users are no longer required to use "python" instead of "python3" whe…

…n trying to run .py executable files directly from the shell

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]

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 = """

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 = """

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]

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 = """

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 = """

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:

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 = """

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.)

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.)

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

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

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

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

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

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

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:

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

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:

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

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

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:

moltemplate/amber2lt.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 # Author: Andrew Jewett
 # License: MIT License  (See LICENSE.md)

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)

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)

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)

moltemplate/dump2data.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
 # Author: Andrew Jewett

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)

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)

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)

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)

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.

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)

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)

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'

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)

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)

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

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)

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)

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)

moltemplate/mol22lt.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 # Author: Andrew Jewett
 # License: MIT License  (See LICENSE.md)

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

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

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)

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)

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)

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)

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)

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)

moltemplate/raw2data.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
 # Author: Andrew Jewett

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)

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)

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)

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)

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

moltemplate/ttree_render.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 # Author: Andrew Jewett ([email protected])
 # License: MIT License  (See LICENSE.md)

tests/test_genpoly_lt.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import math
 import numpy as np