nf-core/pdb2pqr @ 0.0.0-0c7146d
Summary
Convert PDB files to PQR format by assigning charge and radius parameters for electrostatics calculations (e.g. APBS input preparation).
Get started
Add the following snippet to your workflow script to include this module.
include { PDB2PQR } from 'nf-core/pdb2pqr'
License
MIT License
Process
Name
|
PDB2PQR |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
pdb
file
|
Protein structure file in PDB format *.{pdb}
|
Output
4 channels
#1
log
tuple
meta
map
|
Groovy Map containing sample information |
|---|---|
*.log
file
|
Log file produced during PDB2PQR execution *.log
|
#2
pqr
tuple
meta
map
|
Groovy Map containing sample information |
|---|---|
*.pqr
file
|
Protein structure file in PQR format *.pqr
|
#3
conf
tuple
meta
map
|
Groovy Map containing sample information |
|---|---|
*.in
file
|
APBS input configuration file generated by PDB2PQR *.in
|
#4
versions_pdb2pqr
tuple
${task.process}
string
|
The name of the process |
|---|---|
pdb2pqr
string
|
The name of the tool |
pdb2pqr --version | sed 's/^[^ ]* //'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| pdb2pqr | PDB2PQR converts protein structure files in PDB format to PQR format by assigning atomic charges and radii. It is commonly used to prepare structures for electrostatics calculations with APBS. | https://www.poissonboltzmann.org |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:01:55 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fpdb2pqr/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/pdb2pqr/blobs/sha256:f45e15ec88886df22624f0065b2c26bfcf1e1d6ace8d42d1e64a8b2c19b28d79 |
| Size | 2.6 KB |
| Checksum | sha256:f45e15ec88886df22624f0065b2c26bfcf1e1d6ace8d42d1e64a8b2c19b28d79 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:01:55 (UTC) | 1 | 2.6 KB | - |