API docs has not been updated since gemmi 0.6.7.
Modules
- module cif
- CIF file format
Classes
- class Addends
- class AlignmentResult
- class AlignmentScoring
- class Assembly
- class AssemblyList
- class AsuBrick
- class Atom
- class AtomAddress
- class AtomGroup
- class BasicRefinementInfo
- class BatchFloats
- class BatchInts
- class Binner
- class Blob
- class BondIndex
- class C4322Coef
- class CRA
- class Ccp4Base
- class Ccp4Map
- class Ccp4Mask
- class Chain
- class ChemComp
- class ChemCompAtoms
- class ChemCompMap
- class ChemLink
- class ChemLinkMap
- class ChemMod
- class ChemModMap
- class CifToMtz
- class CifWalk
- class CisPep
- class ComplexAsuData
- class ComplexCorrelation
- class ComplexGridBase
- class ComplexHklValue
- class Connection
- class ConnectionList
- class ContactSearch
- class CoorFileWalk
- class Correlation
- class CraGenerator
- class CrystalInfo
- class DensityCalculatorE
- class DensityCalculatorN
- class DensityCalculatorX
- class DiffractionInfo
- class Element
- class EnerLib
- class Entity
- class EntityList
- class ExperimentInfo
- class FTransform
- class FastaSeq
- class FirstConformerAtoms
- class FirstConformerRes
- class FirstConformerResSpan
- class FloatAsuData
- class FloatGrid
- class FloatGridBase
- class FloatHklValue
- class Fractional
- class FractionalBox
- class GridMeta
- class GroupOps
- class GruberVector
- class Helix
- class HelixList
- class HklMatch
- class IT92Coef
- class InfoMap
- class Int8Grid
- class Int8GridBase
- class IntAsuData
- class IntHklValue
- class Intensities
- class ItemsView
- class KeysView
- class LinkHunt
- class MaskedFloatGrid
- class MaskedInt8Grid
- class Mat33
- class Metadata
- class MmcifOutputGroups
- class ModRes
- class Model
- class MonLib
- class Mtz
- class MtzBatches
- class MtzColumns
- class MtzDatasets
- class MtzToCif
- class NcsOp
- class NcsOpList
- class NearestImage
- class NeighborSearch
- class Neutron92
- class Op
- class PdbWriteOptions
- class Position
- class PositionBox
- class ReciprocalAsu
- class ReciprocalComplexGrid
- class ReciprocalFloatGrid
- class ReciprocalInt8Grid
- class RefinementInfo
- class ReflectionsInfo
- class ReflnBlock
- class ReflnBlocks
- class Residue
- class ResidueGroup
- class ResidueId
- class ResidueInfo
- class ResidueSpan
- class ResidueSpanGroups
- class Restraints
- class RestraintsAngles
- class RestraintsBonds
- class RestraintsChirs
- class RestraintsPlanes
- class RestraintsTorsions
- class SMat33d
- class SMat33f
- class Scaling
- class Selection
- class SelectionAtomsProxy
- class SelectionChainsProxy
- class SelectionModelsProxy
- class SelectionResiduesProxy
- class SellingVector
- class SeqId
- class Sheet
- class SheetList
- class SmallStructure
- class SoftwareItem
- class SolventMasker
- class SpaceGroup
- class Structure
- class StructureFactorCalculatorE
- class StructureFactorCalculatorN
- class StructureFactorCalculatorX
- class SupResult
- class TlsGroup
- class Topo
- class TopoAngles
- class TopoBonds
- class TopoChainInfos
- class TopoChirs
- class TopoFinalChemComps
- class TopoLinks
- class TopoMods
- class TopoPlanes
- class TopoResInfos
- class TopoRules
- class TopoTorsions
- class Transform
- class UnitCell
- class ValueSigma
- class ValueSigmaAsuData
- class ValueSigmaHklValue
- class ValuesView
- class Vec3
- class VectorMarkPtr
Enums
