From f87694a5a6ee2cb5b72ea616f05b9a969071728f Mon Sep 17 00:00:00 2001 From: IAlibay Date: Mon, 6 Mar 2023 21:02:53 +0000 Subject: [PATCH 1/8] an initial test --- testsuite/MDAnalysisTests/data/__init__.py | 1 + testsuite/MDAnalysisTests/datafiles.py | 680 ++++++++++----------- 2 files changed, 336 insertions(+), 345 deletions(-) create mode 100644 testsuite/MDAnalysisTests/data/__init__.py diff --git a/testsuite/MDAnalysisTests/data/__init__.py b/testsuite/MDAnalysisTests/data/__init__.py new file mode 100644 index 00000000000..8b137891791 --- /dev/null +++ b/testsuite/MDAnalysisTests/data/__init__.py @@ -0,0 +1 @@ + diff --git a/testsuite/MDAnalysisTests/datafiles.py b/testsuite/MDAnalysisTests/datafiles.py index 68417b9e560..fa5b58b2fbf 100644 --- a/testsuite/MDAnalysisTests/datafiles.py +++ b/testsuite/MDAnalysisTests/datafiles.py @@ -25,7 +25,7 @@ Location of data files for the MDAnalysis unit tests ==================================================== -Real MD simulation data are stored in the ``data/`` sub +Real MD simulation data are stored in the ```` sub directory. Use as :: from MDAnalysis.tests.datafiles import * @@ -230,395 +230,385 @@ "SURFACE_TRR", # full precision coordinates for NSGrid bug #2345 ] -from pkg_resources import resource_filename - -WIN_PDB_multiframe = resource_filename(__name__, - 'data/windows/WIN_nmr_neopetrosiamide.pdb') -WIN_DLP_HISTORY = resource_filename(__name__, - 'data/windows/WIN_HISTORY') -WIN_TRJ = resource_filename(__name__, - 'data/windows/WIN_ache.mdcrd') -WIN_ARC = resource_filename(__name__, - 'data/windows/WIN_test.arc') -WIN_LAMMPSDUMP = resource_filename(__name__, - 'data/windows/WIN_wat.lammpstrj') - -legacy_DCD_NAMD_coords = resource_filename(__name__, -'data/legacy_DCD_NAMD_coords.npy') -legacy_DCD_ADK_coords = resource_filename(__name__, -'data/legacy_DCD_adk_coords.npy') -legacy_DCD_c36_coords = resource_filename(__name__, -'data/legacy_DCD_c36_coords.npy') -AUX_XVG_LOWF = resource_filename(__name__, 'data/test_lowf.xvg') -AUX_XVG_HIGHF = resource_filename(__name__, 'data/test_highf.xvg') -XVG_BAD_NCOL = resource_filename(__name__, 'data/bad_num_col.xvg') -AUX_XVG = resource_filename(__name__, 'data/test.xvg') -AUX_EDR = resource_filename(__name__, 'data/test.edr') -AUX_EDR_RAW = resource_filename(__name__, 'data/aux_edr_raw.txt') -AUX_EDR_TPR = resource_filename(__name__, 'data/aux_edr.tpr') -AUX_EDR_XTC = resource_filename(__name__, 'data/aux_edr.xtc') -AUX_EDR_SINGLE_FRAME = resource_filename(__name__, 'data/single_frame.edr') -ENT = resource_filename(__name__, 'data/testENT.ent') -GRO_missing_atomname = resource_filename(__name__, 'data/missing_atomname.gro') -GRO_empty_atom = resource_filename(__name__, 'data/empty_atom.gro') -GRO_huge_box = resource_filename(__name__, 'data/huge_box.gro') - -COORDINATES_GRO = resource_filename(__name__, 'data/coordinates/test.gro') -COORDINATES_GRO_INCOMPLETE_VELOCITY = resource_filename(__name__, 'data/coordinates/test_incomplete_vel.gro') -COORDINATES_GRO_BZ2 = resource_filename(__name__, 'data/coordinates/test.gro.bz2') -COORDINATES_XYZ = resource_filename(__name__, 'data/coordinates/test.xyz') -COORDINATES_XYZ_BZ2 = resource_filename( - __name__, 'data/coordinates/test.xyz.bz2') -COORDINATES_XTC = resource_filename(__name__, 'data/coordinates/test.xtc') -COORDINATES_TRR = resource_filename(__name__, 'data/coordinates/test.trr') -COORDINATES_TNG = resource_filename(__name__, 'data/coordinates/test.tng') -COORDINATES_H5MD = resource_filename(__name__, 'data/coordinates/test.h5md') -COORDINATES_DCD = resource_filename(__name__, 'data/coordinates/test.dcd') -COORDINATES_TOPOLOGY = resource_filename(__name__, 'data/coordinates/test_topology.pdb') - -PSF = resource_filename(__name__, 'data/adk.psf') -PSF_notop = resource_filename(__name__, 'data/adk_notop.psf') -PSF_BAD = resource_filename(__name__, 'data/adk_notop_BAD.psf') -DCD = resource_filename(__name__, 'data/adk_dims.dcd') -DCD_empty = resource_filename(__name__, 'data/empty.dcd') -CRD = resource_filename(__name__, 'data/adk_open.crd') -PSF_TRICLINIC = resource_filename(__name__, 'data/tip125_tric_C36.psf') -DCD_TRICLINIC = resource_filename(__name__, 'data/tip125_tric_C36.dcd') -DCD2 = resource_filename(__name__, 'data/adk_dims2.dcd') - -PSF_NAMD = resource_filename(__name__, 'data/namd_cgenff.psf') -PDB_NAMD = resource_filename(__name__, 'data/namd_cgenff.pdb') -PDB_multipole = resource_filename(__name__, 'data/water_methane_acetic-acid_ammonia.pdb') -PSF_NAMD_TRICLINIC = resource_filename(__name__, 'data/SiN_tric_namd.psf') -DCD_NAMD_TRICLINIC = resource_filename(__name__, 'data/SiN_tric_namd.dcd') -PSF_NAMD_GBIS = resource_filename(__name__, 'data/adk_closed_NAMD.psf') -DCD_NAMD_GBIS = resource_filename(__name__, 'data/adk_gbis_tmd-fast1_NAMD.dcd') - -PSF_nosegid = resource_filename(__name__, 'data/nosegid.psf') - -PSF_cmap = resource_filename(__name__, 'data/parmed_ala3.psf') - -PDB_small = resource_filename(__name__, 'data/adk_open.pdb') -PDB_closed = resource_filename(__name__, 'data/adk_closed.pdb') - -ALIGN = resource_filename(__name__, 'data/align.pdb') -RNA_PSF = resource_filename(__name__, 'data/analysis/1k5i_c36.psf.gz') -RNA_PDB = resource_filename(__name__, 'data/analysis/1k5i_c36.pdb.gz') -INC_PDB = resource_filename(__name__, 'data/incomplete.pdb') -PDB_cm = resource_filename(__name__, 'data/cryst_then_model.pdb') -PDB_cm_gz = resource_filename(__name__, 'data/cryst_then_model.pdb.gz') -PDB_cm_bz2 = resource_filename(__name__, 'data/cryst_then_model.pdb.bz2') -PDB_mc = resource_filename(__name__, 'data/model_then_cryst.pdb') -PDB_mc_gz = resource_filename(__name__, 'data/model_then_cryst.pdb.gz') -PDB_mc_bz2 = resource_filename(__name__, 'data/model_then_cryst.pdb.bz2') -PDB_chainidnewres = resource_filename(__name__, 'data/chainIDnewres.pdb.gz') -PDB_sameresid_diffresname = resource_filename(__name__, 'data/sameresid_diffresname.pdb') -PDB_chainidrepeat = resource_filename(__name__, 'data/chainIDrepeat.pdb.gz') -PDB_multiframe = resource_filename(__name__, 'data/nmr_neopetrosiamide.pdb') -PDB_helix = resource_filename(__name__, 'data/A6PA6_alpha.pdb') -PDB_conect = resource_filename(__name__, 'data/conect_parsing.pdb') -PDB_conect2TER = resource_filename(__name__, 'data/CONECT2TER.pdb') -PDB_singleconect = resource_filename(__name__, 'data/SINGLECONECT.pdb') -PDB_icodes = resource_filename(__name__, 'data/1osm.pdb.gz') -PDB_CRYOEM_BOX = resource_filename(__name__, 'data/5a7u.pdb') -PDB_CHECK_RIGHTHAND_PA = resource_filename(__name__, 'data/6msm.pdb.bz2') -FHIAIMS = resource_filename(__name__, 'data/fhiaims.in') - -GRO = resource_filename(__name__, 'data/adk_oplsaa.gro') -GRO_velocity = resource_filename(__name__, 'data/sample_velocity_file.gro') -GRO_incomplete_vels = resource_filename(__name__, 'data/grovels.gro') -GRO_large = resource_filename(__name__, 'data/bigbox.gro.bz2') -GRO_residwrap = resource_filename(__name__, 'data/residwrap.gro') -GRO_residwrap_0base = resource_filename(__name__, 'data/residwrap_0base.gro') -GRO_sameresid_diffresname = resource_filename(__name__, 'data/sameresid_diffresname.gro') -PDB = resource_filename(__name__, 'data/adk_oplsaa.pdb') -XTC = resource_filename(__name__, 'data/adk_oplsaa.xtc') -TRR = resource_filename(__name__, 'data/adk_oplsaa.trr') -TPR = resource_filename(__name__, 'data/adk_oplsaa.tpr') -PDB_sub_dry = resource_filename(__name__, 'data/cobrotoxin_dry_neutral_0.pdb') -TRR_sub_sol = resource_filename(__name__, 'data/cobrotoxin.trr') -XTC_sub_sol = resource_filename(__name__, 'data/cobrotoxin.xtc') -PDB_sub_sol = resource_filename(__name__, 'data/cobrotoxin.pdb') -PDB_xlserial = resource_filename(__name__, 'data/xl_serial.pdb') -GRO_MEMPROT = resource_filename(__name__, 'data/analysis/YiiP_lipids.gro.gz') -XTC_MEMPROT = resource_filename(__name__, 'data/analysis/YiiP_lipids.xtc') -XTC_multi_frame = resource_filename( - __name__, 