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Commit 5dbe78d0 authored by Studer Gabriel's avatar Studer Gabriel
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Merge branch 'release-2.9.2'

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CHANGELOG.txt
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Changes in Release 2.9.2
--------------------------------------------------------------------------------
* Examples for comparing macromolecular complexes
* Documentation updates
Changes in Release 2.9.1 Changes in Release 2.9.1
-------------------------------------------------------------------------------- --------------------------------------------------------------------------------
......
CMakeLists.txt
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− 1
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...@@ -15,7 +15,7 @@ project(OpenStructure CXX C) ...@@ -15,7 +15,7 @@ project(OpenStructure CXX C)
set (CMAKE_EXPORT_COMPILE_COMMANDS 1) set (CMAKE_EXPORT_COMPILE_COMMANDS 1)
set (OST_VERSION_MAJOR 2) set (OST_VERSION_MAJOR 2)
set (OST_VERSION_MINOR 9) set (OST_VERSION_MINOR 9)
set (OST_VERSION_PATCH 1) set (OST_VERSION_PATCH 2)
set (OST_VERSION_STRING ${OST_VERSION_MAJOR}.${OST_VERSION_MINOR}.${OST_VERSION_PATCH} ) set (OST_VERSION_STRING ${OST_VERSION_MAJOR}.${OST_VERSION_MINOR}.${OST_VERSION_PATCH} )
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake_support) set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake_support)
include(OST) include(OST)
......
ReadMe.txt → README.md
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================= OpenStructure molecular modelling framework ================== # OpenStructure - A computational structural biology framework
OpenStructure provides a modular, flexible, molecular modelling environment OpenStructure provides a modular, flexible, molecular modelling environment
which allows to integrate, process and visualize information of different origin which allows to integrate, process and visualize information of different origin
...@@ -6,12 +6,52 @@ such as sequences, alignments and 3D structures. ...@@ -6,12 +6,52 @@ such as sequences, alignments and 3D structures.
Please refer to www.openstructure.org for more information and documentation. Please refer to www.openstructure.org for more information and documentation.
Thank you for you interest and enjoy the straightforward way of handling protein Thank you for your interest and enjoy the straightforward way of handling protein
structure data! structure data!
Please do not hesitate to contact us for feedback or troubleshooting: Please do not hesitate to contact us for feedback or troubleshooting:
openstructure-users@maillist.unibas.ch <a href="mailto:&#111;&#112;&#101;&#110;&#115;&#116;&#114;&#117;&#099;&#116;&#117;&#114;&#101;&#045;&#117;&#115;&#101;&#114;&#115;&#064;&#109;&#097;&#105;&#108;&#108;&#105;&#115;&#116;&#046;&#117;&#110;&#105;&#098;&#097;&#115;&#046;&#099;&#104;">&#111;&#112;&#101;&#110;&#115;&#116;&#114;&#117;&#099;&#116;&#117;&#114;&#101;&#045;&#117;&#115;&#101;&#114;&#115;&#064;&#109;&#097;&#105;&#108;&#108;&#105;&#115;&#116;&#046;&#117;&#110;&#105;&#098;&#097;&#115;&#046;&#099;&#104;</a>
## OpenStructure Installation
For a simple and portable setup, we recommend using a containerized
solution. OpenStructure provides its own Docker container registry,
making deployment easier. Deploying a docker image just needs a
docker pull which typically finishes in about a minute depending
on your local hardware and internet connection. Singularity
containers bootstrap from the docker container but must be built
by the user. Detailed instructions can be found here:
* Docker: [OpenStructure Docker Instructions](https://git.scicore.unibas.ch/schwede/openstructure/tree/master/docker)
* Singularity: [OpenStructure Singularity Instructions](https://git.scicore.unibas.ch/schwede/openstructure/tree/master/singularity)
OpenStructure is developed and tested across various Linux distributions.
You can find detailed build instructions and a list of required dependencies here:
https://openstructure.org/docs/install/
## Getting started
The installation and container instructions will help you set up
OpenStructure for scripting. Additionally, here are some advanced
use cases worth highlighting.
### Benchmarking and Scoring
OpenStructure implements a benchmarking suite for comparing macromolecular
complexes. To get started, check out the examples in the [examples/scoring](examples/scoring)
directory of this repository.
### Modeling
[ProMod3](https://git.scicore.unibas.ch/schwede/ProMod3) is a fully featured modeling engine built on top of OpenStructure.
