diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index 2bf42f24a7114df591e71881b158a7aba9fcb1e6..5d58f1cb4e15df04671abc8aa477eb0e726e03c2 100644
--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
@@ -1,4 +1,4 @@
-Changes in Release 1.x.x
+Changes in Release 1.10.0
--------------------------------------------------------------------------------
* Use system provided SQLite3 library.
@@ -9,6 +9,7 @@ Changes in Release 1.x.x
for further details.
* Improved support for recent compilers and libraries.
* Removed support for USE_MESA.
+ * Bugfix of string representation of ResNum which now includes insertion code.
* Several minor bug fixes and improvements.
Changes in Release 1.9.0
diff --git a/CMakeLists.txt b/CMakeLists.txt
index e976dce27a4832c2d059df8f7829cab4446ba155..7b76c4eeabb796d74a31491335e6be9ab53c2a2b 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -6,22 +6,12 @@ cmake_minimum_required(VERSION 2.6.4 FATAL_ERROR)
project(OpenStructure CXX C)
set (CMAKE_EXPORT_COMPILE_COMMANDS 1)
set (OST_VERSION_MAJOR 1)
-set (OST_VERSION_MINOR 9)
+set (OST_VERSION_MINOR 10)
set (OST_VERSION_PATCH 0)
set (OST_VERSION_STRING ${OST_VERSION_MAJOR}.${OST_VERSION_MINOR}.${OST_VERSION_PATCH} )
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake_support)
include(OST)
-
-if (CMAKE_COMPILER_IS_GNUCXX)
- exec_program(gcc ARGS --version OUTPUT_VARIABLE CMAKE_C_COMPILER_VERSION)
- if(CMAKE_C_COMPILER_VERSION MATCHES ".*4\\.[5-9].*")
- set(OST_GCC_45 true)
- else()
- set(OST_GCC_45 false)
- endif()
-endif()
-
option(USE_SHADER "whether to compile with shader support"
OFF)
option(USE_RPATH "embed rpath upon make install"
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 55824c75509a1d2dcec7a05c1bdc0db38b585de5..8ae9ff19e36718f38b319b40e79fea337d883a1f 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -31,7 +31,7 @@ Only model structures are "Molck-ed" in CAMEO. The call to molck is as follows:
molck \\
--complib=<COMPOUND LIB> \\
- --rm=hyd,oxt,unk \\
+ --rm=hyd,oxt,unk,nonstd \\
--fix-ele \\
--map-nonstd \\
--out=<OUTPUT> \\
@@ -45,7 +45,7 @@ compare-structures as follows:
--reference <REF> \\
--output output.json \\
--molck \\
- --remove oxt hyd unk \\
+ --remove oxt hyd unk nonstd \\
--clean-element-column \\
--map-nonstandard-residues \\
--structural-checks \\
@@ -243,7 +243,7 @@ def _ParseArgs():
" * hyd - remove hydrogen atoms\n"
" * oxt - remove terminal oxygens\n"
" * nonstd - remove all residues not one of the 20\n"
- " * standard amino acids\n"
+ " standard amino acids\n"
" * unk - Remove unknown and atoms not following the\n"
" nomenclature\n"
"Defaults to hyd."))
diff --git a/cmake_support/OST.cmake b/cmake_support/OST.cmake
index 4ee0d944049fed084c53ea42b9977132c3f51d37..31c304804c033fc6f4cb142c726c618a45db1138 100644
--- a/cmake_support/OST.cmake
+++ b/cmake_support/OST.cmake
@@ -321,15 +321,15 @@ macro(executable)
if (ENABLE_STATIC AND _ARG_STATIC)
target_link_libraries(${_ARG_NAME} ${STATIC_LIBRARIES})
if (UNIX AND NOT APPLE)
- if (OST_GCC_45)
- set_target_properties(${_ARG_NAME}
- PROPERTIES LINK_SEARCH_END_STATIC TRUE
- LINK_FLAGS "-static-libgcc -static-libstdc++ -static -pthread")
