biology/dsr-pdb 1.0.3_19 FreeBSD
Simple C++ PDB reader (reads the protein description format)
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
97a84ef467- License
- LGPL21
- Categories
- biology
Description
dsr-pdb is a simple C++ PDB reader along with a couple of programs which use it to manipulate pdb files (applying a rigid transform or splitting/merging). The are aimed at people interested in proteins from a geometric viewpoint as they allow easy access to the geometry and bond structure in addition of the biological information. The reader has two modes for reading/writing a pdb file. The simplest one, through the Protein class just reads and writes a single protein from/to a pdb file (which must have only one chain, but can have multiple models). The second, through the PDB class can handle pdb files with multiple models and herogens (although these are just passed through and not currently interpreted).
In the other systems
The newest version among them is 1.0.3, as upstream numbers it.
| System | Port | Version | Vulnerabilities | Status | Maintainer | Last update |
|---|---|---|---|---|---|---|
| FreeBSD | biology/dsr-pdb | 1.0.3_19 newest | none known | - | [email protected] | 2026-09-29 |
| DragonFly | biology/dsr-pdb | 1.0.3_15 newest | none known | - | [email protected] | - |
| HardenedBSD | biology/dsr-pdb | 1.0.3_19 newest | no data | - | [email protected] | - |
| GhostBSD | biology/dsr-pdb | 1.0.3_18 newest | no data | - | [email protected] | - |
Install
Binary package:
pkg install dsr-pdb
From the ports tree:
cd /usr/ports/biology/dsr-pdb/ && make install clean
To depend on this port in another port's Makefile:
RUN_DEPENDS= dsr-pdb>0:biology/dsr-pdb
LIB_DEPENDS= libdsrpdb.so:biology/dsr-pdb
Packages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | - | 1.0.3_19 | 1.0.3_8 | 1.0.3_16 | 1.0.3_19 |
| FreeBSD:14:quarterly | - | 1.0.3_19 | n/a | 1.0.3_16 | 1.0.3_19 |
| FreeBSD:15:latest | - | 1.0.3_19 | n/a | 1.0.3_16 | 1.0.3_16 |
| FreeBSD:15:quarterly | - | 1.0.3_19 | n/a | n/a | n/a |
| FreeBSD:16:latest | - | 1.0.3_19 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependency graph
Ports that need it on the left, what it needs to run on the right; at most 8 of each. "Dependencies" below lists them all.
Dependencies
As this port's Makefile names them.
Library 1
libboost_program_options.so: devel/boost-libs
The full lists below include those, and their dependencies in turn.
Build dependencies 7
Run dependencies 4
No port depends on this one.
Configuration
No options to configure.
- USES
- compiler:c++11-lang gmake libtool localbase:ldflags tar:tgz
- Service scripts
- none
Files
pkg-plist 28
- bin/pdb_align
- bin/pdb_align_points
- bin/pdb_cat
- bin/pdb_distance
- bin/pdb_distance_matrix
- bin/pdb_split
- bin/pdb_stats
- bin/pdb_transform
- include/dsrpdb/Atom.h
- include/dsrpdb/Matrix.h
- include/dsrpdb/Model.h
- include/dsrpdb/PDB.h
- include/dsrpdb/PDB_index.h
- include/dsrpdb/Point.h
- include/dsrpdb/Protein.h
- include/dsrpdb/Residue.h
- include/dsrpdb/Transform.h
- include/dsrpdb/align.h
- include/dsrpdb/config.h
- include/dsrpdb/distance.h
- include/dsrpdb/geometry.h
- include/dsrpdb/geometry_internal.h
- include/dsrpdb/iterator.h
- include/dsrpdb/label.h
- include/dsrpdb/labeled_index.h
- include/dsrpdb/small_map.h
- lib/libdsrpdb.a
- lib/libdsrpdb.so
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| dsr-pdb-1.0.3/dsr-pdb.tgz | 958360 | e9fea9c4b8fc0255ee0e2bca11ab267d10cc9687cf5ba515c704875bcee21837 |
Master sites 1
- https://graphics.stanford.edu/~drussel/