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Makefile

© Copyright 2024, BonvinLab. - Last updated on Oct 29, 2024. + Last updated on Oct 31, 2024.

diff --git a/INSTALL.html b/INSTALL.html index 35319dfa8..622c4ddcc 100644 --- a/INSTALL.html +++ b/INSTALL.html @@ -206,7 +206,7 @@

openmm

© Copyright 2024, BonvinLab. - Last updated on Oct 29, 2024. + Last updated on Oct 31, 2024.

diff --git a/USAGE.html b/USAGE.html index ebe860ef2..608b49d85 100644 --- a/USAGE.html +++ b/USAGE.html @@ -135,7 +135,7 @@

Run HADDOCK3

© Copyright 2024, BonvinLab. - Last updated on Oct 29, 2024. + Last updated on Oct 31, 2024.

diff --git a/_modules/haddock.html b/_modules/haddock.html index ae1096bec..60d3fafc3 100644 --- a/_modules/haddock.html +++ b/_modules/haddock.html @@ -138,7 +138,7 @@

Source code for haddock

 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/clis/cli.html b/_modules/haddock/clis/cli.html
index 2d5b1214e..cd02799ac 100644
--- a/_modules/haddock/clis/cli.html
+++ b/_modules/haddock/clis/cli.html
@@ -310,7 +310,7 @@ 
Source code for haddock.clis.cli
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/clis/cli_analyse.html b/_modules/haddock/clis/cli_analyse.html
index 55faca0bd..979c8e4de 100644
--- a/_modules/haddock/clis/cli_analyse.html
+++ b/_modules/haddock/clis/cli_analyse.html
@@ -854,7 +854,7 @@ 
Source code for haddock.clis.cli_analyse
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/clis/cli_cfg.html b/_modules/haddock/clis/cli_cfg.html
index 614ac9172..5e18acc2c 100644
--- a/_modules/haddock/clis/cli_cfg.html
+++ b/_modules/haddock/clis/cli_cfg.html
@@ -337,7 +337,7 @@ 
Source code for haddock.clis.cli_cfg
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/clis/cli_clean.html b/_modules/haddock/clis/cli_clean.html
index 6122e2a65..964e1b6b0 100644
--- a/_modules/haddock/clis/cli_clean.html
+++ b/_modules/haddock/clis/cli_clean.html
@@ -217,7 +217,7 @@ 
Source code for haddock.clis.cli_clean
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/clis/cli_cp.html b/_modules/haddock/clis/cli_cp.html
index 4ddfafb8f..ee83b0fa2 100644
--- a/_modules/haddock/clis/cli_cp.html
+++ b/_modules/haddock/clis/cli_cp.html
@@ -280,7 +280,7 @@ 
Source code for haddock.clis.cli_cp
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/clis/cli_dmn.html b/_modules/haddock/clis/cli_dmn.html
index 1f626347b..b4fad48c6 100644
--- a/_modules/haddock/clis/cli_dmn.html
+++ b/_modules/haddock/clis/cli_dmn.html
@@ -455,7 +455,7 @@ 
Source code for haddock.clis.cli_dmn
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/clis/cli_mpi.html b/_modules/haddock/clis/cli_mpi.html
index aec9a6de7..f313651dc 100644
--- a/_modules/haddock/clis/cli_mpi.html
+++ b/_modules/haddock/clis/cli_mpi.html
@@ -230,7 +230,7 @@ 
Source code for haddock.clis.cli_mpi
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/clis/cli_pp.html b/_modules/haddock/clis/cli_pp.html
index 10f341128..636066902 100644
--- a/_modules/haddock/clis/cli_pp.html
+++ b/_modules/haddock/clis/cli_pp.html
@@ -269,7 +269,7 @@ 
Source code for haddock.clis.cli_pp
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/clis/cli_re.html b/_modules/haddock/clis/cli_re.html
index 2a81eb09c..06270d89c 100644
--- a/_modules/haddock/clis/cli_re.html
+++ b/_modules/haddock/clis/cli_re.html
@@ -155,7 +155,7 @@ 
Source code for haddock.clis.cli_re
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/clis/cli_restraints.html b/_modules/haddock/clis/cli_restraints.html
index dbb8d4876..20e94593d 100644
--- a/_modules/haddock/clis/cli_restraints.html
+++ b/_modules/haddock/clis/cli_restraints.html
@@ -215,7 +215,7 @@ 
Source code for haddock.clis.cli_restraints
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/clis/cli_score.html b/_modules/haddock/clis/cli_score.html
index bb591a668..d4568903a 100644
--- a/_modules/haddock/clis/cli_score.html
+++ b/_modules/haddock/clis/cli_score.html
@@ -389,7 +389,7 @@ 
Source code for haddock.clis.cli_score
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/clis/cli_traceback.html b/_modules/haddock/clis/cli_traceback.html
index 6991ac1c9..0b8d98f93 100644
--- a/_modules/haddock/clis/cli_traceback.html
+++ b/_modules/haddock/clis/cli_traceback.html
@@ -486,7 +486,7 @@ 
Source code for haddock.clis.cli_traceback
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/clis/cli_unpack.html b/_modules/haddock/clis/cli_unpack.html
index 69c46091e..d00cda355 100644
--- a/_modules/haddock/clis/cli_unpack.html
+++ b/_modules/haddock/clis/cli_unpack.html
@@ -239,7 +239,7 @@ 
Source code for haddock.clis.cli_unpack
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/clis/re/clustfcc.html b/_modules/haddock/clis/re/clustfcc.html
index dd1554c55..9357e8594 100644
--- a/_modules/haddock/clis/re/clustfcc.html
+++ b/_modules/haddock/clis/re/clustfcc.html
@@ -310,7 +310,7 @@ 
Source code for haddock.clis.re.clustfcc
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/clis/re/clustrmsd.html b/_modules/haddock/clis/re/clustrmsd.html
index e185c0116..d072e91c7 100644
--- a/_modules/haddock/clis/re/clustrmsd.html
+++ b/_modules/haddock/clis/re/clustrmsd.html
@@ -387,7 +387,7 @@ 
Source code for haddock.clis.re.clustrmsd
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/clis/re/score.html b/_modules/haddock/clis/re/score.html
index e4be04d62..fc5c7b149 100644
--- a/_modules/haddock/clis/re/score.html
+++ b/_modules/haddock/clis/re/score.html
@@ -243,7 +243,7 @@ 
Source code for haddock.clis.re.score
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/clis/restraints/active_passive_to_ambig.html b/_modules/haddock/clis/restraints/active_passive_to_ambig.html
index c1231dbd0..6dbd586c9 100644
--- a/_modules/haddock/clis/restraints/active_passive_to_ambig.html
+++ b/_modules/haddock/clis/restraints/active_passive_to_ambig.html
@@ -164,7 +164,7 @@ 
Source code for haddock.clis.restraints.active_passive_to_ambig

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/clis/restraints/calc_accessibility.html b/_modules/haddock/clis/restraints/calc_accessibility.html
index f02640885..eb3b77468 100644
--- a/_modules/haddock/clis/restraints/calc_accessibility.html
+++ b/_modules/haddock/clis/restraints/calc_accessibility.html
@@ -413,7 +413,7 @@ 
Source code for haddock.clis.restraints.calc_accessibility

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/clis/restraints/passive_from_active.html b/_modules/haddock/clis/restraints/passive_from_active.html
index bc8fe51ff..23a14d183 100644
--- a/_modules/haddock/clis/restraints/passive_from_active.html
+++ b/_modules/haddock/clis/restraints/passive_from_active.html
@@ -162,7 +162,7 @@ 
Source code for haddock.clis.restraints.passive_from_active

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/clis/restraints/restrain_bodies.html b/_modules/haddock/clis/restraints/restrain_bodies.html
index 2bd5744ee..372135664 100644
--- a/_modules/haddock/clis/restraints/restrain_bodies.html
+++ b/_modules/haddock/clis/restraints/restrain_bodies.html
@@ -167,7 +167,7 @@ 
Source code for haddock.clis.restraints.restrain_bodies

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/clis/restraints/validate_tbl.html b/_modules/haddock/clis/restraints/validate_tbl.html
index d8653def3..38fc19dc3 100644
--- a/_modules/haddock/clis/restraints/validate_tbl.html
+++ b/_modules/haddock/clis/restraints/validate_tbl.html
@@ -153,7 +153,7 @@ 
Source code for haddock.clis.restraints.validate_tbl

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/clis/restraints/z_surface_restraints.html b/_modules/haddock/clis/restraints/z_surface_restraints.html
index 1d70c38be..94f91c28f 100644
--- a/_modules/haddock/clis/restraints/z_surface_restraints.html
+++ b/_modules/haddock/clis/restraints/z_surface_restraints.html
@@ -873,7 +873,7 @@ 
Source code for haddock.clis.restraints.z_surface_restraints

 
diff --git a/_modules/haddock/core/cns_paths.html b/_modules/haddock/core/cns_paths.html
index c6b89d971..2232dd02e 100644
--- a/_modules/haddock/core/cns_paths.html
+++ b/_modules/haddock/core/cns_paths.html
@@ -189,7 +189,7 @@ 
Source code for haddock.core.cns_paths
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/core/exceptions.html b/_modules/haddock/core/exceptions.html
index ce17ebf70..c649eca52 100644
--- a/_modules/haddock/core/exceptions.html
+++ b/_modules/haddock/core/exceptions.html
@@ -201,7 +201,7 @@ 
Source code for haddock.core.exceptions
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/core/supported_molecules.html b/_modules/haddock/core/supported_molecules.html
index 812c60272..9fb44755d 100644
--- a/_modules/haddock/core/supported_molecules.html
+++ b/_modules/haddock/core/supported_molecules.html
@@ -587,7 +587,7 @@ 
Source code for haddock.core.supported_molecules

 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/core/typing.html b/_modules/haddock/core/typing.html
index 19fe330b6..e0d48e032 100644
--- a/_modules/haddock/core/typing.html
+++ b/_modules/haddock/core/typing.html
@@ -295,7 +295,7 @@ 
Source code for haddock.core.typing
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/fcc/calc_fcc_matrix.html b/_modules/haddock/fcc/calc_fcc_matrix.html
index 43fe1649f..160e4ee14 100644
--- a/_modules/haddock/fcc/calc_fcc_matrix.html
+++ b/_modules/haddock/fcc/calc_fcc_matrix.html
@@ -197,7 +197,7 @@ 
Source code for haddock.fcc.calc_fcc_matrix
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/fcc/cluster_fcc.html b/_modules/haddock/fcc/cluster_fcc.html
index 23472eada..1a1aa94ee 100644
--- a/_modules/haddock/fcc/cluster_fcc.html
+++ b/_modules/haddock/fcc/cluster_fcc.html
@@ -306,7 +306,7 @@ 
Source code for haddock.fcc.cluster_fcc
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/gear/clean_steps.html b/_modules/haddock/gear/clean_steps.html
index ff0a2b519..1a018f8ca 100644
--- a/_modules/haddock/gear/clean_steps.html
+++ b/_modules/haddock/gear/clean_steps.html
@@ -341,7 +341,7 @@ 
Source code for haddock.gear.clean_steps
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/gear/config.html b/_modules/haddock/gear/config.html
index c7b825878..07ea76442 100644
--- a/_modules/haddock/gear/config.html
+++ b/_modules/haddock/gear/config.html
@@ -452,7 +452,7 @@ 
Source code for haddock.gear.config
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/gear/expandable_parameters.html b/_modules/haddock/gear/expandable_parameters.html
index 8f5f57af8..52df396d3 100644
--- a/_modules/haddock/gear/expandable_parameters.html
+++ b/_modules/haddock/gear/expandable_parameters.html
@@ -1071,7 +1071,7 @@ 
Source code for haddock.gear.expandable_parameters