+ set_target_properties(${_ARG_NAME} PROPERTIES LINK_SEARCH_START_STATIC TRUE)
+ set_target_properties(${_ARG_NAME} PROPERTIES LINK_SEARCH_END_STATIC TRUE)
+ if (OST_GCC_LESS_45)
+ set_target_properties(${_ARG_NAME} PROPERTIES LINK_FLAGS
+ "-static-libgcc -static -pthread")
else()
- set_target_properties(${_ARG_NAME}
- PROPERTIES LINK_SEARCH_END_STATIC TRUE
- LINK_FLAGS "-static-libgcc -static -pthread")
- endif()
+ set_target_properties(${_ARG_NAME} PROPERTIES LINK_FLAGS
+ "-static-libgcc -static-libstdc++ -static -pthread")
+ endif()
endif()
endif()
install(TARGETS ${_ARG_NAME} DESTINATION bin)
@@ -859,7 +859,7 @@ endmacro()
#-------------------------------------------------------------------------------
function(get_compiler_version _OUTPUT_VERSION)
exec_program(${CMAKE_CXX_COMPILER}
- ARGS ${CMAKE_CXX_COMPILER_ARG1} -dumpversion
+ ARGS ${CMAKE_CXX_COMPILER_ARG1} -dumpfullversion -dumpversion
OUTPUT_VARIABLE _COMPILER_VERSION
)
string(REGEX REPLACE "([0-9])\\.([0-9])(\\.[0-9])?" "\\1\\2"
@@ -899,9 +899,13 @@ macro(setup_compiler_flags)
#message(STATUS "GCC VERSION " ${_GCC_VERSION})
if ((ENABLE_INFO OR ENABLE_GUI) AND _GCC_VERSION LESS "60")
# for older compilers we need to enable C++11 for Qt5
- #message(STATUS "ADDING C++11 FLAG")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
endif()
+ if (_GCC_VERSION LESS "45")
+ set(OST_GCC_LESS_45 true)
+ else()
+ set(OST_GCC_LESS_45 false)
+ endif()
endif()
endmacro()
set(_BOOST_MIN_VERSION 1.31)
diff --git a/modules/db/src/CMakeLists.txt b/modules/db/src/CMakeLists.txt
index 8c536297f304b1a8ec686500c2259159c7002230..8b59de092c830779d896e3a84a6cae83e43646a2 100644
--- a/modules/db/src/CMakeLists.txt
+++ b/modules/db/src/CMakeLists.txt
@@ -23,4 +23,6 @@ if(WIN32)
else(WIN32)
add_definitions(-DSQLITE_OMIT_LOAD_EXTENSION)
endif(WIN32)
-
+if (ENABLE_STATIC AND UNIX AND NOT APPLE)
+ target_link_libraries(ost_db ${CMAKE_DL_LIBS})
+endif()
diff --git a/modules/doc/actions.rst b/modules/doc/actions.rst
index ccda8476eee514ece15815bab7bff2fe0b27de02..993612233e4650e6f76287864fe29bcfa9f7f1d2 100644
--- a/modules/doc/actions.rst
+++ b/modules/doc/actions.rst
@@ -1,4 +1,4 @@
-.. Note on large code blocks: keep max. width to 120 or it will look bad
+.. Note on large code blocks: keep max. width to 100 or it will look bad
on webpage!
.. TODO: look at argparse directive to autogenerate --help output!
@@ -101,7 +101,7 @@ Details on the usage (output of ``ost compare-structures --help``):
molck \
--complib=<COMPOUND LIB> \
- --rm=hyd,oxt,unk \
+ --rm=hyd,oxt,unk,nonstd \
--fix-ele \
--map-nonstd \
--out=<OUTPUT> \
@@ -115,7 +115,7 @@ Details on the usage (output of ``ost compare-structures --help``):
--reference <REF> \
--output output.json \
--molck \
- --remove oxt hyd unk \
+ --remove oxt hyd unk nonstd \
--clean-element-column \
--map-nonstandard-residues \
--structural-checks \
@@ -171,7 +171,7 @@ Details on the usage (output of ``ost compare-structures --help``):
* hyd - remove hydrogen atoms
* oxt - remove terminal oxygens
* nonstd - remove all residues not one of the 20
- * standard amino acids
+ standard amino acids
* unk - Remove unknown and atoms not following the
nomenclature
Defaults to hyd.
