├── .gitignore ├── .gitmodules ├── .travis.yml ├── .ycm_extra_conf.py ├── LICENSE ├── Makefile ├── README.md ├── _vimrc_local.vim ├── doc ├── Doxyfile └── man │ └── pdb++.3 ├── docs ├── README.md └── _config.yml ├── include ├── Exception.hpp ├── PDB.hpp ├── ZDOCK.hpp └── pdb++.h ├── python ├── .gitignore ├── LICENSE ├── README.md ├── setup.py └── zdock │ ├── ZDOCK.py │ └── __init__.py ├── src ├── Centroids.cpp ├── Centroids.hpp ├── CreateLigand.cpp ├── CreateLigand.hpp ├── CreateMultimer.cpp ├── CreateMultimer.hpp ├── FilterConstraints.cpp ├── FilterConstraints.hpp ├── Pruning.cpp ├── Pruning.hpp ├── README.md ├── Split.cpp ├── Split.hpp ├── UnSplit.cpp ├── UnSplit.hpp ├── common │ ├── Exception.hpp │ └── Utils.hpp ├── libpdb++ │ ├── pdb++.cpp │ ├── pdb_chars.cpp │ ├── pdb_read.cpp │ ├── pdb_sprntf.cpp │ ├── pdb_sscanf.cpp │ ├── pdb_type.cpp │ ├── pdbinput.cpp │ ├── pdbrun5_read.i │ ├── pdbrun5_write.i │ ├── pdbrun6_read.i │ ├── pdbrun6_write.i │ ├── read_format.i │ └── write_format.i ├── pdb │ └── PDB.cpp └── zdock │ ├── Constraints.cpp │ ├── Constraints.hpp │ ├── TransformLigand.cpp │ ├── TransformLigand.hpp │ ├── TransformMultimer.cpp │ ├── TransformMultimer.hpp │ ├── TransformUtil.cpp │ ├── TransformUtil.hpp │ └── ZDOCK.cpp └── test ├── Test.cpp ├── Test.hpp ├── data ├── 2OOB │ ├── ligand.1.pdb │ ├── ligand.10.pdb │ ├── ligand.2.pdb │ ├── ligand.3.pdb │ ├── ligand.4.pdb │ ├── ligand.5.pdb │ ├── ligand.6.pdb │ ├── ligand.7.pdb │ ├── ligand.8.pdb │ ├── ligand.9.pdb │ ├── ligand.pdb │ └── zdock.out.pruned └── ZDOCK │ ├── 2MTA.zd.out │ ├── 4EEW.zd.out │ ├── 6GWC.zd.out │ └── mzdock.out ├── prediction.cpp ├── rotation.cpp └── zdock.cpp /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/.gitmodules -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/.travis.yml -------------------------------------------------------------------------------- /.ycm_extra_conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/.ycm_extra_conf.py -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/LICENSE -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/Makefile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/README.md -------------------------------------------------------------------------------- /_vimrc_local.vim: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/_vimrc_local.vim -------------------------------------------------------------------------------- /doc/Doxyfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/doc/Doxyfile -------------------------------------------------------------------------------- /doc/man/pdb++.3: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/doc/man/pdb++.3 -------------------------------------------------------------------------------- /docs/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/docs/README.md -------------------------------------------------------------------------------- /docs/_config.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/docs/_config.yml -------------------------------------------------------------------------------- /include/Exception.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/include/Exception.hpp -------------------------------------------------------------------------------- /include/PDB.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/include/PDB.hpp -------------------------------------------------------------------------------- /include/ZDOCK.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/include/ZDOCK.hpp -------------------------------------------------------------------------------- /include/pdb++.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/include/pdb++.h -------------------------------------------------------------------------------- /python/.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc 2 | /.idea/ 3 | -------------------------------------------------------------------------------- /python/LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/python/LICENSE -------------------------------------------------------------------------------- /python/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/python/README.md -------------------------------------------------------------------------------- /python/setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/python/setup.py -------------------------------------------------------------------------------- /python/zdock/ZDOCK.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/python/zdock/ZDOCK.py -------------------------------------------------------------------------------- /python/zdock/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/python/zdock/__init__.py -------------------------------------------------------------------------------- /src/Centroids.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/Centroids.cpp -------------------------------------------------------------------------------- /src/Centroids.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/Centroids.hpp -------------------------------------------------------------------------------- /src/CreateLigand.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/CreateLigand.cpp -------------------------------------------------------------------------------- /src/CreateLigand.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/CreateLigand.hpp -------------------------------------------------------------------------------- /src/CreateMultimer.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/CreateMultimer.cpp -------------------------------------------------------------------------------- /src/CreateMultimer.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/CreateMultimer.hpp -------------------------------------------------------------------------------- /src/FilterConstraints.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/FilterConstraints.cpp -------------------------------------------------------------------------------- /src/FilterConstraints.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/FilterConstraints.hpp -------------------------------------------------------------------------------- /src/Pruning.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/Pruning.cpp -------------------------------------------------------------------------------- /src/Pruning.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/Pruning.hpp -------------------------------------------------------------------------------- /src/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/README.md -------------------------------------------------------------------------------- /src/Split.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/Split.cpp -------------------------------------------------------------------------------- /src/Split.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/Split.hpp -------------------------------------------------------------------------------- /src/UnSplit.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/UnSplit.cpp -------------------------------------------------------------------------------- /src/UnSplit.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/UnSplit.hpp -------------------------------------------------------------------------------- /src/common/Exception.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/common/Exception.hpp -------------------------------------------------------------------------------- /src/common/Utils.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/common/Utils.hpp -------------------------------------------------------------------------------- /src/libpdb++/pdb++.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/libpdb++/pdb++.cpp -------------------------------------------------------------------------------- /src/libpdb++/pdb_chars.