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/gear/extend_run.html b/_modules/haddock/gear/extend_run.html
index 744d0457b..3aa7a216f 100644
--- a/_modules/haddock/gear/extend_run.html
+++ b/_modules/haddock/gear/extend_run.html
@@ -396,7 +396,7 @@ 
Source code for haddock.gear.extend_run
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/gear/greetings.html b/_modules/haddock/gear/greetings.html
index 11d86d43c..9feb62fbb 100644
--- a/_modules/haddock/gear/greetings.html
+++ b/_modules/haddock/gear/greetings.html
@@ -216,7 +216,7 @@ 
Source code for haddock.gear.greetings
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/gear/haddockmodel.html b/_modules/haddock/gear/haddockmodel.html
index 4a3736b50..23112fe16 100644
--- a/_modules/haddock/gear/haddockmodel.html
+++ b/_modules/haddock/gear/haddockmodel.html
@@ -158,7 +158,7 @@ 
Source code for haddock.gear.haddockmodel
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/gear/known_cns_errors.html b/_modules/haddock/gear/known_cns_errors.html
index 3ba8fbbd3..975376159 100644
--- a/_modules/haddock/gear/known_cns_errors.html
+++ b/_modules/haddock/gear/known_cns_errors.html
@@ -278,7 +278,7 @@ 
Source code for haddock.gear.known_cns_errors

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/gear/prepare_run.html b/_modules/haddock/gear/prepare_run.html
index c1e860704..b99738f9c 100644
--- a/_modules/haddock/gear/prepare_run.html
+++ b/_modules/haddock/gear/prepare_run.html
@@ -1662,7 +1662,7 @@ 
Source code for haddock.gear.prepare_run
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/gear/preprocessing.html b/_modules/haddock/gear/preprocessing.html
index ebafe30c4..19eee171c 100644
--- a/_modules/haddock/gear/preprocessing.html
+++ b/_modules/haddock/gear/preprocessing.html
@@ -1212,7 +1212,7 @@ 
Source code for haddock.gear.preprocessing
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/gear/restart_run.html b/_modules/haddock/gear/restart_run.html
index de38d88ea..dbc0534f6 100644
--- a/_modules/haddock/gear/restart_run.html
+++ b/_modules/haddock/gear/restart_run.html
@@ -162,7 +162,7 @@ 
Source code for haddock.gear.restart_run
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/gear/validations.html b/_modules/haddock/gear/validations.html
index 6b0930cc3..cf5500a8b 100644
--- a/_modules/haddock/gear/validations.html
+++ b/_modules/haddock/gear/validations.html
@@ -208,7 +208,7 @@ 
Source code for haddock.gear.validations
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/gear/yaml2cfg.html b/_modules/haddock/gear/yaml2cfg.html
index bd8a4947d..57f151c74 100644
--- a/_modules/haddock/gear/yaml2cfg.html
+++ b/_modules/haddock/gear/yaml2cfg.html
@@ -388,7 +388,7 @@ 
Source code for haddock.gear.yaml2cfg
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/gear/zerofill.html b/_modules/haddock/gear/zerofill.html
index 1d6f3a439..c3bb73857 100644
--- a/_modules/haddock/gear/zerofill.html
+++ b/_modules/haddock/gear/zerofill.html
@@ -233,7 +233,7 @@ 
Source code for haddock.gear.zerofill
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/libs/libalign.html b/_modules/haddock/libs/libalign.html
index b120c62e4..dc9af6f7a 100644
--- a/_modules/haddock/libs/libalign.html
+++ b/_modules/haddock/libs/libalign.html
@@ -1522,7 +1522,7 @@ 
Source code for haddock.libs.libalign
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/libs/libcli.html b/_modules/haddock/libs/libcli.html
index e5d8f1acd..f5a9c9a68 100644
--- a/_modules/haddock/libs/libcli.html
+++ b/_modules/haddock/libs/libcli.html
@@ -206,7 +206,7 @@ 
Source code for haddock.libs.libcli
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/libs/libclust.html b/_modules/haddock/libs/libclust.html
index 4ea82341b..b261fcf8f 100644
--- a/_modules/haddock/libs/libclust.html
+++ b/_modules/haddock/libs/libclust.html
@@ -423,7 +423,7 @@ 
Source code for haddock.libs.libclust
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/libs/libcns.html b/_modules/haddock/libs/libcns.html
index 6bdcf6a02..752f75980 100644
--- a/_modules/haddock/libs/libcns.html
+++ b/_modules/haddock/libs/libcns.html
@@ -519,7 +519,7 @@ 
Source code for haddock.libs.libcns
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/libs/libfcc.html b/_modules/haddock/libs/libfcc.html
index 852c07cae..2b923cc07 100644
--- a/_modules/haddock/libs/libfcc.html
+++ b/_modules/haddock/libs/libfcc.html
@@ -361,7 +361,7 @@ 
Source code for haddock.libs.libfcc
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/libs/libfunc.html b/_modules/haddock/libs/libfunc.html
index f9d82a2c8..6237334e5 100644
--- a/_modules/haddock/libs/libfunc.html
+++ b/_modules/haddock/libs/libfunc.html
@@ -216,7 +216,7 @@ 
Source code for haddock.libs.libfunc
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/libs/libhpc.html b/_modules/haddock/libs/libhpc.html
index fd5f58ee2..d4393916a 100644
--- a/_modules/haddock/libs/libhpc.html
+++ b/_modules/haddock/libs/libhpc.html
@@ -520,7 +520,7 @@ 
Source code for haddock.libs.libhpc
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/libs/libinteractive.html b/_modules/haddock/libs/libinteractive.html
index d5b303cc5..db88c64c1 100644
--- a/_modules/haddock/libs/libinteractive.html
+++ b/_modules/haddock/libs/libinteractive.html
@@ -303,7 +303,7 @@ 
Source code for haddock.libs.libinteractive
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/libs/libio.html b/_modules/haddock/libs/libio.html
index efb88c406..a1153cbb8 100644
--- a/_modules/haddock/libs/libio.html
+++ b/_modules/haddock/libs/libio.html
@@ -767,7 +767,7 @@ 
Source code for haddock.libs.libio
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/libs/liblog.html b/_modules/haddock/libs/liblog.html
index 8ad39413c..578d0e18d 100644
--- a/_modules/haddock/libs/liblog.html
+++ b/_modules/haddock/libs/liblog.html
@@ -181,7 +181,7 @@ 
Source code for haddock.libs.liblog
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/libs/libmath.html b/_modules/haddock/libs/libmath.html
index f4fa28935..f34292322 100644
--- a/_modules/haddock/libs/libmath.html
+++ b/_modules/haddock/libs/libmath.html
@@ -122,7 +122,7 @@ 
Source code for haddock.libs.libmath
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/libs/libmpi.html b/_modules/haddock/libs/libmpi.html
index 438e3a43e..a8ad5080b 100644
--- a/_modules/haddock/libs/libmpi.html
+++ b/_modules/haddock/libs/libmpi.html
@@ -142,7 +142,7 @@ 
Source code for haddock.libs.libmpi
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/libs/libontology.html b/_modules/haddock/libs/libontology.html
index a4101582b..f44fc2aa4 100644
--- a/_modules/haddock/libs/libontology.html
+++ b/_modules/haddock/libs/libontology.html
@@ -378,7 +378,7 @@ 
Source code for haddock.libs.libontology
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/libs/libparallel.html b/_modules/haddock/libs/libparallel.html
index cd024d087..bf694c5e1 100644
--- a/_modules/haddock/libs/libparallel.html
+++ b/_modules/haddock/libs/libparallel.html
@@ -324,7 +324,7 @@ 
Source code for haddock.libs.libparallel
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/libs/libpdb.html b/_modules/haddock/libs/libpdb.html
index ffbdc5899..7a025181a 100644
--- a/_modules/haddock/libs/libpdb.html
+++ b/_modules/haddock/libs/libpdb.html
@@ -420,7 +420,7 @@ 
Source code for haddock.libs.libpdb
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/libs/libplots.html b/_modules/haddock/libs/libplots.html
index d3191d0ff..cc403584e 100644
--- a/_modules/haddock/libs/libplots.html
+++ b/_modules/haddock/libs/libplots.html
@@ -1746,7 +1746,7 @@ 
Source code for haddock.libs.libplots
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/libs/librestraints.html b/_modules/haddock/libs/librestraints.html
index 9aa3062ac..21b990d4a 100644
--- a/_modules/haddock/libs/librestraints.html
+++ b/_modules/haddock/libs/librestraints.html
@@ -872,7 +872,7 @@ 
Source code for haddock.libs.librestraints
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/libs/libstructure.html b/_modules/haddock/libs/libstructure.html
index 4fbe48431..288c4f4df 100644
--- a/_modules/haddock/libs/libstructure.html
+++ b/_modules/haddock/libs/libstructure.html
@@ -139,7 +139,7 @@ 
Source code for haddock.libs.libstructure
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/libs/libsubprocess.html b/_modules/haddock/libs/libsubprocess.html
index 93fa35f94..545374bf5 100644
--- a/_modules/haddock/libs/libsubprocess.html
+++ b/_modules/haddock/libs/libsubprocess.html
@@ -394,7 +394,7 @@ 
Source code for haddock.libs.libsubprocess
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/libs/libtimer.html b/_modules/haddock/libs/libtimer.html
index eb40ef054..bef3a1087 100644
--- a/_modules/haddock/libs/libtimer.html
+++ b/_modules/haddock/libs/libtimer.html
@@ -170,7 +170,7 @@ 
Source code for haddock.libs.libtimer
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/libs/libutil.html b/_modules/haddock/libs/libutil.html
index 7fa45cc1b..f0fd50c42 100644
--- a/_modules/haddock/libs/libutil.html
+++ b/_modules/haddock/libs/libutil.html
@@ -512,7 +512,7 @@ 
Source code for haddock.libs.libutil
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/libs/libworkflow.html b/_modules/haddock/libs/libworkflow.html
index 5c8727715..ffff8619b 100644
--- a/_modules/haddock/libs/libworkflow.html
+++ b/_modules/haddock/libs/libworkflow.html
@@ -292,7 +292,7 @@ 
Source code for haddock.libs.libworkflow
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules.html b/_modules/haddock/modules.html
index 6b4265931..bac27d420 100644
--- a/_modules/haddock/modules.html
+++ b/_modules/haddock/modules.html
@@ -654,7 +654,7 @@ 
Source code for haddock.modules
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/analysis.html b/_modules/haddock/modules/analysis.html
index 4389f8d7d..34ef112a9 100644
--- a/_modules/haddock/modules/analysis.html
+++ b/_modules/haddock/modules/analysis.html
@@ -149,7 +149,7 @@ 
Source code for haddock.modules.analysis
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/analysis/alascan.html b/_modules/haddock/modules/analysis/alascan.html
index c4674e94f..1c1a52abf 100644
--- a/_modules/haddock/modules/analysis/alascan.html
+++ b/_modules/haddock/modules/analysis/alascan.html
@@ -203,7 +203,7 @@ 
Source code for haddock.modules.analysis.alascan

 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/analysis/alascan/scan.html b/_modules/haddock/modules/analysis/alascan/scan.html
index 1033d5704..e0354498d 100644
--- a/_modules/haddock/modules/analysis/alascan/scan.html
+++ b/_modules/haddock/modules/analysis/alascan/scan.html
@@ -683,7 +683,7 @@ 
Source code for haddock.modules.analysis.alascan.scan

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/analysis/caprieval.html b/_modules/haddock/modules/analysis/caprieval.html
index 7b78a205f..2e1037de7 100644
--- a/_modules/haddock/modules/analysis/caprieval.html
+++ b/_modules/haddock/modules/analysis/caprieval.html
@@ -254,7 +254,7 @@ 
Source code for haddock.modules.analysis.caprieval

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/analysis/caprieval/capri.html b/_modules/haddock/modules/analysis/caprieval/capri.html
index 7a339c550..d1f8962b4 100644
--- a/_modules/haddock/modules/analysis/caprieval/capri.html
+++ b/_modules/haddock/modules/analysis/caprieval/capri.html
@@ -1184,7 +1184,7 @@ 
Source code for haddock.modules.analysis.caprieval.capri

