From 8aca01e21d436fed3f5948addd603e22e8529fff Mon Sep 17 00:00:00 2001 From: Andrew Jewett Date: Sat, 3 Dec 2022 20:45:14 -0800 Subject: [PATCH] users are no longer required to use "python" instead of "python3" when trying to run .py executable files directly from the shell --- .../measure_persistence_length/merge_lines_periodic.py | 2 +- .../measure_persistence_length/raw2blockaverage.py | 2 +- .../measure_persistence_length/raw2subtractlines.py | 2 +- .../merge_lines_periodic.py | 2 +- .../measure_torsional_persistence_length/raw2blockaverage.py | 2 +- .../measure_torsional_persistence_length/raw2subtractlines.py | 2 +- .../moltemplate_files/generate_system_lt.py | 2 +- .../moltemplate_files/interpolate_coords.py | 2 +- .../moltemplate_files/calc_table_angle.py | 2 +- .../moltemplate_files/calc_table_angle.py | 2 +- .../moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py | 2 +- .../calc_table/version_charmm_cutoff/calc_table.py | 2 +- .../moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py | 2 +- .../calc_table/version_charmm_cutoff/calc_table.py | 2 +- .../moltemplate_files/calc_table/calc_table.py | 2 +- .../calc_table/version_charmm_cutoff/calc_table.py | 2 +- .../moltemplate_files/generate_tables/calc_chaperone_table.py | 2 +- .../moltemplate_files/generate_tables/calc_dihedral_table.py | 2 +- .../moltemplate_files/generate_tables/calc_chaperone_table.py | 2 +- .../moltemplate_files/generate_tables/calc_dihedral_table.py | 2 +- .../moltemplate_files/generate_tables/calc_dihedral_table.py | 2 +- .../moltemplate_files/generate_tables/calc_chaperone_table.py | 2 +- moltemplate/amber2lt.py | 2 +- moltemplate/bonds_by_type.py | 2 +- moltemplate/charge_by_bond.py | 2 +- moltemplate/depreciated/oplsaa_moltemplate.py | 2 +- moltemplate/dump2data.py | 2 +- moltemplate/ettree.py | 2 +- moltemplate/extract_espresso_atom_types.py | 2 +- moltemplate/extract_lammps_data.py | 2 +- .../force_fields/convert_EMC_files_to_LT_files/emcprm2lt.py | 2 +- .../force_fields/convert_MSI_files_to_LT_files/msifrc2lt.py | 2 +- .../convert_TINKER_files_to_LT_files/tinkerparm2lt.py | 2 +- moltemplate/genpoly_lt.py | 2 +- moltemplate/genpoly_modify_lt.py | 2 +- moltemplate/interpolate_curve.py | 2 +- moltemplate/ltemplify.py | 2 +- moltemplate/lttree.py | 2 +- moltemplate/lttree_check.py | 2 +- moltemplate/lttree_postprocess.py | 2 +- moltemplate/lttree_styles.py | 2 +- moltemplate/mol22lt.py | 2 +- moltemplate/nbody_by_type.py | 2 +- moltemplate/nbody_by_type_lib.py | 2 +- moltemplate/nbody_fix_ttree_assignments.py | 2 +- moltemplate/nbody_reorder_atoms.py | 2 +- moltemplate/pdbsort.py | 2 +- moltemplate/postprocess_coeffs.py | 2 +- moltemplate/postprocess_input_script.py | 2 +- moltemplate/postprocess_transitions.py | 2 +- moltemplate/raw2data.py | 2 +- moltemplate/recenter_coords.py | 2 +- moltemplate/remove_duplicate_atoms.py | 2 +- moltemplate/remove_duplicates_nbody.py | 2 +- moltemplate/renumber_DATA_first_column.py | 2 +- moltemplate/ttree.py | 2 +- moltemplate/ttree_render.py | 2 +- tests/test_genpoly_lt.py | 2 +- 58 files changed, 58 insertions(+), 58 deletions(-) diff --git a/examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/simple_dna_example/measure_persistence_length/merge_lines_periodic.py b/examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/simple_dna_example/measure_persistence_length/merge_lines_periodic.py index dc71cb43..483da56a 100755 --- a/examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/simple_dna_example/measure_persistence_length/merge_lines_periodic.py +++ b/examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/simple_dna_example/measure_persistence_length/merge_lines_periodic.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 import sys, math g_filename = __file__.split('/')[-1] diff --git a/examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/simple_dna_example/measure_persistence_length/raw2blockaverage.py b/examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/simple_dna_example/measure_persistence_length/raw2blockaverage.py index f49f75f4..023593a3 100755 --- a/examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/simple_dna_example/measure_persistence_length/raw2blockaverage.py +++ b/examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/simple_dna_example/measure_persistence_length/raw2blockaverage.