It powers the [SWISS-MODEL](https://swissmodel.expasy.org) web server and provides advanced modeling
capabilities. Learn more here:
[ProMod3 Documentation](https://openstructure.org/promod3)
## Cite Us
If you like our software and have used it in your research project, please cite If you like our software and have used it in your research project, please cite
the following paper on OpenStructure: the following paper on OpenStructure:
...@@ -34,4 +74,3 @@ following reference: ...@@ -34,4 +74,3 @@ following reference:
quaternary structure of homo- and hetero-oligomers beyond binary interactions quaternary structure of homo- and hetero-oligomers beyond binary interactions
by homology, Scientific Reports, 2017 by homology, Scientific Reports, 2017
================= The OpenStructure Team =======================================
deployment/CMakeLists.txt
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− 1
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...@@ -12,7 +12,7 @@ if(${PROJECT_SOURCE_DIR} STREQUAL ${CMAKE_SOURCE_DIR}) ...@@ -12,7 +12,7 @@ if(${PROJECT_SOURCE_DIR} STREQUAL ${CMAKE_SOURCE_DIR})
set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "OpenStructure Framework") set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "OpenStructure Framework")
set(CPACK_PACKAGE_VENDOR "2008-2020 -- The OpenStructure Team") set(CPACK_PACKAGE_VENDOR "2008-2020 -- The OpenStructure Team")
set(CPACK_PACKAGE_DESCRIPTION_FILE "${PROJECT_SOURCE_DIR}/ReadMe.txt") set(CPACK_PACKAGE_DESCRIPTION_FILE "${PROJECT_SOURCE_DIR}/README.md")
set(CPACK_RESOURCE_FILE_LICENSE "${PROJECT_SOURCE_DIR}/LICENSE.txt") set(CPACK_RESOURCE_FILE_LICENSE "${PROJECT_SOURCE_DIR}/LICENSE.txt")
set(CPACK_PACKAGE_VERSION_MAJOR ${OST_VERSION_MAJOR}) set(CPACK_PACKAGE_VERSION_MAJOR ${OST_VERSION_MAJOR})
set(CPACK_PACKAGE_VERSION_MINOR ${OST_VERSION_MINOR}) set(CPACK_PACKAGE_VERSION_MINOR ${OST_VERSION_MINOR})
......
docker/Dockerfile
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...@@ -2,7 +2,7 @@ FROM ubuntu:22.04 ...@@ -2,7 +2,7 @@ FROM ubuntu:22.04
# ARGUMENTS # ARGUMENTS
########### ###########
ARG OPENSTRUCTURE_VERSION="2.9.1" ARG OPENSTRUCTURE_VERSION="2.9.2"
ARG SRC_FOLDER="/usr/local/src" ARG SRC_FOLDER="/usr/local/src"
ARG CPUS_FOR_MAKE=2 ARG CPUS_FOR_MAKE=2
......
examples/scoring/README.md 0 → 100644
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Structure comparison examples
=============================
OpenStructure provides "actions" for general benchmarking use cases.
* **compare-structures**: Focuses on comparisons involving polymer entities, i.e.
protein, DNA and RNA chains
* **compare-ligand-structures**: Focuses on comparisons of interactions between
polymer entities and non-polymer entities, i.e. small molecule ligands
The example commands here assume an OpenStructure installation
(compile instructions: https://openstructure.org/docs/install/).
Running the computations in containers provide a considerably easier setup than
compiling OpenStructure from source. Instructions for setup and running
equivalent computations are available for
* [Docker](https://git.scicore.unibas.ch/schwede/openstructure/tree/master/docker)
* [Singularity](https://git.scicore.unibas.ch/schwede/openstructure/tree/master/singularity)
A detailed list of options can be found in the
[action documentation](https://openstructure.org/docs/actions/).
Alternatively, the command
```
ost <ACTION> -h
```
will list all available options of the respective action. Both actions compute
scores on an “opt-in” basis and produce output in JSON format. Example to compute
global and per-residue LDDT scores, as well as as QS-scores which are written to
default output (out.json):
```
ost compare-structures -m model.pdb -r reference.cif.gz --lddt --local-lddt --qs-score
```
Results should be computed within seconds and example output can be found
[here](compare-structures_example_out.json). We refer to the action
documentation for in-depth description of the provided data items.
By default, model-reference chains are aligned using Needleman-Wunsch.
Many benchmarking efforts such as CASP and CAMEO assume residue numbers
according to target sequence(s). Both "actions" allow to derive model-reference
chain alignments according to these numbers which should be preferred in these
cases. This can be enabled by adding a `-rna` (residue number alignment) flag:
```
ost compare-structures -m model.pdb -r reference.cif.gz --lddt --local-lddt --qs-score -rna
```
The same example also contains small molecule ligands.
We can compute LDDT-PLI and BiSyRMSD with:
```
ost compare-ligand-structures -m model.pdb -r reference.cif.gz -ml *.sdf --rmsd --lddt-pli
```
Results should be computed within seconds and example output can be found
[here](compare-ligand-structures_example_out.json). We refer to the action
documentation for in-depth description of the provided data items.
Again, it is advised to use the `-rna` flag if applicable. In this example,
reference ligands are directly extracted from the provided mmCIF file based on
"non-polymer" entity types.
This only works in case of mmCIF input AND if the respective ligand is in the
PDB component dictionary which defines connectivity (matching based on compound
name).
Container solutions come with such a dictionary which has been created at build
time. Check the Docker/Singularity instructions linked above on how to set the
latest dictionary, i.e. "Compound Library".
