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Copy pathconstants_last.txt
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189 lines (189 loc) · 10.2 KB
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clean_up_molecule_list_script=True
generate_conformers_using_vconf_script=False
prepare_TMoleX_files_script=False
submit_TMoleX_files_to_cluster_script=False
check_cluster_queue_script=False
grab_files_from_cluster_script=False
write_new_inp_file_script=False
gzip_and_unzip_script=False
check_remote_directory_script=False
extract_data_from_excel_list=True
generate_tsv_file=True
identifier_override=""
max_conformers=1000000000
skip_vconf_exe=False
step_sampling=False
use_default_vconf_settings=True
generate_cosmo_format_files=True
geometry_optimize_lowest_energy_structures=100
percent_enabled=True
clean_temp_directory=True
copy_files_to_timestamped_folder=True
delete_temp_dir_after_transferring_to_timestamped_folder=True
gzip_timestamped_folder=False
only_transfer_cosmo_file=True
pull_from_timestamped_folder=True
timestamp_folder=""
extract_cosmo_files_to_cosmo_folder=True
write_inp_file=True
delete_file_path=""
delete_file_path_toggle=False
gzip_directory_by_name=""
gzip_temp_directory=False
unzip_directory_by_name=""
unzip_temp_directory=False
list_folder_name="Template"
template_name=""
temp_dir="temp_dir"
port="22"
compound_list_directory="Path to Compound_List in PyCharm"
vconf_path="Path to vconf.exe in PyCharm"
Default VConf Settings_SDF_FILENAME="Path to Compound_List in PyCharm\Template\VCONF_outputs\Template.sdf"
Default VConf Settings_OUTPUT_LOG="Path to Compound_List in PyCharm\Template\VCONF_outputs\Template.log"
Default VConf Settings_OUTPUT_SDF="Path to Compound_List in PyCharm\Template\VCONF_outputs\Template_vconf.sdf"
Default VConf Settings_vconf_batch_sdf_path="Path to Compound_List in PyCharm\Template\VCONF_outputs\Template_vconf_batchfile.sdf"
Default VConf Settings_FIRST_MOLECULE="1"
Default VConf Settings_LAST_MOLECULE="None"
Default VConf Settings_FORCEFIELD="dreiding"
Default VConf Settings_USE_GENERALIZED_BORN_SOLVATION="False"
Default VConf Settings_SEARCH_MODE="search"
Default VConf Settings_NUM_STEPS="50000"
Default VConf Settings_RESTRAINED_ATOMS="None"
Default VConf Settings_RANDOM_SEEDS="1111 1111 1111 1111"
Default VConf Settings_SEARCH_WIDTH="0.5"
Default VConf Settings_FORMAL_CHARGE="True"
Default VConf Settings_SULFONAMIDE_NITROGEN="False"
Default VConf Settings_CHIRAL_PRIORITY="pbc"
Default VConf Settings_STEREOCHEMISTRY_RESTRICTIONS="b"
Default VConf Settings_DIELECTRIC_COEFFICIENT="4.0"
Default VConf Settings_NITROGEN_LONE_PAIR="False"
Default VConf Settings_RESONANCE_LIMIT="1000"
Default VConf Settings_SUBSTITUENTS_LEVEL="u"
Default VConf Settings_MIN_RING_SEARCH_STEPS="50"
Default VConf Settings_ADD_RING_SEARCH_STEPS="200"
Default VConf Settings_MAX_RING_CONFS="5"
Default VConf Settings_MAX_RING_ATOMS="200"
Default VConf Settings_RING_ENERGY_CUTOFF="1"
Default VConf Settings_KEEP_LOWEST_ENERGY_RING_COMBINATION="False"
Default VConf Settings_ENERGY_CUTOFF="5"
Default VConf Settings_ENERGY_TOLERANCE="1"
Default VConf Settings_DISTANCE_TOLERANCE="0.2"
Default VConf Settings_ANGLE_TOLERANCE="30"
Default VConf Settings_DO_NOT_FILTER_OUTPUT="False"
Default VConf Settings_SETUP_TIME_LIMIT="120"
Default VConf Settings_FILTER_TIME_LIMIT="120"
Default VConf Settings_NO_TIME_LIMITS="True"
Default VConf Settings_KEEP_UNFILTERED_CONFORMATIONS="False"
Experimental VConf Settings_SDF_FILENAME="Path to Compound_List in PyCharm\Template\VCONF_outputs\Template.sdf"