@@ -250,68 +250,68 @@ The output file has following format:
.. code-block:: none
{
- "result": {
- "<MODEL NAME>": { # Model name extracted from the file name
- "<REFERENCE NAME>": { # Reference name extracted from the file name
- "info": {
- "residue_names_consistent": <Are the residue numbers consistent? true or false>,
- "mapping": {
- "chain_mapping": <Mapping of chains eg. {"A": "B", "B": "A"}>,
- "chain_mapping_scheme": <Scheme used to get mapping, check mapping manually
- if "permissive" or "extensive">,
- "alignments": <list of chain-chain alignments in FASTA format>
- }
- },
- "lddt": {
- # calculated when --lddt (-l) option is selected
- "oligo_lddt": {
- "status": <SUCCESS or FAILURE>,
- "error": <ERROR message if any>,
- "global_score": <calculated oligomeric lDDT score>
- },
- "weighted_lddt": {
- "status": <SUCCESS or FAILURE>,
- "error": <ERROR message if any>,
- "global_score": <calculated weighted lDDT score>
- },
- "single_chain_lddt": [
- # a list of chain-chain lDDTs
- {
- "status": <SUCCESS or FAILURE>,
- "error": <ERROR message if any>,
- "reference_chain": <name of the chain in reference>,
- "model_chain": <name of the chain in model>
- "global_score": <calculated single-chain lDDT score>,
- "conserved_contacts": <number of conserved contacts between model and reference>,
- "total_contacts": <total number of contacts in reference>,
- "per_residue_scores": [
- # per-residue lDDT scores
- # only calculated when --save-per-residue-scores (-spr) option is selected
- {
- "residue_name": <three letter code of the residue in reference chain>,
- "residue_number": <residue number in reference chain>,
- "lddt": <residue lDDT score>,
- "conserved_contacts": <conserved_contacts for given residue>,
- "total_contacts": <total_contacts for given residue>
- },
- .
- .
- .
- ]
- }
- ]
+ "options": { ... }, # Options used to run the script
+ "result": {
+ "<MODEL NAME>": { # Model name extracted from the file name
+ "<REFERENCE NAME>": { # Reference name extracted from the file name
+ "info": {
+ "mapping": {
+ "alignments": <list of chain-chain alignments in FASTA format>,
+ "chain_mapping": <Mapping of chains eg. {"A": "B", "B": "A"}>,
+ "chain_mapping_scheme": <Scheme used to get mapping, check mapping manually
+ if "permissive" or "extensive">
+ },
+ "residue_names_consistent": <Are the residue numbers consistent? true or false>
+ },
+ "lddt": {
+ # calculated when --lddt (-l) option is selected
+ "oligo_lddt": {
+ "error": <ERROR message if any>,
+ "global_score": <calculated oligomeric lDDT score>,
+ "status": <SUCCESS or FAILURE>
+ },
+ "single_chain_lddt": [
+ # a list of chain-chain lDDTs
+ {
+ "conserved_contacts": <number of conserved contacts between model & reference>,
+ "error": <ERROR message if any>,
+ "global_score": <calculated single-chain lDDT score>,
+ "model_chain": <name of the chain in model>,
+ "reference_chain": <name of the chain in reference>,
+ "status": <SUCCESS or FAILURE>,
+ "total_contacts": <total number of contacts in reference>,
+ "per_residue_scores": [
+ # per-residue lDDT scores
+ # only calculated when --save-per-residue-scores (-spr) option is selected
+ {
+ "residue_name": <three letter code of the residue in reference chain>,
+ "residue_number": <residue number in reference chain>,
+ "lddt": <residue lDDT score>,
+ "conserved_contacts": <conserved_contacts for given residue>,
+ "total_contacts": <total_contacts for given residue>
},
- "qs_score": {
- # calculated when --qs-score (-q) option is selected
- "status": <SUCCESS or FAILURE>,
- "error": <ERROR message if any>,
- "global_score": <Global QS-score>,
- "best_score": <Best QS-score>
- }
+ .
+ .
+ .
