gemmi module
GEneral MacroMolecular I/O
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 ReciprocalAsuChecker
- 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 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_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() -> typing.Iterator[SpaceGroup]
- def spacegroup_table_itb() -> typing.Iterator[SpaceGroup]
- 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