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/analysis/clustfcc.html b/_modules/haddock/modules/analysis/clustfcc.html
index 123546145..7f1c4e33a 100644
--- a/_modules/haddock/modules/analysis/clustfcc.html
+++ b/_modules/haddock/modules/analysis/clustfcc.html
@@ -305,7 +305,7 @@ 
Source code for haddock.modules.analysis.clustfcc

 
diff --git a/_modules/haddock/modules/analysis/clustfcc/clustfcc.html b/_modules/haddock/modules/analysis/clustfcc/clustfcc.html
index 836eaea64..e095b7f56 100644
--- a/_modules/haddock/modules/analysis/clustfcc/clustfcc.html
+++ b/_modules/haddock/modules/analysis/clustfcc/clustfcc.html
@@ -310,7 +310,7 @@ 
Source code for haddock.modules.analysis.clustfcc.clustfcc

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/analysis/clustrmsd.html b/_modules/haddock/modules/analysis/clustrmsd.html
index 3af41611a..6db9aea83 100644
--- a/_modules/haddock/modules/analysis/clustrmsd.html
+++ b/_modules/haddock/modules/analysis/clustrmsd.html
@@ -288,7 +288,7 @@ 
Source code for haddock.modules.analysis.clustrmsd

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/analysis/clustrmsd/clustrmsd.html b/_modules/haddock/modules/analysis/clustrmsd/clustrmsd.html
index 54d851161..281e75fc5 100644
--- a/_modules/haddock/modules/analysis/clustrmsd/clustrmsd.html
+++ b/_modules/haddock/modules/analysis/clustrmsd/clustrmsd.html
@@ -525,7 +525,7 @@ 
Source code for haddock.modules.analysis.clustrmsd.clustrmsd

 
diff --git a/_modules/haddock/modules/analysis/contactmap.html b/_modules/haddock/modules/analysis/contactmap.html
index aa792ab0f..1b8aae078 100644
--- a/_modules/haddock/modules/analysis/contactmap.html
+++ b/_modules/haddock/modules/analysis/contactmap.html
@@ -227,7 +227,7 @@ 
Source code for haddock.modules.analysis.contactmap

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/analysis/contactmap/contmap.html b/_modules/haddock/modules/analysis/contactmap/contmap.html
index a536a234d..7011d9ee9 100644
--- a/_modules/haddock/modules/analysis/contactmap/contmap.html
+++ b/_modules/haddock/modules/analysis/contactmap/contmap.html
@@ -2628,7 +2628,7 @@ 
Source code for haddock.modules.analysis.contactmap.contmap

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/analysis/ilrmsdmatrix.html b/_modules/haddock/modules/analysis/ilrmsdmatrix.html
index d466f847c..9c9798cf0 100644
--- a/_modules/haddock/modules/analysis/ilrmsdmatrix.html
+++ b/_modules/haddock/modules/analysis/ilrmsdmatrix.html
@@ -468,7 +468,7 @@ 
Source code for haddock.modules.analysis.ilrmsdmatrix

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/analysis/ilrmsdmatrix/ilrmsd.html b/_modules/haddock/modules/analysis/ilrmsdmatrix/ilrmsd.html
index 649c56593..31de4fe57 100644
--- a/_modules/haddock/modules/analysis/ilrmsdmatrix/ilrmsd.html
+++ b/_modules/haddock/modules/analysis/ilrmsdmatrix/ilrmsd.html
@@ -217,7 +217,7 @@ 
Source code for haddock.modules.analysis.ilrmsdmatrix.ilrmsd

 
diff --git a/_modules/haddock/modules/analysis/rmsdmatrix.html b/_modules/haddock/modules/analysis/rmsdmatrix.html
index d4b5cebf3..4102877fe 100644
--- a/_modules/haddock/modules/analysis/rmsdmatrix.html
+++ b/_modules/haddock/modules/analysis/rmsdmatrix.html
@@ -328,7 +328,7 @@ 
Source code for haddock.modules.analysis.rmsdmatrix

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/analysis/rmsdmatrix/rmsd.html b/_modules/haddock/modules/analysis/rmsdmatrix/rmsd.html
index 1af3ddf87..fbe8edc47 100644
--- a/_modules/haddock/modules/analysis/rmsdmatrix/rmsd.html
+++ b/_modules/haddock/modules/analysis/rmsdmatrix/rmsd.html
@@ -240,7 +240,7 @@ 
Source code for haddock.modules.analysis.rmsdmatrix.rmsd

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/analysis/seletop.html b/_modules/haddock/modules/analysis/seletop.html
index 2fdf13416..12ac0f39b 100644
--- a/_modules/haddock/modules/analysis/seletop.html
+++ b/_modules/haddock/modules/analysis/seletop.html
@@ -162,7 +162,7 @@ 
Source code for haddock.modules.analysis.seletop

 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/analysis/seletopclusts.html b/_modules/haddock/modules/analysis/seletopclusts.html
index c8a27f036..91adabafe 100644
--- a/_modules/haddock/modules/analysis/seletopclusts.html
+++ b/_modules/haddock/modules/analysis/seletopclusts.html
@@ -186,7 +186,7 @@ 
Source code for haddock.modules.analysis.seletopclusts

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/analysis/seletopclusts/seletopclusts.html b/_modules/haddock/modules/analysis/seletopclusts/seletopclusts.html
index b39d52aca..224108fe6 100644
--- a/_modules/haddock/modules/analysis/seletopclusts/seletopclusts.html
+++ b/_modules/haddock/modules/analysis/seletopclusts/seletopclusts.html
@@ -351,7 +351,7 @@ 
Source code for haddock.modules.analysis.seletopclusts.seletopclusts

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/base_cns_module.html b/_modules/haddock/modules/base_cns_module.html
index 8d017358e..e7b0ede31 100644
--- a/_modules/haddock/modules/base_cns_module.html
+++ b/_modules/haddock/modules/base_cns_module.html
@@ -262,7 +262,7 @@ 
Source code for haddock.modules.base_cns_module
<
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/extras/exit.html b/_modules/haddock/modules/extras/exit.html
index 33fcef2c7..2a99ef3c2 100644
--- a/_modules/haddock/modules/extras/exit.html
+++ b/_modules/haddock/modules/extras/exit.html
@@ -164,7 +164,7 @@ 
Source code for haddock.modules.extras.exit
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/refinement/emref.html b/_modules/haddock/modules/refinement/emref.html
index ae74e1235..e92eb6099 100644
--- a/_modules/haddock/modules/refinement/emref.html
+++ b/_modules/haddock/modules/refinement/emref.html
@@ -238,7 +238,7 @@ 
Source code for haddock.modules.refinement.emref

 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/refinement/flexref.html b/_modules/haddock/modules/refinement/flexref.html
index b3bad4b9e..955990414 100644
--- a/_modules/haddock/modules/refinement/flexref.html
+++ b/_modules/haddock/modules/refinement/flexref.html
@@ -255,7 +255,7 @@ 
Source code for haddock.modules.refinement.flexref

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/refinement/mdref.html b/_modules/haddock/modules/refinement/mdref.html
index 5a93bf9cf..0e611af55 100644
--- a/_modules/haddock/modules/refinement/mdref.html
+++ b/_modules/haddock/modules/refinement/mdref.html
@@ -252,7 +252,7 @@ 
Source code for haddock.modules.refinement.mdref

 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/refinement/openmm.html b/_modules/haddock/modules/refinement/openmm.html
index 734491512..ad27b2f97 100644
--- a/_modules/haddock/modules/refinement/openmm.html
+++ b/_modules/haddock/modules/refinement/openmm.html
@@ -295,7 +295,7 @@ 
Source code for haddock.modules.refinement.openmm

 
diff --git a/_modules/haddock/modules/sampling/gdock.html b/_modules/haddock/modules/sampling/gdock.html
index 9ca07e2de..a3e07f9ab 100644
--- a/_modules/haddock/modules/sampling/gdock.html
+++ b/_modules/haddock/modules/sampling/gdock.html
@@ -251,7 +251,7 @@ 
Source code for haddock.modules.sampling.gdock

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/sampling/lightdock.html b/_modules/haddock/modules/sampling/lightdock.html
index 17679355d..e9fc673e6 100644
--- a/_modules/haddock/modules/sampling/lightdock.html
+++ b/_modules/haddock/modules/sampling/lightdock.html
@@ -256,7 +256,7 @@ 
Source code for haddock.modules.sampling.lightdock

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/sampling/rigidbody.html b/_modules/haddock/modules/sampling/rigidbody.html
index ccc365ae8..dba1721fd 100644
--- a/_modules/haddock/modules/sampling/rigidbody.html
+++ b/_modules/haddock/modules/sampling/rigidbody.html
@@ -353,7 +353,7 @@ 
Source code for haddock.modules.sampling.rigidbody

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/scoring.html b/_modules/haddock/modules/scoring.html
index a1cad82ee..7641010ad 100644
--- a/_modules/haddock/modules/scoring.html
+++ b/_modules/haddock/modules/scoring.html
@@ -271,7 +271,7 @@ 
Source code for haddock.modules.scoring
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/scoring/emscoring.html b/_modules/haddock/modules/scoring/emscoring.html
index d0153845a..b4c9f6423 100644
--- a/_modules/haddock/modules/scoring/emscoring.html
+++ b/_modules/haddock/modules/scoring/emscoring.html
@@ -202,7 +202,7 @@ 
Source code for haddock.modules.scoring.emscoring

 
diff --git a/_modules/haddock/modules/scoring/mdscoring.html b/_modules/haddock/modules/scoring/mdscoring.html
index fdb4392da..cf2cf4b0d 100644
--- a/_modules/haddock/modules/scoring/mdscoring.html
+++ b/_modules/haddock/modules/scoring/mdscoring.html
@@ -202,7 +202,7 @@ 
Source code for haddock.modules.scoring.mdscoring

 
diff --git a/_modules/haddock/modules/scoring/sasascore.html b/_modules/haddock/modules/scoring/sasascore.html
index d96194a6d..c4cf98f42 100644
--- a/_modules/haddock/modules/scoring/sasascore.html
+++ b/_modules/haddock/modules/scoring/sasascore.html
@@ -172,7 +172,7 @@ 
Source code for haddock.modules.scoring.sasascore
self.output_models: list[PDBFile] = []
         # initialize jobs
         sasascore_jobs: list[AccScore] = []
-        for model_to_be_evaluated in models_to_score:
+        for i, model_to_be_evaluated in enumerate(models_to_score):
             accscore_obj = AccScore(
                 model=model_to_be_evaluated,
                 path=Path("."),
@@ -180,6 +180,7 @@ 
Source code for haddock.modules.scoring.sasascore
acc_resdic=acc_resdic,
                 cutoff=self.params["cutoff"],
                 probe_radius=self.params["probe_radius"],
+                identificator=i,
                 )
             sasascore_jobs.append(accscore_obj)
             # append model to output models
@@ -194,8 +195,12 @@ 
Source code for haddock.modules.scoring.sasascore
# extract results and overwrite scores
         sasascore_jobs = engine.results
-        for i, pdb in enumerate(self.output_models):
-            pdb.score = sasascore_jobs[i].data[3]
+        sasascore_jobs = sorted(sasascore_jobs,
+                                key=lambda accscore: accscore.identificator)
+        
+        for i, job in enumerate(sasascore_jobs):
+            pdb = self.output_models[i]
+            pdb.score = job.data[3]
         output_name = Path("sasascore.tsv")
         self.output(output_name)
 
