nuget
The lightweight PDB structure file reader.
StructureIO
01 Syntax
SMRUCC.genomics.Data.RCSB.PDB.Structures.StructureIO
02 Methods
| Name | Overloads | Summary |
|---|---|---|
| ReadPdb | 1 | Read the first MODEL frame of the given PDB file. |
| ReadPdb | 1 | Read the first MODEL frame of the given PDB file into a caller supplied container type. |
| ReadPdbFrames | 1 | Read all of the MODEL frames of the given PDB file, each frame is returned as an individual molecule object. |
| ReadPdbFrames | 1 | Read all of the MODEL frames of the given PDB file into a caller supplied container type. |
| PerceiveBonds | 1 | Perceive the covalent connectivity of the given molecule by the distance criterion: two heavy atoms are bonded when r < 1.3 * (r_cov_i + r_cov_j). |
| ReadPdb | 1 | |
| ReadPdbFrames | 1 | |
| PerceiveBonds | 1 |
03 Members
ReadPdb``1(
String)Read the first MODEL frame of the given PDB file.
Type Parameters
| Name | Description |
|---|---|
T | The atom model type, derived from Atom. |
Parameters
| Name | Type | Description |
|---|---|---|
path | String | The file path of the PDB structure file. |
ReadPdb``2(
String)Read the first MODEL frame of the given PDB file into a caller supplied container type.
Type Parameters
| Name | Description |
|---|---|
T | The atom model type, derived from Atom. |
TMol | The molecule container type, derived from Molecule. Naming the concrete container type lets the caller keep a strongly typed subclass (e.g. the AutoDock Vina molecule) without any down-casting. |
Parameters
| Name | Type | Description |
|---|---|---|
path | String | The file path of the PDB structure file. |
ReadPdbFrames``1(
String)Read all of the MODEL frames of the given PDB file, each frame is returned as an individual molecule object.
Type Parameters
| Name | Description |
|---|---|
T | The atom model type, derived from Atom. |
Parameters
| Name | Type | Description |
|---|---|---|
path | String | The file path of the PDB structure file. |
ReadPdbFrames``2(
String)Read all of the MODEL frames of the given PDB file into a caller supplied container type.
Type Parameters
| Name | Description |
|---|---|
T | The atom model type, derived from Atom. |
TMol | The molecule container type, derived from Molecule. |
Parameters
| Name | Type | Description |
|---|---|---|
path | String | The file path of the PDB structure file. |
PerceiveBonds``1(Molecule(Of ``0))
Perceive the covalent connectivity of the given molecule by the distance criterion: two heavy atoms are bonded when r < 1.3 * (r_cov_i + r_cov_j).
Remarks
The covalent radii come from the CovalentRadii table of this library, which covers 118 elements. The 1.3 tolerance factor is kept from the original implementation on purpose: switching to the theoretical bond length +/- tolerance criterion of CovalentRadii.MeasureBonds() would introduce the bond order 2/3 into the result and then change the downstream rotatable bond detection.
Type Parameters
| Name | Description |
|---|---|
T | The atom model type, derived from Atom. |
Parameters
| Name | Type | Description |
|---|---|---|
mol | Molecule(Of ``0) | The molecule object that will be modified in place. |
ReadPdb(
String)ReadPdbFrames(
String)PerceiveBonds(Molecule(Of T))