gemmi module

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

Contents

Modules

module cif
CIF file format

Classes

class AlignmentResult
class AlignmentScoring
class Assembly
class AssemblyList
class Atom
class AtomAddress
class AtomGroup
class BondIndex
class CRA
class Ccp4Map
class Ccp4Mask
class Chain
class ChemComp
class ChemCompAtoms
class ChemCompMap
class ChemLink
class ChemLinkMap
class ChemMod
class ChemModMap
class CifWalk
class ComplexGrid
class ComplexGridBase
class Connection
class ConnectionList
class ContactSearch
class CoorFileWalk
class CraGenerator
class Element
class Entity
class EntityList
class FTransform
class FirstConformerAtoms
class FirstConformerRes
class FirstConformerResSpan
class FloatGrid
class FloatGridBase
class Fractional
class GroupOps
class IT92Coef
class InfoMap
class Int8Grid
class Int8GridBase
class LinkHunt
class MaskedComplexGrid
class MaskedFloatGrid
class MaskedInt8Grid
class Mat33
class Model
class MonLib
class Mtz
class MtzBatches
class MtzColumnRefs
class MtzColumns
class MtzDatasets
class NcsOp
class NcsOpList
class NeighborSearch
class Op
class Position
class ReciprocalAsu
class ReciprocalComplexGrid
class ReciprocalFloatGrid
class ReciprocalInt8Grid
class ReflnBlock
class ReflnBlocks
class Residue
class ResidueGroup
class ResidueId
class ResidueInfo
class ResidueSpan
class ResidueSpanGroups
class Restraints
class RestraintsBonds
class SMat33d
class SMat33f
class Selection
class SelectionAtomsProxy
class SelectionChainsProxy
class SelectionModelsProxy
class SelectionResidusProxy
class SeqId
class SmallStructure
class SpaceGroup
class Structure
class SymImage
class Topo
class TopoBonds
class TopoExtraLinks
class TranList
class Transform
class UnitCell
class Vec3
class VectorMarkPtr

Enums

class Asu: Same = 0 Different = 1 Any = 2
Members:
class AxisOrder: XYZ = 1 ZYX = 2
Members:
class BondType: Unspec = 0 Single = 1 Double = 2 Triple = 3 Aromatic = 4 Deloc = 5 Metal = 6
Members:
class ConnectionType: Covale = 0 Disulf = 1 Hydrog = 2 MetalC = 3 Unknown = 4
Members:
class CoorFormat: Unknown = 0 UnknownAny = 1 Pdb = 2 Mmcif = 3 Mmjson = 4 ChemComp = 5
Members:
class EntityType: Unknown = 0 Polymer = 1 NonPolymer = 2 Water = 3
Members:
class HowToNameCopiedChains: Short = 0 AddNumber = 1 Dup = 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:

Functions

def align_sequence_to_polymer(full_seq: typing.List[str], polymer: ResidueSpan, polymer_type: PolymerType, scoring: AlignmentScoring = gemmi.AlignmentScoring()) -> AlignmentResult
def align_string_sequences(query: typing.List[str], target: typing.List[str], free_gapo: typing.List[bool], scoring: AlignmentScoring = gemmi.AlignmentScoring()) -> AlignmentResult
def as_refln_blocks(arg0: cif.Document, /) -> ReflnBlocks
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_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(prev_residue: Residue, residue: Residue, next_residue: Residue) -> typing.List[float[2]]
def calculate_sequence_weight(sequence: typing.List[str], unknown: float = 0.0) -> float
def count_reflections(cell: UnitCell, spacegroup: SpaceGroup, dmin: float, dmax: float = 0.0, unique: bool = True) -> int
def cromer_libermann(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_pdb_code_to_path(arg0: str, arg1: str, /) -> str
def expand_protein_one_letter(arg0: str, /) -> str
def expand_protein_one_letter_string(arg0: str, /) -> typing.List[str]
def find_spacegroup_by_change_of_basis(arg0: SpaceGroup, arg1: Op, /) -> SpaceGroup
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 generators_from_hall(hall: str) -> GroupOps
Parse Hall notation.
def get_spacegroup_reference_setting(number: int) -> SpaceGroup
def hkl_cif_as_refln_block(block: cif.Block) -> ReflnBlock
def is_pdb_code(arg0: str, /) -> bool
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[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(x: int, y: int, z: int, w: int, style: str = 'x') -> str
Make one of the three parts of a triplet.
def one_letter_code(arg0: typing.List[str], /) -> str
def one_letter_code(arg0: ResidueSpan, /) -> str
def parse_cid(arg0: str, /) -> Selection
def parse_triplet(triplet: str) -> Op
Parse coordinate triplet into gemmi.Op.
def parse_triplet_part(s: str) -> typing.List[int[4]]
Parse one of the three parts of a triplet.
def prepare_blosum62_scoring() -> AlignmentScoring
def read_ccp4_map(path: str) -> Ccp4Map
Reads a CCP4 file, mode 2 (floating-point data).
def read_ccp4_mask(path: str) -> Ccp4Mask
Reads a CCP4 file, mode 0 (int8_t data, usually 0/1 masks).
def read_monomer_cif(arg0: str, /) -> MonLib
def read_monomer_lib(arg0: str, arg1: typing.List[str], /) -> 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_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) -> Structure
Reads a coordinate file into Structure.
def spacegroup_table() -> iterator
def spacegroup_table_itb() -> iterator
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) -> ReciprocalComplexGrid

Data

hc = 12398.4197386209