gemmi module

Python bindings to GEMMI - a library used in macromolecular crystallography and related fields

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[str, gemmi.ChemComp]
class ItemsView[str, gemmi.ChemLink]
class ItemsView[str, gemmi.ChemMod]
class ItemsView[str, str]
class KeysView[str]
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[gemmi.ChemComp]
class ValuesView[gemmi.ChemLink]
class ValuesView[gemmi.ChemMod]
class ValuesView[str]
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_chemcomp_to_block(arg0: ChemComp, arg1: cif.Block, /) -> None
def adp_symmetry_constraints(…)
def align_sequence_to_polymer(full_seq: typing.List[str], polymer: ResidueSpan, polymer_type: PolymerType, scoring: AlignmentScoring = None) -> AlignmentResult
def align_string_sequences(query: typing.List[str], target: typing.List[str], target_gapo: typing.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]) -> typing.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: typing.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) -> typing.List[SupResult]
def check_data_type_under_symmetry(arg0: ReflnBlock, /) -> typing.Tuple[DataType, int]
def check_data_type_under_symmetry(arg0: Mtz, /) -> typing.Tuple[DataType, int]
def combine_correlations(arg0: typing.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) -> typing.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, /) -> typing.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) -> typing.List[Blob]
def find_lattice_2fold_ops(reduced_cell: UnitCell, max_obliq: float) -> typing.List[typing.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) -> 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) -> typing.List[Op]
def flood_fill_above(grid: FloatGrid, seeds: typing.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: typing.List[str], /) -> str
def parse_triplet(triplet: str) -> Op
Parse coordinate triplet into gemmi.Op.
def parse_triplet_part(…)
Parse one of the three parts of a triplet.
def pdbx_one_letter_code(arg0: typing.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: typing.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, /) -> typing.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
def spacegroup_table_itb() -> typing.Iterator
def superpose_positions(pos1: typing.List[Position], pos2: typing.List[Position], weight: typing.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