+ ]
}
+ ],
+ "weighted_lddt": {
+ "error": <ERROR message if any>,
+ "global_score": <calculated weighted lDDT score>,
+ "status": <SUCCESS or FAILURE>
+ }
+ },
+ "qs_score": {
+ # calculated when --qs-score (-q) option is selected
+ "best_score": <Best QS-score>,
+ "error": <ERROR message if any>,
+ "global_score": <Global QS-score>,
+ "status": <SUCCESS or FAILURE>
}
- },
- "options": {} # Options used to run the script
+ }
+ }
+ }
}
The "result" filed is a dictionary mapping from model to reference as eg. in
@@ -322,64 +322,34 @@ Example usage:
.. code-block:: console
- $ CAMEO_TARGET_URL=https://www.cameo3d.org/static/data/modeling/2018.03.03/5X7J_B
+ $ CAMEO_TARGET_URL=https://www.cameo3d.org/static/data/modeling/2019.07.13/6PO4_F
$ curl $CAMEO_TARGET_URL/bu_target_01.pdb > reference.pdb
- $ curl $CAMEO_TARGET_URL/servers/server11/oligo_model-1/superposed_oligo_model-1.pdb > model.pdb
+ $ curl $CAMEO_TARGET_URL/servers/server20/oligomodel-1/oligomodel-1.pdb > model.pdb
$ $OST_ROOT/bin/ost compare-structures \
--model model.pdb --reference reference.pdb --output output.json \
--qs-score --residue-number-alignment --lddt --structural-checks \
--consistency-checks --inclusion-radius 15.0 --bond-tolerance 15.0 \
- --angle-tolerance 15.0 --molck --remove oxt hyd unk \
+ --angle-tolerance 15.0 --molck --remove oxt hyd unk nonstd \
--clean-element-column --map-nonstandard-residues
################################################################################
Reading input files (fault_tolerant=False)
--> reading model from model.pdb
- imported 2 chains, 396 residues, 3106 atoms; with 0 helices and 0 strands
+ imported 2 chains, 462 residues, 3400 atoms; with 0 helices and 0 strands
--> reading reference from reference.pdb
- imported 3 chains, 408 residues, 3011 atoms; with 0 helices and 0 strands
+ imported 3 chains, 471 residues, 3465 atoms; with 0 helices and 0 strands
################################################################################
Cleaning up input with Molck
removing hydrogen atoms
--> removed 0 hydrogen atoms
removing OXT atoms
- --> removed 0 OXT atoms
- residue A.GLN54 is missing 4 atoms: 'CG', 'CD', 'OE1', 'NE2'
- residue A.GLU55 is missing 4 atoms: 'CG', 'CD', 'OE1', 'OE2'
- residue A.ARG139 is missing 6 atoms: 'CG', 'CD', 'NE', 'CZ', 'NH1', 'NH2'
- residue B.THR53 is missing 1 atom: 'CG2'
- residue B.GLN54 is missing 4 atoms: 'CG', 'CD', 'OE1', 'NE2'
- residue B.GLU55 is missing 4 atoms: 'CG', 'CD', 'OE1', 'OE2'
- residue B.GLU61 is missing 1 atom: 'OE2'
- residue B.GLU117 is missing 1 atom: 'O'
- residue B.ARG120 is missing 2 atoms: 'NH1', 'NH2'
- residue B.ARG142 is missing 2 atoms: 'NH1', 'NH2'
- residue B.GLU148 is missing 4 atoms: 'CG', 'CD', 'OE1', 'OE2'
- residue B.PRO198 is missing 1 atom: 'O'
- _.CL1 is not a standard amino acid
- _.CL2 is not a standard amino acid
- _.CL3 is not a standard amino acid
- _.CL4 is not a standard amino acid
- _.CA5 is not a standard amino acid
- _.CA6 is not a standard amino acid
- _.CA7 is not a standard amino acid
- _.CA8 is not a standard amino acid
- _.CA9 is not a standard amino acid
- _.CL10 is not a standard amino acid
- _.CL11 is not a standard amino acid
- _.CL12 is not a standard amino acid
- _.CL13 is not a standard amino acid
- _.CL14 is not a standard amino acid
- _.CL15 is not a standard amino acid
- _.CA16 is not a standard amino acid
- _.CA17 is not a standard amino acid
- _.CA18 is not a standard amino acid
- _.CA19 is not a standard amino acid
- _.CA20 is not a standard amino acid
- _.EDO21 is not a standard amino acid
- _.EDO22 is not a standard amino acid
- _.EDO23 is not a standard amino acid
- _.EDO24 is not a standard amino acid
+ --> removed 3 OXT atoms
+ _.HCS1 is not a standard amino acid --> removed
+ _.ADE2 is not a standard amino acid --> removed
+ _.BO33 is not a standard amino acid --> removed
+ _.ADE4 is not a standard amino acid --> removed
+ _.HCS5 is not a standard amino acid --> removed
+ _.BO36 is not a standard amino acid --> removed
removing hydrogen atoms
--> removed 0 hydrogen atoms
removing OXT atoms
@@ -389,29 +359,30 @@ Example usage:
--> for reference(s)
Checking reference.pdb
Checking stereo-chemistry
- Average Z-Score for bond lengths: 0.13694
- Bonds outside of tolerance range: 0 out of 2654
+ Average Z-Score for bond lengths: 0.33163
+ Bonds outside of tolerance range: 0 out of 2993
Bond Avg Length Avg zscore Num Bonds
- C-C 1.50876 0.09299 1501
