1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
|
Supported Structure File Formats
================================================================================
.. currentmodule:: ost.io
The following file formats are supported by :func:`LoadEntity`:
CRD - CARD format file used by CHARMM
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
This trajectory file format is used by the CHARMM program suite (Molecular Modelling).
*Recognized File Extensions*
.crd
PDB - Brookhaven PDB File
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Fine grained control over PDB file import is available via the :func:`LoadPDB`
function. The PDB importer supports loading gzipped PDB files, which are auto-
detected by the .gz file extension.
*Recognized File Extensions*
.ent, .pdb, .ent.gz, .pdb.gz
*Format Name*
pdb
mmCIF - macromolecular Crystallographic Information File
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Fine grained control over mmCIFile import is available via the :func:`LoadMMCIF`
function. Most notably, this gives you access to the :class:`MMCifInfo` class.
The mmCIF importer supports loading gzipped files, which are auto-detected by
the .gz file extension.
*Recognized File Extensions*
.cif, .cif.gz
*Format Name*
cif
PQR
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
A variant of the PDB format that contains data related to atom charges and
radii.
*Recognized File Extensions*
.pqr
*Format Name*
pqr
SDF - Structured Data File
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Chemical table (Ctab) file format, aka SDF, aka MDL Molfile, originally named
after Molecular Design Limited, Inc. Follows the "BIOVIA Databases 2020" format
specification (V2000; read-only V3000 experimental support).
The SDF importer supports loading gzipped files, which are auto-detected by the
.gz file extension.
The SDF format does not support residues, chains or atom names natively.
The reader assigns 1-based atom indices as atom names.
SDF files containing several molecules are loaded into distinct chains,
named after the molecule name in the MOLfile header with a numerical prefix.
Residues are named after the name in the MOLfile header as well.
Chains are written as separate molecules. If a chain contains more than one
residue, they will be merged into a single molecule.
*Recognized File Extensions*
.sdf, .sdf.gz, .mol, .mol.gz
|
