Readers¶
sinccity.load ¶
load(path, *, include_hetatm: bool = False, residues=None, masses=None, elements=None, unwrap='auto') -> Structure
Read a structure file, choosing the reader by extension.
Options a format does not have are ignored with a note.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
path
|
A |
required | |
include_hetatm
|
bool
|
PDB only; also read |
False
|
residues
|
PDB and GRO; the residue names to read, and only those. |
None
|
|
masses
|
PDB and GRO; by residue name, the atom masses in u in topology order. Each mass gives the element of nearest mass. |
None
|
|
elements
|
PDB and GRO; by residue name, the element symbols in order. |
None
|
|
unwrap
|
PDB and GRO; make the aggregate whole across the periodic
box. |
'auto'
|
sinccity.read_pdb ¶
read_pdb(path, *, include_hetatm: bool = False, residues=None, masses=None, elements=None, unwrap='auto') -> Structure
Read the atoms of a PDB file.
Policies: the first MODEL only; one alternate-location ID for the whole
structure (blank plus the first non-blank ID seen); occupancy not applied;
waters never read. Residue names are read from columns 18-21, where MD
programs write four-letter names; a residue number that is not a decimal
integer (hybrid-36 past 9999) starts a new residue whenever it changes. The
CRYST1 box is stored unless it is unreadable or a placeholder (a side of
1 Å or less). Each policy that drops or ignores something adds a note.
Elements per residue name come from masses, elements, the element
column 77-78 when it is filled for the whole residue, or SasView's guess
from the atom name, in that order.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
path
|
The PDB file. |
required | |
include_hetatm
|
bool
|
Also read |
False
|
residues
|
The residue names to read. When given, it is the whole
selection: the water and |
None
|
|
masses
|
As |
None
|
|
elements
|
As |
None
|
|
unwrap
|
As |
'auto'
|
sinccity.read_gro ¶
read_gro(path, *, residues=None, masses=None, elements=None, unwrap='auto') -> Structure
Read the atoms of a GROMACS .gro file.
Fields are cut at their fixed columns, since names may touch numbers. As
GROMACS defines it, the width of a position field is the distance between
the decimal points of the first atom's x and y, which covers files written
with -ndec. Positions are converted from nm to Å; velocities are
ignored. The box on the last line is used for unwrapping. Elements per
residue name come from masses, elements, or a guess from the atom
names (see sinccity.elements.guess_stem), in that order.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
path
|
The |
required | |
residues
|
The residue names to read. A solvated system needs it: there is no water rule, and the reader notes when it reads more than one residue name without a selection. |
None
|
|
masses
|
As |
None
|
|
elements
|
As |
None
|
|
unwrap
|
As |
'auto'
|
sinccity.read_sld ¶
read_sld(path) -> Structure
Read a SasView SLD text file.
The first line is a header and is always skipped. Columns: x y z sld
(4), x y z sld mx my mz (7) or x y z sld mx my mz volume (8);
six columns are magnetic-only and refused. Without a volume column the
points must form a lattice, and each pixel's volume is the product of the
steps. A sparse subset that skips planes looks like a coarser lattice, so
such files need the volume column.
sinccity.read_vtk ¶
read_vtk(path) -> Structure
Read a legacy ASCII VTK UNSTRUCTURED_GRID as one point per cell.
Supports cell types 10 (tetrahedron), 11 (voxel), 12 (hexahedron), 13
(wedge) and 14 (pyramid), in the classic and the 5.1 OFFSETS layout.
The nuclear SLD is the single one-component SCALARS field, given per
cell or per point (point values are averaged to cells with SasView's
inverse-square weights about the cell's vertex mean). Three-component
fields are magnetic and ignored. Each cell becomes a point at its volume
centroid with the cell's volume and SLD. Units are taken as Å and Å⁻².