'data/xtc_test_only_10_frame_10_atoms.xtc' -) -TRR_multi_frame = resource_filename( - __name__, 'data/trr_test_only_10_frame_10_atoms.trr' -) -TNG_traj = resource_filename(__name__, 'data/argon_npt_compressed.tng') -TNG_traj_gro = resource_filename(__name__, 'data/argon_npt_compressed.gro.gz') -TNG_traj_uneven_blocks = resource_filename(__name__, 'data/argon_npt_compressed_uneven.tng') -TNG_traj_vels_forces = resource_filename(__name__, 'data/argon_npt_compressed_vels_forces.tng') -PDB_xvf = resource_filename(__name__, 'data/cobrotoxin.pdb') -TPR_xvf = resource_filename(__name__, 'data/cobrotoxin.tpr') -TRR_xvf = resource_filename(__name__, 'data/cobrotoxin.trr') -H5MD_xvf = resource_filename(__name__, 'data/cobrotoxin.h5md') -XVG_BZ2 = resource_filename(__name__, 'data/cobrotoxin_protein_forces.xvg.bz2') - -XPDB_small = resource_filename(__name__, 'data/5digitResid.pdb') +from importlib import resources +import MDAnalysisTests.data + +data_ref = resources.files('MDAnalysisTests.data') + +WIN_PDB_multiframe = data_ref / 'windows/WIN_nmr_neopetrosiamide.pdb' +WIN_DLP_HISTORY = data_ref / 'windows/WIN_HISTORY' +WIN_TRJ = data_ref / 'windows/WIN_ache.mdcrd' +WIN_ARC = data_ref / 'windows/WIN_test.arc' +WIN_LAMMPSDUMP = data_ref / 'windows/WIN_wat.lammpstrj' + +legacy_DCD_NAMD_coords = data_ref / 'legacy_DCD_NAMD_coords.npy' +legacy_DCD_ADK_coords = data_ref / 'legacy_DCD_adk_coords.npy' +legacy_DCD_c36_coords = data_ref / 'legacy_DCD_c36_coords.npy' +AUX_XVG_LOWF = data_ref / 'test_lowf.xvg' +AUX_XVG_HIGHF = data_ref / 'test_highf.xvg' +XVG_BAD_NCOL = data_ref / 'bad_num_col.xvg' +AUX_XVG = data_ref / 'test.xvg' +AUX_EDR = data_ref / 'test.edr' +AUX_EDR_RAW = data_ref / 'aux_edr_raw.txt' +AUX_EDR_TPR = data_ref / 'aux_edr.tpr' +AUX_EDR_XTC = data_ref / 'aux_edr.xtc' +AUX_EDR_SINGLE_FRAME = data_ref / 'single_frame.edr' +ENT = data_ref / 'testENT.ent' +GRO_missing_atomname = data_ref / 'missing_atomname.gro' +GRO_empty_atom = data_ref / 'empty_atom.gro' +GRO_huge_box = data_ref / 'huge_box.gro' + +COORDINATES_GRO = data_ref / 'coordinates/test.gro' +COORDINATES_GRO_INCOMPLETE_VELOCITY = data_ref / 'coordinates/test_incomplete_vel.gro' +COORDINATES_GRO_BZ2 = data_ref / 'coordinates/test.gro.bz2' +COORDINATES_XYZ = data_ref / 'coordinates/test.xyz' +COORDINATES_XYZ_BZ2 = data_ref / 'coordinates/test.xyz.bz2' +COORDINATES_XTC = data_ref / 'coordinates/test.xtc' +COORDINATES_TRR = data_ref / 'coordinates/test.trr' +COORDINATES_TNG = data_ref / 'coordinates/test.tng' +COORDINATES_H5MD = data_ref / 'coordinates/test.h5md' +COORDINATES_DCD = data_ref / 'coordinates/test.dcd' +COORDINATES_TOPOLOGY = data_ref / 'coordinates/test_topology.pdb' + +PSF = data_ref / 'adk.psf' +PSF_notop = data_ref / 'adk_notop.psf' +PSF_BAD = data_ref / 'adk_notop_BAD.psf' +DCD = data_ref / 'adk_dims.dcd' +DCD_empty = data_ref / 'empty.dcd' +CRD = data_ref / 'adk_open.crd' +PSF_TRICLINIC = data_ref / 'tip125_tric_C36.psf' +DCD_TRICLINIC = data_ref / 'tip125_tric_C36.dcd' +DCD2 = data_ref / 'adk_dims2.dcd' + +PSF_NAMD = data_ref / 'namd_cgenff.psf' +PDB_NAMD = data_ref / 'namd_cgenff.pdb' +PDB_multipole = data_ref / 'water_methane_acetic-acid_ammonia.pdb' +PSF_NAMD_TRICLINIC = data_ref / 'SiN_tric_namd.psf' +DCD_NAMD_TRICLINIC = data_ref / 'SiN_tric_namd.dcd' +PSF_NAMD_GBIS = data_ref / 'adk_closed_NAMD.psf' +DCD_NAMD_GBIS = data_ref / 'adk_gbis_tmd-fast1_NAMD.dcd' + +PSF_nosegid = data_ref / 'nosegid.psf' + +PSF_cmap = data_ref / 'parmed_ala3.psf' + +PDB_small = data_ref / 'adk_open.pdb' +PDB_closed = data_ref / 'adk_closed.pdb' + +ALIGN = data_ref / 'align.pdb' +RNA_PSF = data_ref / 'analysis/1k5i_c36.psf.gz' +RNA_PDB = data_ref / 'analysis/1k5i_c36.pdb.gz' +INC_PDB = data_ref / 'incomplete.pdb' +PDB_cm = data_ref / 'cryst_then_model.pdb' +PDB_cm_gz = data_ref / 'cryst_then_model.pdb.gz' +PDB_cm_bz2 = data_ref / 'cryst_then_model.pdb.bz2' +PDB_mc = data_ref / 'model_then_cryst.pdb' +PDB_mc_gz = data_ref / 'model_then_cryst.pdb.gz' +PDB_mc_bz2 = data_ref / 'model_then_cryst.pdb.bz2' +PDB_chainidnewres = data_ref / 'chainIDnewres.pdb.gz' +PDB_sameresid_diffresname = data_ref / 'sameresid_diffresname.pdb' +PDB_chainidrepeat = data_ref / 'chainIDrepeat.pdb.gz' +PDB_multiframe = data_ref / 'nmr_neopetrosiamide.pdb' +PDB_helix = data_ref / 'A6PA6_alpha.pdb' +PDB_conect = data_ref / 'conect_parsing.pdb' +PDB_conect2TER = data_ref / 'CONECT2TER.pdb' +PDB_singleconect = data_ref / 'SINGLECONECT.pdb' +PDB_icodes = data_ref / '1osm.pdb.gz' +PDB_CRYOEM_BOX = data_ref / '5a7u.pdb' +PDB_CHECK_RIGHTHAND_PA = data_ref / '6msm.pdb.bz2' +FHIAIMS = data_ref / 'fhiaims.in' + +GRO = data_ref / 'adk_oplsaa.gro' +GRO_velocity = data_ref / 'sample_velocity_file.gro' +GRO_incomplete_vels = data_ref / 'grovels.gro' +GRO_large = data_ref / 'bigbox.gro.bz2' +GRO_residwrap = data_ref / 'residwrap.gro' +GRO_residwrap_0base = data_ref / 'residwrap_0base.gro' +GRO_sameresid_diffresname = data_ref / 'sameresid_diffresname.gro' +PDB = data_ref / 'adk_oplsaa.pdb' +XTC = data_ref / 'adk_oplsaa.xtc' +TRR = data_ref / 'adk_oplsaa.trr' +TPR = data_ref / 'adk_oplsaa.tpr' +PDB_sub_dry = data_ref / 'cobrotoxin_dry_neutral_0.pdb' +TRR_sub_sol = data_ref / 'cobrotoxin.trr' +XTC_sub_sol = data_ref / 'cobrotoxin.xtc' +PDB_sub_sol = data_ref / 'cobrotoxin.pdb' +PDB_xlserial = data_ref / 'xl_serial.pdb' +GRO_MEMPROT = data_ref / 'analysis/YiiP_lipids.gro.gz' +XTC_MEMPROT = data_ref / 'analysis/YiiP_lipids.xtc' +XTC_multi_frame = data_ref / 'xtc_test_only_10_frame_10_atoms.xtc' +TRR_multi_frame = data_ref / 'trr_test_only_10_frame_10_atoms.trr' +TNG_traj = data_ref / 'argon_npt_compressed.tng' +TNG_traj_gro = data_ref / 'argon_npt_compressed.gro.gz' +TNG_traj_uneven_blocks = data_ref / 'argon_npt_compressed_uneven.tng' +TNG_traj_vels_forces = data_ref / 'argon_npt_compressed_vels_forces.tng' +PDB_xvf = data_ref / 'cobrotoxin.pdb' +TPR_xvf = data_ref / 'cobrotoxin.tpr' +TRR_xvf = data_ref / 'cobrotoxin.trr' +H5MD_xvf = data_ref / 'cobrotoxin.h5md' +XVG_BZ2 = data_ref / 'cobrotoxin_protein_forces.xvg.bz2' + +XPDB_small = data_ref / '5digitResid.pdb' # number is the gromacs version -TPR400 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.0.tpr') -TPR402 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.0.2.tpr') -TPR403 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.0.3.tpr') -TPR404 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.0.4.tpr') -TPR405 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.0.5.tpr') -TPR406 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.0.6.tpr') -TPR407 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.0.7.tpr') -TPR450 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.5.tpr') -TPR451 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.5.1.tpr') -TPR452 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.5.2.tpr') -TPR453 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.5.3.tpr') -TPR454 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.5.4.tpr') -TPR455 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.5.5.tpr') -TPR502 = resource_filename(__name__, 'data/tprs/2lyz_gmx_5.0.2.tpr') -TPR504 = resource_filename(__name__, 'data/tprs/2lyz_gmx_5.0.4.tpr') -TPR505 = resource_filename(__name__, 'data/tprs/2lyz_gmx_5.0.5.tpr') -TPR510 = resource_filename(__name__, 'data/tprs/2lyz_gmx_5.1.tpr') -TPR2016 = resource_filename(__name__, 'data/tprs/2lyz_gmx_2016.tpr') -TPR2018 = resource_filename(__name__, 'data/tprs/2lyz_gmx_2018.tpr') -TPR2019B3 = resource_filename(__name__, 'data/tprs/2lyz_gmx_2019-beta3.tpr') -TPR2020B2 = resource_filename(__name__, 'data/tprs/2lyz_gmx_2020-beta2.tpr') -TPR2020 = resource_filename(__name__, 'data/tprs/2lyz_gmx_2020.tpr') -TPR2021 = resource_filename(__name__, 'data/tprs/2lyz_gmx_2021.tpr') -TPR2022RC1 = resource_filename(__name__, 'data/tprs/2lyz_gmx_2022-rc1.tpr') -TPR2023 = resource_filename(__name__, 