Merge branch 'main' into bugfix_traceback_contactmap

src/haddock/gear/yaml2cfg.py

@@ -96,7 +96,7 @@ def _yaml2cfg_text(
     exp_level_idx = exp_levels[explevel]
 
     # define set of undesired parameter keys
-    undesired = ("default", "explevel", "short", "type")
+    undesired = ("default", "explevel", "type")
     if not details:
         undesired = undesired + ("long",)  # type: ignore
 

src/haddock/modules/defaults.yaml

@@ -89,7 +89,7 @@ concat:
   precision: 0
   title: Number of models to produce per job.
   short: Multiple models can be calculated within one job
-  long: The defins the number of models that will be generated within on job script. 
+  long: This defines the number of models that will be generated within on job script. 
     This allows to concatenate the generation of models into one script. 
     In that way jobs might run longer in the batch system and reduce the load on the scheduler.
   group: 'execution'

tests/configs/yaml2cfg_converted.cfg

@@ -1,33 +1,33 @@
 [topoaa]
-autohis = true  # $title Automatic HIS protonation state / $group molecule
-delenph = true  # $title Keep or remove non-polar hydrogen atoms / $group molecule
-log_level = 'verbose'  # $minchars 0 / $maxchars 100 / $title Log level verbosity for CNS / $group module
-iniseed = 917  # $min 0 / $max 9999999999999999 / $precision 3 / $title Random seed / $group molecule
-ligand_param_fname = ''  # $title No title yet
-ligand_top_fname = ''  # $title No title yet
-limit = true  # $title No title yet
-tolerance = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
+autohis = true  # $title Automatic HIS protonation state / $short The protonation state of histidine (+1: HIS or 0: HISD/HISE) will be automatically set by HADDOCK / $group molecule
+delenph = true  # $title Keep or remove non-polar hydrogen atoms / $short If set to true, non-polar hydrogen atoms will be discarded to save computing time / $group molecule
+log_level = 'verbose'  # $minchars 0 / $maxchars 100 / $title Log level verbosity for CNS / $short Set the log level verbosity for CNS (minimal or verbose) / $group module
+iniseed = 917  # $min 0 / $max 9999999999999999 / $precision 3 / $title Random seed / $short Random seed used in CNS to initialize the random seed function / $group molecule
+ligand_param_fname = ''  # $title No title yet / $short No short description yet
+ligand_top_fname = ''  # $title No title yet / $short No short description yet
+limit = true  # $title No title yet / $short No short description yet
+tolerance = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet / $short No short description yet
 
 [topoaa.mol1]
-prot_segid = 'A'  # $minchars 0 / $maxchars 100 / $title No title yet
-fix_origin = false  # $title No title yet
-dna = false  # $title No title yet
-shape = false  # $title No title yet
-cg = false  # $title No title yet
-cyclicpept = false  # $title No title yet
-nhisd = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
-hisd_1 = nan  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
-nhise = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
-hise_1 = nan  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
+prot_segid = 'A'  # $minchars 0 / $maxchars 100 / $title No title yet / $short No short description yet
+fix_origin = false  # $title No title yet / $short No short description yet
+dna = false  # $title No title yet / $short No short description yet
+shape = false  # $title No title yet / $short No short description yet
+cg = false  # $title No title yet / $short No short description yet
+cyclicpept = false  # $title No title yet / $short No short description yet
+nhisd = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet / $short No short description yet
+hisd_1 = nan  # $min -9999 / $max 9999 / $precision 3 / $title No title yet / $short No short description yet
+nhise = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet / $short No short description yet
+hise_1 = nan  # $min -9999 / $max 9999 / $precision 3 / $title No title yet / $short No short description yet
 
 [topoaa.mol2]
-prot_segid = 'B'  # $minchars 0 / $maxchars 100 / $title No title yet
-fix_origin = false  # $title No title yet
-dna = false  # $title No title yet
-shape = false  # $title No title yet
-cg = false  # $title No title yet
-cyclicpept = false  # $title No title yet
-nhisd = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
-hisd_1 = nan  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
-nhise = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
-hise_1 = nan  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
+prot_segid = 'B'  # $minchars 0 / $maxchars 100 / $title No title yet / $short No short description yet
+fix_origin = false  # $title No title yet / $short No short description yet
+dna = false  # $title No title yet / $short No short description yet
+shape = false  # $title No title yet / $short No short description yet
+cg = false  # $title No title yet / $short No short description yet
+cyclicpept = false  # $title No title yet / $short No short description yet
+nhisd = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet / $short No short description yet
+hisd_1 = nan  # $min -9999 / $max 9999 / $precision 3 / $title No title yet / $short No short description yet
+nhise = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet / $short No short description yet
+hise_1 = nan  # $min -9999 / $max 9999 / $precision 3 / $title No title yet / $short No short description yet

