From 8aef965bd7e917700ad7f9f08333e5c6ddf89243 Mon Sep 17 00:00:00 2001
From: Rafal Gumienny <r.gumienny@unibas.ch>
Date: Wed, 18 Apr 2018 15:04:32 +0200
Subject: [PATCH] docs: SCHWED-3121 Format help a bit better
---
actions/ost-compare-structures | 149 +++++++++++++++++----------------
1 file changed, 75 insertions(+), 74 deletions(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 6aa18d7ba..8df951933 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -2,64 +2,65 @@
eg.
- ost compare-structures \
- -m <MODEL> \
- -r <REF> \
- -o output.json \
- -l \
- -sc \
- -cc \
- -ml \
- -rm oxt hyd \
- -mn
-
-CAMEO calls lddt binary as follows:
-
- lddt \
- -p <PARAMETER FILE> \
- -f \
- -a 15 \
- -b 15 \
- -r 15 \
- <MODEL> \
- <REF>
+ ost compare-structures \\
+ --model <MODEL> \\
+ --reference <REF> \\
+ --output output.json \\
+ --lddt \\
+ --structural-checks \\
+ --consistency-checks \\
+ --molck \\
+ --remove oxt hyd \\
+ --map-nonstandard-residues
+
+If desired one can recreate what CAMEO is calculating. CAMEO calls lddt binary
+as follows:
+
+ lddt \\
+ -p <PARAMETER FILE> \\
+ -f \\
+ -a 15 \\
+ -b 15 \\
+ -r 15 \\
+ <MODEL> \\
+ <REF>
Only model structures are "Molck-ed" in CAMEO. The call to molck is as follows:
- molck \
- --complib=<COMPOUND LIB> \
- --rm=hyd,oxt,unk \
- --fix-ele \
- --map-nonstd <FILEPATH> \
- --out=<OUTPUT>
+ molck \\
+ --complib=<COMPOUND LIB> \\
+ --rm=hyd,oxt,unk \\
+ --fix-ele \\
+ --map-nonstd <FILEPATH> \\
+ --out=<OUTPUT>
To be as much compatible with with CAMEO as possible one should call
compare-structures as follows:
- ost compare-structures \
- # General parameters
- ####################
- --model <MODEL> \
- --reference <REF> \
- --output output.json \
- # QS-score parameters
- #####################
- --qs-score \
- --residue-number-alignment \
- # lDDT parameters
- #################
- --lddt \
- --structural-checks \
- --consistency-checks \
- --inclusion-radius 15.0 \
- --bond-tolerance 15.0 \
- --angle-tolerance 15.0 \
- # Molck parameters
- ##################
- --molck \
- --remove oxt hyd unk \
- --clean-element-column \
- --map-nonstandard-residues
+ ost compare-structures \\
+ # General parameters
+ ####################
+ --model <MODEL> \\
+ --reference <REF> \\
+ --output output.json \\
+ # QS-score parameters
+ #####################
+ --qs-score \\
+ --residue-number-alignment \\
+ # lDDT parameters
+ #################
+ --lddt \\
+ --structural-checks \\
+ --consistency-checks \\
+ --inclusion-radius 15.0 \\
+ --bond-tolerance 15.0 \\
+ --angle-tolerance 15.0 \\
+ # Molck parameters
+ ##################
+ --molck \\
+ --remove oxt hyd unk \\
+ --clean-element-column \\
+ --map-nonstandard-residues
"""
import os
@@ -154,7 +155,7 @@ def _ParseArgs():
# General options
#
parser = argparse.ArgumentParser(
- formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+ formatter_class=argparse.RawTextHelpFormatter,
description=__doc__,
prog="ost compare-structures")
@@ -197,9 +198,9 @@ def _ParseArgs():
nargs="+",
type=lambda x: x.split(":"),
dest="chain_mapping",
- help=("Mapping of chains between the model and the reference. "
- "Each separate mapping consist of key:value pairs where key "
- "is the chain name in model and value is the chain name in "
+ help=("Mapping of chains between the model and the reference.\n"
+ "Each separate mapping consist of key:value pairs where key\n"
+ "is the chain name in model and value is the chain name in\n"
"reference."))
parser.add_argument(
"-rna",
@@ -207,7 +208,7 @@ def _ParseArgs():
dest="residue_number_alignment",
default=False,
action="store_true",
- help=("Make alignment based on residue number instead of using "
+ help=("Make alignment based on residue number instead of using\n"
"Clustal."))
#
# lDDT options
@@ -251,10 +252,10 @@ def _ParseArgs():
"--parameter-file",
dest="parameter_file",
action=_DefaultStereochemicalParamAction,
- help=("Location of the stereochemical parameter file "
- "(stereo_chemical_props.txt). "
- "If not provided, the following locations are searched in this "
- "order: 1. Working directory, 2. OpenStructure standard library "
+ help=("Location of the stereochemical parameter file\n"
+ "(stereo_chemical_props.txt).\n"
+ "If not provided, the following locations are searched in this\n"
+ "order: 1. Working directory, 2. OpenStructure standard library\n"
"location."))
parser.add_argument(
"-bt",
@@ -283,8 +284,8 @@ def _ParseArgs():
dest="sequence_separation",
type=int,
default=0,
- help=("Sequence separation. Only distances between residues whose "
- "separation is higher than the provided parameter are "
+ help=("Sequence separation. Only distances between residues whose\n"
+ "separation is higher than the provided parameter are\n"
"considered when computing the score"))
parser.add_argument(
"-cc",
@@ -315,10 +316,10 @@ def _ParseArgs():
"--compound-library",
dest="compound_library",
action=_DefaultCompoundLibraryAction,
- help=("Location of the compound library file (compounds.chemlib). "
- "If not provided, the following locations are searched in this "
- "order: 1. Working directory, 2. OpenStructure standard library "
- "location."))
+ help=("Location of the compound library file (compounds.chemlib).\n"
+ "If not provided, the following locations are searched in this\n"
+ "order: 1. Working directory, 2. OpenStructure standard library"
+ "\nlocation."))
parser.add_argument(
"-rm",
"--remove",
@@ -326,13 +327,13 @@ def _ParseArgs():
nargs="+", # *, +, ?, N
required=False,
default=["hyd"],
- help=("Remove atoms and residues matching some criteria: "
- "zeroocc - Remove atoms with zero occupancy, "
- "hyd - remove hydrogen atoms, "
- "oxt - remove terminal oxygens, "
- "nonstd - remove all residues not one of the 20 "
- "standard amino acids, "
- "unk - Remove unknown and atoms not following the nomenclature"))
+ help=("Remove atoms and residues matching some criteria:\n"
+ " * zeroocc - Remove atoms with zero occupancy\n"
+ " * hyd - remove hydrogen atoms\n"
+ " * oxt - remove terminal oxygens\n"
+ " * nonstd - remove all residues not one of the 20\n"
+ " * standard amino acids\n"
+ " * unk - Remove unknown and atoms not following the nomenclature"))
parser.add_argument(
"-ce",
"--clean-element-column",
@@ -346,7 +347,7 @@ def _ParseArgs():
dest="map_nonstandard_residues",
default=False,
action="store_true",
- help=("Map modified residues back to the parent amino acid, for "
+ help=("Map modified residues back to the parent amino acid, for\n"
"example MSE -> MET, SEP -> SER."))
# Print full help is no arguments provided
--
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