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 err_msg = """ diff --git a/examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/simple_dna_example/measure_persistence_length/raw2subtractlines.py b/examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/simple_dna_example/measure_persistence_length/raw2subtractlines.py index dd01e783..bea4be35 100755 --- a/examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/simple_dna_example/measure_persistence_length/raw2subtractlines.py +++ b/examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/simple_dna_example/measure_persistence_length/raw2subtractlines.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 err_msg = """ diff --git a/examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/simple_dna_example/measure_torsional_persistence_length/merge_lines_periodic.py b/examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/simple_dna_example/measure_torsional_persistence_length/merge_lines_periodic.py index dc71cb43..483da56a 100755 --- a/examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/simple_dna_example/measure_torsional_persistence_length/merge_lines_periodic.py +++ b/examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/simple_dna_example/measure_torsional_persistence_length/merge_lines_periodic.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 import sys, math g_filename = __file__.split('/')[-1] diff --git a/examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/simple_dna_example/measure_torsional_persistence_length/raw2blockaverage.py b/examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/simple_dna_example/measure_torsional_persistence_length/raw2blockaverage.py index f49f75f4..023593a3 100755 --- a/examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/simple_dna_example/measure_torsional_persistence_length/raw2blockaverage.py +++ b/examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/simple_dna_example/measure_torsional_persistence_length/raw2blockaverage.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 err_msg = """ diff --git a/examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/simple_dna_example/measure_torsional_persistence_length/raw2subtractlines.py b/examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/simple_dna_example/measure_torsional_persistence_length/raw2subtractlines.py index dd01e783..bea4be35 100755 --- a/examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/simple_dna_example/measure_torsional_persistence_length/raw2subtractlines.py +++ b/examples/coarse_grained/DNA_models/dsDNA_only/2strands/3bp_2particles/simple_dna_example/measure_torsional_persistence_length/raw2subtractlines.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 err_msg = """ diff --git a/examples/coarse_grained/DNA_models/dsDNA_only/Kratky-Porod/chromosome_metaphase_Naumova2013/moltemplate_files/generate_system_lt.py b/examples/coarse_grained/DNA_models/dsDNA_only/Kratky-Porod/chromosome_metaphase_Naumova2013/moltemplate_files/generate_system_lt.py index 21f263d3..a71c6250 100755 --- a/examples/coarse_grained/DNA_models/dsDNA_only/Kratky-Porod/chromosome_metaphase_Naumova2013/moltemplate_files/generate_system_lt.py +++ b/examples/coarse_grained/DNA_models/dsDNA_only/Kratky-Porod/chromosome_metaphase_Naumova2013/moltemplate_files/generate_system_lt.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 err_msg = """ Usage: diff --git a/examples/coarse_grained/DNA_models/dsDNA_only/Kratky-Porod/chromosome_metaphase_Naumova2013/moltemplate_files/interpolate_coords.py b/examples/coarse_grained/DNA_models/dsDNA_only/Kratky-Porod/chromosome_metaphase_Naumova2013/moltemplate_files/interpolate_coords.py index 8ae294c9..d9a320f3 100755 --- a/examples/coarse_grained/DNA_models/dsDNA_only/Kratky-Porod/chromosome_metaphase_Naumova2013/moltemplate_files/interpolate_coords.py +++ b/examples/coarse_grained/DNA_models/dsDNA_only/Kratky-Porod/chromosome_metaphase_Naumova2013/moltemplate_files/interpolate_coords.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 err_msg = """ diff --git a/examples/coarse_grained/DNA_models/dsDNA_only/twistable_Kratky-Porod/42bp_3particles/nucleoid_Ccrescentus_DNA_only/moltemplate_files/calc_table_angle.py b/examples/coarse_grained/DNA_models/dsDNA_only/twistable_Kratky-Porod/42bp_3particles/nucleoid_Ccrescentus_DNA_only/moltemplate_files/calc_table_angle.py index 8d31381c..c5e62481 100755 --- a/examples/coarse_grained/DNA_models/dsDNA_only/twistable_Kratky-Porod/42bp_3particles/nucleoid_Ccrescentus_DNA_only/moltemplate_files/calc_table_angle.py +++ b/examples/coarse_grained/DNA_models/dsDNA_only/twistable_Kratky-Porod/42bp_3particles/nucleoid_Ccrescentus_DNA_only/moltemplate_files/calc_table_angle.