<commit_before>#!/bin/bash

# 
# Script to run toxd test case
#

# Always need to supply the path to the Rosetta directory
ROSETTA_DIR=/opt/rosetta-3.5

# Change the below if the path to these external dependencies of AMPLE
# cannot be found in your standard PATH
export PATH=\
/opt/shelx:\
$PATH

# Set which ample binary we are using
AMPLE=$CCP4/bin/ample
#AMPLE=/opt/ample-dev1/bin/ample

$AMPLE \
-rosetta_dir $ROSETTA_DIR \
-fasta toxd_.fasta \
-mtz 1dtx.mtz \
-frags_3mers aat000_03_05.200_v1_3 \
-frags_9mers aat000_09_05.200_v1_3 \
-nmodels 30 \
-percent 50 \
-use_shelxe True \
-use_arpwarp False \
-use_buccaneer False \
-molrep_only True \
-nproc 2 \

#-models_dir ${AMPLEDIR}/examples/toxd-example/ROSETTA_MR_0/models \
#-ensembles_dir ${AMPLEDIR}/examples/toxd-example/ROSETTA_MR_0/ensembles_1 \<commit_msg>Cleaned up script<commit_after>#!/bin/bash

# 
# Script to run toxd test case
#

# Change the below if the path to these external dependencies of AMPLE
# cannot be found in your standard PATH
export PATH=\
/opt/shelx:\
$PATH

$CCP4/bin/ample \
-rosetta_dir /opt/rosetta-3.5 \
-fasta toxd_.fasta \
-mtz 1dtx.mtz \
-frags_3mers aat000_03_05.200_v1_3 \
-frags_9mers aat000_09_05.200_v1_3 \
-nmodels 30 \
-percent 50 \
-quick_mode True \
-use_shelxe True \
-nproc 2 \

#-models_dir ./models \
#-ensembles_dir ./ROSETTA_MR_0/ensembles_1 \
{'fraction_non_alphanumeric': 0.1123429416112343, 'fraction_numerical': 0.05617147080561715, 'mean_word_length': 3.621160409556314, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1978052', 'n_tokens_mistral': 619, 'n_tokens_neox': 564, 'n_words': 138}