@@ -218,7 +223,7 @@ 
Source code for haddock.modules.scoring.sasascore

 
diff --git a/_modules/haddock/modules/scoring/sasascore/sasascore.html b/_modules/haddock/modules/scoring/sasascore/sasascore.html
index b29943e76..4e65416f4 100644
--- a/_modules/haddock/modules/scoring/sasascore/sasascore.html
+++ b/_modules/haddock/modules/scoring/sasascore/sasascore.html
@@ -154,6 +154,7 @@ 
Source code for haddock.modules.scoring.sasascore.sasascore
acc_resdic,
             cutoff,
             probe_radius,
+            identificator,
             ):
         """Initialise AccScore class."""
         self.model = model
@@ -165,6 +166,7 @@ 
Source code for haddock.modules.scoring.sasascore.sasascore
self.violations = []
         self.probe_radius = probe_radius
         self.violations_data = [self.model.file_name]
+        self.identificator = identificator
 
 

 [docs]
@@ -253,7 +255,7 @@ 
Source code for haddock.modules.scoring.sasascore.sasascore

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/haddock/modules/topology/topoaa.html b/_modules/haddock/modules/topology/topoaa.html
index 9c9cce044..50d847eb4 100644
--- a/_modules/haddock/modules/topology/topoaa.html
+++ b/_modules/haddock/modules/topology/topoaa.html
@@ -439,7 +439,7 @@ 
Source code for haddock.modules.topology.topoaa
<
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/_modules/index.html b/_modules/index.html
index 1036187c2..c9037735c 100644
--- a/_modules/index.html
+++ b/_modules/index.html
@@ -186,7 +186,7 @@ 
All modules for which code is available

 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/citing.html b/citing.html
index 084464048..4dfff340e 100644
--- a/citing.html
+++ b/citing.html
@@ -102,7 +102,7 @@ 
Citing<
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.cli.html b/clients/haddock.clis.cli.html
index f758c99b0..bf140ab8c 100644
--- a/clients/haddock.clis.cli.html
+++ b/clients/haddock.clis.cli.html
@@ -171,7 +171,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.cli_analyse.html b/clients/haddock.clis.cli_analyse.html
index e0b9207bf..5c303f444 100644
--- a/clients/haddock.clis.cli_analyse.html
+++ b/clients/haddock.clis.cli_analyse.html
@@ -329,7 +329,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.cli_cfg.html b/clients/haddock.clis.cli_cfg.html
index e48e67d1d..e307dc6cc 100644
--- a/clients/haddock.clis.cli_cfg.html
+++ b/clients/haddock.clis.cli_cfg.html
@@ -177,7 +177,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.cli_clean.html b/clients/haddock.clis.cli_clean.html
index baa683e69..80593f896 100644
--- a/clients/haddock.clis.cli_clean.html
+++ b/clients/haddock.clis.cli_clean.html
@@ -181,7 +181,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.cli_cp.html b/clients/haddock.clis.cli_cp.html
index 4cedf357c..72e31f4f3 100644
--- a/clients/haddock.clis.cli_cp.html
+++ b/clients/haddock.clis.cli_cp.html
@@ -194,7 +194,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.cli_dmn.html b/clients/haddock.clis.cli_dmn.html
index 2ac9b0cec..0a25b18cd 100644
--- a/clients/haddock.clis.cli_dmn.html
+++ b/clients/haddock.clis.cli_dmn.html
@@ -277,7 +277,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.cli_mpi.html b/clients/haddock.clis.cli_mpi.html
index e6bb957a5..daabb007c 100644
--- a/clients/haddock.clis.cli_mpi.html
+++ b/clients/haddock.clis.cli_mpi.html
@@ -172,7 +172,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.cli_pp.html b/clients/haddock.clis.cli_pp.html
index 25ade2000..27a1f4134 100644
--- a/clients/haddock.clis.cli_pp.html
+++ b/clients/haddock.clis.cli_pp.html
@@ -175,7 +175,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.cli_re.html b/clients/haddock.clis.cli_re.html
index 11b683416..673f63e67 100644
--- a/clients/haddock.clis.cli_re.html
+++ b/clients/haddock.clis.cli_re.html
@@ -134,7 +134,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.cli_restraints.html b/clients/haddock.clis.cli_restraints.html
index b56c61b7b..d36dff52a 100644
--- a/clients/haddock.clis.cli_restraints.html
+++ b/clients/haddock.clis.cli_restraints.html
@@ -149,7 +149,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.cli_score.html b/clients/haddock.clis.cli_score.html
index fc57c5a03..69d109f5d 100644
--- a/clients/haddock.clis.cli_score.html
+++ b/clients/haddock.clis.cli_score.html
@@ -177,7 +177,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.cli_traceback.html b/clients/haddock.clis.cli_traceback.html
index ce0792763..fb6748e6d 100644
--- a/clients/haddock.clis.cli_traceback.html
+++ b/clients/haddock.clis.cli_traceback.html
@@ -256,7 +256,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.cli_unpack.html b/clients/haddock.clis.cli_unpack.html
index 1d332e145..1a064db70 100644
--- a/clients/haddock.clis.cli_unpack.html
+++ b/clients/haddock.clis.cli_unpack.html
@@ -186,7 +186,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.html b/clients/haddock.clis.html
index de893db2e..c73476a8b 100644
--- a/clients/haddock.clis.html
+++ b/clients/haddock.clis.html
@@ -158,7 +158,7 @@ 
Submodules
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.re.clustfcc.html b/clients/haddock.clis.re.clustfcc.html
index 4d7d6adc8..3928393a5 100644
--- a/clients/haddock.clis.re.clustfcc.html
+++ b/clients/haddock.clis.re.clustfcc.html
@@ -143,7 +143,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.re.clustrmsd.html b/clients/haddock.clis.re.clustrmsd.html
index 978a4f2b9..ec8a76cdf 100644
--- a/clients/haddock.clis.re.clustrmsd.html
+++ b/clients/haddock.clis.re.clustrmsd.html
@@ -152,7 +152,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.re.html b/clients/haddock.clis.re.html
index 1f64f93cc..8c7938896 100644
--- a/clients/haddock.clis.re.html
+++ b/clients/haddock.clis.re.html
@@ -123,7 +123,7 @@ 
Submodules
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.re.score.html b/clients/haddock.clis.re.score.html
index 89348d3d7..f54440c51 100644
--- a/clients/haddock.clis.re.score.html
+++ b/clients/haddock.clis.re.score.html
@@ -124,7 +124,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.restraints.active_passive_to_ambig.html b/clients/haddock.clis.restraints.active_passive_to_ambig.html
index 040c1aef5..cc27a6c20 100644
--- a/clients/haddock.clis.restraints.active_passive_to_ambig.html
+++ b/clients/haddock.clis.restraints.active_passive_to_ambig.html
@@ -144,7 +144,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.restraints.calc_accessibility.html b/clients/haddock.clis.restraints.calc_accessibility.html
index 3eda23195..6259dbc4c 100644
--- a/clients/haddock.clis.restraints.calc_accessibility.html
+++ b/clients/haddock.clis.restraints.calc_accessibility.html
@@ -177,7 +177,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.restraints.html b/clients/haddock.clis.restraints.html
index 1c7e77081..4552d19b1 100644
--- a/clients/haddock.clis.restraints.html
+++ b/clients/haddock.clis.restraints.html
@@ -127,7 +127,7 @@ 
Submodules
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.restraints.passive_from_active.html b/clients/haddock.clis.restraints.passive_from_active.html
index 8957ac2a4..1497fc46a 100644
--- a/clients/haddock.clis.restraints.passive_from_active.html
+++ b/clients/haddock.clis.restraints.passive_from_active.html
@@ -132,7 +132,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.restraints.restrain_bodies.html b/clients/haddock.clis.restraints.restrain_bodies.html
index f73703d90..535fad84a 100644
--- a/clients/haddock.clis.restraints.restrain_bodies.html
+++ b/clients/haddock.clis.restraints.restrain_bodies.html
@@ -139,7 +139,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.restraints.validate_tbl.html b/clients/haddock.clis.restraints.validate_tbl.html
index 59ca8f798..52ae30af7 100644
--- a/clients/haddock.clis.restraints.validate_tbl.html
+++ b/clients/haddock.clis.restraints.validate_tbl.html
@@ -129,7 +129,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.restraints.webservice.html b/clients/haddock.clis.restraints.webservice.html
index 368254303..1a4ed6bb6 100644
--- a/clients/haddock.clis.restraints.webservice.html
+++ b/clients/haddock.clis.restraints.webservice.html
@@ -111,7 +111,7 @@ 
haddock.clis.restraints.webservice module
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/clients/haddock.clis.restraints.z_surface_restraints.html b/clients/haddock.clis.restraints.z_surface_restraints.html
index 2c9dcddf9..e5c9c98e1 100644
--- a/clients/haddock.clis.restraints.z_surface_restraints.html
+++ b/clients/haddock.clis.restraints.z_surface_restraints.html
@@ -390,7 +390,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/contributing.html b/contributing.html
index 009854721..87972ff7a 100644
--- a/contributing.html
+++ b/contributing.html
@@ -431,7 +431,7 @@ 
2. Contributing with documentation
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/examples.html b/examples.html
index fda962165..fa056c48f 100644
--- a/examples.html
+++ b/examples.html
@@ -259,7 +259,7 @@ 
general analysis tasks
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/genindex.html b/genindex.html
index 273e2dbc7..cd69d98a9 100644
--- a/genindex.html
+++ b/genindex.html
@@ -3007,7 +3007,7 @@ 
Z