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/libpdb++/pdb_chars.cpp -------------------------------------------------------------------------------- /src/libpdb++/pdb_read.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/libpdb++/pdb_read.cpp -------------------------------------------------------------------------------- /src/libpdb++/pdb_sprntf.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/libpdb++/pdb_sprntf.cpp -------------------------------------------------------------------------------- /src/libpdb++/pdb_sscanf.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/libpdb++/pdb_sscanf.cpp -------------------------------------------------------------------------------- /src/libpdb++/pdb_type.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/libpdb++/pdb_type.cpp -------------------------------------------------------------------------------- /src/libpdb++/pdbinput.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/libpdb++/pdbinput.cpp -------------------------------------------------------------------------------- /src/libpdb++/pdbrun5_read.i: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/libpdb++/pdbrun5_read.i -------------------------------------------------------------------------------- /src/libpdb++/pdbrun5_write.i: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/libpdb++/pdbrun5_write.i -------------------------------------------------------------------------------- /src/libpdb++/pdbrun6_read.i: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/libpdb++/pdbrun6_read.i -------------------------------------------------------------------------------- /src/libpdb++/pdbrun6_write.i: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/libpdb++/pdbrun6_write.i -------------------------------------------------------------------------------- /src/libpdb++/read_format.i: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/libpdb++/read_format.i -------------------------------------------------------------------------------- /src/libpdb++/write_format.i: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/libpdb++/write_format.i -------------------------------------------------------------------------------- /src/pdb/PDB.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/pdb/PDB.cpp -------------------------------------------------------------------------------- /src/zdock/Constraints.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/zdock/Constraints.cpp -------------------------------------------------------------------------------- /src/zdock/Constraints.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/zdock/Constraints.hpp -------------------------------------------------------------------------------- /src/zdock/TransformLigand.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/zdock/TransformLigand.cpp -------------------------------------------------------------------------------- /src/zdock/TransformLigand.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/zdock/TransformLigand.hpp -------------------------------------------------------------------------------- /src/zdock/TransformMultimer.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/zdock/TransformMultimer.cpp -------------------------------------------------------------------------------- /src/zdock/TransformMultimer.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/zdock/TransformMultimer.hpp -------------------------------------------------------------------------------- /src/zdock/TransformUtil.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/zdock/TransformUtil.cpp -------------------------------------------------------------------------------- /src/zdock/TransformUtil.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/zdock/TransformUtil.hpp -------------------------------------------------------------------------------- /src/zdock/ZDOCK.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/src/zdock/ZDOCK.cpp -------------------------------------------------------------------------------- /test/Test.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/test/Test.cpp -------------------------------------------------------------------------------- /test/Test.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/test/Test.hpp -------------------------------------------------------------------------------- /test/data/2OOB/ligand.1.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/test/data/2OOB/ligand.1.pdb -------------------------------------------------------------------------------- /test/data/2OOB/ligand.10.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/test/data/2OOB/ligand.10.pdb -------------------------------------------------------------------------------- /test/data/2OOB/ligand.2.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/test/data/2OOB/ligand.2.pdb -------------------------------------------------------------------------------- /test/data/2OOB/ligand.3.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/test/data/2OOB/ligand.3.pdb -------------------------------------------------------------------------------- /test/data/2OOB/ligand.4.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/test/data/2OOB/ligand.4.pdb -------------------------------------------------------------------------------- /test/data/2OOB/ligand.5.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/test/data/2OOB/ligand.5.pdb -------------------------------------------------------------------------------- /test/data/2OOB/ligand.6.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/test/data/2OOB/ligand.6.pdb -------------------------------------------------------------------------------- /test/data/2OOB/ligand.7.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/test/data/2OOB/ligand.7.pdb -------------------------------------------------------------------------------- /test/data/2OOB/ligand.8.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/test/data/2OOB/ligand.8.pdb -------------------------------------------------------------------------------- /test/data/2OOB/ligand.9.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/test/data/2OOB/ligand.9.pdb -------------------------------------------------------------------------------- /test/data/2OOB/ligand.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/test/data/2OOB/ligand.pdb -------------------------------------------------------------------------------- /test/data/2OOB/zdock.out.pruned: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/test/data/2OOB/zdock.out.pruned -------------------------------------------------------------------------------- /test/data/ZDOCK/2MTA.zd.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/test/data/ZDOCK/2MTA.zd.out -------------------------------------------------------------------------------- /test/data/ZDOCK/4EEW.zd.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/test/data/ZDOCK/4EEW.zd.out -------------------------------------------------------------------------------- /test/data/ZDOCK/6GWC.zd.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/test/data/ZDOCK/6GWC.zd.out -------------------------------------------------------------------------------- /test/data/ZDOCK/mzdock.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/test/data/ZDOCK/mzdock.out -------------------------------------------------------------------------------- /test/prediction.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/test/prediction.cpp -------------------------------------------------------------------------------- /test/rotation.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/test/rotation.cpp -------------------------------------------------------------------------------- /test/zdock.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weng-lab/libzdock/HEAD/test/zdock.cpp --------------------------------------------------------------------------------