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # We keep track of the program name and version. # (This is only used for generating error messages.) diff --git a/examples/coarse_grained/DNA_models/dsDNA_only/twistable_Kratky-Porod/42bp_3particles/twist_motor_supercoiling/moltemplate_files/calc_table_angle.py b/examples/coarse_grained/DNA_models/dsDNA_only/twistable_Kratky-Porod/42bp_3particles/twist_motor_supercoiling/moltemplate_files/calc_table_angle.py index 8d31381c..c5e62481 100755 --- a/examples/coarse_grained/DNA_models/dsDNA_only/twistable_Kratky-Porod/42bp_3particles/twist_motor_supercoiling/moltemplate_files/calc_table_angle.py +++ b/examples/coarse_grained/DNA_models/dsDNA_only/twistable_Kratky-Porod/42bp_3particles/twist_motor_supercoiling/moltemplate_files/calc_table_angle.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # We keep track of the program name and version. # (This is only used for generating error messages.) diff --git a/examples/coarse_grained/membrane_examples/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py b/examples/coarse_grained/membrane_examples/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py index 8223ccbb..f34eac0f 100755 --- a/examples/coarse_grained/membrane_examples/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py +++ b/examples/coarse_grained/membrane_examples/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Calculate a table of pairwise energies and forces between "INT" atoms # in the lipid membrane model described in diff --git a/examples/coarse_grained/membrane_examples/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py b/examples/coarse_grained/membrane_examples/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py index 12554149..a39d6531 100755 --- a/examples/coarse_grained/membrane_examples/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py +++ b/examples/coarse_grained/membrane_examples/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Calculate a table of pairwise energies and forces between "INT" atoms # in the lipid membrane model described in diff --git a/examples/coarse_grained/membrane_examples/membrane+protein_vesicle_Br2005+Be2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py b/examples/coarse_grained/membrane_examples/membrane+protein_vesicle_Br2005+Be2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py index 8223ccbb..f34eac0f 100755 --- a/examples/coarse_grained/membrane_examples/membrane+protein_vesicle_Br2005+Be2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py +++ b/examples/coarse_grained/membrane_examples/membrane+protein_vesicle_Br2005+Be2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Calculate a table of pairwise energies and forces between "INT" atoms # in the lipid membrane model described in diff --git a/examples/coarse_grained/membrane_examples/membrane+protein_vesicle_Br2005+Be2010/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py b/examples/coarse_grained/membrane_examples/membrane+protein_vesicle_Br2005+Be2010/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py index 12554149..a39d6531 100755 --- a/examples/coarse_grained/membrane_examples/membrane+protein_vesicle_Br2005+Be2010/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py +++ b/examples/coarse_grained/membrane_examples/membrane+protein_vesicle_Br2005+Be2010/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Calculate a table of pairwise energies and forces between "INT" atoms # in the lipid membrane model described in diff --git a/examples/coarse_grained/membrane_examples/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py b/examples/coarse_grained/membrane_examples/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py index 8223ccbb..f34eac0f 100755 --- a/examples/coarse_grained/membrane_examples/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py +++ b/examples/coarse_grained/membrane_examples/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Calculate a table of pairwise energies and forces between "INT" atoms # in the lipid membrane model described in diff --git a/examples/coarse_grained/membrane_examples/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py b/examples/coarse_grained/membrane_examples/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py index 12554149..a39d6531 100755 --- a/examples/coarse_grained/membrane_examples/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py +++ b/examples/coarse_grained/membrane_examples/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Calculate a table of pairwise energies and forces between "INT" atoms # in the lipid membrane model described in diff --git a/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py b/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py index 