 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/haddock.fcc.calc_fcc_matrix.html b/haddock.fcc.calc_fcc_matrix.html
index 8518d35b9..9f28e3fef 100644
--- a/haddock.fcc.calc_fcc_matrix.html
+++ b/haddock.fcc.calc_fcc_matrix.html
@@ -128,7 +128,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/haddock.fcc.cluster_fcc.html b/haddock.fcc.cluster_fcc.html
index 5dd592633..b044811d9 100644
--- a/haddock.fcc.cluster_fcc.html
+++ b/haddock.fcc.cluster_fcc.html
@@ -202,7 +202,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/haddock.fcc.html b/haddock.fcc.html
index 8f1076ce2..8bb05c29c 100644
--- a/haddock.fcc.html
+++ b/haddock.fcc.html
@@ -103,7 +103,7 @@ 
Submodules
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/haddock.html b/haddock.html
index 2a18d84c3..5c40f4927 100644
--- a/haddock.html
+++ b/haddock.html
@@ -111,7 +111,7 @@ 
Subpackages
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/haddock.modules.base_cns_module.html b/haddock.modules.base_cns_module.html
index 3e54aadf7..455e4074d 100644
--- a/haddock.modules.base_cns_module.html
+++ b/haddock.modules.base_cns_module.html
@@ -138,7 +138,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/haddock.modules.html b/haddock.modules.html
index 9fe53fa9e..7d5952423 100644
--- a/haddock.modules.html
+++ b/haddock.modules.html
@@ -335,7 +335,7 @@ 
Submodules
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/haddock.modules.topology.topocg.html b/haddock.modules.topology.topocg.html
index 8f901f058..5dcf947c8 100644
--- a/haddock.modules.topology.topocg.html
+++ b/haddock.modules.topology.topocg.html
@@ -96,7 +96,7 @@ 
haddock.modules.topology.topocg package
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/index.html b/index.html
index e5bb8c6ed..698737d3b 100644
--- a/index.html
+++ b/index.html
@@ -121,7 +121,7 @@ 
Indices and tables
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/intro.html b/intro.html
index 757847e17..9fc43e06e 100644
--- a/intro.html
+++ b/intro.html
@@ -220,7 +220,7 @@ 
A brief introduction to HADDOCK3
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules.html b/modules.html
index eb3d09899..b2d8859e3 100644
--- a/modules.html
+++ b/modules.html
@@ -96,7 +96,7 @@ 
haddock
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/haddock.modules.analysis.alascan.html b/modules/analysis/haddock.modules.analysis.alascan.html
index 4955247e9..9a3f6d345 100644
--- a/modules/analysis/haddock.modules.analysis.alascan.html
+++ b/modules/analysis/haddock.modules.analysis.alascan.html
@@ -233,7 +233,7 @@ 
resdic
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/haddock.modules.analysis.alascan.scan.html b/modules/analysis/haddock.modules.analysis.alascan.scan.html
index 019594e2c..306896039 100644
--- a/modules/analysis/haddock.modules.analysis.alascan.scan.html
+++ b/modules/analysis/haddock.modules.analysis.alascan.scan.html
@@ -286,7 +286,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/haddock.modules.analysis.caprieval.capri.html b/modules/analysis/haddock.modules.analysis.caprieval.capri.html
index 2913e0d34..a072beab5 100644
--- a/modules/analysis/haddock.modules.analysis.caprieval.capri.html
+++ b/modules/analysis/haddock.modules.analysis.caprieval.capri.html
@@ -371,7 +371,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/haddock.modules.analysis.caprieval.html b/modules/analysis/haddock.modules.analysis.caprieval.html
index d961bf4e5..2c0c95e57 100644
--- a/modules/analysis/haddock.modules.analysis.caprieval.html
+++ b/modules/analysis/haddock.modules.analysis.caprieval.html
@@ -416,7 +416,7 @@ 
sortby<
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/haddock.modules.analysis.clustfcc.clustfcc.html b/modules/analysis/haddock.modules.analysis.clustfcc.clustfcc.html
index 77d6755b2..b7b0fdccb 100644
--- a/modules/analysis/haddock.modules.analysis.clustfcc.clustfcc.html
+++ b/modules/analysis/haddock.modules.analysis.clustfcc.clustfcc.html
@@ -205,7 +205,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/haddock.modules.analysis.clustfcc.html b/modules/analysis/haddock.modules.analysis.clustfcc.html
index 718256205..739e69fc4 100644
--- a/modules/analysis/haddock.modules.analysis.clustfcc.html
+++ b/modules/analysis/haddock.modules.analysis.clustfcc.html
@@ -247,7 +247,7 @@ 
executable
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/haddock.modules.analysis.clustrmsd.clustrmsd.html b/modules/analysis/haddock.modules.analysis.clustrmsd.clustrmsd.html
index 86a56c87f..9d79e7c50 100644
--- a/modules/analysis/haddock.modules.analysis.clustrmsd.clustrmsd.html
+++ b/modules/analysis/haddock.modules.analysis.clustrmsd.clustrmsd.html
@@ -315,7 +315,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/haddock.modules.analysis.clustrmsd.html b/modules/analysis/haddock.modules.analysis.clustrmsd.html
index 80c8a185f..3c563069c 100644
--- a/modules/analysis/haddock.modules.analysis.clustrmsd.html
+++ b/modules/analysis/haddock.modules.analysis.clustrmsd.html
@@ -265,7 +265,7 @@ 
linkage
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/haddock.modules.analysis.contactmap.contmap.html b/modules/analysis/haddock.modules.analysis.contactmap.contmap.html
index dd2b5a666..245d53148 100644
--- a/modules/analysis/haddock.modules.analysis.contactmap.contmap.html
+++ b/modules/analysis/haddock.modules.analysis.contactmap.contmap.html
@@ -945,7 +945,7 @@ 
Paramters<
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/haddock.modules.analysis.contactmap.html b/modules/analysis/haddock.modules.analysis.contactmap.html
index ac4c3398b..6e251ef1e 100644
--- a/modules/analysis/haddock.modules.analysis.contactmap.html
+++ b/modules/analysis/haddock.modules.analysis.contactmap.html
@@ -288,7 +288,7 @@ 
topX<
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/haddock.modules.analysis.ilrmsdmatrix.html b/modules/analysis/haddock.modules.analysis.ilrmsdmatrix.html
index 786444ffc..968ba00aa 100644
--- a/modules/analysis/haddock.modules.analysis.ilrmsdmatrix.html
+++ b/modules/analysis/haddock.modules.analysis.ilrmsdmatrix.html
@@ -251,7 +251,7 @@ 
max_models
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/haddock.modules.analysis.ilrmsdmatrix.ilrmsd.html b/modules/analysis/haddock.modules.analysis.ilrmsdmatrix.ilrmsd.html
index fbc7c27e4..06bfa3357 100644
--- a/modules/analysis/haddock.modules.analysis.ilrmsdmatrix.ilrmsd.html
+++ b/modules/analysis/haddock.modules.analysis.ilrmsdmatrix.ilrmsd.html
@@ -158,7 +158,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/haddock.modules.analysis.rmsdmatrix.html b/modules/analysis/haddock.modules.analysis.rmsdmatrix.html
index eb653ae02..3cb718952 100644
--- a/modules/analysis/haddock.modules.analysis.rmsdmatrix.html
+++ b/modules/analysis/haddock.modules.analysis.rmsdmatrix.html
@@ -239,7 +239,7 @@ 
resdic
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/haddock.modules.analysis.rmsdmatrix.rmsd.html b/modules/analysis/haddock.modules.analysis.rmsdmatrix.rmsd.html
index b9a86da8d..44c7d025a 100644
--- a/modules/analysis/haddock.modules.analysis.rmsdmatrix.rmsd.html
+++ b/modules/analysis/haddock.modules.analysis.rmsdmatrix.rmsd.html
@@ -181,7 +181,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/haddock.modules.analysis.seletop.html b/modules/analysis/haddock.modules.analysis.seletop.html
index 697fea2fe..1720aa935 100644
--- a/modules/analysis/haddock.modules.analysis.seletop.html
+++ b/modules/analysis/haddock.modules.analysis.seletop.html
@@ -171,7 +171,7 @@ 
select<
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/haddock.modules.analysis.seletopclusts.html b/modules/analysis/haddock.modules.analysis.seletopclusts.html
index af61f6de2..08d9ab7e7 100644
--- a/modules/analysis/haddock.modules.analysis.seletopclusts.html
+++ b/modules/analysis/haddock.modules.analysis.seletopclusts.html
@@ -206,7 +206,7 @@ 
top_models
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/haddock.modules.analysis.seletopclusts.seletopclusts.html b/modules/analysis/haddock.modules.analysis.seletopclusts.seletopclusts.html
index f3c54cd93..1903512d8 100644
--- a/modules/analysis/haddock.modules.analysis.seletopclusts.seletopclusts.html
+++ b/modules/analysis/haddock.modules.analysis.seletopclusts.seletopclusts.html
@@ -239,7 +239,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/index.html b/modules/analysis/index.html
index 3041e020f..487437ec0 100644
--- a/modules/analysis/index.html
+++ b/modules/analysis/index.html
@@ -177,7 +177,7 @@ 
Subpackages
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/params/alascan.html b/modules/analysis/params/alascan.html
index 594415e1c..775914fb2 100644
--- a/modules/analysis/params/alascan.html
+++ b/modules/analysis/params/alascan.html
@@ -157,7 +157,7 @@ 
resdic
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/params/caprieval.html b/modules/analysis/params/caprieval.html
index 65c01b7e9..203e300c5 100644
--- a/modules/analysis/params/caprieval.html
+++ b/modules/analysis/params/caprieval.html
@@ -303,7 +303,7 @@ 
sortby<
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/params/clustfcc.html b/modules/analysis/params/clustfcc.html
index 779f0b7c6..4bc56510a 100644
--- a/modules/analysis/params/clustfcc.html
+++ b/modules/analysis/params/clustfcc.html
@@ -174,7 +174,7 @@ 
executable
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/params/clustrmsd.html b/modules/analysis/params/clustrmsd.html
index 1d0bb87e7..47798feb8 100644
--- a/modules/analysis/params/clustrmsd.html
+++ b/modules/analysis/params/clustrmsd.html
@@ -174,7 +174,7 @@ 
linkage
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/params/contactmap.html b/modules/analysis/params/contactmap.html
index 031ad7d49..2aba8be5b 100644
--- a/modules/analysis/params/contactmap.html
+++ b/modules/analysis/params/contactmap.html
@@ -211,7 +211,7 @@ 
topX<
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/params/ilrmsdmatrix.html b/modules/analysis/params/ilrmsdmatrix.html
index 1699f29bd..189d6fd81 100644
--- a/modules/analysis/params/ilrmsdmatrix.html
+++ b/modules/analysis/params/ilrmsdmatrix.html
@@ -172,7 +172,7 @@ 
max_models
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/params/rmsdmatrix.html b/modules/analysis/params/rmsdmatrix.html
index e210db181..e8d5b1ad6 100644
--- a/modules/analysis/params/rmsdmatrix.html
+++ b/modules/analysis/params/rmsdmatrix.html
@@ -143,7 +143,7 @@ 
resdic
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/params/seletop.html b/modules/analysis/params/seletop.html
index 74e1889ef..001363ac2 100644
--- a/modules/analysis/params/seletop.html
+++ b/modules/analysis/params/seletop.html
@@ -105,7 +105,7 @@ 
select<
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/analysis/params/seletopclusts.html b/modules/analysis/params/seletopclusts.html
index c6713b8c0..a0c21e9ae 100644
--- a/modules/analysis/params/seletopclusts.html
+++ b/modules/analysis/params/seletopclusts.html
@@ -131,7 +131,7 @@ 
top_models
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/extras/haddock.modules.extras.exit.html b/modules/extras/haddock.modules.extras.exit.html
index 16d3852eb..d86f95a1e 100644
--- a/modules/extras/haddock.modules.extras.exit.html
+++ b/modules/extras/haddock.modules.extras.exit.html
@@ -178,7 +178,7 @@ 
message
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/extras/index.html b/modules/extras/index.html
index 133da3504..6af40ab35 100644
--- a/modules/extras/index.html
+++ b/modules/extras/index.html
@@ -129,7 +129,7 @@ 
Subpackages
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/extras/params/exit.html b/modules/extras/params/exit.html
index 2f8bbff84..47eb6b36f 100644
--- a/modules/extras/params/exit.html
+++ b/modules/extras/params/exit.html
@@ -103,7 +103,7 @@ 
message
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/general_module_params.html b/modules/general_module_params.html
index 91b47ce05..0c31a174b 100644
--- a/modules/general_module_params.html
+++ b/modules/general_module_params.html
@@ -249,7 +249,7 @@ 
self_contained
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/index.html b/modules/index.html
index 3b58934d2..5c1629536 100644
--- a/modules/index.html
+++ b/modules/index.html
@@ -779,7 +779,7 @@ 
self_contained
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/refinement/haddock.modules.refinement.emref.html b/modules/refinement/haddock.modules.refinement.emref.html
index dc48ef355..7736525ee 100644
--- a/modules/refinement/haddock.modules.refinement.emref.html
+++ b/modules/refinement/haddock.modules.refinement.emref.html
@@ -2612,7 +2612,7 @@ 
log_level
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/refinement/haddock.modules.refinement.flexref.html b/modules/refinement/haddock.modules.refinement.flexref.html
index 003b42b49..c8ce6d010 100644
--- a/modules/refinement/haddock.modules.refinement.flexref.html
+++ b/modules/refinement/haddock.modules.refinement.flexref.html
@@ -3108,7 +3108,7 @@ 
timestep
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/refinement/haddock.modules.refinement.mdref.html b/modules/refinement/haddock.modules.refinement.mdref.html
index f4e48bea8..c57d4b65e 100644
--- a/modules/refinement/haddock.modules.refinement.mdref.html
+++ b/modules/refinement/haddock.modules.refinement.mdref.html
@@ -2728,7 +2728,7 @@ 
timestep
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/refinement/haddock.modules.refinement.openmm.html b/modules/refinement/haddock.modules.refinement.openmm.html
index 0d151d4c7..66cac4686 100644
--- a/modules/refinement/haddock.modules.refinement.openmm.html
+++ b/modules/refinement/haddock.modules.refinement.openmm.html
@@ -541,7 +541,7 @@ 
timestep_ps
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/refinement/haddock.modules.refinement.openmm.openmm.html b/modules/refinement/haddock.modules.refinement.openmm.openmm.html
index f48564d5b..46b307793 100644
--- a/modules/refinement/haddock.modules.refinement.openmm.openmm.html
+++ b/modules/refinement/haddock.modules.refinement.openmm.openmm.html
@@ -120,7 +120,7 @@ 
haddock.modules.refinement.openmm.openmm module
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/refinement/index.html b/modules/refinement/index.html
index 231771ba0..cc920e680 100644
--- a/modules/refinement/index.html
+++ b/modules/refinement/index.html
@@ -133,7 +133,7 @@ 
Subpackages
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/refinement/params/emref.html b/modules/refinement/params/emref.html
index 988c16f2a..208e8b9ac 100644
--- a/modules/refinement/params/emref.html
+++ b/modules/refinement/params/emref.html
@@ -2552,7 +2552,7 @@ 
log_level
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/refinement/params/flexref.html b/modules/refinement/params/flexref.html
index 0bcad70b7..4bcfa2a66 100644
--- a/modules/refinement/params/flexref.html
+++ b/modules/refinement/params/flexref.html
@@ -3036,7 +3036,7 @@ 
timestep
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/refinement/params/mdref.html b/modules/refinement/params/mdref.html
index d01b010e2..106438f71 100644
--- a/modules/refinement/params/mdref.html
+++ b/modules/refinement/params/mdref.html
@@ -2659,7 +2659,7 @@ 
timestep
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/refinement/params/openmm.html b/modules/refinement/params/openmm.html
index 7d171e750..0996f1452 100644
--- a/modules/refinement/params/openmm.html
+++ b/modules/refinement/params/openmm.html
@@ -426,7 +426,7 @@ 
timestep_ps
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/sampling/haddock.modules.sampling.gdock.html b/modules/sampling/haddock.modules.sampling.gdock.html
index ff6ea4b7a..6ff8d68c2 100644
--- a/modules/sampling/haddock.modules.sampling.gdock.html
+++ b/modules/sampling/haddock.modules.sampling.gdock.html
@@ -164,7 +164,7 @@ 
ambig_fname
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/sampling/haddock.modules.sampling.lightdock.html b/modules/sampling/haddock.modules.sampling.lightdock.html
index 4119aaaaf..3aaae2ef5 100644
--- a/modules/sampling/haddock.modules.sampling.lightdock.html
+++ b/modules/sampling/haddock.modules.sampling.lightdock.html
@@ -322,7 +322,7 @@ 
top
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/sampling/haddock.modules.sampling.rigidbody.html b/modules/sampling/haddock.modules.sampling.rigidbody.html
index 40a66bc61..bc92972cc 100644
--- a/modules/sampling/haddock.modules.sampling.rigidbody.html
+++ b/modules/sampling/haddock.modules.sampling.rigidbody.html
@@ -2607,7 +2607,7 @@ 
rigidtrans
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/sampling/index.html b/modules/sampling/index.html
index a14fafb95..096da7414 100644
--- a/modules/sampling/index.html
+++ b/modules/sampling/index.html
@@ -131,7 +131,7 @@ 
Subpackages
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/sampling/params/gdock.html b/modules/sampling/params/gdock.html
index a93fc8591..6394dcb56 100644
--- a/modules/sampling/params/gdock.html
+++ b/modules/sampling/params/gdock.html
@@ -103,7 +103,7 @@ 
ambig_fname
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/sampling/params/lightdock.html b/modules/sampling/params/lightdock.html
index d88e8d6f1..8b541ac4f 100644
--- a/modules/sampling/params/lightdock.html
+++ b/modules/sampling/params/lightdock.html
@@ -267,7 +267,7 @@ 
top
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/sampling/params/rigidbody.html b/modules/sampling/params/rigidbody.html
index 3bca05862..8fe7498ef 100644
--- a/modules/sampling/params/rigidbody.html
+++ b/modules/sampling/params/rigidbody.html
@@ -2513,7 +2513,7 @@ 
rigidtrans
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/scoring/haddock.modules.scoring.emscoring.html b/modules/scoring/haddock.modules.scoring.emscoring.html
index 0486a3bfd..2470b304e 100644
--- a/modules/scoring/haddock.modules.scoring.emscoring.html
+++ b/modules/scoring/haddock.modules.scoring.emscoring.html
@@ -378,7 +378,7 @@ 
log_level
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/scoring/haddock.modules.scoring.mdscoring.html b/modules/scoring/haddock.modules.scoring.mdscoring.html
index 9a0e8456a..91103ab76 100644
--- a/modules/scoring/haddock.modules.scoring.mdscoring.html
+++ b/modules/scoring/haddock.modules.scoring.mdscoring.html
@@ -524,7 +524,7 @@ 
timestep
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/scoring/haddock.modules.scoring.sasascore.html b/modules/scoring/haddock.modules.scoring.sasascore.html
index 0eec01de2..d3af49290 100644
--- a/modules/scoring/haddock.modules.scoring.sasascore.html
+++ b/modules/scoring/haddock.modules.scoring.sasascore.html
@@ -222,7 +222,7 @@ 
probe_radius
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/scoring/haddock.modules.scoring.sasascore.sasascore.html b/modules/scoring/haddock.modules.scoring.sasascore.sasascore.html
index 188c4c6af..a79c6fec8 100644
--- a/modules/scoring/haddock.modules.scoring.sasascore.sasascore.html
+++ b/modules/scoring/haddock.modules.scoring.sasascore.sasascore.html
@@ -108,7 +108,7 @@
 