Experimental VConf Settings_OUTPUT_LOG="Path to Compound_List in PyCharm\Template\VCONF_outputs\Template.log"
Experimental VConf Settings_OUTPUT_SDF="Path to Compound_List in PyCharm\Template\VCONF_outputs\Template_vconf.sdf"
Experimental VConf Settings_vconf_batch_sdf_path="Path to Compound_List in PyCharm\Template\VCONF_outputs\Template_vconf_batchfile.sdf"
Experimental VConf Settings_FIRST_MOLECULE="1"
Experimental VConf Settings_LAST_MOLECULE="None"
Experimental VConf Settings_FORCEFIELD="dreiding"
Experimental VConf Settings_USE_GENERALIZED_BORN_SOLVATION="False"
Experimental VConf Settings_SEARCH_MODE="search"
Experimental VConf Settings_NUM_STEPS="5000"
Experimental VConf Settings_RESTRAINED_ATOMS="None"
Experimental VConf Settings_RANDOM_SEEDS="1111 1111 1111 1111"
Experimental VConf Settings_SEARCH_WIDTH="0.5"
Experimental VConf Settings_FORMAL_CHARGE="True"
Experimental VConf Settings_SULFONAMIDE_NITROGEN="False"
Experimental VConf Settings_CHIRAL_PRIORITY="pbc"
Experimental VConf Settings_STEREOCHEMISTRY_RESTRICTIONS="b"
Experimental VConf Settings_DIELECTRIC_COEFFICIENT="4.0"
Experimental VConf Settings_NITROGEN_LONE_PAIR="False"
Experimental VConf Settings_RESONANCE_LIMIT="1000"
Experimental VConf Settings_SUBSTITUENTS_LEVEL="u"
Experimental VConf Settings_MIN_RING_SEARCH_STEPS="50"
Experimental VConf Settings_ADD_RING_SEARCH_STEPS="200"
Experimental VConf Settings_MAX_RING_CONFS="5"
Experimental VConf Settings_MAX_RING_ATOMS="200"
Experimental VConf Settings_RING_ENERGY_CUTOFF="1"
Experimental VConf Settings_KEEP_LOWEST_ENERGY_RING_COMBINATION="False"
Experimental VConf Settings_ENERGY_CUTOFF="5"
Experimental VConf Settings_ENERGY_TOLERANCE="1"
Experimental VConf Settings_DISTANCE_TOLERANCE="0.2"
Experimental VConf Settings_ANGLE_TOLERANCE="30"
Experimental VConf Settings_DO_NOT_FILTER_OUTPUT="False"
Experimental VConf Settings_SETUP_TIME_LIMIT="120"
Experimental VConf Settings_FILTER_TIME_LIMIT="120"
Experimental VConf Settings_NO_TIME_LIMITS="True"
Experimental VConf Settings_KEEP_UNFILTERED_CONFORMATIONS="False"
default_vconf_settings_SDF_FILENAME="Path to Compound_List in PyCharm\Template\VCONF_outputs\Template.sdf"
default_vconf_settings_OUTPUT_LOG="Path to Compound_List in PyCharm\Template\VCONF_outputs\Template.log"
default_vconf_settings_OUTPUT_SDF="Path to Compound_List in PyCharm\Template\VCONF_outputs\Template_vconf.sdf"
default_vconf_settings_vconf_batch_sdf_path="Path to Compound_List in PyCharm\Template\VCONF_outputs\Template_vconf_batchfile.sdf"
default_vconf_settings_FIRST_MOLECULE=1
default_vconf_settings_LAST_MOLECULE=None
default_vconf_settings_FORCEFIELD="dreiding"
default_vconf_settings_USE_GENERALIZED_BORN_SOLVATION=False
default_vconf_settings_SEARCH_MODE="search"
default_vconf_settings_NUM_STEPS=50000
default_vconf_settings_RESTRAINED_ATOMS=None
default_vconf_settings_RANDOM_SEEDS="1111 1111 1111 1111"
default_vconf_settings_SEARCH_WIDTH="0.5"
default_vconf_settings_FORMAL_CHARGE=True
default_vconf_settings_SULFONAMIDE_NITROGEN=False
default_vconf_settings_CHIRAL_PRIORITY="pbc"
default_vconf_settings_STEREOCHEMISTRY_RESTRICTIONS="b"
default_vconf_settings_DIELECTRIC_COEFFICIENT="4.0"
default_vconf_settings_NITROGEN_LONE_PAIR=False
default_vconf_settings_RESONANCE_LIMIT=1000
default_vconf_settings_SUBSTITUENTS_LEVEL="u"
default_vconf_settings_MIN_RING_SEARCH_STEPS=50
default_vconf_settings_ADD_RING_SEARCH_STEPS=200
default_vconf_settings_MAX_RING_CONFS=5
default_vconf_settings_MAX_RING_ATOMS=200
default_vconf_settings_RING_ENERGY_CUTOFF=1
