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Commit 8aef965b authored by Rafal Gumienny's avatar Rafal Gumienny
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docs: SCHWED-3121 Format help a bit better

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......@@ -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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