Accessibility scoring calculations.

 

 

-class haddock.modules.scoring.sasascore.sasascore.AccScore(model, path, buried_resdic, acc_resdic, cutoff, probe_radius)[source]

+class haddock.modules.scoring.sasascore.sasascore.AccScore(model, path, buried_resdic, acc_resdic, cutoff, probe_radius, identificator)[source]
 
Bases: object

 
AccScore class.

 

@@ -176,7 +176,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/scoring/index.html b/modules/scoring/index.html
index f414eeeeb..a409c552e 100644
--- a/modules/scoring/index.html
+++ b/modules/scoring/index.html
@@ -193,7 +193,7 @@ 
Subpackages
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/scoring/params/emscoring.html b/modules/scoring/params/emscoring.html
index ec611fe52..e329d2d21 100644
--- a/modules/scoring/params/emscoring.html
+++ b/modules/scoring/params/emscoring.html
@@ -321,7 +321,7 @@ 
log_level
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/scoring/params/mdscoring.html b/modules/scoring/params/mdscoring.html
index 5098036eb..43b58cee5 100644
--- a/modules/scoring/params/mdscoring.html
+++ b/modules/scoring/params/mdscoring.html
@@ -467,7 +467,7 @@ 
timestep
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/scoring/params/sasascore.html b/modules/scoring/params/sasascore.html
index 4e1d1404a..211f375dd 100644
--- a/modules/scoring/params/sasascore.html
+++ b/modules/scoring/params/sasascore.html
@@ -146,7 +146,7 @@ 
probe_radius
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/topology/haddock.modules.topology.topoaa.html b/modules/topology/haddock.modules.topology.topoaa.html
index 54862902f..9ff13ef42 100644
--- a/modules/topology/haddock.modules.topology.topoaa.html
+++ b/modules/topology/haddock.modules.topology.topoaa.html
@@ -412,7 +412,7 @@ 
log_level
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/topology/index.html b/modules/topology/index.html
index 4453aa872..3b65431ca 100644
--- a/modules/topology/index.html
+++ b/modules/topology/index.html
@@ -127,7 +127,7 @@ 
Subpackages
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/modules/topology/params/topoaa.html b/modules/topology/params/topoaa.html
index 08424b5bb..f1ad5d080 100644
--- a/modules/topology/params/topoaa.html
+++ b/modules/topology/params/topoaa.html
@@ -316,7 +316,7 @@ 
log_level
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/py-modindex.html b/py-modindex.html
index 562a33df0..b610459b1 100644
--- a/py-modindex.html
+++ b/py-modindex.html
@@ -667,7 +667,7 @@ 
Python Module Index