You can override automatic extraction by providing SDF files with ligand
coordinates and connectivity information. If the receptor is provided in
PDB format, ligands must be provided in SDF format.
examples/scoring/compare-ligand-structures_example_out.json 0 → 100644
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{
"model_ligands": [
"model_ligand-1.sdf",
"model_ligand-2.sdf",
"model_ligand-3.sdf"
],
"reference_ligands": [
"C.1.",
"D.1.",
"E.1."
],
"lddt_pli": {
"assigned_scores": [
{
"score": 0.791304349899292,
"coverage": 1.0,
"lddt_pli_n_contacts": 1035,
"model_ligand": "model_ligand-1.sdf",
"reference_ligand": "D.1.",
"bs_ref_res": [
"A.233.",
"A.95.",
"A.38.",
"A.113.",
"A.248.",
"A.229.",
"A.57.",
"A.126.",
"A.122.",
"A.244.",
"A.36.",
"A.137.",
"A.118.",
"A.98.",
"A.127.",
"A.94.",
"A.133.",
"A.226.",
"A.246.",
"A.54.",
"A.60.",
"A.52.",
"A.91.",
"A.111.",
"A.45.",
"A.33.",
"A.228.",
"A.132.",
"A.225.",
"A.96.",
"A.116.",
"A.100.",
"A.135.",
"A.124.",
"A.34.",
"A.58.",
"A.129.",
"A.93.",
"A.101.",
"A.110.",
"A.109.",
"A.245.",
"A.232.",
"A.235.",
"A.119.",
"A.251.",
"A.153.",
"A.50.",
"A.103.",
"A.134.",
"A.130.",
"A.66.",
"A.92.",
"A.61.",
"A.63.",
"A.55.",
"A.131.",
"A.230.",
"A.247.",
"A.56.",
"A.112.",
"A.222.",
"A.64.",
"A.236.",
"A.102.",
"A.99.",
"A.65.",
"A.97.",
"A.136.",
"A.35.",
"A.62.",
"A.123.",
"A.231.",
"A.37.",
"A.49.",
"A.32.",
"A.128.",
"A.234.",
"A.125.",
"A.59.",
"A.53.",
"A.224.",
"A.120.",
"A.51.",
"A.88.",
"A.114.",
"A.227.",
"A.157."
],
"bs_mdl_res": [
"B.54.",
"B.136.",
"B.95.",
"B.236.",
"B.62.",
"B.243.",
"B.233.",
"B.232.",
"B.130.",
"B.91.",
"B.240.",
"B.57.",
"B.132.",
"B.128.",
"B.92.",
"B.247.",
"B.244.",
"B.61.",
"B.118.",
"B.96.",
"B.55.",
"B.229.",
"B.59.",
"B.98.",
"B.51.",
"B.241.",
"B.112.",
"B.133.",
"B.129.",
"B.58.",
"B.56.",
"B.99.",
"B.110.",
"B.242.",
"B.102."
]
},
{
"score": 0.0,
"coverage": 1.0,
"lddt_pli_n_contacts": 1338,
"model_ligand": "model_ligand-3.sdf",
"reference_ligand": "E.1.",
"bs_ref_res": [
"B.250.",
"B.57.",
"B.98.",
"B.36.",
"B.230.",
"B.94.",
"B.157.",
"B.112.",
"B.222.",
"B.241.",
"B.128.",
"B.54.",
"B.60.",
"B.52.",
"B.123.",
"B.231.",
"B.242.",
"B.248.",
"B.91.",
"B.137.",
"B.33.",
"B.234.",
"B.243.",
"B.133.",
"B.96.",
"B.100.",
"B.34.",
"B.120.",
"B.224.",
"B.244.",
"B.110.",
"B.58.",
"B.93.",
"B.101.",
"B.114.",
"B.227.",
"B.130.",
"B.233.",
"B.50.",
"B.103.",
"B.113.",
"B.246.",
"B.229.",
"B.122.",
"B.131.",
"B.135.",
"B.66.",
"B.61.",
"B.92.",
"B.63.",
"B.118.",
"B.55.",
"B.56.",
"B.64.",
"B.153.",
"B.99.",
"B.102.",
"B.226.",
"B.65.",
"B.134.",
"B.109.",
"B.251.",
"B.97.",
"B.35.",
"B.126.",
"B.62.",
"B.37.",
"B.245.",
"B.49.",
"B.32.",
"B.111.",
"B.127.",
"B.129.",
"B.228.",
"B.116.",
"B.53.",
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"B.59.",
"B.124.",
"B.51.",
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"B.47.",
"B.136.",
"B.88.",
"B.119.",
"B.125.",
"B.232.",
"B.132.",
"B.95."
],
"bs_mdl_res": [
"B.70.",
"B.80.",
"B.77.",
"B.78.",
"B.79.",
"B.179.",
"B.74.",
"B.249.",
"B.252.",
"B.76.",
"B.83.",
"B.75.",
"B.253.",
"B.178.",
"B.175.",
"B.182.",
"B.255.",
"B.254."
