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install_commands
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install_commands
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#########################################################################################
# #
# Install commands #
# #
#########################################################################################
#MosAT based programs
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/2d_enrichment.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/2d_enrichment_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/3d_enrichment.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/3d_enrichment_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/2d_kinetics.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/2d_kinetics_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/apl.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/apl_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/apl_3d.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/apl_3d_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/atoms_in_2_planes.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/atoms_in_2_planes_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/atom_select.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/atom_select_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/b_stamp.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/b_stamp_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/b_stamp_grid.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/b_stamp_grid_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/bilayer_z.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/bilayer_z_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/check_broken_mols.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/check_broken_mols_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/contact_kinetics.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/contact_kinetics_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/contact_rmsf.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/contact_rmsf_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/h_bond_kinetics.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/h_bond_kinetics_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/interdigitation.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/interdigitation_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/inter_leaflet_contacts.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/inter_leaflet_contacts_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/inter_leaflet_contacts_3d.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/inter_leaflet_contacts_3d_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/lipid_contacts.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/lipid_contacts_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/lipid_contacts_3d.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/lipid_contacts_3d_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/lipid_density.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/lipid_density_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/lipid_density_3d.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/lipid_density_3d_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/lipid_distances.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/lipid_distances_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/lipid_distances_3d.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/lipid_distances_3d_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/lipid_flip.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/lipid_flip_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/lipid_gyration.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/lipid_gyration_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/lipid_h_bonds.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/lipid_h_bonds_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/lipid_immobilization.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/lipid_immobilization_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/lipid_mixing.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/lipid_mixing_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/lipid_msd.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/lipid_msd_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/lipid_orientation.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/lipid_orientation_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/lipid_orientation_3d.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/lipid_orientation_3d_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/lipid_protein_min_dist.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/lipid_protein_min_dist_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/lipid_salt_bridges.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/lipid_salt_bridges_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/mean_coords.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/mean_coords_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/mean_lipid_coords.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/mean_lipid_coords_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/mean_lipid_coords_3d.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/mean_lipid_coords_3d_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/mean_protein_coords.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/mean_protein_coords_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/membrane_thickness.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/membrane_thickness_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/mosat.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/mosat_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/nearest_neighbors.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/nearest_neighbors_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/nearest_neighbors_3d.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/nearest_neighbors_3d_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/p2.