 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/core/haddock.core.cns_paths.html b/reference/core/haddock.core.cns_paths.html
index ebe74eb2c..9eb59fb73 100644
--- a/reference/core/haddock.core.cns_paths.html
+++ b/reference/core/haddock.core.cns_paths.html
@@ -159,7 +159,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/core/haddock.core.defaults.html b/reference/core/haddock.core.defaults.html
index 25c690892..2417965f3 100644
--- a/reference/core/haddock.core.defaults.html
+++ b/reference/core/haddock.core.defaults.html
@@ -158,7 +158,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/core/haddock.core.exceptions.html b/reference/core/haddock.core.exceptions.html
index 65282e5ea..73a6c0e35 100644
--- a/reference/core/haddock.core.exceptions.html
+++ b/reference/core/haddock.core.exceptions.html
@@ -192,7 +192,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/core/haddock.core.html b/reference/core/haddock.core.html
index b5576a892..0ecec04c7 100644
--- a/reference/core/haddock.core.html
+++ b/reference/core/haddock.core.html
@@ -129,7 +129,7 @@ 
Submodules
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/core/haddock.core.supported_molecules.html b/reference/core/haddock.core.supported_molecules.html
index 213a42bef..5caa966bc 100644
--- a/reference/core/haddock.core.supported_molecules.html
+++ b/reference/core/haddock.core.supported_molecules.html
@@ -390,7 +390,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/core/haddock.core.typing.html b/reference/core/haddock.core.typing.html
index f00d3f924..a7a6c7c34 100644
--- a/reference/core/haddock.core.typing.html
+++ b/reference/core/haddock.core.typing.html
@@ -284,7 +284,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/core/mandatory_parameters.html b/reference/core/mandatory_parameters.html
index 077852e65..27e0d2ce6 100644
--- a/reference/core/mandatory_parameters.html
+++ b/reference/core/mandatory_parameters.html
@@ -118,7 +118,7 @@ 
run_dir
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/gear/haddock.gear.clean_steps.html b/reference/gear/haddock.gear.clean_steps.html
index 907f6da88..f223c99ad 100644
--- a/reference/gear/haddock.gear.clean_steps.html
+++ b/reference/gear/haddock.gear.clean_steps.html
@@ -214,7 +214,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/gear/haddock.gear.config.html b/reference/gear/haddock.gear.config.html
index 8fb160058..dfd1ed94b 100644
--- a/reference/gear/haddock.gear.config.html
+++ b/reference/gear/haddock.gear.config.html
@@ -286,7 +286,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/gear/haddock.gear.expandable_parameters.html b/reference/gear/haddock.gear.expandable_parameters.html
index f6940c90a..effbd1293 100644
--- a/reference/gear/haddock.gear.expandable_parameters.html
+++ b/reference/gear/haddock.gear.expandable_parameters.html
@@ -651,7 +651,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/gear/haddock.gear.extend_run.html b/reference/gear/haddock.gear.extend_run.html
index f77314d82..7c4be9d27 100644
--- a/reference/gear/haddock.gear.extend_run.html
+++ b/reference/gear/haddock.gear.extend_run.html
@@ -279,7 +279,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/gear/haddock.gear.greetings.html b/reference/gear/haddock.gear.greetings.html
index f4c08a30f..be60f7c38 100644
--- a/reference/gear/haddock.gear.greetings.html
+++ b/reference/gear/haddock.gear.greetings.html
@@ -166,7 +166,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/gear/haddock.gear.haddockmodel.html b/reference/gear/haddock.gear.haddockmodel.html
index 1839b2067..f2ce51329 100644
--- a/reference/gear/haddock.gear.haddockmodel.html
+++ b/reference/gear/haddock.gear.haddockmodel.html
@@ -137,7 +137,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/gear/haddock.gear.html b/reference/gear/haddock.gear.html
index 6e5bf021d..016c49cf2 100644
--- a/reference/gear/haddock.gear.html
+++ b/reference/gear/haddock.gear.html
@@ -150,7 +150,7 @@ 
Submodules
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/gear/haddock.gear.known_cns_errors.html b/reference/gear/haddock.gear.known_cns_errors.html
index e386b1786..f3423a231 100644
--- a/reference/gear/haddock.gear.known_cns_errors.html
+++ b/reference/gear/haddock.gear.known_cns_errors.html
@@ -154,7 +154,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/gear/haddock.gear.parameters.html b/reference/gear/haddock.gear.parameters.html
index 652c2bd24..29eada5ed 100644
--- a/reference/gear/haddock.gear.parameters.html
+++ b/reference/gear/haddock.gear.parameters.html
@@ -136,7 +136,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/gear/haddock.gear.prepare_run.html b/reference/gear/haddock.gear.prepare_run.html
index 02b33bedd..7128dfced 100644
--- a/reference/gear/haddock.gear.prepare_run.html
+++ b/reference/gear/haddock.gear.prepare_run.html
@@ -577,7 +577,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/gear/haddock.gear.preprocessing.html b/reference/gear/haddock.gear.preprocessing.html
index 71a0ae024..642623246 100644
--- a/reference/gear/haddock.gear.preprocessing.html
+++ b/reference/gear/haddock.gear.preprocessing.html
@@ -536,7 +536,7 @@ 
Additional information
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/gear/haddock.gear.restart_run.html b/reference/gear/haddock.gear.restart_run.html
index 32482b117..ce309398d 100644
--- a/reference/gear/haddock.gear.restart_run.html
+++ b/reference/gear/haddock.gear.restart_run.html
@@ -156,7 +156,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/gear/haddock.gear.validations.html b/reference/gear/haddock.gear.validations.html
index fc563c341..5cfcad804 100644
--- a/reference/gear/haddock.gear.validations.html
+++ b/reference/gear/haddock.gear.validations.html
@@ -166,7 +166,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/gear/haddock.gear.yaml2cfg.html b/reference/gear/haddock.gear.yaml2cfg.html
index ae6d904d0..4d2d29ec2 100644
--- a/reference/gear/haddock.gear.yaml2cfg.html
+++ b/reference/gear/haddock.gear.yaml2cfg.html
@@ -199,7 +199,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/gear/haddock.gear.zerofill.html b/reference/gear/haddock.gear.zerofill.html
index 7c555fb2f..a2e48eeaa 100644
--- a/reference/gear/haddock.gear.zerofill.html
+++ b/reference/gear/haddock.gear.zerofill.html
@@ -164,7 +164,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/index.html b/reference/index.html
index 29f092a72..b8aa4b8e1 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -109,7 +109,7 @@ 
Library Reference
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/libs/haddock.libs.assets.html b/reference/libs/haddock.libs.assets.html
index 4677fc7e6..04900fd52 100644
--- a/reference/libs/haddock.libs.assets.html
+++ b/reference/libs/haddock.libs.assets.html
@@ -120,7 +120,7 @@ 
haddock.libs.assets package
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/libs/haddock.libs.html b/reference/libs/haddock.libs.html
index e86ffc58d..fe0b1214b 100644
--- a/reference/libs/haddock.libs.html
+++ b/reference/libs/haddock.libs.html
@@ -175,7 +175,7 @@ 
Submodules
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/libs/haddock.libs.libalign.html b/reference/libs/haddock.libs.libalign.html
index 4e3870bb2..937afd30e 100644
--- a/reference/libs/haddock.libs.libalign.html
+++ b/reference/libs/haddock.libs.libalign.html
@@ -467,7 +467,7 @@ 
Main functions
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/libs/haddock.libs.libcli.html b/reference/libs/haddock.libs.libcli.html
index 37728946c..aa39f7d4b 100644
--- a/reference/libs/haddock.libs.libcli.html
+++ b/reference/libs/haddock.libs.libcli.html
@@ -157,7 +157,7 @@ 
libcli: functions helping clients
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/libs/haddock.libs.libclust.html b/reference/libs/haddock.libs.libclust.html
index 729352bae..61f3aebcd 100644
--- a/reference/libs/haddock.libs.libclust.html
+++ b/reference/libs/haddock.libs.libclust.html
@@ -250,7 +250,7 @@ 
Main functions
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/libs/haddock.libs.libcns.html b/reference/libs/haddock.libs.libcns.html
index 459e97483..239d4d054 100644
--- a/reference/libs/haddock.libs.libcns.html
+++ b/reference/libs/haddock.libs.libcns.html
@@ -329,7 +329,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/libs/haddock.libs.libfcc.html b/reference/libs/haddock.libs.libfcc.html
index 4e33fe423..dc195b3d6 100644
--- a/reference/libs/haddock.libs.libfcc.html
+++ b/reference/libs/haddock.libs.libfcc.html
@@ -262,7 +262,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/libs/haddock.libs.libfunc.html b/reference/libs/haddock.libs.libfunc.html
index ab9f44b45..9d532edcb 100644
--- a/reference/libs/haddock.libs.libfunc.html
+++ b/reference/libs/haddock.libs.libfunc.html
@@ -214,7 +214,7 @@ 
libfunc: functional-programming helping tools
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/libs/haddock.libs.libhpc.html b/reference/libs/haddock.libs.libhpc.html
index 12f130659..70a4435e2 100644
--- a/reference/libs/haddock.libs.libhpc.html
+++ b/reference/libs/haddock.libs.libhpc.html
@@ -269,7 +269,7 @@ 
libhpc: HPC execution functions
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/libs/haddock.libs.libinteractive.html b/reference/libs/haddock.libs.libinteractive.html
index dd27c8a7b..681e4237d 100644
--- a/reference/libs/haddock.libs.libinteractive.html
+++ b/reference/libs/haddock.libs.libinteractive.html
@@ -199,7 +199,7 @@ 
libinteractive: functions related to interactive tasks
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/libs/haddock.libs.libio.html b/reference/libs/haddock.libs.libio.html
index 0b630a0e7..6d603ce5f 100644
--- a/reference/libs/haddock.libs.libio.html
+++ b/reference/libs/haddock.libs.libio.html
@@ -466,7 +466,7 @@ 
libio: I/O helping functions
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/libs/haddock.libs.liblog.html b/reference/libs/haddock.libs.liblog.html
index b04c76b3f..27fdaa4b0 100644
--- a/reference/libs/haddock.libs.liblog.html
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@@ -175,7 +175,7 @@ 
liblog: Logging helping functions
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/libs/haddock.libs.libmath.html b/reference/libs/haddock.libs.libmath.html
index 98f693642..aff216945 100644
--- a/reference/libs/haddock.libs.libmath.html
+++ b/reference/libs/haddock.libs.libmath.html
@@ -148,7 +148,7 @@ 
libmath: Math helping functions
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/libs/haddock.libs.libmpi.html b/reference/libs/haddock.libs.libmpi.html
index 1ba8f2ef3..f84e2a2bd 100644
--- a/reference/libs/haddock.libs.libmpi.html
+++ b/reference/libs/haddock.libs.libmpi.html
@@ -146,7 +146,7 @@ 
libmpi: MPI execution functions
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/libs/haddock.libs.libontology.html b/reference/libs/haddock.libs.libontology.html
index 9629a2352..0b9fa866f 100644
--- a/reference/libs/haddock.libs.libontology.html
+++ b/reference/libs/haddock.libs.libontology.html
@@ -256,7 +256,7 @@ 
libontology: module communication
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/libs/haddock.libs.libparallel.html b/reference/libs/haddock.libs.libparallel.html
index a248c89aa..5297ca93d 100644
--- a/reference/libs/haddock.libs.libparallel.html
+++ b/reference/libs/haddock.libs.libparallel.html
@@ -206,7 +206,7 @@ 
libparallel: multiprocessing helping functions
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/libs/haddock.libs.libpdb.html b/reference/libs/haddock.libs.libpdb.html
index 59e16d842..da4d2f3e7 100644
--- a/reference/libs/haddock.libs.libpdb.html
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@@ -262,7 +262,7 @@ 
libpdb: PDB helping functions
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/libs/haddock.libs.libplots.html b/reference/libs/haddock.libs.libplots.html
index 20484e13a..8ad7ee39d 100644
--- a/reference/libs/haddock.libs.libplots.html
+++ b/reference/libs/haddock.libs.libplots.html
@@ -557,7 +557,7 @@ 
libplots: plotting functionalities
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/libs/haddock.libs.librestraints.html b/reference/libs/haddock.libs.librestraints.html
index 65af4329e..d6c203b6a 100644
--- a/reference/libs/haddock.libs.librestraints.html
+++ b/reference/libs/haddock.libs.librestraints.html
@@ -247,7 +247,7 @@ 
librestraints: functions related to restraints
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/libs/haddock.libs.libstructure.html b/reference/libs/haddock.libs.libstructure.html
index e285f4173..c9d0a836b 100644
--- a/reference/libs/haddock.libs.libstructure.html
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@@ -158,7 +158,7 @@ 
libstructure: functions related to structures
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/libs/haddock.libs.libsubprocess.html b/reference/libs/haddock.libs.libsubprocess.html
index c797d95bf..7dd5efdd5 100644
--- a/reference/libs/haddock.libs.libsubprocess.html
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@@ -228,7 +228,7 @@ 
libsubprocess: subprocess execution functions
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/libs/haddock.libs.libtimer.html b/reference/libs/haddock.libs.libtimer.html
index f7488048f..5c763e312 100644
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+++ b/reference/libs/haddock.libs.libtimer.html
@@ -182,7 +182,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/reference/libs/haddock.libs.libutil.html b/reference/libs/haddock.libs.libutil.html
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@@ -331,7 +331,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
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@@ -190,7 +190,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/search.html b/search.html
index c97e02fe0..75913b66d 100644
--- a/search.html
+++ b/search.html
@@ -100,7 +100,7 @@
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/searchindex.js b/searchindex.js
index 9dd3b26cc..69d9104f5 100644
--- a/searchindex.js
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"haddock.clis.restraints.validate_tbl module", "haddock.clis.restraints.webservice module", "haddock.clis.restraints.z_surface_restraints module", "Contributing to HADDOCK3", "Workflow Examples", "haddock package", "haddock.fcc package", "haddock.fcc.calc_fcc_matrix module", "haddock.fcc.cluster_fcc module", "haddock.modules package", "haddock.modules.base_cns_module module", "haddock.modules.topology.topocg package", "Welcome to HADDOCK3 Documentation!", "A brief introduction to HADDOCK3", "haddock", "Alanine Scanning module", "haddock.modules.analysis.alascan.scan module", "CAPRI Evaluation module", "haddock.modules.analysis.caprieval.capri module", "FCC Clustering module", "haddock.modules.analysis.clustfcc.clustfcc module", "RMSD Clustering module", "haddock.modules.analysis.clustrmsd.clustrmsd module", "Contact Map module", "haddock.modules.analysis.contactmap.contmap module", "Interface Ligand RMSD Matrix calculation module", "haddock.modules.analysis.ilrmsdmatrix.ilrmsd module", "RMSD Matrix calculation module", "haddock.modules.analysis.rmsdmatrix.rmsd module", "Selection of top models module", "Selection of top clusters module", "haddock.modules.analysis.seletopclusts.seletopclusts module", "Analysis Modules", "Easy", "Easy", "Easy", "Easy", "Easy", "Easy", "Easy", "Easy", "Easy", "Exit module", "Extra Modules", "Easy", "Easy", "Modules", "Energy Minimization refinement module", "Flexible refinement module", "Water refinement module", "OpenMM Molecular Dynamics module", "haddock.modules.refinement.openmm.openmm module", "Model Refinement Modules", "Easy", "Easy", "Easy", "Easy", "Gdock sampling module", "LightDock sampling module", "Rigid body docking sampling module", "Sampling Modules", "Easy", "Easy", "Easy", "Energy Minimization scoring module", "Molecular Dynamics scoring module", "Surface Accessibility Scoring module", "haddock.modules.scoring.sasascore.sasascore module", "Scoring Modules", "Easy", "Easy", "Easy", "All-atom topology module", "Topology Modules", "Easy", "Core Reference", "CNS paths definitions", "Defaults definitions", "Exceptions", "Supported molecules", "typing", "Mandatory Parameters", "Gear Reference", "Clean output from step folders", "Configuration file I/O", "Expandable parameters", "Start from copy", "Greetings messages", "HADDOCK models", "Known CNS errors", "Parameters helper", "Prepare run", "PDB preprocessing", "Restart run", "Validations", "YAML configs", "Zero fill prefix", "Library Reference", "Libs Reference", "haddock.libs.assets package", "libalign: sequence and structural alignments", "libcli: functions helping clients", "libclust: functions related to clustering", "libcns: creating CNS files", "haddock.libs.libfcc module", "libfunc: functional-programming helping tools", "libhpc: HPC execution functions", "libinteractive: functions related to interactive tasks", "libio: I/O helping functions", "liblog: Logging helping functions", "libmath: Math helping functions", "libmpi: MPI execution functions", "libontology: module communication", "libparallel: multiprocessing helping functions", "libpdb: PDB helping functions", "libplots: plotting functionalities", "librestraints: functions related to restraints", "libstructure: functions related to structures", "libsubprocess: subprocess execution functions", "libtimer: timing functions", "libutil: utility functions", "libworkflow: workflow functions", "Testing", "Running integration tests manually", "Editing and extending runs", "Advanced features", "Running HADDOCK3 with MPI", "Workflow configuration files"], "titleterms": {"1": [0, 30, 119, 150], "2": [0, 30, 119], "3": [0, 30, 119, 150], "4": [0, 30, 150], "5": [0, 30, 150], "6": 30, "A": 40, "access": 93, "active_passive_to_ambig": 23, "add_extra_particles_for_forcefield": [77, 83], "addit": [30, 119, 150, 151], "advanc": 152, "alanin": 42, "alascan": 43, "align": 127, "alignment_method": [44, 61], "all": 99, "allatom": [44, 52, 54, 61, 65, 66], "ambig": 31, "ambig_cool1": 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\ No newline at end of file
+Search.setIndex({"alltitles": {"(Optional) Install MPI libraries if you intend to run HADDOCK3 with MPI": [[1, "optional-install-mpi-libraries-if-you-intend-to-run-haddock3-with-mpi"]], "(Optional) Install web service dependencies if you intend to run HADDOCK3 restraints web service": [[1, "optional-install-web-service-dependencies-if-you-intend-to-run-haddock3-restraints-web-service"]], "1. Contributing new code": [[30, "contributing-new-code"]], "1. Downloading CNS": [[0, "downloading-cns"]], "1. Install HADDOCK3 main branch separately": [[150, "install-haddock3-main-branch-separately"]], "1. System not recognized": [[0, "system-not-recognized"]], "1.1 Contributing with code (additional details)": [[30, "contributing-with-code-additional-details"]], "1.2 Contributing with tests (additional details)": [[30, "contributing-with-tests-additional-details"]], "1.3 Dependencies": [[30, "dependencies"]], "1.4 Code style": [[30, "code-style"]], "1.5 Code structure": [[30, "code-structure"]], "1.6 Creating a new module": [[30, "creating-a-new-module"]], "2. Compiler": [[0, "compiler"]], "2. Configuring CNS": [[0, "configuring-cns"]], "2. Contributing with documentation": [[30, "contributing-with-documentation"]], "3. Makefile": [[0, "makefile"]], "3. Patch CNS with HADDOCK custom files": [[0, "patch-cns-with-haddock-custom-files"]], "3. Running the tests in the main": [[150, "running-the-tests-in-the-main"]], "4. Compiling CNS": [[0, "compiling-cns"]], "4. Running the tests on your branch": [[150, "running-the-tests-on-your-branch"]], "5. Comparing both runs": [[150, "comparing-both-runs"]], "5. Installing the created CNS executable into haddock3": [[0, "installing-the-created-cns-executable-into-haddock3"]], "A brief introduction to HADDOCK3": [[40, null]], "Additional considerations": [[150, "additional-considerations"], [151, "additional-considerations"]], "Additional information": [[119, "additional-information"]], "Advanced features": [[152, null]], "Alanine Scanning module": [[42, null]], "All-atom topology module": [[99, null]], "Analysis Modules": [[59, null]], "Analysis client": [[6, null]], "Benchmark Daemon": [[10, null]], "CAPRI Evaluation module": [[44, null]], "CNS Installation": [[0, null]], "CNS paths definitions": [[103, null]], "Calculate score": [[15, null]], "Citing": [[3, null]], "Clean HADDOCK3 runs": [[8, null]], "Clean output from step folders": [[110, null]], "Command-line interfaces": [[4, null]], "Compatibility with TOML": [[154, "compatibility-with-toml"]], "Configuration file I/O": [[111, null]], "Contact Map module": [[50, null]], "Content": [[39, "content"]], "Contributing to HADDOCK3": [[30, null]], "Copy steps to new run": [[9, null]], "Core Reference": [[102, null]], "Corrections performed on 1)": [[119, "corrections-performed-on-1"]], "Corrections performed on 2)": [[119, "corrections-performed-on-2"]], "Corrections performed on 3)": [[119, "corrections-performed-on-3"]], "Default Parameters": [[42, "default-parameters"], [44, "default-parameters"], [46, "default-parameters"], [48, "default-parameters"], [50, "default-parameters"], [52, "default-parameters"], [54, "default-parameters"], [56, "default-parameters"], [57, "default-parameters"], [69, "default-parameters"], [74, "default-parameters"], [75, "default-parameters"], [76, "default-parameters"], [77, "default-parameters"], [84, "default-parameters"], [85, "default-parameters"], [86, "default-parameters"], [91, "default-parameters"], [92, "default-parameters"], [93, "default-parameters"], [99, "default-parameters"]], "Defaults definitions": [[104, null]], "Easy": [[42, 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29, "z_surface_restraint": 22, "zero": [36, 73, 109, 151], "zero_fil": [113, 123], "zerofil": [113, 123], "zfnum": 123, "zip": [6, 30, 135], "zip_top_rank": 6, "zn": [106, 119], "zn2": [106, 119], "zxvf": 0, "\u00e5": [42, 44, 60, 61]}, "titles": ["CNS Installation", "Installation", "Usage", "Citing", "Command-line interfaces", "Run HADDOCK3", "Analysis client", "Retrieve config", "Clean HADDOCK3 runs", "Copy steps to new run", "Benchmark Daemon", "HADDOCK3 MPI Run", "PDB preprocessing client", "Interactive run client", "Generate restraints", "Calculate score", "PDB Traceback client", "Unpack HADDOCK3 run", "Interactive sucommands", "haddock.clis.re.clustfcc module", "haddock.clis.re.clustrmsd module", "haddock.clis.re.score module", "Restraints-related subcommands", "haddock.clis.restraints.active_passive_to_ambig module", "haddock.clis.restraints.calc_accessibility module", "haddock.clis.restraints.passive_from_active module", "haddock.clis.restraints.restrain_bodies module", "haddock.clis.restraints.validate_tbl module", "haddock.clis.restraints.webservice module", "haddock.clis.restraints.z_surface_restraints module", "Contributing to HADDOCK3", "Workflow Examples", "haddock package", "haddock.fcc package", "haddock.fcc.calc_fcc_matrix module", "haddock.fcc.cluster_fcc module", "haddock.modules package", "haddock.modules.base_cns_module module", "haddock.modules.topology.topocg package", "Welcome to HADDOCK3 Documentation!", "A brief introduction to HADDOCK3", "haddock", "Alanine Scanning module", "haddock.modules.analysis.alascan.scan module", "CAPRI Evaluation module", "haddock.modules.analysis.caprieval.capri module", "FCC Clustering module", "haddock.modules.analysis.clustfcc.clustfcc module", "RMSD Clustering module", "haddock.modules.analysis.clustrmsd.clustrmsd module", "Contact Map module", "haddock.modules.analysis.contactmap.contmap module", "Interface Ligand RMSD Matrix calculation module", "haddock.modules.analysis.ilrmsdmatrix.ilrmsd module", "RMSD Matrix calculation module", "haddock.modules.analysis.rmsdmatrix.rmsd module", "Selection of top models module", "Selection of top clusters module", "haddock.modules.analysis.seletopclusts.seletopclusts module", "Analysis Modules", "Easy", "Easy", "Easy", "Easy", "Easy", "Easy", "Easy", "Easy", "Easy", "Exit module", "Extra Modules", "Easy", "Easy", "Modules", "Energy Minimization refinement module", "Flexible refinement module", "Water refinement module", "OpenMM Molecular Dynamics module", "haddock.modules.refinement.openmm.openmm module", "Model Refinement Modules", "Easy", "Easy", "Easy", "Easy", "Gdock sampling module", "LightDock sampling module", "Rigid body docking sampling module", "Sampling Modules", "Easy", "Easy", "Easy", "Energy Minimization scoring module", "Molecular Dynamics scoring module", "Surface Accessibility Scoring module", "haddock.modules.scoring.sasascore.sasascore module", "Scoring Modules", "Easy", "Easy", "Easy", "All-atom topology module", "Topology Modules", "Easy", "Core Reference", "CNS paths definitions", "Defaults definitions", "Exceptions", "Supported molecules", "typing", "Mandatory Parameters", "Gear Reference", "Clean output from step folders", "Configuration file I/O", "Expandable parameters", "Start from copy", "Greetings messages", "HADDOCK models", "Known CNS errors", "Parameters helper", "Prepare run", "PDB preprocessing", "Restart run", "Validations", "YAML configs", "Zero fill prefix", "Library Reference", "Libs Reference", "haddock.libs.assets package", "libalign: sequence and structural alignments", "libcli: functions helping clients", "libclust: functions related to clustering", "libcns: creating CNS files", "haddock.libs.libfcc module", "libfunc: functional-programming helping tools", "libhpc: HPC execution functions", "libinteractive: functions related to interactive tasks", "libio: I/O helping functions", "liblog: Logging helping functions", "libmath: Math helping functions", "libmpi: MPI execution 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\ No newline at end of file
diff --git a/testing/index.html b/testing/index.html
index d1a1db513..292ac270d 100644
--- a/testing/index.html
+++ b/testing/index.html
@@ -104,7 +104,7 @@ 
Testing
 