- class AssemblySpecialKind: NA = 0 CompleteIcosahedral = 1 RepresentativeHelical = 2 CompletePoint = 3
- Members:
- class Asu: Same = 0 Different = 1 Any = 2
- Members:
- class AtomicRadiiSet: VanDerWaals = 0 Cctbx = 1 Refmac = 2 Constant = 3
- Members:
- class AxisOrder: Unknown = 0 XYZ = 1 ZYX = 2
- Members:
- class BondType: Unspec = 0 Single = 1 Double = 2 Triple = 3 Aromatic = 4 Deloc = 5 Metal = 6
- Members:
- class CalcFlag: NotSet = 0 NoHydrogen = 1 Determined = 2 Calculated = 3 Dummy = 4
- Members:
- class ChiralityType: Positive = 0 Negative = 1 Both = 2
- Members:
- class ConnectionType: Covale = 0 Disulf = 1 Hydrog = 2 MetalC = 3 Unknown = 4
- Members:
- class CoorFormat: Unknown = 0 Detect = 1 Pdb = 2 Mmcif = 3 Mmjson = 4 ChemComp = 5
- Members:
- class CrystalSystem: Triclinic = 0 Monoclinic = 1 Orthorhombic = 2 Tetragonal = 3 Trigonal = 4 Hexagonal = 5 Cubic = 6
- Members:
- class DataType: Unknown = 0 Unmerged = 1 Mean = 2 Anomalous = 3
- Members:
- class EntityType: Unknown = 0 Polymer = 1 NonPolymer = 2 Branched = 3 Water = 4
- Members:
- class GridSizeRounding: Nearest = 0 Up = 1 Down = 2
- Members:
- class HowToNameCopiedChain: Short = 0 AddNumber = 1 Dup = 2
- Members:
- class HydrogenChange: NoChange = 0 Shift = 1 Remove = 2 ReAdd = 3 ReAddButWater = 4 ReAddKnown = 5
- Members:
- class MapSetup: Full = 0 NoSymmetry = 1 ReorderOnly = 2
- Members:
- class PolymerType: PeptideL = 1 PeptideD = 2 Dna = 3 Rna = 4 DnaRnaHybrid = 5 SaccharideD = 6 SaccharideL = 7 Pna = 8 CyclicPseudoPeptide = 9 Other = 10 Unknown = 0
- Members:
- class RKind: Bond = 0 Angle = 1 Torsion = 2 Chirality = 3 Plane = 4
- Members:
- class ResidueKind: UNKNOWN = 0 AA = 1 AAD = 2 PAA = 3 MAA = 4 RNA = 5 DNA = 6 BUF = 7 HOH = 8 PYR = 9 KET = 10 ELS = 11
- Members:
- class SupSelect: CaP = 0 MainChain = 1 All = 2
- Members:
Functions
- def IT92_get_exact(arg0: Element, arg1: int, /) -> IT92Coef
- def IT92_get_ignore_charge() -> bool
- def IT92_normalize() -> None
- def IT92_set_ignore_charge(arg0: bool, /) -> None
- def add_automatic_links(arg0: Model, arg1: Structure, arg2: MonLib, /) -> None
- def add_chemcomp_to_block(arg0: ChemComp, arg1: cif.Block, /) -> None
- def add_dictionary_blocks(arg0: cif.Document, arg1: list[str], arg2: Topo, arg3: MonLib, /) -> None
- def adp_symmetry_constraints(…)
- def align_sequence_to_polymer(full_seq: list[str], polymer: ResidueSpan, polymer_type: PolymerType, scoring: AlignmentScoring = None) -> AlignmentResult
- def align_string_sequences(query: list[str], target: list[str], target_gapo: list[int], scoring: AlignmentScoring = None) -> AlignmentResult
- def as_refln_blocks(arg0: cif.Document, /) -> ReflnBlocks
- def bessel_i1_over_i0(arg0: numpy.ndarray[numpy.float64], /) -> object
- def bincorr(nbins: numpy.ndarray[numpy.int32], obs: numpy.ndarray[numpy.float64], calc: numpy.ndarray[numpy.float64]) -> list[Correlation]
- def binmean(nbins: numpy.ndarray[numpy.int32], values: numpy.ndarray[numpy.float64]) -> numpy.ndarray[numpy.float64]
- def binrfactor(nbins: numpy.ndarray[numpy.int32], obs: numpy.ndarray[numpy.float64], calc: numpy.ndarray[numpy.float64], riso: bool = False) -> numpy.ndarray[numpy.float64]
- def calculate_amplitude_normalizers(arg0: Mtz, arg1: str, arg2: Binner, /) -> numpy.ndarray[numpy.float64]
- def calculate_angle(arg0: Position, arg1: Position, arg2: Position, /) -> float
- Input: three points. Output: angle in radians.