]
}
],
"model_ligand_unassigned_reason": {
"model_ligand-2.sdf": [
"no_iso",
"No full isomorphic match could be found - enabling substructure_match might allow a match"
]
},
"reference_ligand_unassigned_reason": {
"C.1.": [
"no_iso",
"No full isomorphic match could be found - enabling substructure_match might allow a match"
]
}
},
"rmsd": {
"assigned_scores": [
{
"score": 1.3892921209335327,
"coverage": 1.0,
"lddt_lp": 0.9220483938256153,
"bb_rmsd": 0.6037176251411438,
"model_ligand": "model_ligand-1.sdf",
"reference_ligand": "D.1.",
"chain_mapping": {
"A": "B"
},
"bs_ref_res": [
"A.51.",
"A.54.",
"A.55.",
"A.57.",
"A.58.",
"A.59.",
"A.61.",
"A.91.",
"A.92.",
"A.95.",
"A.96.",
"A.99.",
"A.102.",
"A.112.",
"A.129.",
"A.132.",
"A.133.",
"A.136.",
"A.232.",
"A.233.",
"A.244.",
"A.247."
],
"bs_ref_res_mapped": [
"A.51.",
"A.54.",
"A.55.",
"A.57.",
"A.58.",
"A.59.",
"A.61.",
"A.91.",
"A.92.",
"A.95.",
"A.96.",
"A.99.",
"A.102.",
"A.112.",
"A.129.",
"A.132.",
"A.133.",
"A.136.",
"A.232.",
"A.233.",
"A.244.",
"A.247."
],
"bs_mdl_res_mapped": [
"B.51.",
"B.54.",
"B.55.",
"B.57.",
"B.58.",
"B.59.",
"B.61.",
"B.91.",
"B.92.",
"B.95.",
"B.96.",
"B.99.",
"B.102.",
"B.112.",
"B.129.",
"B.132.",
"B.133.",
"B.136.",
"B.232.",
"B.233.",
"B.244.",
"B.247."
],
"inconsistent_residues": [],
"transform": [
[
-0.3686985373497009,
0.3980128765106201,
0.8400280475616455,
7.079176902770996
],
[
-0.8913460969924927,
-0.40779373049736023,
-0.19800609350204468,
-3.9579238891601562
],
[
0.26374921202659607,
-0.8217602968215942,
0.5051202774047852,
6.306806564331055
],
[
0.0,
0.0,
0.0,
1.0
]
]
},
{
"score": 29.482725143432617,
"coverage": 1.0,
"lddt_lp": 0.9362713153035733,
"bb_rmsd": 0.3739512264728546,
"model_ligand": "model_ligand-3.sdf",
"reference_ligand": "E.1.",
"chain_mapping": {
"B": "B"
},
"bs_ref_res": [
"B.54.",
"B.55.",
"B.58.",
"B.59.",
"B.61.",
"B.62.",
"B.91.",
"B.92.",
"B.95.",
"B.96.",
"B.99.",
"B.102.",
"B.112.",
"B.129.",
"B.132.",
"B.133.",
"B.136.",
"B.233.",
"B.247."
],
"bs_ref_res_mapped": [
"B.54.",
"B.55.",
"B.58.",
"B.59.",
"B.61.",
"B.62.",
"B.91.",
"B.92.",
"B.95.",
"B.96.",
"B.99.",
"B.102.",
"B.112.",
"B.129.",
"B.132.",
"B.133.",
"B.136.",
"B.233.",
"B.247."
],
"bs_mdl_res_mapped": [
"B.54.",
"B.55.",
"B.58.",
"B.59.",
"B.61.",
"B.62.",
"B.91.",
"B.92.",
"B.95.",
"B.96.",
"B.99.",
"B.102.",
"B.112.",
"B.129.",
"B.132.",
"B.133.",
"B.136.",
"B.233.",
"B.247."