tests/configs/yaml2cfg_converted_no_header.cfg

@@ -1,32 +1,32 @@
-autohis = true  # $title Automatic HIS protonation state / $group molecule
-delenph = true  # $title Keep or remove non-polar hydrogen atoms / $group molecule
-log_level = 'verbose'  # $minchars 0 / $maxchars 100 / $title Log level verbosity for CNS / $group module
-iniseed = 917  # $min 0 / $max 9999999999999999 / $precision 3 / $title Random seed / $group molecule
-ligand_param_fname = ''  # $title No title yet
-ligand_top_fname = ''  # $title No title yet
-limit = true  # $title No title yet
-tolerance = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
+autohis = true  # $title Automatic HIS protonation state / $short The protonation state of histidine (+1: HIS or 0: HISD/HISE) will be automatically set by HADDOCK / $group molecule
+delenph = true  # $title Keep or remove non-polar hydrogen atoms / $short If set to true, non-polar hydrogen atoms will be discarded to save computing time / $group molecule
+log_level = 'verbose'  # $minchars 0 / $maxchars 100 / $title Log level verbosity for CNS / $short Set the log level verbosity for CNS (minimal or verbose) / $group module
+iniseed = 917  # $min 0 / $max 9999999999999999 / $precision 3 / $title Random seed / $short Random seed used in CNS to initialize the random seed function / $group molecule
+ligand_param_fname = ''  # $title No title yet / $short No short description yet
+ligand_top_fname = ''  # $title No title yet / $short No short description yet
+limit = true  # $title No title yet / $short No short description yet
+tolerance = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet / $short No short description yet
 
 [mol1]
-prot_segid = 'A'  # $minchars 0 / $maxchars 100 / $title No title yet
-fix_origin = false  # $title No title yet
-dna = false  # $title No title yet
-shape = false  # $title No title yet
-cg = false  # $title No title yet
-cyclicpept = false  # $title No title yet
-nhisd = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
-hisd_1 = nan  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
-nhise = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
-hise_1 = nan  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
+prot_segid = 'A'  # $minchars 0 / $maxchars 100 / $title No title yet / $short No short description yet
+fix_origin = false  # $title No title yet / $short No short description yet
+dna = false  # $title No title yet / $short No short description yet
+shape = false  # $title No title yet / $short No short description yet
+cg = false  # $title No title yet / $short No short description yet
+cyclicpept = false  # $title No title yet / $short No short description yet
+nhisd = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet / $short No short description yet
+hisd_1 = nan  # $min -9999 / $max 9999 / $precision 3 / $title No title yet / $short No short description yet
+nhise = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet / $short No short description yet
+hise_1 = nan  # $min -9999 / $max 9999 / $precision 3 / $title No title yet / $short No short description yet
 
 [mol2]
-prot_segid = 'B'  # $minchars 0 / $maxchars 100 / $title No title yet
-fix_origin = false  # $title No title yet
-dna = false  # $title No title yet
-shape = false  # $title No title yet
-cg = false  # $title No title yet
-cyclicpept = false  # $title No title yet
-nhisd = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
-hisd_1 = nan  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
-nhise = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
-hise_1 = nan  # $min -9999 / $max 9999 / $precision 3 / $title No title yet
+prot_segid = 'B'  # $minchars 0 / $maxchars 100 / $title No title yet / $short No short description yet
+fix_origin = false  # $title No title yet / $short No short description yet
+dna = false  # $title No title yet / $short No short description yet
+shape = false  # $title No title yet / $short No short description yet
+cg = false  # $title No title yet / $short No short description yet
+cyclicpept = false  # $title No title yet / $short No short description yet
+nhisd = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet / $short No short description yet
+hisd_1 = nan  # $min -9999 / $max 9999 / $precision 3 / $title No title yet / $short No short description yet
+nhise = 0  # $min -9999 / $max 9999 / $precision 3 / $title No title yet / $short No short description yet
+hise_1 = nan  # $min -9999 / $max 9999 / $precision 3 / $title No title yet / $short No short description yet