- def calculate_b_est(arg0: Atom, /) -> float
- def calculate_current_rmsd(fixed: ResidueSpan, movable: ResidueSpan, ptype: PolymerType, sel: SupSelect, altloc: str = '\x00') -> SupResult
- def calculate_dihedral(arg0: Position, arg1: Position, arg2: Position, arg3: Position, /) -> float
- Input: four points. Output: dihedral angle in radians.
- def calculate_omega(residue: Residue, next_residue: Residue) -> float
- def calculate_phi_psi(…)
- def calculate_sequence_weight(sequence: list[str], unknown: float = 0.0) -> float
- def calculate_superposition(fixed: ResidueSpan, movable: ResidueSpan, ptype: PolymerType, sel: SupSelect, trim_cycles: int = 0, trim_cutoff: float = 2.0, altloc: str = '\x00') -> SupResult
- def calculate_superpositions_in_moving_window(fixed: ResidueSpan, movable: ResidueSpan, ptype: PolymerType, radius: float = 10.0) -> list[SupResult]
- def check_data_type_under_symmetry(arg0: ReflnBlock, /) -> tuple[DataType, int]
- def check_data_type_under_symmetry(arg0: Mtz, /) -> tuple[DataType, int]
- def combine_correlations(arg0: list[Correlation], /) -> Correlation
- def count_reflections(cell: UnitCell, spacegroup: SpaceGroup, dmin: float, dmax: float = 0.0, unique: bool = True) -> int
- def cromer_liberman(z: int, energy: float) -> tuple[float, float]
- def estimate_uncompressed_size(path: str) -> int
- Returns uncompressed size of a .gz file (not always reliable)
- def expand_if_pdb_code(code: str, filetype: str = 'M') -> str
- def expand_ncs_model(arg0: Model, arg1: NcsOpList, arg2: HowToNameCopiedChain, /) -> Model
- def expand_one_letter(arg0: str, arg1: ResidueKind, /) -> str
- def expand_one_letter_sequence(arg0: str, arg1: ResidueKind, /) -> list[str]
- def expand_pdb_code_to_path(code: str, filetype: str, throw_if_unset: bool = False) -> str
- def find_asu_brick(arg0: SpaceGroup, /) -> AsuBrick
- def find_best_plane(…)
- def find_blobs_by_flood_fill(grid: FloatGrid, cutoff: float, min_volume: float = 10.0, min_score: float = 15.0, min_peak: float = 0.0, negate: bool = False) -> list[Blob]
- def find_lattice_2fold_ops(reduced_cell: UnitCell, max_obliq: float) -> list[tuple[Op, float]]
- def find_lattice_symmetry(cell: UnitCell, centring: str, max_obliq: float) -> GroupOps
- def find_lattice_symmetry_r(arg0: UnitCell, arg1: float, /) -> GroupOps
- def find_spacegroup_by_name(hm: str, alpha: float = 0.0, gamma: float = 0.0, prefer: str = None) -> SpaceGroup
- Returns space-group with given name.
- def find_spacegroup_by_number(ccp4: int) -> SpaceGroup
- Returns space-group of given number.
- def find_spacegroup_by_ops(group_ops: GroupOps) -> SpaceGroup
- Returns space-group with identical operations.
- def find_tabulated_residue(name: str) -> ResidueInfo
- Find chemical component information in the internal table.
- def find_twin_laws(cell: UnitCell, sg: SpaceGroup, max_obliq: float, all_ops: bool) -> list[Op]
- def flood_fill_above(grid: FloatGrid, seeds: list[Position], threshold: float, negate: bool = False) -> Int8Grid
- def generators_from_hall(hall: str) -> GroupOps
- Parse Hall notation.