4c787de5..ab0d8b26 100755 --- a/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py +++ b/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Calculate a table of pairwise energies and forces between atoms in the # protein and a chaperone provided in the supplemental materials section of: diff --git a/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py b/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py index 907732fa..d2bee94d 100755 --- a/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py +++ b/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Calculate a table of dihedral angle interactions used in the alpha-helix # and beta-sheet regions of the frustrated protein model described in diff --git a/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py b/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py index 4c787de5..ab0d8b26 100755 --- a/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py +++ b/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Calculate a table of pairwise energies and forces between atoms in the # protein and a chaperone provided in the supplemental materials section of: diff --git a/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py b/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py index 907732fa..d2bee94d 100755 --- a/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py +++ b/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Calculate a table of dihedral angle interactions used in the alpha-helix # and beta-sheet regions of the frustrated protein model described in diff --git a/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py b/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py index 907732fa..d2bee94d 100755 --- a/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py +++ b/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Calculate a table of dihedral angle interactions used in the alpha-helix # and beta-sheet regions of the frustrated protein model described in diff --git a/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py b/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py index 4c787de5..ab0d8b26 100755 --- a/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py +++ b/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Calculate a table of pairwise energies and forces between atoms in the # protein and a chaperone provided in the supplemental materials section of: diff --git a/moltemplate/amber2lt.py b/moltemplate/amber2lt.py index 419b289c..7fd06b7d 100755 --- a/moltemplate/amber2lt.py +++ b/moltemplate/amber2lt.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett # License: MIT License (See LICENSE.md) diff --git a/moltemplate/bonds_by_type.py b/moltemplate/bonds_by_type.py index c343a6d7..b652fcf3 100755 --- a/moltemplate/bonds_by_type.py +++ b/moltemplate/bonds_by_type.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett (jewett.aij at g mail) # License: MIT License (See LICENSE.md) diff --git a/moltemplate/charge_by_bond.py b/moltemplate/charge_by_bond.py index b86dd49f..d28e3814 100755 --- a/moltemplate/charge_by_bond.py +++ b/moltemplate/charge_by_bond.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett (jewett.aij at g mail) # License: MIT License (See LICENSE.md) diff --git a/moltemplate/depreciated/oplsaa_moltemplate.py b/moltemplate/depreciated/oplsaa_moltemplate.py index 1190b9c2..66fb60c3 100644 --- a/moltemplate/depreciated/oplsaa_moltemplate.py +++ b/moltemplate/depreciated/oplsaa_moltemplate.py @@ -1,4 +1,4 @@ -#! /usr/bin/env python +#! /usr/bin/env python3 # # Author: Jason Lambert # (some additional corrections by Miguel Gonzalez, Yue Chun Chiu and others) diff --git a/moltemplate/dump2data.py b/moltemplate/dump2data.py index cfa3e808..11e549c8 100755 --- a/moltemplate/dump2data.py +++ b/moltemplate/dump2data.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # -*- coding: utf-8 -*- # Author: Andrew Jewett diff --git a/moltemplate/ettree.py b/moltemplate/ettree.py index d0eca31c..05bb1fda 100755 --- a/moltemplate/ettree.py +++ b/moltemplate/ettree.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett (jewett.aij at g mail) # License: MIT License (See LICENSE.md) diff --git a/moltemplate/extract_espresso_atom_types.py b/moltemplate/extract_espresso_atom_types.py index da8fe216..488cac74 100755 --- a/moltemplate/extract_espresso_atom_types.py +++ b/moltemplate/extract_espresso_atom_types.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett (jewett.aij at g mail) # License: MIT License (See LICENSE.md) diff --git a/moltemplate/extract_lammps_data.py b/moltemplate/extract_lammps_data.py index fedd8e41..d58edeb4 100755 --- a/moltemplate/extract_lammps_data.py +++ b/moltemplate/extract_lammps_data.