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/p2_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/p2_3d.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/p2_3d_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/pbc_gen.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/pbc_gen_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/pbc_xy.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/pbc_xy_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/pbc_z.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/pbc_z_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/protein_lipid_contacts.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/protein_lipid_contacts_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/protein_orientation.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/protein_orientation_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/protein_residue_enrichment.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/protein_residue_enrichment_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/protein_translator.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/protein_translator_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/surface_residue_finder.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/surface_residue_finder_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/symmetry_enforcer.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/symmetry_enforcer_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/system_translator.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/system_translator_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/traj_prep.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/traj_prep_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/traj_time.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/traj_time_mpi
$MPI_CPP_COMP -I src -std=c++11 src/MosAT/programs/zcoord.cpp src/xdr/src/xdrfile_xtc.cpp src/xdr/src/xdrfile.cpp src/xdr/src/xdrfile_trr.cpp src/xdr/src/xdr_seek.cpp -o build/zcoord_mpi
#non MosAT mpi
$MPI_CPP_COMP -I src -std=c++11 src/other_tools/2d_enrichment_distance_projection.cpp -o build/2d_enrichment_distance_projection_mpi
$MPI_CPP_COMP -I src -std=c++11 src/other_tools/2d_kinetics_percent_visited.cpp -o build/2d_kinetics_percent_visited_mpi
$MPI_CPP_COMP -I src -std=c++11 src/other_tools/2d_kinetics_distance_projection_global.cpp -o build/2d_kinetics_distance_projection_global_mpi
$MPI_CPP_COMP -I src -std=c++11 src/other_tools/2d_kinetics_distance_projection_window.cpp -o build/2d_kinetics_distance_projection_window_mpi
$MPI_CPP_COMP -I src -std=c++11 src/other_tools/binding_contributors.cpp -o build/binding_contributors_mpi
$MPI_CPP_COMP -I src -std=c++11 src/other_tools/binding_events_analyzer.cpp -o build/binding_events_analyzer_mpi
$MPI_CPP_COMP -I src -std=c++11 src/other_tools/binding_events_analyzer_single.cpp -o build/binding_events_analyzer_single_mpi
$MPI_CPP_COMP -I src -std=c++11 src/other_tools/binding_events_merger.cpp -o build/binding_events_merger_mpi
$MPI_CPP_COMP -I src -std=c++11 src/other_tools/binding_events_video.cpp -o build/binding_events_video_mpi
$MPI_CPP_COMP -I src -std=c++11 src/other_tools/binding_extractor.cpp -o build/binding_extractor_mpi
$MPI_CPP_COMP -I src -std=c++11 src/other_tools/binding_lipids.cpp -o build/binding_lipids_mpi
$MPI_CPP_COMP -I src -std=c++11 src/other_tools/binding_list.cpp -o build/binding_list_mpi
$MPI_CPP_COMP -I src -std=c++11 src/other_tools/binding_occupancy.cpp -o build/binding_occupancy_mpi
$MPI_CPP_COMP -I src -std=c++11 src/other_tools/binding_time_line.cpp -o build/binding_time_line_mpi
$MPI_CPP_COMP -I src -std=c++11 src/other_tools/grid_distance_projection.cpp -o build/grid_distance_projection_mpi
$MPI_CPP_COMP -I src -std=c++11 src/other_tools/lipid_exchange.cpp -o build/lipid_exchange_mpi
$MPI_CPP_COMP -I src -std=c++11 src/other_tools/lipid_exchange_distances.cpp -o build/lipid_exchange_distances_mpi
$MPI_CPP_COMP -I src -std=c++11 src/other_tools/single_frame_distributions.cpp -o build/single_frame_distributions_mpi
$MPI_CPP_COMP -I src -std=c++11 src/other_tools/single_frame_error.cpp -o build/single_frame_error_mpi
$MPI_CPP_COMP -I src -std=c++11 src/other_tools/solvation_shells.cpp -o build/solvation_shells_mpi
#non MosAT serial
$CPP_COMP -I src -std=c++11 src/other_tools/bilayer_free_energy.cpp -o build/bilayer_free_energ
$CPP_COMP -I src -std=c++11 src/other_tools/bonds_generator.cpp -o build/bonds_generator
$CPP_COMP -I src -std=c++11 src/other_tools/data_averager.cpp -o build/data_averager
$CPP_COMP -I src -std=c++11 src/other_tools/delta_plot.cpp -o build/delta_plot
$CPP_COMP -I src -std=c++11 src/other_tools/grid_addition.cpp -o build/grid_addition
$CPP_COMP -I src -std=c++11 src/other_tools/grid_data_excluder.cpp -o build/grid_data_excluder
$CPP_COMP -I src -std=c++11 src/other_tools/grid_editor.cpp -o build/grid_editor
$CPP_COMP -I src -std=c++11 src/other_tools/grid_region_integrator.cpp -o build/grid_region_integrator
$CPP_COMP -I src -std=c++11 src/other_tools/histogram.cpp -o build/histogram
$CPP_COMP -I src -std=c++11 src/other_tools/leaflet_averager.cpp -o build/leaflet_averager
$CPP_COMP -I src -std=c++11 src/other_tools/mask_maker.cpp -o build/mask_maker
$CPP_COMP -I src -std=c++11 src/other_tools/mean_coords_row_selector.cpp -o build/mean_coords_row_selector
$CPP_COMP -I src -std=c++11 src/other_tools/midplane.cpp -o build/midplane
$CPP_COMP -I src -std=c++11 src/other_tools/nan_selector.cpp -o build/nan_selector
$CPP_COMP -I src -std=c++11 src/other_tools/orientation_histogram.cpp -o build/orientation_histogram
$CPP_COMP -I src -std=c++11 src/other_tools/protein_mask.cpp -o build/protein_mask
$CPP_COMP -I src -std=c++11 src/other_tools/protein_mask_grower.cpp -o build/protein_mask_grower
#########################################################################################
# #
# Set permissions #
# #
#########################################################################################
#for user
chmod u+rx build/*
#for group
chmod g+rx build/*
#for others
chmod o+rx build/*
#for all
chmod a+rx build/*