default_vconf_settings_KEEP_LOWEST_ENERGY_RING_COMBINATION=False
default_vconf_settings_ENERGY_CUTOFF=5
default_vconf_settings_ENERGY_TOLERANCE=1
default_vconf_settings_DISTANCE_TOLERANCE="0.2"
default_vconf_settings_ANGLE_TOLERANCE=30
default_vconf_settings_DO_NOT_FILTER_OUTPUT=False
default_vconf_settings_SETUP_TIME_LIMIT=120
default_vconf_settings_FILTER_TIME_LIMIT=120
default_vconf_settings_NO_TIME_LIMITS=True
default_vconf_settings_KEEP_UNFILTERED_CONFORMATIONS=False
experimental_vconf_settings_SDF_FILENAME="Path to Compound_List in PyCharm\Template\VCONF_outputs\Template.sdf"
experimental_vconf_settings_OUTPUT_LOG="Path to Compound_List in PyCharm\Template\VCONF_outputs\Template.log"
experimental_vconf_settings_OUTPUT_SDF="Path to Compound_List in PyCharm\Template\VCONF_outputs\Template_vconf.sdf"
experimental_vconf_settings_vconf_batch_sdf_path="Path to Compound_List in PyCharm\Template\VCONF_outputs\Template_vconf_batchfile.sdf"
experimental_vconf_settings_FIRST_MOLECULE=1
experimental_vconf_settings_LAST_MOLECULE=None
experimental_vconf_settings_FORCEFIELD="dreiding"
experimental_vconf_settings_USE_GENERALIZED_BORN_SOLVATION=False
experimental_vconf_settings_SEARCH_MODE="search"
experimental_vconf_settings_NUM_STEPS=5000
experimental_vconf_settings_RESTRAINED_ATOMS=None
experimental_vconf_settings_RANDOM_SEEDS="1111 1111 1111 1111"
experimental_vconf_settings_SEARCH_WIDTH="0.5"
experimental_vconf_settings_FORMAL_CHARGE=True
experimental_vconf_settings_SULFONAMIDE_NITROGEN=False
experimental_vconf_settings_CHIRAL_PRIORITY="pbc"
experimental_vconf_settings_STEREOCHEMISTRY_RESTRICTIONS="b"
experimental_vconf_settings_DIELECTRIC_COEFFICIENT="4.0"
experimental_vconf_settings_NITROGEN_LONE_PAIR=False
experimental_vconf_settings_RESONANCE_LIMIT=1000
experimental_vconf_settings_SUBSTITUENTS_LEVEL="u"
experimental_vconf_settings_MIN_RING_SEARCH_STEPS=50
experimental_vconf_settings_ADD_RING_SEARCH_STEPS=200
experimental_vconf_settings_MAX_RING_CONFS=5
experimental_vconf_settings_MAX_RING_ATOMS=200
experimental_vconf_settings_RING_ENERGY_CUTOFF=1
experimental_vconf_settings_KEEP_LOWEST_ENERGY_RING_COMBINATION=False
experimental_vconf_settings_ENERGY_CUTOFF=5
experimental_vconf_settings_ENERGY_TOLERANCE=1
experimental_vconf_settings_DISTANCE_TOLERANCE="0.2"
experimental_vconf_settings_ANGLE_TOLERANCE=30
experimental_vconf_settings_DO_NOT_FILTER_OUTPUT=False
experimental_vconf_settings_SETUP_TIME_LIMIT=120
experimental_vconf_settings_FILTER_TIME_LIMIT=120
experimental_vconf_settings_NO_TIME_LIMITS=True
experimental_vconf_settings_KEEP_UNFILTERED_CONFORMATIONS=False
define_sh_content=define << EOF\n\n\na coord\ndesy\nired\n*\nno\nb all def2-TZVP\n*\neht\n\n{charge}\n\n\nrex\n-int\n*\n-polish\n*\n*\n*\n*\n*\n*\n*\nscf\niter\n200\n\ndft\nfunc\nb3-lyp\non\n\nri\non\n\n*\nEOF
cosmoprep_sh_content=cosmoprep << EOF\n\n\n\n\n\n\n\n\n\n\n\nr all o\n*\n\n\nEOF
subscript_sh_content=#!/bin/bash\n#\n#$ -q speedy\n#$ -cwd\n#$ -j y\n#$ -S /bin/bash\n#$ -N {mol_name}\n#$ -pe orte 10\n#$ -R y\n\n######## ENTER YOUR TURBOMOLE INSTALLATION PATH HERE ##########\nexport TURBODIR=/state/partition1/TURBOMOLE/TURBOMOLE\n###############################################################\nexport PATH=$TURBODIR/scripts:$PATH\nexport PARA_ARCH=MPI\nexport PATH=$TURBODIR/bin/`sysname`:$PATH\nexport PARNODES=10\nulimit -s unlimited\nmodule load openmpi-x86_64\npwd\njobex -c 400 -ri > job.out
go_define_sh_content=define << EOF\n\n\na coord\ndesy\nired\n*\nno\nb all def2-TZVP\n*\neht\n\n{charge}\n\n\nscf\niter\n200\n\ndft\non\n\nri\non\n\n*\nEOF
gzip_and_unzip_script=False