],
"inconsistent_residues": [],
"transform": [
[
-0.5568894743919373,
-0.6022372841835022,
-0.5720000267028809,
41.09874725341797
],
[
-0.7276356816291809,
0.021647661924362183,
0.6856220960617065,
-26.01633644104004
],
[
-0.4005247950553894,
0.7980234622955322,
-0.4502646327018738,
42.01909637451172
],
[
0.0,
0.0,
0.0,
1.0
]
]
}
],
"model_ligand_unassigned_reason": {
"model_ligand-2.sdf": [
"no_iso",
"No full isomorphic match could be found - enabling substructure_match might allow a match"
]
},
"reference_ligand_unassigned_reason": {
"C.1.": [
"no_iso",
"No full isomorphic match could be found - enabling substructure_match might allow a match"
]
}
},
"model": "model.pdb",
"reference": "reference.cif.gz",
"model_cleanup_log": {
"cleaned_residues": {
"no_clib": [],
"not_linking": []
},
"cleaned_atoms": {
"unknown_atoms": []
}
},
"reference_cleanup_log": {
"cleaned_residues": {
"no_clib": [],
"not_linking": []
},
"cleaned_atoms": {
"unknown_atoms": []
}
},
"resnum_alignments": false,
"substructure_match": false,
"coverage_delta": 0.2,
"max_symmetries": 10000.0,
"ost_version": "2.9.2",
"status": "SUCCESS"
}
\ No newline at end of file
examples/scoring/compare-structures_example_out.json 0 → 100644
+ 562
− 0
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{
"reference_chains": [
"A",
"B",
"C"
],
"model_chains": [
"A",
"B"
],
"chem_groups": [
[
"A",
"B"
]
],
"chem_mapping": [
[
"A",
"B"
]
],
"chain_mapping": {
"A": "B",
"B": "A"
},
"aln": [
">reference:A\nLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTF--STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSM-------LSDLLLEMLDAHRL\n>model:B\n----LTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKSKNVVPLSDLLLEMLDAHR-",
">reference:B\nLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY---------LEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYS-----VVPLSDLLLEMLDA-\n>model:A\n-----TADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKSKNVVPLSDLLLEMLDAH"
],
"inconsistent_residues": [],
"lddt": 0.874,
"local_lddt": {
"A.19.": 0.797,
"A.20.": 0.868,
"A.21.": 0.726,
"A.22.": 0.783,
"A.23.": 0.735,
"A.24.": 0.881,
"A.25.": 0.849,
"A.26.": 0.873,
"A.27.": 0.911,
"A.28.": 0.94,
"A.29.": 0.919,
"A.30.": 0.933,
"A.31.": 0.972,
"A.32.": 0.952,
"A.33.": 0.946,
"A.34.": 0.972,
"A.35.": 0.949,
"A.36.": 0.916,
"A.37.": 0.817,
"A.38.": 0.724,
"A.39.": 0.694,
"A.40.": 0.776,
"A.41.": 0.655,
"A.42.": 0.769,
"A.43.": 0.692,
"A.44.": 0.676,
"A.45.": 0.741,
"A.46.": 0.655,
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}
\ No newline at end of file
examples/scoring/model.pdb 0 → 100644
+ 3802
− 0
View file @ 5dbe78d0
Source diff could not be displayed: it is too large. Options to address this: view the blob.
examples/scoring/model_ligand-1.sdf 0 → 100644
+ 155
− 0
View file @ 5dbe78d0
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35 68 1 0 0 0
36 37 1 0 0 0
36 38 1 0 0 0
37 38 1 0 0 0
37 69 1 0 0 0
37 70 1 0 0 0
38 71 1 0 0 0
38 72 1 0 0 0
M END
$$$$
examples/scoring/model_ligand-2.sdf 0 → 100644
+ 46
− 0
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LIG
OST02122508393D
20 20 0 0 0 0 999 V2000
14.5030 17.7260 35.6290 N 0 3 0 0 0 0
14.6340 17.4680 34.2040 C 0 0 0 0 0 0
15.9580 16.7510 33.9650 C 0 0 0 0 0 0
17.0760 17.4970 34.5970 C 0 0 0 0 0 0
17.8840 18.3940 33.9480 C 0 0 0 0 0 0
18.7760 18.8660 34.8320 N 0 0 0 0 0 0
18.5470 18.2880 36.0220 C 0 0 0 0 0 0
17.5090 17.4570 35.8620 N 0 0 0 0 0 0
13.5190 16.6000 33.7450 C 0 0 0 0 0 0
13.0900 16.6000 32.5610 O 0 0 0 0 0 0