'data/tprs/2lyz_gmx_2023.tpr') +TPR400 = data_ref / 'tprs/2lyz_gmx_4.0.tpr' +TPR402 = data_ref / 'tprs/2lyz_gmx_4.0.2.tpr' +TPR403 = data_ref / 'tprs/2lyz_gmx_4.0.3.tpr' +TPR404 = data_ref / 'tprs/2lyz_gmx_4.0.4.tpr' +TPR405 = data_ref / 'tprs/2lyz_gmx_4.0.5.tpr' +TPR406 = data_ref / 'tprs/2lyz_gmx_4.0.6.tpr' +TPR407 = data_ref / 'tprs/2lyz_gmx_4.0.7.tpr' +TPR450 = data_ref / 'tprs/2lyz_gmx_4.5.tpr' +TPR451 = data_ref / 'tprs/2lyz_gmx_4.5.1.tpr' +TPR452 = data_ref / 'tprs/2lyz_gmx_4.5.2.tpr' +TPR453 = data_ref / 'tprs/2lyz_gmx_4.5.3.tpr' +TPR454 = data_ref / 'tprs/2lyz_gmx_4.5.4.tpr' +TPR455 = data_ref / 'tprs/2lyz_gmx_4.5.5.tpr' +TPR502 = data_ref / 'tprs/2lyz_gmx_5.0.2.tpr' +TPR504 = data_ref / 'tprs/2lyz_gmx_5.0.4.tpr' +TPR505 = data_ref / 'tprs/2lyz_gmx_5.0.5.tpr' +TPR510 = data_ref / 'tprs/2lyz_gmx_5.1.tpr' +TPR2016 = data_ref / 'tprs/2lyz_gmx_2016.tpr' +TPR2018 = data_ref / 'tprs/2lyz_gmx_2018.tpr' +TPR2019B3 = data_ref / 'tprs/2lyz_gmx_2019-beta3.tpr' +TPR2020B2 = data_ref / 'tprs/2lyz_gmx_2020-beta2.tpr' +TPR2020 = data_ref / 'tprs/2lyz_gmx_2020.tpr' +TPR2021 = data_ref / 'tprs/2lyz_gmx_2021.tpr' +TPR2022RC1 = data_ref / 'tprs/2lyz_gmx_2022-rc1.tpr' +TPR2023 = data_ref / 'tprs/2lyz_gmx_2023.tpr' # double precision -TPR455Double = resource_filename(__name__, 'data/tprs/drew_gmx_4.5.5.double.tpr') -TPR460 = resource_filename(__name__, 'data/tprs/ab42_gmx_4.6.tpr') -TPR461 = resource_filename(__name__, 'data/tprs/ab42_gmx_4.6.1.tpr') -TPR2020Double = resource_filename(__name__, 'data/tprs/2lyz_gmx_2020_double.tpr') -TPR2021Double = resource_filename(__name__, 'data/tprs/2lyz_gmx_2021_double.tpr') +TPR455Double = data_ref / 'tprs/drew_gmx_4.5.5.double.tpr' +TPR460 = data_ref / 'tprs/ab42_gmx_4.6.tpr' +TPR461 = data_ref / 'tprs/ab42_gmx_4.6.1.tpr' +TPR2020Double = data_ref / 'tprs/2lyz_gmx_2020_double.tpr' +TPR2021Double = data_ref / 'tprs/2lyz_gmx_2021_double.tpr' # all bonded interactions -TPR334_bonded = resource_filename(__name__, 'data/tprs/all_bonded/dummy_3.3.4.tpr') -TPR510_bonded = resource_filename(__name__, 'data/tprs/all_bonded/dummy_5.1.tpr') -TPR2016_bonded = resource_filename(__name__, 'data/tprs/all_bonded/dummy_2016.tpr') -TPR2018_bonded = resource_filename(__name__, 'data/tprs/all_bonded/dummy_2018.tpr') -TPR2019B3_bonded = resource_filename(__name__, 'data/tprs/all_bonded/dummy_2019-beta3.tpr') -TPR2020B2_bonded = resource_filename(__name__, 'data/tprs/all_bonded/dummy_2020-beta2.tpr') -TPR2020_bonded = resource_filename(__name__, 'data/tprs/all_bonded/dummy_2020.tpr') -TPR2020_double_bonded = resource_filename(__name__, 'data/tprs/all_bonded/dummy_2020_double.tpr') -TPR2021_bonded = resource_filename(__name__, 'data/tprs/all_bonded/dummy_2021.tpr') -TPR2021_double_bonded = resource_filename(__name__, 'data/tprs/all_bonded/dummy_2021_double.tpr') -TPR2022RC1_bonded = resource_filename(__name__, 'data/tprs/all_bonded/dummy_2022-rc1.tpr') -TPR2023_bonded = resource_filename(__name__, 'data/tprs/all_bonded/dummy_2023.tpr') +TPR334_bonded = data_ref / 'tprs/all_bonded/dummy_3.3.4.tpr' +TPR510_bonded = data_ref / 'tprs/all_bonded/dummy_5.1.tpr' +TPR2016_bonded = data_ref / 'tprs/all_bonded/dummy_2016.tpr' +TPR2018_bonded = data_ref / 'tprs/all_bonded/dummy_2018.tpr' +TPR2019B3_bonded = data_ref / 'tprs/all_bonded/dummy_2019-beta3.tpr' +TPR2020B2_bonded = data_ref / 'tprs/all_bonded/dummy_2020-beta2.tpr' +TPR2020_bonded = data_ref / 'tprs/all_bonded/dummy_2020.tpr' +TPR2020_double_bonded = data_ref / 'tprs/all_bonded/dummy_2020_double.tpr' +TPR2021_bonded = data_ref / 'tprs/all_bonded/dummy_2021.tpr' +TPR2021_double_bonded = data_ref / 'tprs/all_bonded/dummy_2021_double.tpr' +TPR2022RC1_bonded = data_ref / 'tprs/all_bonded/dummy_2022-rc1.tpr' +TPR2023_bonded = data_ref / 'tprs/all_bonded/dummy_2023.tpr' # all interactions -TPR_EXTRA_2023 = resource_filename(__name__, 'data/tprs/virtual_sites/extra-interactions-2023.tpr') -TPR_EXTRA_2022RC1 = resource_filename(__name__, 'data/tprs/virtual_sites/extra-interactions-2022-rc1.tpr') -TPR_EXTRA_2021 = resource_filename(__name__, 'data/tprs/virtual_sites/extra-interactions-2021.tpr') -TPR_EXTRA_2020 = resource_filename(__name__, 'data/tprs/virtual_sites/extra-interactions-2020.tpr') -TPR_EXTRA_2018 = resource_filename(__name__, 'data/tprs/virtual_sites/extra-interactions-2018.tpr') -TPR_EXTRA_2016 = resource_filename(__name__, 'data/tprs/virtual_sites/extra-interactions-2016.3.tpr') -TPR_EXTRA_407 = resource_filename(__name__, 'data/tprs/virtual_sites/extra-interactions-4.0.7.tpr') +TPR_EXTRA_2023 = data_ref / 'tprs/virtual_sites/extra-interactions-2023.tpr' +TPR_EXTRA_2022RC1 = data_ref / 'tprs/virtual_sites/extra-interactions-2022-rc1.tpr' +TPR_EXTRA_2021 = data_ref / 'tprs/virtual_sites/extra-interactions-2021.tpr' +TPR_EXTRA_2020 = data_ref / 'tprs/virtual_sites/extra-interactions-2020.tpr' +TPR_EXTRA_2018 = data_ref / 'tprs/virtual_sites/extra-interactions-2018.tpr' +TPR_EXTRA_2016 = data_ref / 'tprs/virtual_sites/extra-interactions-2016.3.tpr' +TPR_EXTRA_407 = data_ref / 'tprs/virtual_sites/extra-interactions-4.0.7.tpr' -XYZ_psf = resource_filename(__name__, 'data/2r9r-1b.psf') -XYZ_bz2 = resource_filename(__name__, 'data/2r9r-1b.xyz.bz2') -XYZ = resource_filename(__name__, 'data/2r9r-1b.xyz') -XYZ_mini = resource_filename(__name__, 'data/mini.xyz') -XYZ_five = resource_filename(__name__, 'data/five.xyz') -TXYZ = resource_filename(__name__, 'data/coordinates/test.txyz') -ARC = resource_filename(__name__, 'data/coordinates/test.arc') -ARC_PBC = resource_filename(__name__, 'data/coordinates/new_hexane.arc') +XYZ_psf = data_ref / '2r9r-1b.psf' +XYZ_bz2 = data_ref / '2r9r-1b.xyz.bz2' +XYZ = data_ref / '2r9r-1b.xyz' +XYZ_mini = data_ref / 'mini.xyz' +XYZ_five = data_ref / 'five.xyz' +TXYZ = data_ref / 'coordinates/test.txyz' +ARC = data_ref / 'coordinates/test.arc' +ARC_PBC = data_ref / 'coordinates/new_hexane.arc' -PRM = resource_filename(__name__, 'data/Amber/ache.prmtop') -TRJ = resource_filename(__name__, 'data/Amber/ache.mdcrd') -INPCRD = resource_filename(__name__, 'data/Amber/test.inpcrd') -TRJ_bz2 = resource_filename(__name__, 'data/Amber/ache.mdcrd.bz2') -PFncdf_Top = resource_filename(__name__, 'data/Amber/posfor.top') -PFncdf_Trj = resource_filename(__name__, 'data/Amber/posfor.ncdf') +PRM = data_ref / 'Amber/ache.prmtop' +TRJ = data_ref / 'Amber/ache.mdcrd' +INPCRD = data_ref / 'Amber/test.inpcrd' +TRJ_bz2 = data_ref / 'Amber/ache.mdcrd.bz2' +PFncdf_Top = data_ref / 'Amber/posfor.top' +PFncdf_Trj = data_ref / 'Amber/posfor.ncdf' -PRMpbc = resource_filename(__name__, 'data/Amber/capped-ala.prmtop') -TRJpbc_bz2 = resource_filename(__name__, 'data/Amber/capped-ala.mdcrd.bz2') +PRMpbc = data_ref / 'Amber/capped-ala.prmtop' +TRJpbc_bz2 = data_ref / 'Amber/capped-ala.mdcrd.bz2' -PRMncdf = resource_filename(__name__, 'data/Amber/bala.prmtop') -TRJncdf = resource_filename(__name__, 'data/Amber/bala.trj') -NCDF = resource_filename(__name__, 'data/Amber/bala.ncdf') +PRMncdf = data_ref / 'Amber/bala.prmtop' +TRJncdf = data_ref / 'Amber/bala.trj' +NCDF = data_ref / 'Amber/bala.ncdf' -PRM12 = resource_filename(__name__, 'data/Amber/anti.top') -TRJ12_bz2 = resource_filename(__name__, 'data/Amber/anti_md1.mdcrd.bz2') +PRM12 = data_ref / 'Amber/anti.top' +TRJ12_bz2 = data_ref / 'Amber/anti_md1.mdcrd.bz2' -PRM7 = resource_filename(__name__, 'data/Amber/tz2.truncoct.parm7.bz2') -NCDFtruncoct = resource_filename(__name__, 'data/Amber/tz2.truncoct.nc') +PRM7 = data_ref / 'Amber/tz2.truncoct.parm7.bz2' +NCDFtruncoct = data_ref / 'Amber/tz2.truncoct.nc' -PRMcs = resource_filename(__name__, 'data/Amber/chitosan.prmtop') +PRMcs = data_ref / 'Amber/chitosan.prmtop' -PRMNCRST = resource_filename(__name__, 'data/Amber/ace_mbondi3.parm7') +PRMNCRST = data_ref / 'Amber/ace_mbondi3.parm7' -PRM_NCBOX = resource_filename(__name__, 'data/Amber/ace_tip3p.parm7') -TRJ_NCBOX = resource_filename(__name__, 