- C-N 1.42978 0.17690 635
- C-O 1.25079 0.21528 518
- Average Z-Score angle widths: 0.07562
- Angles outside of tolerance range: 0 out of 2941
+ C-C 1.51236 0.03971 1682
+ C-N 1.46198 0.96819 603
+ C-O 1.25794 0.49967 674
+ C-S 1.80242 0.15292 34
+ Average Z-Score angle widths: -0.12077
+ Angles outside of tolerance range: 0 out of 3260
Filtering non-bonded clashes
0 non-bonded short-range distances shorter than tolerance distance
Distances shorter than tolerance are on average shorter by: 0.00000
--> for model(s)
Checking model.pdb
Checking stereo-chemistry
- Average Z-Score for bond lengths: -0.22524
- Bonds outside of tolerance range: 0 out of 2774
+ Average Z-Score for bond lengths: 0.23693
+ Bonds outside of tolerance range: 0 out of 2976
Bond Avg Length Avg zscore Num Bonds
- C-C 1.50225 -0.20158 1558
- C-N 1.42294 -0.12261 666
- C-O 1.24232 -0.42115 546
- C-S 1.80215 0.20858 4
- Average Z-Score angle widths: -0.06767
- Angles outside of tolerance range: 0 out of 3079
+ C-C 1.52020 0.40359 1674
+ C-N 1.43936 -0.19949 598
+ C-O 1.25221 0.20230 670
+ C-S 1.81182 0.38936 34
+ Average Z-Score angle widths: 0.04946
+ Angles outside of tolerance range: 0 out of 3241
Filtering non-bonded clashes
0 non-bonded short-range distances shorter than tolerance distance
Distances shorter than tolerance are on average shorter by: 0.00000
@@ -419,25 +390,25 @@ Example usage:
Comparing model.pdb to reference.pdb
Chains in reference.pdb: AB
Chains in model.pdb: AB
- Chemically equivalent chain-groups in reference.pdb: [['B', 'A']]
+ Chemically equivalent chain-groups in reference.pdb: [['A', 'B']]
Chemically equivalent chain-groups in model.pdb: [['A', 'B']]
- Chemical chain-groups mapping: {('B', 'A'): ('A', 'B')}
+ Chemical chain-groups mapping: {('A', 'B'): ('A', 'B')}
Identifying Symmetry Groups...
Symmetry threshold 0.1 used for angles of reference.pdb
Symmetry threshold 0.1 used for axis of reference.pdb
Symmetry threshold 0.1 used for angles of model.pdb
Symmetry threshold 0.1 used for axis of model.pdb
Selecting Symmetry Groups...
- Symmetry-groups used in reference.pdb: [('B',), ('A',)]
+ Symmetry-groups used in reference.pdb: [('A',), ('B',)]
Symmetry-groups used in model.pdb: [('A',), ('B',)]
Closed Symmetry with strict parameters
- Mapping found: {'A': 'B', 'B': 'A'}
+ Mapping found: {'A': 'A', 'B': 'B'}
--------------------------------------------------------------------------------
Checking consistency between model.pdb and reference.pdb
Consistency check: OK
--------------------------------------------------------------------------------
Computing QS-score
- QSscore reference.pdb, model.pdb: best: 0.90, global: 0.90
+ QSscore reference.pdb, model.pdb: best: 0.96, global: 0.96
--------------------------------------------------------------------------------
Computing lDDT scores
lDDT settings:
@@ -446,21 +417,21 @@ Example usage:
Cutoffs: 0.5, 1, 2, 4
Residue properties label: lddt
===
- --> Computing lDDT between model chain B and reference chain A
- Coverage: 1 (187 out of 187 residues)
- Global LDDT score: 0.8257
- (877834 conserved distances out of 1063080 checked, over 4 thresholds)
- --> Computing lDDT between model chain A and reference chain B
- Coverage: 1 (197 out of 197 residues)
- Global LDDT score: 0.7854
- (904568 conserved distances out of 1151664 checked, over 4 thresholds)
+ --> Computing lDDT between model chain A and reference chain A
+ Coverage: 0.991416 (231 out of 233 residues)
+ Global LDDT score: 0.8955
+ (1194245 conserved distances out of 1333644 checked, over 4 thresholds)
+ --> Computing lDDT between model chain B and reference chain B
+ Coverage: 0.991379 (230 out of 232 residues)
+ Global LDDT score: 0.8998
+ (1200391 conserved distances out of 1334056 checked, over 4 thresholds)
--> Computing oligomeric lDDT score
Reference reference.pdb has: 2 chains
Model model.pdb has: 2 chains
- Coverage: 1 (384 out of 384 residues)
- Oligo lDDT score: 0.8025
+ Coverage: 0.991398 (461 out of 465 residues)
+ Oligo lDDT score: 0.8977
--> Computing weighted lDDT score
- Weighted lDDT score: 0.8048
+ Weighted lDDT score: 0.8976
################################################################################
Saving output into output.json
@@ -475,112 +446,114 @@ alignments were cut in display here for readability):
new_alns = list()
for aln in mapping["alignments"]:
aln_lines = aln.splitlines()
- aln_lines[1] = aln_lines[1][:20] + "..."