12.9120 15.7440 34.6560 O 0 5 0 0 0 0
15.4250 17.9670 36.0330 H 0 0 0 0 0 0
14.1590 16.8270 36.0620 H 0 0 0 0 0 0
13.7950 18.4920 35.7430 H 0 0 0 0 0 0
14.6038 18.4166 33.6478 H 0 0 0 0 0 0
15.9061 15.7413 34.3984 H 0 0 0 0 0 0
16.1388 16.6903 32.8817 H 0 0 0 0 0 0
17.8134 18.6774 32.8875 H 0 0 0 0 0 0
19.5230 19.5620 34.6410 H 0 0 0 0 0 0
19.1064 18.4638 36.9527 H 0 0 0 0 0 0
1 2 1 0 0 0
1 12 1 0 0 0
1 13 1 0 0 0
1 14 1 0 0 0
2 3 1 0 0 0
2 9 1 0 0 0
2 15 1 0 0 0
3 4 1 0 0 0
3 16 1 0 0 0
3 17 1 0 0 0
4 5 2 0 0 0
4 8 1 0 0 0
5 6 1 0 0 0
5 18 1 0 0 0
6 7 1 0 0 0
6 19 1 0 0 0
7 8 2 0 0 0
7 20 1 0 0 0
9 10 2 0 0 0
9 11 1 0 0 0
M END
$$$$
examples/scoring/model_ligand-3.sdf 0 → 100644
+ 159
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LIG
OST02122508393D
74 79 0 0 0 0 999 V2000
12.4190 4.5510 -2.7930 O 0 0 0 0 0 0
12.0190 4.4310 -4.0260 C 0 0 0 0 0 0
11.1680 3.2690 -4.1990 C 0 0 0 0 0 0
11.6010 1.9680 -4.3190 C 0 0 0 0 0 0
10.7390 0.9160 -4.5410 C 0 0 0 0 0 0
9.3830 1.1340 -4.6520 C 0 0 0 0 0 0
8.8950 2.4170 -4.5400 C 0 0 0 0 0 0
9.7790 3.4270 -4.3210 C 0 0 0 0 0 0
12.4790 5.4060 -4.8800 N 0 0 0 0 0 0
12.1160 6.7850 -5.0820 C 0 0 0 0 0 0
11.7080 7.6360 -4.0250 C 0 0 0 0 0 0
11.1470 7.1340 -2.8800 C 0 0 0 0 0 0
10.7360 7.9710 -1.8360 C 0 0 0 0 0 0
10.8730 9.3220 -1.9110 C 0 0 0 0 0 0
10.4590 10.1350 -0.8630 O 0 0 0 0 0 0
10.1380 11.4780 -1.1770 C 0 0 0 0 0 0
9.0670 12.0230 -0.2570 C 0 0 0 0 0 0
9.7170 13.1580 0.5200 C 0 0 0 0 0 0
9.0230 13.0220 1.8600 C 0 0 0 0 0 0
8.8160 11.6130 2.0600 N 0 3 0 0 0 0
7.8740 11.2800 3.0670 C 0 0 0 0 0 0
6.8120 10.2970 2.7280 C 0 0 0 0 0 0
6.3780 9.3930 3.8480 C 0 0 0 0 0 0
5.5450 8.3930 3.3490 F 0 0 0 0 0 0
8.6370 11.0000 0.7800 C 0 0 0 0 0 0
11.4380 9.8270 -3.0690 C 0 0 0 0 0 0
11.8470 9.0170 -4.1020 C 0 0 0 0 0 0
11.3500 6.7770 -6.3380 C 0 0 0 0 0 0
10.0500 7.1170 -6.5250 C 0 0 0 0 0 0
9.5430 7.0240 -7.8300 C 0 0 0 0 0 0
10.3100 6.6090 -8.8810 C 0 0 0 0 0 0
9.8140 6.5130 -10.1870 O 0 0 0 0 0 0
11.6490 6.2570 -8.6840 C 0 0 0 0 0 0
12.1520 6.3440 -7.4210 C 0 0 0 0 0 0
13.5400 5.9540 -7.0840 C 0 0 0 0 0 0
13.4600 4.9620 -5.9190 C 0 0 0 0 0 0
13.4910 3.5460 -6.3540 C 0 0 0 0 0 0
14.6540 4.2220 -5.6000 C 0 0 0 0 0 0
12.6778 1.7597 -4.2343 H 0 0 0 0 0 0
11.1366 -0.1058 -4.6303 H 0 0 0 0 0 0
8.6974 0.2921 -4.8282 H 0 0 0 0 0 0
7.8172 2.6197 -4.6255 H 0 0 0 0 0 0
9.3741 4.4460 -4.2327 H 0 0 0 0 0 0
13.0367 7.3845 -5.1357 H 0 0 0 0 0 0
11.0164 6.0465 -2.7788 H 0 0 0 0 0 0
10.2917 7.5255 -0.9337 H 0 0 0 0 0 0
11.0433 12.0947 -1.0761 H 0 0 0 0 0 0
9.7553 11.5090 -2.2078 H 0 0 0 0 0 0
8.1937 12.3179 -0.8574 H 0 0 0 0 0 0
10.8039 13.0152 0.6111 H 0 0 0 0 0 0
9.6116 14.1479 0.0520 H 0 0 0 0 0 0
9.6554 13.4326 2.6610 H 0 0 0 0 0 0
8.0721 13.5747 1.8784 H 0 0 0 0 0 0
9.7660 11.2560 2.4300 H 0 0 0 0 0 0
8.4366 10.8733 3.9203 H 0 0 0 0 0 0
7.3313 12.2176 3.2580 H 0 0 0 0 0 0
5.9298 10.8575 2.3851 H 0 0 0 0 0 0
7.2473 9.6378 1.9626 H 0 0 0 0 0 0
7.2637 8.9337 4.3112 H 0 0 0 0 0 0
5.8310 9.9812 4.5996 H 0 0 0 0 0 0
9.2593 10.0963 0.7020 H 0 0 0 0 0 0
7.5901 10.6984 0.6283 H 0 0 0 0 0 0
11.5644 10.9154 -3.1665 H 0 0 0 0 0 0
12.2904 9.4681 -5.0020 H 0 0 0 0 0 0
9.4195 7.4518 -5.6881 H 0 0 0 0 0 0
8.4925 7.2944 -8.0127 H 0 0 0 0 0 0
8.9380 6.0000 -10.3050 H 0 0 0 0 0 0
12.2764 5.9204 -9.5225 H 0 0 0 0 0 0
14.0194 5.4783 -7.9522 H 0 0 0 0 0 0
14.1376 6.8351 -6.8072 H 0 0 0 0 0 0
12.8631 2.7941 -5.8536 H 0 0 0 0 0 0
13.3666 3.0018 -7.3018 H 0 0 0 0 0 0
14.8697 3.9460 -4.5573 H 0 0 0 0 0 0
15.7299 4.3582 -5.7843 H 0 0 0 0 0 0