- def get_distance_from_plane(…)
- def get_spacegroup_reference_setting(number: int) -> SpaceGroup
- def hkl_cif_as_refln_block(block: cif.Block) -> ReflnBlock
- def interpolate_grid(dest: FloatGrid, src: FloatGrid, tr: Transform, order: int = 2) -> None
- def interpolate_grid_of_aligned_model2(dest: FloatGrid, src: FloatGrid, tr: Transform, dest_model: Model, radius: float, order: int = 2) -> None
- def is_pdb_code(arg0: str, /) -> bool
- def log_bessel_i0(arg0: numpy.ndarray[numpy.float64], /) -> object
- def log_cosh(arg0: numpy.ndarray[numpy.float64], /) -> object
- def make_address(arg0: Chain, arg1: Residue, arg2: Atom, /) -> AtomAddress
- def make_assembly(arg0: Assembly, arg1: Model, arg2: HowToNameCopiedChain, /) -> Model
- def make_chemcomp_from_block(arg0: cif.Block, /) -> ChemComp
- def make_miller_array(cell: UnitCell, spacegroup: SpaceGroup, dmin: float, dmax: float = 0.0, unique: bool = True) -> numpy.ndarray[numpy.int32]
- def make_small_structure_from_block(block: cif.Block) -> SmallStructure
- Takes CIF block and returns SmallStructure.
- def make_structure_from_block(block: cif.Block) -> Structure
- Takes mmCIF block and returns Structure.
- def make_structure_from_chemcomp_block(block: cif.Block) -> Structure
- CIF block from CCD or monomer library -> single-residue Structure.
- def make_triplet_part(…)
- Make one of the three parts of a triplet.
- def merge_atoms_in_expanded_model(model: Model, cell: UnitCell, max_dist: float = 0.2, compare_serial: bool = True) -> None
- def mott_bethe_const() -> float
- def mx_to_sx_structure(st: Structure, n: int = 0) -> SmallStructure
- def one_letter_code(arg0: list[str], /) -> str
- def parse_triplet(triplet: str) -> Op
- Parse coordinate triplet into gemmi.Op.
- def parse_triplet_as_ftransform(arg0: str, /) -> FTransform
- def parse_triplet_part(…)
- Parse one of the three parts of a triplet.
- def pdbx_one_letter_code(arg0: list[str], arg1: ResidueKind, /) -> str
- def prepare_refmac_crd(arg0: Structure, arg1: Topo, arg2: MonLib, arg3: HydrogenChange, /) -> cif.Document
- def prepare_topology(st: Structure, monlib: MonLib, model_index: int = 0, h_change: HydrogenChange = HydrogenChange.NoChange, reorder: bool = False, warnings: object = None, ignore_unknown_links: bool = False, use_cispeps: bool = False) -> Topo
- def read_ccp4_map(path: str, setup: bool = False) -> Ccp4Map
- Reads a CCP4 file, mode 2 (floating-point data).
- def read_ccp4_mask(path: str, setup: bool = False) -> Ccp4Mask
- Reads a CCP4 file, mode 0 (int8_t data, usually 0/1 masks).
- def read_monomer_lib(monomer_dir: str, resnames: list[str], libin: str = '', ignore_missing: bool = False) -> MonLib
- def read_mtz_file(path: str) -> Mtz
- def read_pdb(filename: str, max_line_length: int = 0, split_chain_on_ter: bool = False) -> Structure
- def read_pdb_string(s: str, max_line_length: int = 0, split_chain_on_ter: bool = False) -> Structure
- Reads a string as PDB file.
- def read_pir_or_fasta(arg0: str, /) -> list[FastaSeq]
- def read_small_structure(path: str) -> SmallStructure
- Reads a small molecule CIF file.
- def read_structure(path: str, merge_chain_parts: bool = True, format: CoorFormat = CoorFormat.Unknown, save_doc: cif.Document = None) -> Structure
- Reads a coordinate file into Structure.
- def seitz_to_op(…)
- def sequence_kind(arg0: PolymerType, /) -> ResidueKind
- def setup_for_crd(arg0: Structure, /) -> None
- def spacegroup_table() -> typing.Iterator[SpaceGroup]
- def spacegroup_table_itb() -> typing.Iterator[SpaceGroup]
- def superpose_positions(pos1: list[Position], pos2: list[Position], weight: list[float] = []) -> SupResult
- def symops_from_hall(hall: str) -> GroupOps
- Parse Hall notation.
- def transform_f_phi_grid_to_map(grid: ReciprocalComplexGrid) -> FloatGrid
- def transform_map_to_f_phi(map: FloatGrid, half_l: bool = False, use_scale: bool = True) -> ReciprocalComplexGrid
Data
- hc = 12398.4197386209