- aln_lines[3] = aln_lines[3][:20] + "..."
+ aln_lines[1] = aln_lines[1][:15] + "..."
+ aln_lines[3] = aln_lines[3][:15] + "..."
new_alns.append("\n".join(aln_lines))
mapping["alignments"] = new_alns
json_data["options"]["parameter_file"] = "Path to stage/share/openstructure/stereo_chemical_props.txt"
json_data["options"]["compound_library"] = "Path to stage/share/openstructure/compounds.chemlib"
+ json_data["options"]["cwd"] = "Path to current working directory"
with open("output_fixed.json", "w") as outfile:
- json.dump(json_data, outfile, indent=4, sort_keys=True)
+ json.dump(json_data, outfile, indent=2, sort_keys=True)
.. code-block:: json
{
- "options": {
- "angle_tolerance": 15.0,
- "bond_tolerance": 15.0,
- "c_alpha_only": false,
- "chain_mapping": null,
- "clean_element_column": true,
- "compound_library": "Path to stage/share/openstructure/compounds.chemlib",
- "consistency_checks": true,
- "cwd": "/home/taurielg/GT/Code/ost/build",
- "dump_structures": false,
- "dump_suffix": ".compare.structures.pdb",
- "fault_tolerant": false,
- "inclusion_radius": 15.0,
- "lddt": true,
- "map_nonstandard_residues": true,
- "model": "model.pdb",
- "model_selection": "",
- "molck": true,
- "output": "output.json",
- "parameter_file": "Path to stage/share/openstructure/stereo_chemical_props.txt",
- "qs_max_mappings_extensive": 1000000,
- "qs_rmsd": false,
- "qs_score": true,
- "reference": "reference.pdb",
- "reference_selection": "",
- "remove": [
- "oxt",
- "hyd",
- "unk"
- ],
- "residue_number_alignment": true,
- "save_per_residue_scores": false,
- "sequence_separation": 0,
- "structural_checks": true,
- "verbosity": 3
- },
- "result": {
- "model.pdb": {
- "reference.pdb": {
- "info": {
- "mapping": {
- "alignments": [
- ">reference:A\n-PGLFLTLEGLDGSGKTTQA...\n>model:B\nMPGLFLTLEGLDGSGKTTQA...",
- ">reference:B\n-PGLFLTLEGLDGSGKTTQA...\n>model:A\nMPGLFLTLEGLDGSGKTTQA..."
- ],
- "chain_mapping": {
- "A": "B",
- "B": "A"
- },
- "chain_mapping_scheme": "strict"
- },
- "residue_names_consistent": true
- },
- "lddt": {
- "oligo_lddt": {
- "error": "",
- "global_score": 0.8025223275721413,
- "status": "SUCCESS"
- },
- "single_chain_lddt": [
- {
- "conserved_contacts": 877834,
- "error": "",
- "global_score": 0.8257459402084351,
- "model_chain": "B",
- "reference_chain": "A",
- "status": "SUCCESS",
- "total_contacts": 1063080
- },
- {
- "conserved_contacts": 904568,
- "error": "",
- "global_score": 0.7854443788528442,
- "model_chain": "A",
- "reference_chain": "B",
- "status": "SUCCESS",
- "total_contacts": 1151664
- }
- ],
- "weighted_lddt": {
- "error": "",
- "global_score": 0.804789180710712,
- "status": "SUCCESS"
- }
- },
- "qs_score": {
- "best_score": 0.9022811630070536,
- "error": "",
- "global_score": 0.8974384796108209,
- "status": "SUCCESS"
- }
+ "options": {
+ "angle_tolerance": 15.0,
+ "bond_tolerance": 15.0,
+ "c_alpha_only": false,
+ "chain_mapping": null,
+ "clean_element_column": true,
+ "compound_library": "Path to stage/share/openstructure/compounds.chemlib",
+ "consistency_checks": true,
+ "cwd": "Path to current working directory",
+ "dump_structures": false,
+ "dump_suffix": ".compare.structures.pdb",
+ "fault_tolerant": false,
+ "inclusion_radius": 15.0,
+ "lddt": true,
+ "map_nonstandard_residues": true,
+ "model": "model.pdb",
+ "model_selection": "",
+ "molck": true,
+ "output": "output.json",
+ "parameter_file": "Path to stage/share/openstructure/stereo_chemical_props.txt",
+ "qs_max_mappings_extensive": 1000000,
+ "qs_rmsd": false,
+ "qs_score": true,
+ "reference": "reference.pdb",
+ "reference_selection": "",
+ "remove": [
+ "oxt",
+ "hyd",
+ "unk",
+ "nonstd"
+ ],
+ "residue_number_alignment": true,
+ "save_per_residue_scores": false,
+ "sequence_separation": 0,
+ "structural_checks": true,
+ "verbosity": 3
+ },
+ "result": {
+ "model.pdb": {
+ "reference.pdb": {
+ "info": {
+ "mapping": {
+ "alignments": [
+ ">reference:A\n-NAMKIGIVGAMAQE...\n>model:A\n---MKIGIVGAMAQE...",
+ ">reference:B\n-NAMKIGIVGAMAQE...\n>model:B\n---MKIGIVGAMAQE..."