1 2 2 0 0 0
2 3 1 0 0 0
2 9 1 0 0 0
3 4 2 0 0 0
3 8 1 0 0 0
4 5 1 0 0 0
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5 6 2 0 0 0
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10 44 1 0 0 0
11 12 2 0 0 0
11 27 1 0 0 0
12 13 1 0 0 0
12 45 1 0 0 0
13 14 2 0 0 0
13 46 1 0 0 0
14 15 1 0 0 0
14 26 1 0 0 0
15 16 1 0 0 0
16 17 1 0 0 0
16 47 1 0 0 0
16 48 1 0 0 0
17 18 1 0 0 0
17 25 1 0 0 0
17 49 1 0 0 0
18 19 1 0 0 0
18 50 1 0 0 0
18 51 1 0 0 0
19 20 1 0 0 0
19 52 1 0 0 0
19 53 1 0 0 0
20 21 1 0 0 0
20 25 1 0 0 0
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21 22 1 0 0 0
21 55 1 0 0 0
21 56 1 0 0 0
22 23 1 0 0 0
22 57 1 0 0 0
22 58 1 0 0 0
23 24 1 0 0 0
23 59 1 0 0 0
23 60 1 0 0 0
25 61 1 0 0 0
25 62 1 0 0 0
26 27 2 0 0 0
26 63 1 0 0 0
27 64 1 0 0 0
28 29 2 0 0 0
28 34 1 0 0 0
29 30 1 0 0 0
29 65 1 0 0 0
30 31 2 0 0 0
30 66 1 0 0 0
31 32 1 0 0 0
31 33 1 0 0 0
32 67 1 0 0 0
33 34 2 0 0 0
33 68 1 0 0 0
34 35 1 0 0 0
35 36 1 0 0 0
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35 70 1 0 0 0
36 37 1 0 0 0
36 38 1 0 0 0
37 38 1 0 0 0
37 71 1 0 0 0
37 72 1 0 0 0
38 73 1 0 0 0
38 74 1 0 0 0
M END
$$$$
examples/scoring/reference.cif.gz 0 → 100644
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File added
modules/doc/install.rst
+ 34
− 78
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...@@ -310,108 +310,58 @@ observed for OpenMM versions 6.1 until 7.1.1 when compiling with gcc versions >= ...@@ -310,108 +310,58 @@ observed for OpenMM versions 6.1 until 7.1.1 when compiling with gcc versions >=
from source. from source.
**Ubuntu 20.04 LTS / Debian 10 with GUI** **Ubuntu 24.04 LTS**
Besides the molecular mechanics module, we also enable parasail here.
All the dependencies can be installed from the package manager as follows: All the dependencies can be installed from the package manager as follows:
.. code-block:: bash .. code-block:: bash
sudo apt-get install cmake g++ libtiff-dev libfftw3-dev libeigen3-dev \ sudo apt-get install cmake g++ libtiff-dev libfftw3-dev libeigen3-dev \
libpng-dev python3-all python3-pyqt5 libboost-all-dev \ libpng-dev python3-all python3-pyqt5 libboost-all-dev \
qt5-qmake qtbase5-dev libpng-dev libsqlite3-dev qt5-qmake qtbase5-dev libpng-dev libsqlite3-dev \
libopenmm-dev libopenmm-plugins libparasail-dev
Now, all dependencies are located in standard locations and cmake will Now, all dependencies are located in standard locations and cmake will
automatically find them without the need to pass any additional parameters. automatically find them. As a single quirk, we need to specify the
We add -DOPTIMIZE, which will tell cmake to build an optimised version of OpenMM plugin directory. Lets do a proper out of source build here:
OpenStructure.
.. code-block:: bash .. code-block:: bash
cmake . -DOPTIMIZE=ON mkdir build
cd build
cmake .. -DOPTIMIZE=ON -DENABLE_MM=1 -DENABLE_PARASAIL=1 \
-DOPEN_MM_PLUGIN_DIR=/lib/x86_64-linux-gnu/openmm/plugins
Building the Project
--------------------------------------------------------------------------------
Type ``make``. If you are using a multi-core machine, you can use the `-j` flag
to run multiple jobs at once.
What's next?
--------------------------------------------------------------------------------
**macOS (Catalina/ Big Sur/ Monterey) with Homebrew** One thing is missing for a fully functional OpenStructure installation.
The compound library. It is used at various places for connectivity
.. note:: information and certain algorithms do not work without.