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett (jewett.aij at g mail) # License: MIT License (See LICENSE.md) diff --git a/moltemplate/force_fields/convert_EMC_files_to_LT_files/emcprm2lt.py b/moltemplate/force_fields/convert_EMC_files_to_LT_files/emcprm2lt.py index d9a270cd..5d8ade76 100755 --- a/moltemplate/force_fields/convert_EMC_files_to_LT_files/emcprm2lt.py +++ b/moltemplate/force_fields/convert_EMC_files_to_LT_files/emcprm2lt.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: David Stelter, Andrew Jewett # License: MIT License (See LICENSE.md) diff --git a/moltemplate/force_fields/convert_MSI_files_to_LT_files/msifrc2lt.py b/moltemplate/force_fields/convert_MSI_files_to_LT_files/msifrc2lt.py index 48978e42..d5509f8c 100755 --- a/moltemplate/force_fields/convert_MSI_files_to_LT_files/msifrc2lt.py +++ b/moltemplate/force_fields/convert_MSI_files_to_LT_files/msifrc2lt.py @@ -1,4 +1,4 @@ -#! /usr/bin/env python +#! /usr/bin/env python3 # Author: Andrew Jewett (jewett.aij at g mail) # Copyright (c) 2017, California Institute of Technology # All rights reserved. diff --git a/moltemplate/force_fields/convert_TINKER_files_to_LT_files/tinkerparm2lt.py b/moltemplate/force_fields/convert_TINKER_files_to_LT_files/tinkerparm2lt.py index 9b99896d..86063b5e 100755 --- a/moltemplate/force_fields/convert_TINKER_files_to_LT_files/tinkerparm2lt.py +++ b/moltemplate/force_fields/convert_TINKER_files_to_LT_files/tinkerparm2lt.py @@ -1,4 +1,4 @@ -#! /usr/bin/env python +#! /usr/bin/env python3 # Author: Jason Lambert, Andrew Jewett (jewett.aij at g mail) # (some additional corrections by Miguel Gonzalez, Yue Chun Chiu and others) diff --git a/moltemplate/genpoly_lt.py b/moltemplate/genpoly_lt.py index 4c13c837..76b42003 100755 --- a/moltemplate/genpoly_lt.py +++ b/moltemplate/genpoly_lt.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett (jewett.aij at g mail) # License: MIT License (See LICENSE.md) diff --git a/moltemplate/genpoly_modify_lt.py b/moltemplate/genpoly_modify_lt.py index 6dcd90a4..d4806472 100755 --- a/moltemplate/genpoly_modify_lt.py +++ b/moltemplate/genpoly_modify_lt.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 g_program_name = __file__.split('/')[-1] g_version_str = '0.3.8' diff --git a/moltemplate/interpolate_curve.py b/moltemplate/interpolate_curve.py index e96c3e64..67138f8c 100755 --- a/moltemplate/interpolate_curve.py +++ b/moltemplate/interpolate_curve.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett (jewett.aij at g mail) # License: MIT License (See LICENSE.md) diff --git a/moltemplate/ltemplify.py b/moltemplate/ltemplify.py index accd97ea..260e0305 100755 --- a/moltemplate/ltemplify.py +++ b/moltemplate/ltemplify.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # -*- coding: utf-8 -*- # Author: Andrew Jewett (jewett.aij at g mail) diff --git a/moltemplate/lttree.py b/moltemplate/lttree.py index 2acfef19..8c5d78d9 100755 --- a/moltemplate/lttree.py +++ b/moltemplate/lttree.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett (jewett.aij at g mail) # http://www.moltemplate.org diff --git a/moltemplate/lttree_check.py b/moltemplate/lttree_check.py index 93aab6dd..09a96fb1 100755 --- a/moltemplate/lttree_check.py +++ b/moltemplate/lttree_check.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett (jewett.aij at g mail) # License: MIT License (See LICENSE.md) diff --git a/moltemplate/lttree_postprocess.py b/moltemplate/lttree_postprocess.py index dea010ea..02823d92 100755 --- a/moltemplate/lttree_postprocess.py +++ b/moltemplate/lttree_postprocess.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett (jewett.aij at g mail) # License: MIT License (See LICENSE.md) diff --git a/moltemplate/lttree_styles.py b/moltemplate/lttree_styles.py index f4be5090..b5470490 100644 --- a/moltemplate/lttree_styles.py +++ b/moltemplate/lttree_styles.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # -*- coding: utf-8 -*- # Author: Andrew Jewett (jewett.aij at g mail) diff --git a/moltemplate/mol22lt.py b/moltemplate/mol22lt.py index 5eb35c6a..bb25b513 100755 --- a/moltemplate/mol22lt.py +++ b/moltemplate/mol22lt.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett # License: MIT License (See LICENSE.md) diff --git a/moltemplate/nbody_by_type.py b/moltemplate/nbody_by_type.py index bd079920..95e36e89 100755 --- a/moltemplate/nbody_by_type.py +++ b/moltemplate/nbody_by_type.