+ ],
+ "chain_mapping": {
+ "A": "A",
+ "B": "B"
+ },
+ "chain_mapping_scheme": "strict"
+ },
+ "residue_names_consistent": true
+ },
+ "lddt": {
+ "oligo_lddt": {
+ "error": "",
+ "global_score": 0.8977285786061329,
+ "status": "SUCCESS"
+ },
+ "single_chain_lddt": [
+ {
+ "conserved_contacts": 1194245,
+ "error": "",
+ "global_score": 0.8954750895500183,
+ "model_chain": "A",
+ "reference_chain": "A",
+ "status": "SUCCESS",
+ "total_contacts": 1333644
+ },
+ {
+ "conserved_contacts": 1200391,
+ "error": "",
+ "global_score": 0.8998055458068848,
+ "model_chain": "B",
+ "reference_chain": "B",
+ "status": "SUCCESS",
+ "total_contacts": 1334056
}
+ ],
+ "weighted_lddt": {
+ "error": "",
+ "global_score": 0.8976406520766181,
+ "status": "SUCCESS"
+ }
+ },
+ "qs_score": {
+ "best_score": 0.9619749105661133,
+ "error": "",
+ "global_score": 0.9619749105661133,
+ "status": "SUCCESS"
}
+ }
}
+ }
}
If all the structures are clean and have matching residue numbers, one can omit
@@ -595,31 +568,32 @@ all the checking steps and calculate scores directly as here:
################################################################################
Reading input files (fault_tolerant=False)
--> reading model from model.pdb
- imported 2 chains, 396 residues, 3106 atoms; with 0 helices and 0 strands
+ imported 2 chains, 462 residues, 3400 atoms; with 0 helices and 0 strands
--> reading reference from reference.pdb
- imported 3 chains, 408 residues, 3011 atoms; with 0 helices and 0 strands
+ imported 3 chains, 471 residues, 3465 atoms; with 0 helices and 0 strands
################################################################################
Comparing model.pdb to reference.pdb
+ Chains removed from reference.pdb: _
Chains in reference.pdb: AB
Chains in model.pdb: AB
- Chemically equivalent chain-groups in reference.pdb: [['B', 'A']]
+ Chemically equivalent chain-groups in reference.pdb: [['A', 'B']]
Chemically equivalent chain-groups in model.pdb: [['A', 'B']]
- Chemical chain-groups mapping: {('B', 'A'): ('A', 'B')}
+ Chemical chain-groups mapping: {('A', 'B'): ('A', 'B')}
Identifying Symmetry Groups...
Symmetry threshold 0.1 used for angles of reference.pdb
Symmetry threshold 0.1 used for axis of reference.pdb
Symmetry threshold 0.1 used for angles of model.pdb
Symmetry threshold 0.1 used for axis of model.pdb
Selecting Symmetry Groups...
- Symmetry-groups used in reference.pdb: [('B',), ('A',)]
+ Symmetry-groups used in reference.pdb: [('A',), ('B',)]
Symmetry-groups used in model.pdb: [('A',), ('B',)]
Closed Symmetry with strict parameters
- Mapping found: {'A': 'B', 'B': 'A'}
+ Mapping found: {'A': 'A', 'B': 'B'}
--------------------------------------------------------------------------------
Checking consistency between model.pdb and reference.pdb
Consistency check: OK
--------------------------------------------------------------------------------
Computing QS-score
- QSscore reference.pdb, model.pdb: best: 0.90, global: 0.90
+ QSscore reference.pdb, model.pdb: best: 0.96, global: 0.96
################################################################################
Saving output into output_qs.json
diff --git a/modules/doc/install.rst b/modules/doc/install.rst
index 55a9cddaad94e61ebf758efe9950629395ab90f7..b86672515a32ada004e5a40b97acd8750997f773 100644
--- a/modules/doc/install.rst
+++ b/modules/doc/install.rst
@@ -234,7 +234,9 @@ Build Options
* `ENABLE_STATIC` allows some parts of OpenStructure to be statically linked
and thus can be used more easily across a heterogeneous setup, e.g. older
- systems and newer systems. By default, this is switched off.