Besides an OpenStructure executable, we just built the
When switching the Qt version used for compiling OST with support for the chemdict_tool which converts the PDB chemical component dictionary
graphical user interface, dng may start behaving weird. Symptoms are that the into our internal format:
user interface starts being unresponsive to mouse clicks. An easy solution
may be to close dng and remove
``$HOME/Library/Preferences/org.openstructure.dng.plist`` and start dng again.
`Homebrew <https://brew.sh/>`_ can be used to conveniently install all
dependencies. The current Python version, as of writing these instructions, is
3.9.10 but works so far. Boost comes as 1.76.0 which seems to be OK. Do not
forget to also install boost-python3 (your system may have a lower version of
Python than 3.9.10 but it seems like boost-python3 was compiled for 3.9.10).
Eigen and SQLite also seem to be unproblematic concerning higher version
numbers. To build the graphical user interface, use Qt version 5 by installing
packages qt@5 and pyqt@5 from Homebrew.
If you want to build the info module or the graphical user interface, make sure
you have the Xcode app installed. Just the Xcode command line tools which are
sufficient for Homebrew, will not work with Qt5.
Before running CMake, some environment variables need to be set on the command
line. If omitted, the linker will throw a bunch of warnings later:
.. code-block:: bash
export SDKROOT=/Applications/Xcode.app/Contents/Developer/Platforms/\
MacOSX.platform/Developer/SDKs/MacOSX.sdk
If building the info module or with graphical user interface, get the Qt
binaries in your Path for CMake to determine its configuration:
.. code-block:: bash .. code-block:: bash
export PATH="/usr/local/opt/qt@5/bin:$PATH" wget https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
stage/bin/chemdict_tool create components.cif.gz <compounds.chemlib>
Homebrew installs all the software under /usr/local. Thus we have to tell cmake We can rerun cmake and make. All cmake parameters from the original
where to find Python. Also the Python headers and libraries are not located as configuration remain in the cache.
they are on Linux and hence they must be specified too. To get rid of a ton of
compilation warnings from third party software, we add some dedicated C flags:
.. code-block:: bash .. code-block:: bash
cmake . -DPython_INCLUDE_DIRS=/usr/local/opt/python@3.9/Frameworks/\ cmake .. -DCOMPOUND_LIB=<compounds.chemlib>
Python.framework/Versions/Current/include/python3.9/ \ make
-DPython_LIBRARIES=/usr/local/opt/python@3.9/Frameworks/\
Python.framework/Versions/Current/lib/libpython3.9.dylib \
-DPython_ROOT_DIR=/usr/local/opt/python@3.9/ \
-DBOOST_ROOT=/usr/local \
-DSYS_ROOT=/usr/local \
-DOPTIMIZE=ON \
-DCMAKE_C_FLAGS="-isystem /Applications/Xcode.app/Contents/\
Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/\
Library/Frameworks/OpenGL.framework/Headers/ -isystem /usr/local/opt/\
qt@5/lib/QtCore.framework/Headers/ -isystem /usr/local/opt/qt@5/lib/\
QtWidgets.framework/Headers/ -isystem /Applications/Xcode.app/\
Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/\
MacOSX.sdk/System/Library/Frameworks/Security.framework/ \
-isystem /usr/local/opt/qt@5/lib/QtGui.framework/Headers/" \
-DCMAKE_CXX_FLAGS="-isystem /Applications/Xcode.app/\
Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/\
System/Library/Frameworks/OpenGL.framework/Headers/ -isystem /usr/local/opt/\
qt@5/lib/QtCore.framework/Headers/ -isystem /usr/local/opt/qt@5/lib/\
QtWidgets.framework/Headers/ -isystem /Applications/Xcode.app/\
Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/\
MacOSX.sdk/System/Library/Frameworks/Security.framework/ \
-isystem /usr/local/opt/qt@5/lib/QtGui.framework/Headers/"
Building the Project
--------------------------------------------------------------------------------
Type ``make``. If you are using a multi-core machine, you can use the `-j` flag
to run multiple jobs at once.
What's next?
--------------------------------------------------------------------------------
On Linux and macOS, you can start dng from the command-line. The binaries are On Linux and macOS, you can start dng from the command-line. The binaries are
all located in stage/bin: all located in stage/bin:
...@@ -426,6 +376,12 @@ or, to start the command-line interpreter: ...@@ -426,6 +376,12 @@ or, to start the command-line interpreter:
stage/bin/ost stage/bin/ost
But hey, good citizen run the unit tests first:
.. code-block:: bash
make check
If you repeatedly use OpenStructure, it is recommended to add If you repeatedly use OpenStructure, it is recommended to add
/path/to/ost/stage/bin to your path. /path/to/ost/stage/bin to your path.
......
singularity/Singularity
+ 1
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BootStrap: docker BootStrap: docker
From: registry.scicore.unibas.ch/schwede/openstructure:2.9.1 From: registry.scicore.unibas.ch/schwede/openstructure:2.9.2
%post %post
############################################################################## ##############################################################################
# POST # POST
......
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