'data/Amber/ace_tip3p.nc') +PRM_NCBOX = data_ref / 'Amber/ace_tip3p.parm7' +TRJ_NCBOX = data_ref / 'Amber/ace_tip3p.nc' -PRMNEGATIVE = resource_filename(__name__, 'data/Amber/ace_mbondi3.negative.parm7') +PRMNEGATIVE = data_ref / 'Amber/ace_mbondi3.negative.parm7' -PRMErr1 = resource_filename(__name__, 'data/Amber/ace_mbondi3.error1.parm7') -PRMErr2 = resource_filename(__name__, 'data/Amber/ace_mbondi3.error2.parm7') -PRMErr3 = resource_filename(__name__, 'data/Amber/ace_mbondi3.error3.parm7') +PRMErr1 = data_ref / 'Amber/ace_mbondi3.error1.parm7' +PRMErr2 = data_ref / 'Amber/ace_mbondi3.error2.parm7' +PRMErr3 = data_ref / 'Amber/ace_mbondi3.error3.parm7' -PRM_UreyBradley = resource_filename(__name__, 'data/Amber/parmed_fad.prmtop') -PRM7_ala2 = resource_filename(__name__, 'data/Amber/parmed_ala2_solv.parm7') -RST7_ala2 = resource_filename(__name__, 'data/Amber/parmed_ala2_solv.rst7') +PRM_UreyBradley = data_ref / 'Amber/parmed_fad.prmtop' +PRM7_ala2 = data_ref / 'Amber/parmed_ala2_solv.parm7' +RST7_ala2 = data_ref / 'Amber/parmed_ala2_solv.rst7' -PRM19SBOPC = resource_filename(__name__, 'data/Amber/ala.ff19SB.OPC.parm7.bz2') +PRM19SBOPC = data_ref / 'Amber/ala.ff19SB.OPC.parm7.bz2' -PQR = resource_filename(__name__, 'data/adk_open.pqr') -PQR_icodes = resource_filename(__name__, 'data/1A2C.pqr') +PQR = data_ref / 'adk_open.pqr' +PQR_icodes = data_ref / '1A2C.pqr' -PDBQT_input = resource_filename(__name__, 'data/pdbqt_inputpdbqt.pdbqt') -PDBQT_querypdb = resource_filename(__name__, 'data/pdbqt_querypdb.pdb') +PDBQT_input = data_ref / 'pdbqt_inputpdbqt.pdbqt' +PDBQT_querypdb = data_ref / 'pdbqt_querypdb.pdb' -FASTA = resource_filename(__name__, 'data/test.fasta') -HELANAL_BENDING_MATRIX = resource_filename(__name__, 'data/helanal_bending_matrix_AdK_DIMS_H8.dat') -HELANAL_BENDING_MATRIX_SUBSET = resource_filename(__name__, 'data/helanal_bending_matrix_AdK_DIMS_H8_frames10to79.dat') +FASTA = data_ref / 'test.fasta' +HELANAL_BENDING_MATRIX = data_ref / 'helanal_bending_matrix_AdK_DIMS_H8.dat' +HELANAL_BENDING_MATRIX_SUBSET = data_ref / 'helanal_bending_matrix_AdK_DIMS_H8_frames10to79.dat' -PDB_HOLE = resource_filename(__name__, 'data/1grm_single.pdb') -MULTIPDB_HOLE = resource_filename(__name__, 'data/1grm_elNemo_mode7.pdb.bz2') +PDB_HOLE = data_ref / '1grm_single.pdb' +MULTIPDB_HOLE = data_ref / '1grm_elNemo_mode7.pdb.bz2' -DMS = resource_filename(__name__, 'data/adk_closed.dms') -DMS_DOMAINS = resource_filename(__name__, 'data/adk_closed_domains.dms') -DMS_NO_SEGID = resource_filename(__name__, 'data/adk_closed_no_segid.dms') +DMS = data_ref / 'adk_closed.dms' +DMS_DOMAINS = data_ref / 'adk_closed_domains.dms' +DMS_NO_SEGID = data_ref / 'adk_closed_no_segid.dms' -CONECT = resource_filename(__name__, 'data/1hvr.pdb') -CONECT_ERROR = resource_filename(__name__, 'data/conect_error.pdb') +CONECT = data_ref / '1hvr.pdb' +CONECT_ERROR = data_ref / 'conect_error.pdb' -TRZ = resource_filename(__name__, 'data/trzfile.trz') -TRZ_psf = resource_filename(__name__, 'data/trz_psf.psf') +TRZ = data_ref / 'trzfile.trz' +TRZ_psf = data_ref / 'trz_psf.psf' -TRIC = resource_filename(__name__, 'data/dppc_vesicle_hg.gro') +TRIC = data_ref / 'dppc_vesicle_hg.gro' -PDB_full = resource_filename(__name__, "data/4E43.pdb") +PDB_full = data_ref / "4E43.pdb" -merge_protein = resource_filename(__name__, "data/merge/2zmm/protein.pdb") -merge_ligand = resource_filename(__name__, "data/merge/2zmm/ligand.pdb") -merge_water = resource_filename(__name__, "data/merge/2zmm/water.pdb") +merge_protein = data_ref / "merge/2zmm/protein.pdb" +merge_ligand = data_ref / "merge/2zmm/ligand.pdb" +merge_water = data_ref / "merge/2zmm/water.pdb" -mol2_molecules = resource_filename(__name__, "data/mol2/Molecules.mol2") -mol2_molecule = resource_filename(__name__, "data/mol2/Molecule.mol2") -mol2_ligand = resource_filename(__name__, "data/mol2/Ligand.mol2") -mol2_broken_molecule = resource_filename(__name__, "data/mol2/BrokenMolecule.mol2") -mol2_comments_header = resource_filename(__name__, "data/mol2/Molecule_comments_header.mol2") +mol2_molecules = data_ref / "mol2/Molecules.mol2" +mol2_molecule = data_ref / "mol2/Molecule.mol2" +mol2_ligand = data_ref / "mol2/Ligand.mol2" +mol2_broken_molecule = data_ref / "mol2/BrokenMolecule.mol2" +mol2_comments_header = data_ref / "mol2/Molecule_comments_header.mol2" # MOL2 file without substructure field -mol2_zinc = resource_filename(__name__, "data/mol2/zinc_856218.mol2") +mol2_zinc = data_ref / "mol2/zinc_856218.mol2" # MOL2 file without bonds -mol2_sodium_ion = resource_filename(__name__, "data/mol2/sodium_ion.mol2") - -capping_input = resource_filename(__name__, "data/capping/aaqaa.gro") -capping_output = resource_filename(__name__, "data/capping/maestro_aaqaa_capped.pdb") -capping_ace = resource_filename(__name__, "data/capping/ace.pdb") -capping_nma = resource_filename(__name__, "data/capping/nma.pdb") - -contacts_villin_folded = resource_filename(__name__, "data/contacts/villin_folded.gro.bz2") -contacts_villin_unfolded = resource_filename(__name__, "data/contacts/villin_unfolded.gro.bz2") -contacts_file = resource_filename(__name__, "data/contacts/2F4K_qlist5_remap.dat") - -trz4data = resource_filename(__name__, "data/lammps/datatest.trz") -LAMMPSdata = resource_filename(__name__, "data/lammps/datatest.data") -LAMMPSdata_mini = resource_filename(__name__, "data/lammps/mini.data") -LAMMPSdata2 = resource_filename(__name__, "data/lammps/ifabp_apo_100mM.data.bz2") -LAMMPSdcd2 = resource_filename(__name__, "data/lammps/ifabp_apo_100mM.dcd") -LAMMPScnt = resource_filename(__name__, "data/lammps/cnt-hexagonal-class1.data") -LAMMPScnt2 = resource_filename(__name__, "data/lammps/cnt-hexagonal-class1.data2") -LAMMPShyd = resource_filename(__name__, "data/lammps/hydrogen-class1.data") -LAMMPShyd2 = resource_filename(__name__, "data/lammps/hydrogen-class1.data2") -LAMMPSdata_deletedatoms = resource_filename(__name__, 'data/lammps/deletedatoms.data') -LAMMPSdata_triclinic = resource_filename(__name__, "data/lammps/albite_triclinic.data") -LAMMPSdata_PairIJ = resource_filename(__name__, "data/lammps/pairij_coeffs.data.bz2") -LAMMPSDUMP = resource_filename(__name__, "data/lammps/wat.lammpstrj.bz2") -LAMMPSDUMP_long = resource_filename(__name__, "data/lammps/wat.lammpstrj_long.bz2") -LAMMPSDUMP_allcoords = resource_filename(__name__, "data/lammps/spce_all_coords.lammpstrj.bz2") -LAMMPSDUMP_nocoords = resource_filename(__name__, "data/lammps/spce_no_coords.lammpstrj.bz2") -LAMMPSDUMP_triclinic = resource_filename(__name__, "data/lammps/albite_triclinic.dump") -LAMMPSDUMP_image_vf = resource_filename(__name__, "data/lammps/image_vf.lammpstrj") -LAMMPS_image_vf = resource_filename(__name__, "data/lammps/image_vf.data") - -unordered_res = resource_filename(__name__, "data/unordered_res.pdb") - -GMS_ASYMOPT = resource_filename(__name__, "data/gms/c1opt.gms.gz") -GMS_SYMOPT = resource_filename(__name__, "data/gms/symopt.gms") -GMS_ASYMSURF = resource_filename(__name__, "data/gms/surf2wat.gms") - -two_water_gro = resource_filename(__name__, "data/two_water_gro.gro") -two_water_gro_multiframe = resource_filename(__name__, "data/two_water_gro_multiframe.gro") -two_water_gro_nonames = resource_filename(__name__, "data/two_water_gro_nonames.gro") -two_water_gro_widebox = resource_filename(__name__, "data/two_water_gro_widebox.gro") - -DLP_CONFIG = resource_filename(__name__, "data/dlpoly/CONFIG") -DLP_CONFIG_order = resource_filename(__name__, "data/dlpoly/CONFIG_order") -DLP_CONFIG_minimal = resource_filename(__name__, "data/dlpoly/CONFIG_minimal") -DLP_HISTORY = resource_filename(__name__, "data/dlpoly/HISTORY") -DLP_HISTORY_order = resource_filename(__name__, "data/dlpoly/HISTORY_order") -DLP_HISTORY_minimal = resource_filename(__name__, "data/dlpoly/HISTORY_minimal") -DLP_HISTORY_minimal_cell = resource_filename(__name__, "data/dlpoly/HISTORY_minimal_cell") -DLP_HISTORY_classic = resource_filename(__name__, "data/dlpoly/HISTORY_classic") - -waterPSF = resource_filename(__name__, 'data/watdyn.psf') -waterDCD = resource_filename(__name__, 'data/watdyn.dcd') - -rmsfArray = resource_filename(__name__, 'data/adk_oplsaa_CA_rmsf.npy') - -HoomdXMLdata = resource_filename(__name__, 'data/C12x64.xml.bz2') - -Make_Whole = resource_filename(__name__, 'data/make_whole.gro') -fullerene = resource_filename(__name__, 'data/fullerene.pdb.gz') - -Plength = resource_filename(__name__, 'data/plength.gro') -Martini_membrane_gro = resource_filename(__name__, 'data/martini_dppc_chol_bilayer.gro') +mol2_sodium_ion = data_ref / "mol2/sodium_ion.mol2" + +capping_input = data_ref / "capping/aaqaa.gro" +capping_output = data_ref / "capping/maestro_aaqaa_capped.pdb" +capping_ace = data_ref / "capping/ace.pdb" +capping_nma = data_ref / "capping/nma.pdb" + +contacts_villin_folded = data_ref / "contacts/villin_folded.gro.bz2" +contacts_villin_unfolded = data_ref / "contacts/villin_unfolded.gro.bz2" +contacts_file = data_ref / "contacts/2F4K_qlist5_remap.dat" + +trz4data = data_ref / "lammps/datatest.trz" +LAMMPSdata = data_ref / "lammps/datatest.data" +LAMMPSdata_mini = data_ref / "lammps/mini.data" +LAMMPSdata2 = data_ref / "lammps/ifabp_apo_100mM.data.bz2" +LAMMPSdcd2 = data_ref / "lammps/ifabp_apo_100mM.dcd" +LAMMPScnt = data_ref / "lammps/cnt-hexagonal-class1.data" +LAMMPScnt2 = data_ref / "lammps/cnt-hexagonal-class1.data2" +LAMMPShyd = data_ref / "lammps/hydrogen-class1.data" +LAMMPShyd2 = data_ref / "lammps/hydrogen-class1.data2" +LAMMPSdata_deletedatoms = data_ref / 'lammps/deletedatoms.data' +LAMMPSdata_triclinic = data_ref / "lammps/albite_triclinic.data" +LAMMPSdata_PairIJ = data_ref / "lammps/pairij_coeffs.data.bz2" +LAMMPSDUMP = data_ref / "lammps/wat.lammpstrj.bz2" +LAMMPSDUMP_long = data_ref / "lammps/wat.lammpstrj_long.bz2" +LAMMPSDUMP_allcoords = data_ref / "lammps/spce_all_coords.lammpstrj.bz2" +LAMMPSDUMP_nocoords = data_ref / "lammps/spce_no_coords.lammpstrj.bz2" +LAMMPSDUMP_triclinic = data_ref / "lammps/albite_triclinic.dump" +LAMMPSDUMP_image_vf = data_ref / "lammps/image_vf.lammpstrj" +LAMMPS_image_vf = data_ref / "lammps/image_vf.data" + +unordered_res = data_ref / "unordered_res.pdb" + +GMS_ASYMOPT = data_ref / "gms/c1opt.gms.gz" +GMS_SYMOPT = data_ref / "gms/symopt.gms" +GMS_ASYMSURF = data_ref / "gms/surf2wat.gms" + +two_water_gro = data_ref / "two_water_gro.gro" +two_water_gro_multiframe = data_ref / "two_water_gro_multiframe.gro" +two_water_gro_nonames = data_ref / "two_water_gro_nonames.gro" +two_water_gro_widebox = data_ref / "two_water_gro_widebox.gro" + +DLP_CONFIG = data_ref / "dlpoly/CONFIG" +DLP_CONFIG_order = data_ref / "dlpoly/CONFIG_order" +DLP_CONFIG_minimal = data_ref / "dlpoly/CONFIG_minimal" +DLP_HISTORY = data_ref / "dlpoly/HISTORY" +DLP_HISTORY_order = data_ref / "dlpoly/HISTORY_order" +DLP_HISTORY_minimal = data_ref / "dlpoly/HISTORY_minimal" +DLP_HISTORY_minimal_cell = data_ref / "dlpoly/HISTORY_minimal_cell" +DLP_HISTORY_classic = data_ref / "dlpoly/HISTORY_classic" + +waterPSF = data_ref / 'watdyn.psf' +waterDCD = data_ref / 'watdyn.dcd' + +rmsfArray = data_ref / 'adk_oplsaa_CA_rmsf.npy' + +HoomdXMLdata = data_ref / 'C12x64.xml.bz2' + +Make_Whole = data_ref / 'make_whole.gro' +fullerene = data_ref / 'fullerene.pdb.gz' + +Plength = data_ref / 'plength.gro' +Martini_membrane_gro = data_ref / 'martini_dppc_chol_bilayer.gro' # Contains one of each residue in 'nucleic' selections -NUCLsel = resource_filename(__name__, 'data/nucl_res.pdb') +NUCLsel = data_ref / 'nucl_res.pdb' -RANDOM_WALK = resource_filename(__name__, 'data/xyz_random_walk.xtc') -RANDOM_WALK_TOPO = resource_filename(__name__, 'data/RANDOM_WALK_TOPO.pdb') +RANDOM_WALK = data_ref / 'xyz_random_walk.xtc' +RANDOM_WALK_TOPO = data_ref / 'RANDOM_WALK_TOPO.pdb' -MMTF = resource_filename(__name__, 'data/173D.mmtf') -MMTF_gz = resource_filename(__name__, 'data/5KIH.mmtf.gz') -MMTF_skinny = resource_filename(__name__, 'data/1ubq-less-optional.mmtf') -MMTF_skinny2 = resource_filename(__name__, 'data/3NJW-onlyrequired.mmtf') -MMTF_NOCRYST = resource_filename(__name__, "data/6QYR.mmtf.gz") +MMTF = data_ref / '173D.mmtf' +MMTF_gz = data_ref / '5KIH.mmtf.gz' +MMTF_skinny = data_ref / '1ubq-less-optional.mmtf' +MMTF_skinny2 = data_ref / '3NJW-onlyrequired.mmtf' +MMTF_NOCRYST = data_ref / "6QYR.mmtf.gz" -ALIGN_BOUND = resource_filename(__name__, 'data/analysis/align_bound.pdb.gz') -ALIGN_UNBOUND = resource_filename(__name__, 'data/analysis/align_unbound.pdb.gz') +ALIGN_BOUND = data_ref / 'analysis/align_bound.pdb.gz' +ALIGN_UNBOUND = data_ref / 'analysis/align_unbound.pdb.gz' -GSD = resource_filename(__name__, 'data/example.gsd') -GSD_bonds = resource_filename(__name__, 'data/example_bonds.gsd') -GSD_long = resource_filename(__name__, 'data/example_longer.gsd') +GSD = data_ref / 'example.gsd' +GSD_bonds = data_ref / 'example_bonds.gsd' +GSD_long = data_ref / 'example_longer.gsd' -DihedralArray = resource_filename(__name__, 'data/adk_oplsaa_dihedral.npy') -DihedralsArray = resource_filename(__name__, 'data/adk_oplsaa_dihedral_list.npy') -RamaArray = resource_filename(__name__, 'data/adk_oplsaa_rama.npy') -GLYRamaArray = resource_filename(__name__, 'data/adk_oplsaa_GLY_rama.npy') -JaninArray = resource_filename(__name__, 'data/adk_oplsaa_janin.npy') -LYSJaninArray = resource_filename(__name__, 'data/adk_oplsaa_LYS_janin.npy') -PDB_rama = resource_filename(__name__, 'data/19hc.pdb.gz') -PDB_janin = resource_filename(__name__, 'data/1a28.pdb.gz') +DihedralArray = data_ref / 'adk_oplsaa_dihedral.npy' +DihedralsArray = data_ref / 'adk_oplsaa_dihedral_list.npy' +RamaArray = data_ref / 'adk_oplsaa_rama.npy' +GLYRamaArray = data_ref / 'adk_oplsaa_GLY_rama.npy' +JaninArray = data_ref / 'adk_oplsaa_janin.npy' +LYSJaninArray = data_ref / 'adk_oplsaa_LYS_janin.npy' +PDB_rama = data_ref / '19hc.pdb.gz' +PDB_janin = data_ref / '1a28.pdb.gz' -BATArray = resource_filename(__name__, 'data/mol2_comments_header_bat.npy') +BATArray = data_ref / 'mol2_comments_header_bat.npy' -ITP = resource_filename(__name__, 'data/gromacs_ala10.itp') -ITP_nomass = resource_filename(__name__, 'data/itp_nomass.itp') -ITP_atomtypes = resource_filename(__name__, 'data/atomtypes.itp') -ITP_charges = resource_filename(__name__, 'data/atomtypes_charge.itp') -ITP_edited = resource_filename(__name__, 'data/edited_itp.itp') -ITP_tip5p = resource_filename(__name__, "data/tip5p.itp") -ITP_spce = resource_filename(__name__, 'data/spce.itp') +ITP = data_ref / 'gromacs_ala10.itp' +ITP_nomass = data_ref / 'itp_nomass.itp' +ITP_atomtypes = data_ref / 'atomtypes.itp' +ITP_charges = data_ref / 'atomtypes_charge.itp' +ITP_edited = data_ref / 'edited_itp.itp' +ITP_tip5p = data_ref / "tip5p.itp" +ITP_spce = data_ref / 'spce.itp' -GMX_TOP = resource_filename(__name__, 'data/gromacs_ala10.top') -GMX_DIR = resource_filename(__name__, 'data/gromacs/') -GMX_TOP_BAD = resource_filename(__name__, 'data/bad_top.top') -ITP_no_endif = resource_filename(__name__, 'data/no_endif_spc.itp') +GMX_TOP = data_ref / 'gromacs_ala10.top' +GMX_DIR = data_ref / 'gromacs/' +GMX_TOP_BAD = data_ref / 'bad_top.top' +ITP_no_endif = data_ref / 'no_endif_spc.itp' -NAMDBIN = resource_filename(__name__, 'data/adk_open.coor') +NAMDBIN = data_ref / 'adk_open.coor' -SDF_molecule = resource_filename(__name__, 'data/molecule.sdf') +SDF_molecule = data_ref / 'molecule.sdf' -PDB_elements = resource_filename(__name__, 'data/elements.pdb') -PDB_charges = resource_filename(__name__, 'data/charges.pdb') +PDB_elements = data_ref / 'elements.pdb' +PDB_charges = data_ref / 'charges.pdb' -PDBX = resource_filename(__name__, "data/4x8u.pdbx") +PDBX = data_ref / "4x8u.pdbx" -SURFACE_PDB = resource_filename(__name__, 'data/surface.pdb.bz2') -SURFACE_TRR = resource_filename(__name__, 'data/surface.trr') +SURFACE_PDB = data_ref / 'surface.pdb.bz2' +SURFACE_TRR = data_ref / 'surface.trr' # This should be the last line: clean up namespace -del resource_filename +del resources From 80be0a12a174d1eac1dd6824a22320e7c769f304 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Mon, 6 Mar 2023 21:18:08 +0000 Subject: [PATCH 2/8] the simpler approach --- testsuite/MDAnalysisTests/datafiles.py | 656 ++++++++++++------------- 1 file changed, 328 insertions(+), 328 deletions(-) diff --git a/testsuite/MDAnalysisTests/datafiles.py b/testsuite/MDAnalysisTests/datafiles.py index fa5b58b2fbf..c988330bbc2 100644 --- a/testsuite/MDAnalysisTests/datafiles.py +++ b/testsuite/MDAnalysisTests/datafiles.py @@ -235,379 +235,379 @@ data_ref = resources.files('MDAnalysisTests.data') -WIN_PDB_multiframe = data_ref / 'windows/WIN_nmr_neopetrosiamide.pdb' -WIN_DLP_HISTORY = data_ref / 'windows/WIN_HISTORY' -WIN_TRJ = data_ref / 'windows/WIN_ache.mdcrd' -WIN_ARC = data_ref / 'windows/WIN_test.arc' -WIN_LAMMPSDUMP = data_ref / 'windows/WIN_wat.lammpstrj' - -legacy_DCD_NAMD_coords = data_ref / 'legacy_DCD_NAMD_coords.npy' -legacy_DCD_ADK_coords = data_ref / 'legacy_DCD_adk_coords.npy' -legacy_DCD_c36_coords = data_ref / 'legacy_DCD_c36_coords.npy' -AUX_XVG_LOWF = data_ref / 'test_lowf.xvg' -AUX_XVG_HIGHF = data_ref / 'test_highf.xvg' -XVG_BAD_NCOL = data_ref / 'bad_num_col.xvg' -AUX_XVG = data_ref / 'test.xvg' -AUX_EDR = data_ref / 'test.edr' -AUX_EDR_RAW = data_ref / 'aux_edr_raw.txt' -AUX_EDR_TPR = data_ref / 'aux_edr.tpr' -AUX_EDR_XTC = data_ref / 'aux_edr.xtc' -AUX_EDR_SINGLE_FRAME = data_ref / 'single_frame.edr' -ENT = data_ref / 'testENT.ent' -GRO_missing_atomname = data_ref / 'missing_atomname.gro' -GRO_empty_atom = data_ref / 'empty_atom.gro' -GRO_huge_box = data_ref / 'huge_box.gro' - -COORDINATES_GRO = data_ref / 'coordinates/test.gro' -COORDINATES_GRO_INCOMPLETE_VELOCITY = data_ref / 'coordinates/test_incomplete_vel.gro' -COORDINATES_GRO_BZ2 = data_ref / 'coordinates/test.gro.bz2' -COORDINATES_XYZ = data_ref / 'coordinates/test.xyz' -COORDINATES_XYZ_BZ2 = data_ref / 'coordinates/test.xyz.bz2' -COORDINATES_XTC = data_ref / 'coordinates/test.xtc' -COORDINATES_TRR = data_ref / 'coordinates/test.trr' -COORDINATES_TNG = data_ref / 'coordinates/test.tng' -COORDINATES_H5MD = data_ref / 'coordinates/test.h5md' -COORDINATES_DCD = data_ref / 'coordinates/test.dcd' -COORDINATES_TOPOLOGY = data_ref / 'coordinates/test_topology.pdb' - -PSF = data_ref / 'adk.psf' -PSF_notop = data_ref / 'adk_notop.psf' -PSF_BAD = data_ref / 'adk_notop_BAD.psf' -DCD = data_ref / 'adk_dims.dcd' -DCD_empty = data_ref / 'empty.dcd' -CRD = data_ref / 'adk_open.crd' -PSF_TRICLINIC = data_ref / 'tip125_tric_C36.psf' -DCD_TRICLINIC = data_ref / 'tip125_tric_C36.dcd' -DCD2 = data_ref / 'adk_dims2.dcd' - -PSF_NAMD = data_ref / 'namd_cgenff.psf' -PDB_NAMD = data_ref / 'namd_cgenff.pdb' -PDB_multipole = data_ref / 'water_methane_acetic-acid_ammonia.pdb' -PSF_NAMD_TRICLINIC = data_ref / 'SiN_tric_namd.psf' -DCD_NAMD_TRICLINIC = data_ref / 'SiN_tric_namd.dcd' -PSF_NAMD_GBIS = data_ref / 'adk_closed_NAMD.psf' -DCD_NAMD_GBIS = data_ref / 'adk_gbis_tmd-fast1_NAMD.dcd' - -PSF_nosegid = data_ref / 'nosegid.psf' - -PSF_cmap = data_ref / 'parmed_ala3.psf' - -PDB_small = data_ref / 'adk_open.pdb' -PDB_closed = data_ref / 'adk_closed.pdb' - -ALIGN = data_ref / 'align.pdb' -RNA_PSF = data_ref / 'analysis/1k5i_c36.psf.gz' -RNA_PDB = data_ref / 'analysis/1k5i_c36.pdb.gz' -INC_PDB = data_ref / 'incomplete.pdb' -PDB_cm = data_ref / 'cryst_then_model.pdb' -PDB_cm_gz = data_ref / 'cryst_then_model.pdb.gz' -PDB_cm_bz2 = data_ref / 'cryst_then_model.pdb.bz2' -PDB_mc = data_ref / 'model_then_cryst.pdb' -PDB_mc_gz = data_ref / 'model_then_cryst.pdb.gz' -PDB_mc_bz2 = data_ref / 'model_then_cryst.pdb.bz2' -PDB_chainidnewres = data_ref / 'chainIDnewres.pdb.gz' -PDB_sameresid_diffresname = data_ref / 'sameresid_diffresname.pdb' -PDB_chainidrepeat = data_ref / 'chainIDrepeat.pdb.gz' -PDB_multiframe = data_ref / 'nmr_neopetrosiamide.pdb' -PDB_helix = data_ref / 'A6PA6_alpha.pdb' -PDB_conect = data_ref / 'conect_parsing.pdb' -PDB_conect2TER = data_ref / 'CONECT2TER.pdb' -PDB_singleconect = data_ref / 'SINGLECONECT.pdb' -PDB_icodes = data_ref / '1osm.pdb.gz' -PDB_CRYOEM_BOX = data_ref / '5a7u.pdb' -PDB_CHECK_RIGHTHAND_PA = data_ref / '6msm.pdb.bz2' -FHIAIMS = data_ref / 'fhiaims.in' - -GRO = data_ref / 'adk_oplsaa.gro' -GRO_velocity = data_ref / 'sample_velocity_file.gro' -GRO_incomplete_vels = data_ref / 'grovels.gro' -GRO_large = data_ref / 'bigbox.gro.bz2' -GRO_residwrap = data_ref / 'residwrap.gro' -GRO_residwrap_0base = data_ref / 'residwrap_0base.gro' -GRO_sameresid_diffresname = data_ref / 'sameresid_diffresname.gro' -PDB = data_ref / 'adk_oplsaa.pdb' -XTC = data_ref / 'adk_oplsaa.xtc' -TRR = data_ref / 'adk_oplsaa.trr' -TPR = data_ref / 'adk_oplsaa.tpr' -PDB_sub_dry = data_ref / 'cobrotoxin_dry_neutral_0.pdb' -TRR_sub_sol = data_ref / 'cobrotoxin.trr' -XTC_sub_sol = data_ref / 'cobrotoxin.xtc' -PDB_sub_sol = data_ref / 'cobrotoxin.pdb' -PDB_xlserial = data_ref / 'xl_serial.pdb' -GRO_MEMPROT = data_ref / 'analysis/YiiP_lipids.gro.gz' -XTC_MEMPROT = data_ref / 'analysis/YiiP_lipids.xtc' -XTC_multi_frame = data_ref / 'xtc_test_only_10_frame_10_atoms.xtc' -TRR_multi_frame = data_ref / 'trr_test_only_10_frame_10_atoms.trr' -TNG_traj = data_ref / 'argon_npt_compressed.tng' -TNG_traj_gro = data_ref / 'argon_npt_compressed.gro.gz' -TNG_traj_uneven_blocks = data_ref / 'argon_npt_compressed_uneven.tng' -TNG_traj_vels_forces = data_ref / 'argon_npt_compressed_vels_forces.tng' -PDB_xvf = data_ref / 'cobrotoxin.pdb' -TPR_xvf = data_ref / 'cobrotoxin.tpr' -TRR_xvf = data_ref / 'cobrotoxin.trr' -H5MD_xvf = data_ref / 'cobrotoxin.h5md' -XVG_BZ2 = data_ref / 'cobrotoxin_protein_forces.xvg.bz2' - -XPDB_small = data_ref / '5digitResid.pdb' +WIN_PDB_multiframe = str(data_ref / 'windows/WIN_nmr_neopetrosiamide.pdb') +WIN_DLP_HISTORY = str(data_ref / 'windows/WIN_HISTORY') +WIN_TRJ = str(data_ref / 'windows/WIN_ache.mdcrd') +WIN_ARC = str(data_ref / 'windows/WIN_test.arc') +WIN_LAMMPSDUMP = str(data_ref / 'windows/WIN_wat.lammpstrj') + +legacy_DCD_NAMD_coords = str(data_ref / 'legacy_DCD_NAMD_coords.npy') +legacy_DCD_ADK_coords = str(data_ref / 'legacy_DCD_adk_coords.npy') +legacy_DCD_c36_coords = str(data_ref / 'legacy_DCD_c36_coords.npy') +AUX_XVG_LOWF = str(data_ref / 'test_lowf.xvg') +AUX_XVG_HIGHF = str(data_ref / 'test_highf.xvg') +XVG_BAD_NCOL = str(data_ref / 'bad_num_col.xvg') +AUX_XVG = str(data_ref / 'test.xvg') +AUX_EDR = str(data_ref / 'test.edr') +AUX_EDR_RAW = str(data_ref / 'aux_edr_raw.txt') +AUX_EDR_TPR = str(data_ref / 'aux_edr.tpr') +AUX_EDR_XTC = str(data_ref / 'aux_edr.xtc') +AUX_EDR_SINGLE_FRAME = str(data_ref / 'single_frame.edr') +ENT = str(data_ref / 'testENT.ent') +GRO_missing_atomname = str(data_ref / 'missing_atomname.gro') +GRO_empty_atom = str(data_ref / 'empty_atom.gro') +GRO_huge_box = str(data_ref / 'huge_box.gro') + +COORDINATES_GRO = str(data_ref / 'coordinates/test.gro') +COORDINATES_GRO_INCOMPLETE_VELOCITY = str(data_ref / 'coordinates/test_incomplete_vel.gro') +COORDINATES_GRO_BZ2 = str(data_ref / 'coordinates/test.gro.bz2') +COORDINATES_XYZ = str(data_ref / 'coordinates/test.xyz') +COORDINATES_XYZ_BZ2 = str(data_ref / 'coordinates/test.xyz.bz2') +COORDINATES_XTC = str(data_ref / 'coordinates/test.xtc') +COORDINATES_TRR = str(data_ref / 'coordinates/test.trr') +COORDINATES_TNG = str(data_ref / 'coordinates/test.tng') +COORDINATES_H5MD = str(data_ref / 'coordinates/test.h5md') +COORDINATES_DCD = str(data_ref / 'coordinates/test.dcd') +COORDINATES_TOPOLOGY = str(data_ref / 'coordinates/test_topology.pdb') + +PSF = str(data_ref / 'adk.psf') +PSF_notop = str(data_ref / 'adk_notop.psf') +PSF_BAD = str(data_ref / 'adk_notop_BAD.psf') +DCD = str(data_ref / 'adk_dims.dcd') +DCD_empty = str(data_ref / 'empty.dcd') +CRD = str(data_ref / 'adk_open.crd') +PSF_TRICLINIC = str(data_ref / 'tip125_tric_C36.psf') +DCD_TRICLINIC = str(data_ref / 'tip125_tric_C36.dcd') +DCD2 = str(data_ref / 'adk_dims2.dcd') + +PSF_NAMD = str(data_ref / 'namd_cgenff.psf') +PDB_NAMD = str(data_ref / 'namd_cgenff.pdb') +PDB_multipole = str(data_ref / 'water_methane_acetic-acid_ammonia.pdb') +PSF_NAMD_TRICLINIC = str(data_ref / 'SiN_tric_namd.psf') +DCD_NAMD_TRICLINIC = str(data_ref / 'SiN_tric_namd.dcd') +PSF_NAMD_GBIS = str(data_ref / 'adk_closed_NAMD.psf') +DCD_NAMD_GBIS = str(data_ref / 'adk_gbis_tmd-fast1_NAMD.dcd') + +PSF_nosegid = str(data_ref / 'nosegid.psf') + +PSF_cmap = str(data_ref / 'parmed_ala3.psf') + +PDB_small = str(data_ref / 'adk_open.pdb') +PDB_closed = str(data_ref / 'adk_closed.pdb') + +ALIGN = str(data_ref / 'align.pdb') +RNA_PSF = str(data_ref / 'analysis/1k5i_c36.psf.gz') +RNA_PDB = str(data_ref / 'analysis/1k5i_c36.pdb.gz') +INC_PDB = str(data_ref / 'incomplete.pdb') +PDB_cm = str(data_ref / 'cryst_then_model.pdb') +PDB_cm_gz = str(data_ref / 'cryst_then_model.pdb.gz') +PDB_cm_bz2 = str(data_ref / 'cryst_then_model.pdb.bz2') +PDB_mc = str(data_ref / 'model_then_cryst.pdb') +PDB_mc_gz = str(data_ref / 'model_then_cryst.pdb.gz') +PDB_mc_bz2 = str(data_ref / 'model_then_cryst.pdb.bz2') +PDB_chainidnewres = str(data_ref / 'chainIDnewres.pdb.gz') +PDB_sameresid_diffresname = str(data_ref / 'sameresid_diffresname.pdb') +PDB_chainidrepeat = str(data_ref / 'chainIDrepeat.pdb.gz') +PDB_multiframe = str(data_ref / 'nmr_neopetrosiamide.pdb') +PDB_helix = str(data_ref / 'A6PA6_alpha.pdb') +PDB_conect = str(data_ref / 'conect_parsing.pdb') +PDB_conect2TER = str(data_ref / 'CONECT2TER.pdb') +PDB_singleconect = str(data_ref / 'SINGLECONECT.pdb') +PDB_icodes = str(data_ref / '1osm.pdb.gz') +PDB_CRYOEM_BOX = str(data_ref / '5a7u.pdb') +PDB_CHECK_RIGHTHAND_PA = str(data_ref / '6msm.pdb.bz2') +FHIAIMS = str(data_ref / 'fhiaims.in') + +GRO = str(data_ref / 'adk_oplsaa.gro') +GRO_velocity = str(data_ref / 'sample_velocity_file.gro') +GRO_incomplete_vels = str(data_ref / 'grovels.gro') +GRO_large = str(data_ref / 'bigbox.gro.bz2') +GRO_residwrap = str(data_ref / 'residwrap.gro') +GRO_residwrap_0base = str(data_ref / 'residwrap_0base.gro') +GRO_sameresid_diffresname = str(data_ref / 'sameresid_diffresname.gro') +PDB = str(data_ref / 'adk_oplsaa.pdb') +XTC = str(data_ref / 'adk_oplsaa.xtc') +TRR = str(data_ref / 'adk_oplsaa.trr') +TPR = str(data_ref / 'adk_oplsaa.tpr') +PDB_sub_dry = str(data_ref / 'cobrotoxin_dry_neutral_0.pdb') +TRR_sub_sol = str(data_ref / 'cobrotoxin.trr') +XTC_sub_sol = str(data_ref / 'cobrotoxin.xtc') +PDB_sub_sol = str(data_ref / 'cobrotoxin.pdb') +PDB_xlserial = str(data_ref / 'xl_serial.pdb') +GRO_MEMPROT = str(data_ref / 'analysis/YiiP_lipids.gro.gz') +XTC_MEMPROT = str(data_ref / 'analysis/YiiP_lipids.xtc') +XTC_multi_frame = str(data_ref / 'xtc_test_only_10_frame_10_atoms.xtc') +TRR_multi_frame = str(data_ref / 'trr_test_only_10_frame_10_atoms.trr') +TNG_traj = str(data_ref / 'argon_npt_compressed.tng') +TNG_traj_gro = str(data_ref / 'argon_npt_compressed.gro.gz') +TNG_traj_uneven_blocks = str(data_ref / 'argon_npt_compressed_uneven.tng') +TNG_traj_vels_forces = str(data_ref / 'argon_npt_compressed_vels_forces.tng') +PDB_xvf = str(data_ref / 'cobrotoxin.pdb') +TPR_xvf = str(data_ref / 'cobrotoxin.tpr') +TRR_xvf = str(data_ref / 'cobrotoxin.trr') +H5MD_xvf = str(data_ref / 'cobrotoxin.h5md') +XVG_BZ2 = str(data_ref / 'cobrotoxin_protein_forces.xvg.bz2') + +XPDB_small = str(data_ref / '5digitResid.pdb') # number is the gromacs version -TPR400 = data_ref / 'tprs/2lyz_gmx_4.0.tpr' -TPR402 = data_ref / 'tprs/2lyz_gmx_4.0.2.tpr' -TPR403 = data_ref / 'tprs/2lyz_gmx_4.0.3.tpr' -TPR404 = data_ref / 'tprs/2lyz_gmx_4.0.4.tpr' -TPR405 = data_ref / 'tprs/2lyz_gmx_4.0.5.tpr' -TPR406 = data_ref / 'tprs/2lyz_gmx_4.0.6.tpr' -TPR407 = data_ref / 'tprs/2lyz_gmx_4.0.7.tpr' -TPR450 = data_ref / 'tprs/2lyz_gmx_4.5.tpr' -TPR451 = data_ref / 'tprs/2lyz_gmx_4.5.1.tpr' -TPR452 = data_ref / 'tprs/2lyz_gmx_4.5.2.tpr' -TPR453 = data_ref / 'tprs/2lyz_gmx_4.5.3.tpr' -TPR454 = data_ref / 'tprs/2lyz_gmx_4.5.4.tpr' -TPR455 = data_ref / 'tprs/2lyz_gmx_4.5.5.tpr' -TPR502 = data_ref / 'tprs/2lyz_gmx_5.0.2.tpr' -TPR504 = data_ref / 'tprs/2lyz_gmx_5.0.4.tpr' -TPR505 = data_ref / 'tprs/2lyz_gmx_5.0.5.tpr' -TPR510 = data_ref / 'tprs/2lyz_gmx_5.1.tpr' -TPR2016 = data_ref / 'tprs/2lyz_gmx_2016.tpr' -TPR2018 = data_ref / 'tprs/2lyz_gmx_2018.tpr' -TPR2019B3 = data_ref / 'tprs/2lyz_gmx_2019-beta3.tpr' -TPR2020B2 = data_ref / 'tprs/2lyz_gmx_2020-beta2.tpr' -TPR2020 = data_ref / 'tprs/2lyz_gmx_2020.tpr' -TPR2021 = data_ref / 'tprs/2lyz_gmx_2021.tpr' -TPR2022RC1 = data_ref / 'tprs/2lyz_gmx_2022-rc1.tpr' -TPR2023 = data_ref / 'tprs/2lyz_gmx_2023.tpr' +TPR400 = str(data_ref / 'tprs/2lyz_gmx_4.0.tpr') +TPR402 = str(data_ref / 'tprs/2lyz_gmx_4.0.2.tpr') +TPR403 = str(data_ref / 'tprs/2lyz_gmx_4.0.3.tpr') +TPR404 = str(data_ref / 'tprs/2lyz_gmx_4.0.4.tpr') +TPR405 = str(data_ref / 'tprs/2lyz_gmx_4.0.5.tpr') +TPR406 = str(data_ref / 'tprs/2lyz_gmx_4.0.6.tpr') +TPR407 = str(data_ref / 'tprs/2lyz_gmx_4.0.7.tpr') +TPR450 = str(data_ref / 'tprs/2lyz_gmx_4.5.tpr') +TPR451 = str(data_ref / 'tprs/2lyz_gmx_4.5.1.tpr') +TPR452 = str(data_ref / 'tprs/2lyz_gmx_4.5.2.tpr') +TPR453 = str(data_ref / 'tprs/2lyz_gmx_4.5.3.tpr') +TPR454 = str(data_ref / 'tprs/2lyz_gmx_4.5.4.tpr') +TPR455 = str(data_ref / 'tprs/2lyz_gmx_4.5.5.tpr') +TPR502 = str(data_ref / 'tprs/2lyz_gmx_5.0.2.tpr') +TPR504 = str(data_ref / 'tprs/2lyz_gmx_5.0.4.tpr') +TPR505 = str(data_ref / 'tprs/2lyz_gmx_5.0.5.tpr') +TPR510 = str(data_ref / 'tprs/2lyz_gmx_5.1.tpr') +TPR2016 = str(data_ref / 'tprs/2lyz_gmx_2016.tpr') +TPR2018 = str(data_ref / 'tprs/2lyz_gmx_2018.tpr') +TPR2019B3 = str(data_ref / 'tprs/2lyz_gmx_2019-beta3.tpr') +TPR2020B2 = str(data_ref / 'tprs/2lyz_gmx_2020-beta2.tpr') +TPR2020 = str(data_ref / 'tprs/2lyz_gmx_2020.tpr') +TPR2021 = str(data_ref / 'tprs/2lyz_gmx_2021.tpr') +TPR2022RC1 = str(data_ref / 'tprs/2lyz_gmx_2022-rc1.tpr') +TPR2023 = str(data_ref / 'tprs/2lyz_gmx_2023.tpr') # double precision -TPR455Double = data_ref / 'tprs/drew_gmx_4.5.5.double.tpr' -TPR460 = data_ref / 'tprs/ab42_gmx_4.6.tpr' -TPR461 = data_ref / 'tprs/ab42_gmx_4.6.1.tpr' -TPR2020Double = data_ref / 'tprs/2lyz_gmx_2020_double.tpr' -TPR2021Double = data_ref / 'tprs/2lyz_gmx_2021_double.tpr' +TPR455Double = str(data_ref / 'tprs/drew_gmx_4.5.5.double.tpr') +TPR460 = str(data_ref / 'tprs/ab42_gmx_4.6.tpr') +TPR461 = str(data_ref / 'tprs/ab42_gmx_4.6.1.tpr') +TPR2020Double = str(data_ref / 'tprs/2lyz_gmx_2020_double.tpr') +TPR2021Double = str(data_ref / 'tprs/2lyz_gmx_2021_double.tpr') # all bonded interactions -TPR334_bonded = data_ref / 'tprs/all_bonded/dummy_3.3.4.tpr' -TPR510_bonded = data_ref / 'tprs/all_bonded/dummy_5.1.tpr' -TPR2016_bonded = data_ref / 'tprs/all_bonded/dummy_2016.tpr' -TPR2018_bonded = data_ref / 'tprs/all_bonded/dummy_2018.tpr' -TPR2019B3_bonded = data_ref / 'tprs/all_bonded/dummy_2019-beta3.tpr' -TPR2020B2_bonded = data_ref / 'tprs/all_bonded/dummy_2020-beta2.tpr' -TPR2020_bonded = data_ref / 'tprs/all_bonded/dummy_2020.tpr' -TPR2020_double_bonded = data_ref / 'tprs/all_bonded/dummy_2020_double.tpr' -TPR2021_bonded = data_ref / 'tprs/all_bonded/dummy_2021.tpr' -TPR2021_double_bonded = data_ref / 'tprs/all_bonded/dummy_2021_double.tpr' -TPR2022RC1_bonded = data_ref / 'tprs/all_bonded/dummy_2022-rc1.tpr' -TPR2023_bonded = data_ref / 'tprs/all_bonded/dummy_2023.tpr' +TPR334_bonded = str(data_ref / 'tprs/all_bonded/dummy_3.3.4.tpr') +TPR510_bonded = str(data_ref / 'tprs/all_bonded/dummy_5.1.tpr') +TPR2016_bonded = str(data_ref / 'tprs/all_bonded/dummy_2016.tpr') +TPR2018_bonded = str(data_ref / 'tprs/all_bonded/dummy_2018.tpr') +TPR2019B3_bonded = str(data_ref / 'tprs/all_bonded/dummy_2019-beta3.tpr') +TPR2020B2_bonded = str(data_ref / 