+ systems and newer systems. Note that enabling this flag will not compile the
+ full OpenStructure package and it is not guaranteed to lead to fully portable
+ binaries. By default, this is switched off.
* For deployment of OpenStructure with `make install` there are two relevant
settings to consider:
diff --git a/modules/index.rst b/modules/index.rst
index 4b1b1d3c11c7a6b2c0ae585919ebe8479764576f..9727d322be7f61df6d9c20dd71f457ab6326f4be 100644
--- a/modules/index.rst
+++ b/modules/index.rst
@@ -37,7 +37,7 @@ OpenStructure documentation
For Starters
--------------------------------------------------------------------------------
-**Installation**: `install from binary <http://www.openstructure.org/download/>`_ | :doc:`install from source <install>`
+**Installation**: :doc:`install from source <install>`
**Tutorial Style**: :doc:`introduction <intro>` | :doc:`molecules intro <intro-01>` | :doc:`images intro <intro-02>` | :doc:`graphics intro <intro-03>`
diff --git a/modules/mol/alg/doc/molck.rst b/modules/mol/alg/doc/molck.rst
index 1dfaf6addeb0eca91744505ad34d9efb4a0eb6a2..7ffd414ae95c5f2f10c6cb739398dd164718792b 100644
--- a/modules/mol/alg/doc/molck.rst
+++ b/modules/mol/alg/doc/molck.rst
@@ -1,3 +1,6 @@
+.. Note on large code blocks: keep max. width to 100 or it will look bad
+ on webpage!
+
=========================
Molecular Checker (Molck)
=========================
@@ -37,23 +40,23 @@ please find them following:
.. code-block:: bash
usage: molck [options] file1.pdb [file2.pdb [...]]
- options
- --complib=path location of the compound library file. If not provided, the
- following locations are searched in this order:
- 1. Working directory,
- 2. OpenStructure standard library location (if the
- executable is part of a standard OpenStructure installation)
+ options
+ --complib=path location of the compound library file. If not provided, the
+ following locations are searched in this order:
+ 1. Working directory,
+ 2. OpenStructure standard library location (if the
+ executable is part of a standard OpenStructure installation)
--rm=<a>,<b> remove atoms and residues matching some criteria:
- - zeroocc - Remove atoms with zero occupancy
- - hyd - Remove hydrogen atoms
- - oxt - Remove terminal oxygens
- - nonstd - Remove all residues not one of the 20 standard amino acids
- - unk - Remove unknown and atoms not following the nomenclature
+ - zeroocc - Remove atoms with zero occupancy
+ - hyd - Remove hydrogen atoms
+ - oxt - Remove terminal oxygens
+ - nonstd - Remove all residues not one of the 20 standard amino acids
+ - unk - Remove unknown and atoms not following the nomenclature
--fix-ele clean up element column
- --stdout write cleaned file(s) to stdout
- --out=filename write cleaned file(s) to disk. % characters in the filename are
- replaced with the basename of the input file without extension.
- Default: %-molcked.pdb
+ --stdout write cleaned file(s) to stdout
+ --out=filename write cleaned file(s) to disk. % characters in the filename are
+ replaced with the basename of the input file without extension.
+ Default: %-molcked.pdb
--color=auto|on|off whether output should be colored
--map-nonstd maps modified residues back to the parent amino acid, for example
MSE -> MET, SEP -> SER.
diff --git a/singularity/Singularity b/singularity/Singularity
index 0a6c58eaac787d83b890f85426ae91c69b7fa918..429cb86a501f77822f52648490f7cf89e8a6ad61 100644
--- a/singularity/Singularity
+++ b/singularity/Singularity
@@ -214,7 +214,7 @@ cd /home
# ENVIRONMENT
##############################################################################
export OST_ROOT="/usr/local"
-export OPENSTRUCTURE_VERSION="1.9.0"
+export OPENSTRUCTURE_VERSION="1.10.0"
export OPENMM_LIB_PATH=/usr/local/openmm/lib/
export PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib64:${OPENMM_LIB_PATH}"