   

     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
       

   

 
diff --git a/testing/integration_tests.html b/testing/integration_tests.html
index a62953f2f..02c34ada9 100644
--- a/testing/integration_tests.html
+++ b/testing/integration_tests.html
@@ -223,7 +223,7 @@ 
Running individual test cases
     
© Copyright 2024, BonvinLab.
-      Last updated on Oct 29, 2024.
+      Last updated on Oct 31, 2024.
diff --git a/tutorials/continuing_runs.html b/tutorials/continuing_runs.html index dcb8029d0..bdf46a947 100644 --- a/tutorials/continuing_runs.html +++ b/tutorials/continuing_runs.html @@ -259,7 +259,7 @@

Additional considerations

© Copyright 2024, BonvinLab. - Last updated on Oct 29, 2024. + Last updated on Oct 31, 2024.

diff --git a/tutorials/index.html b/tutorials/index.html index deb1148b2..e1ecc38b0 100644 --- a/tutorials/index.html +++ b/tutorials/index.html @@ -125,7 +125,7 @@

Tutorials for developers

© Copyright 2024, BonvinLab. - Last updated on Oct 29, 2024. + Last updated on Oct 31, 2024.

diff --git a/tutorials/mpi.html b/tutorials/mpi.html index 737266b3f..cd0dd8ae8 100644 --- a/tutorials/mpi.html +++ b/tutorials/mpi.html @@ -153,7 +153,7 @@

Running HADDOCK3 with MPI

© Copyright 2024, BonvinLab. - Last updated on Oct 29, 2024. + Last updated on Oct 31, 2024.

diff --git a/tutorials/user_config.html b/tutorials/user_config.html index ebe88e741..8520f1a07 100644 --- a/tutorials/user_config.html +++ b/tutorials/user_config.html @@ -276,7 +276,7 @@

Compatibility with TOML

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