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett (jewett.aij at g mail) # http://www.chem.ucsb.edu/~sheagroup diff --git a/moltemplate/nbody_by_type_lib.py b/moltemplate/nbody_by_type_lib.py index 9549a371..31205159 100644 --- a/moltemplate/nbody_by_type_lib.py +++ b/moltemplate/nbody_by_type_lib.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett (jewett.aij at g mail) # http://www.chem.ucsb.edu/~sheagroup diff --git a/moltemplate/nbody_fix_ttree_assignments.py b/moltemplate/nbody_fix_ttree_assignments.py index 76ef37f8..c69d0a6c 100755 --- a/moltemplate/nbody_fix_ttree_assignments.py +++ b/moltemplate/nbody_fix_ttree_assignments.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett (jewett.aij at g mail) # License: MIT License (See LICENSE.md) diff --git a/moltemplate/nbody_reorder_atoms.py b/moltemplate/nbody_reorder_atoms.py index 0694d7d7..fa999521 100755 --- a/moltemplate/nbody_reorder_atoms.py +++ b/moltemplate/nbody_reorder_atoms.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett (jewett.aij at g mail) # License: MIT License (See LICENSE.md) diff --git a/moltemplate/pdbsort.py b/moltemplate/pdbsort.py index eac294bc..f4602075 100755 --- a/moltemplate/pdbsort.py +++ b/moltemplate/pdbsort.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett (jewett.aij at g mail) # License: MIT License (See LICENSE.md) diff --git a/moltemplate/postprocess_coeffs.py b/moltemplate/postprocess_coeffs.py index b164c720..19d7c147 100755 --- a/moltemplate/postprocess_coeffs.py +++ b/moltemplate/postprocess_coeffs.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett (jewett.aij at g mail) # License: MIT License (See LICENSE.md) diff --git a/moltemplate/postprocess_input_script.py b/moltemplate/postprocess_input_script.py index fb71b5bb..26dc336a 100755 --- a/moltemplate/postprocess_input_script.py +++ b/moltemplate/postprocess_input_script.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett (jewett.aij at g mail) # License: MIT License (See LICENSE.md) diff --git a/moltemplate/postprocess_transitions.py b/moltemplate/postprocess_transitions.py index a9056b66..46963e50 100755 --- a/moltemplate/postprocess_transitions.py +++ b/moltemplate/postprocess_transitions.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett (jewett.aij at g mail) # License: MIT License (See LICENSE.md) diff --git a/moltemplate/raw2data.py b/moltemplate/raw2data.py index b2b2fb7f..d4ce3c60 100755 --- a/moltemplate/raw2data.py +++ b/moltemplate/raw2data.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # -*- coding: utf-8 -*- # Author: Andrew Jewett diff --git a/moltemplate/recenter_coords.py b/moltemplate/recenter_coords.py index b6edce38..d1f32634 100755 --- a/moltemplate/recenter_coords.py +++ b/moltemplate/recenter_coords.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett (jewett.aij at g mail) # License: MIT License (See LICENSE.md) diff --git a/moltemplate/remove_duplicate_atoms.py b/moltemplate/remove_duplicate_atoms.py index 3963b299..4c474ed9 100755 --- a/moltemplate/remove_duplicate_atoms.py +++ b/moltemplate/remove_duplicate_atoms.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett (jewett.aij at g mail) # License: MIT License (See LICENSE.md) diff --git a/moltemplate/remove_duplicates_nbody.py b/moltemplate/remove_duplicates_nbody.py index ca8dc8a2..1d7ac40f 100755 --- a/moltemplate/remove_duplicates_nbody.py +++ b/moltemplate/remove_duplicates_nbody.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett (jewett.aij at g mail) # License: MIT License (See LICENSE.md) diff --git a/moltemplate/renumber_DATA_first_column.py b/moltemplate/renumber_DATA_first_column.py index 4e548554..c2f9887d 100755 --- a/moltemplate/renumber_DATA_first_column.py +++ b/moltemplate/renumber_DATA_first_column.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett (jewett.aij at g mail) # License: MIT License (See LICENSE.md) diff --git a/moltemplate/ttree.py b/moltemplate/ttree.py index f265d7f5..504a5c16 100755 --- a/moltemplate/ttree.py +++ b/moltemplate/ttree.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett (jewett.aij at g mail) # http://www.moltemplate.org diff --git a/moltemplate/ttree_render.py b/moltemplate/ttree_render.py index 675934ac..ef18f78a 100755 --- a/moltemplate/ttree_render.py +++ b/moltemplate/ttree_render.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # Author: Andrew Jewett (jewett.aij@gmail.com) # License: MIT License (See LICENSE.md) diff --git a/tests/test_genpoly_lt.py b/tests/test_genpoly_lt.py index f12d9820..f4c3bd9c 100755 --- a/tests/test_genpoly_lt.py +++ b/tests/test_genpoly_lt.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 import math import numpy as np