'tprs/all_bonded/dummy_2020-beta2.tpr') +TPR2020_bonded = str(data_ref / 'tprs/all_bonded/dummy_2020.tpr') +TPR2020_double_bonded = str(data_ref / 'tprs/all_bonded/dummy_2020_double.tpr') +TPR2021_bonded = str(data_ref / 'tprs/all_bonded/dummy_2021.tpr') +TPR2021_double_bonded = str(data_ref / 'tprs/all_bonded/dummy_2021_double.tpr') +TPR2022RC1_bonded = str(data_ref / 'tprs/all_bonded/dummy_2022-rc1.tpr') +TPR2023_bonded = str(data_ref / 'tprs/all_bonded/dummy_2023.tpr') # all interactions -TPR_EXTRA_2023 = data_ref / 'tprs/virtual_sites/extra-interactions-2023.tpr' -TPR_EXTRA_2022RC1 = data_ref / 'tprs/virtual_sites/extra-interactions-2022-rc1.tpr' -TPR_EXTRA_2021 = data_ref / 'tprs/virtual_sites/extra-interactions-2021.tpr' -TPR_EXTRA_2020 = data_ref / 'tprs/virtual_sites/extra-interactions-2020.tpr' -TPR_EXTRA_2018 = data_ref / 'tprs/virtual_sites/extra-interactions-2018.tpr' -TPR_EXTRA_2016 = data_ref / 'tprs/virtual_sites/extra-interactions-2016.3.tpr' -TPR_EXTRA_407 = data_ref / 'tprs/virtual_sites/extra-interactions-4.0.7.tpr' +TPR_EXTRA_2023 = str(data_ref / 'tprs/virtual_sites/extra-interactions-2023.tpr') +TPR_EXTRA_2022RC1 = str(data_ref / 'tprs/virtual_sites/extra-interactions-2022-rc1.tpr') +TPR_EXTRA_2021 = str(data_ref / 'tprs/virtual_sites/extra-interactions-2021.tpr') +TPR_EXTRA_2020 = str(data_ref / 'tprs/virtual_sites/extra-interactions-2020.tpr') +TPR_EXTRA_2018 = str(data_ref / 'tprs/virtual_sites/extra-interactions-2018.tpr') +TPR_EXTRA_2016 = str(data_ref / 'tprs/virtual_sites/extra-interactions-2016.3.tpr') +TPR_EXTRA_407 = str(data_ref / 'tprs/virtual_sites/extra-interactions-4.0.7.tpr') -XYZ_psf = data_ref / '2r9r-1b.psf' -XYZ_bz2 = data_ref / '2r9r-1b.xyz.bz2' -XYZ = data_ref / '2r9r-1b.xyz' -XYZ_mini = data_ref / 'mini.xyz' -XYZ_five = data_ref / 'five.xyz' -TXYZ = data_ref / 'coordinates/test.txyz' -ARC = data_ref / 'coordinates/test.arc' -ARC_PBC = data_ref / 'coordinates/new_hexane.arc' +XYZ_psf = str(data_ref / '2r9r-1b.psf') +XYZ_bz2 = str(data_ref / '2r9r-1b.xyz.bz2') +XYZ = str(data_ref / '2r9r-1b.xyz') +XYZ_mini = str(data_ref / 'mini.xyz') +XYZ_five = str(data_ref / 'five.xyz') +TXYZ = str(data_ref / 'coordinates/test.txyz') +ARC = str(data_ref / 'coordinates/test.arc') +ARC_PBC = str(data_ref / 'coordinates/new_hexane.arc') -PRM = data_ref / 'Amber/ache.prmtop' -TRJ = data_ref / 'Amber/ache.mdcrd' -INPCRD = data_ref / 'Amber/test.inpcrd' -TRJ_bz2 = data_ref / 'Amber/ache.mdcrd.bz2' -PFncdf_Top = data_ref / 'Amber/posfor.top' -PFncdf_Trj = data_ref / 'Amber/posfor.ncdf' +PRM = str(data_ref / 'Amber/ache.prmtop') +TRJ = str(data_ref / 'Amber/ache.mdcrd') +INPCRD = str(data_ref / 'Amber/test.inpcrd') +TRJ_bz2 = str(data_ref / 'Amber/ache.mdcrd.bz2') +PFncdf_Top = str(data_ref / 'Amber/posfor.top') +PFncdf_Trj = str(data_ref / 'Amber/posfor.ncdf') -PRMpbc = data_ref / 'Amber/capped-ala.prmtop' -TRJpbc_bz2 = data_ref / 'Amber/capped-ala.mdcrd.bz2' +PRMpbc = str(data_ref / 'Amber/capped-ala.prmtop') +TRJpbc_bz2 = str(data_ref / 'Amber/capped-ala.mdcrd.bz2') -PRMncdf = data_ref / 'Amber/bala.prmtop' -TRJncdf = data_ref / 'Amber/bala.trj' -NCDF = data_ref / 'Amber/bala.ncdf' +PRMncdf = str(data_ref / 'Amber/bala.prmtop') +TRJncdf = str(data_ref / 'Amber/bala.trj') +NCDF = str(data_ref / 'Amber/bala.ncdf') -PRM12 = data_ref / 'Amber/anti.top' -TRJ12_bz2 = data_ref / 'Amber/anti_md1.mdcrd.bz2' +PRM12 = str(data_ref / 'Amber/anti.top') +TRJ12_bz2 = str(data_ref / 'Amber/anti_md1.mdcrd.bz2') -PRM7 = data_ref / 'Amber/tz2.truncoct.parm7.bz2' -NCDFtruncoct = data_ref / 'Amber/tz2.truncoct.nc' +PRM7 = str(data_ref / 'Amber/tz2.truncoct.parm7.bz2') +NCDFtruncoct = str(data_ref / 'Amber/tz2.truncoct.nc') -PRMcs = data_ref / 'Amber/chitosan.prmtop' +PRMcs = str(data_ref / 'Amber/chitosan.prmtop') -PRMNCRST = data_ref / 'Amber/ace_mbondi3.parm7' +PRMNCRST = str(data_ref / 'Amber/ace_mbondi3.parm7') -PRM_NCBOX = data_ref / 'Amber/ace_tip3p.parm7' -TRJ_NCBOX = data_ref / 'Amber/ace_tip3p.nc' +PRM_NCBOX = str(data_ref / 'Amber/ace_tip3p.parm7') +TRJ_NCBOX = str(data_ref / 'Amber/ace_tip3p.nc') -PRMNEGATIVE = data_ref / 'Amber/ace_mbondi3.negative.parm7' +PRMNEGATIVE = str(data_ref / 'Amber/ace_mbondi3.negative.parm7') -PRMErr1 = data_ref / 'Amber/ace_mbondi3.error1.parm7' -PRMErr2 = data_ref / 'Amber/ace_mbondi3.error2.parm7' -PRMErr3 = data_ref / 'Amber/ace_mbondi3.error3.parm7' +PRMErr1 = str(data_ref / 'Amber/ace_mbondi3.error1.parm7') +PRMErr2 = str(data_ref / 'Amber/ace_mbondi3.error2.parm7') +PRMErr3 = str(data_ref / 'Amber/ace_mbondi3.error3.parm7') -PRM_UreyBradley = data_ref / 'Amber/parmed_fad.prmtop' -PRM7_ala2 = data_ref / 'Amber/parmed_ala2_solv.parm7' -RST7_ala2 = data_ref / 'Amber/parmed_ala2_solv.rst7' +PRM_UreyBradley = str(data_ref / 'Amber/parmed_fad.prmtop') +PRM7_ala2 = str(data_ref / 'Amber/parmed_ala2_solv.parm7') +RST7_ala2 = str(data_ref / 'Amber/parmed_ala2_solv.rst7') -PRM19SBOPC = data_ref / 'Amber/ala.ff19SB.OPC.parm7.bz2' +PRM19SBOPC = str(data_ref / 'Amber/ala.ff19SB.OPC.parm7.bz2') -PQR = data_ref / 'adk_open.pqr' -PQR_icodes = data_ref / '1A2C.pqr' +PQR = str(data_ref / 'adk_open.pqr') +PQR_icodes = str(data_ref / '1A2C.pqr') -PDBQT_input = data_ref / 'pdbqt_inputpdbqt.pdbqt' -PDBQT_querypdb = data_ref / 'pdbqt_querypdb.pdb' +PDBQT_input = str(data_ref / 'pdbqt_inputpdbqt.pdbqt') +PDBQT_querypdb = str(data_ref / 'pdbqt_querypdb.pdb') -FASTA = data_ref / 'test.fasta' -HELANAL_BENDING_MATRIX = data_ref / 'helanal_bending_matrix_AdK_DIMS_H8.dat' -HELANAL_BENDING_MATRIX_SUBSET = data_ref / 'helanal_bending_matrix_AdK_DIMS_H8_frames10to79.dat' +FASTA = str(data_ref / 'test.fasta') +HELANAL_BENDING_MATRIX = str(data_ref / 'helanal_bending_matrix_AdK_DIMS_H8.dat') +HELANAL_BENDING_MATRIX_SUBSET = str(data_ref / 'helanal_bending_matrix_AdK_DIMS_H8_frames10to79.dat') -PDB_HOLE = data_ref / '1grm_single.pdb' -MULTIPDB_HOLE = data_ref / '1grm_elNemo_mode7.pdb.bz2' +PDB_HOLE = str(data_ref / '1grm_single.pdb') +MULTIPDB_HOLE = str(data_ref / '1grm_elNemo_mode7.pdb.bz2') -DMS = data_ref / 'adk_closed.dms' -DMS_DOMAINS = data_ref / 'adk_closed_domains.dms' -DMS_NO_SEGID = data_ref / 'adk_closed_no_segid.dms' +DMS = str(data_ref / 'adk_closed.dms') +DMS_DOMAINS = str(data_ref / 'adk_closed_domains.dms') +DMS_NO_SEGID = str(data_ref / 'adk_closed_no_segid.dms') -CONECT = data_ref / '1hvr.pdb' -CONECT_ERROR = data_ref / 'conect_error.pdb' +CONECT = str(data_ref / '1hvr.pdb') +CONECT_ERROR = str(data_ref / 'conect_error.pdb') -TRZ = data_ref / 'trzfile.trz' -TRZ_psf = data_ref / 'trz_psf.psf' +TRZ = str(data_ref / 'trzfile.trz') +TRZ_psf = str(data_ref / 'trz_psf.psf') -TRIC = data_ref / 'dppc_vesicle_hg.gro' +TRIC = str(data_ref / 'dppc_vesicle_hg.gro') -PDB_full = data_ref / "4E43.pdb" +PDB_full = str(data_ref / "4E43.pdb") -merge_protein = data_ref / "merge/2zmm/protein.pdb" -merge_ligand = data_ref / "merge/2zmm/ligand.pdb" -merge_water = data_ref / "merge/2zmm/water.pdb" +merge_protein = str(data_ref / "merge/2zmm/protein.pdb") +merge_ligand = str(data_ref / "merge/2zmm/ligand.pdb") +merge_water = str(data_ref / "merge/2zmm/water.pdb") -mol2_molecules = data_ref / "mol2/Molecules.mol2" -mol2_molecule = data_ref / "mol2/Molecule.mol2" -mol2_ligand = data_ref / "mol2/Ligand.mol2" -mol2_broken_molecule = data_ref / "mol2/BrokenMolecule.mol2" -mol2_comments_header = data_ref / "mol2/Molecule_comments_header.mol2" +mol2_molecules = str(data_ref / "mol2/Molecules.mol2") +mol2_molecule = str(data_ref / "mol2/Molecule.mol2") +mol2_ligand = str(data_ref / "mol2/Ligand.mol2") +mol2_broken_molecule = str(data_ref / "mol2/BrokenMolecule.mol2") +mol2_comments_header = str(data_ref / "mol2/Molecule_comments_header.mol2") # MOL2 file without substructure field -mol2_zinc = data_ref / "mol2/zinc_856218.mol2" +mol2_zinc = str(data_ref / "mol2/zinc_856218.mol2") # MOL2 file without bonds -mol2_sodium_ion = data_ref / "mol2/sodium_ion.mol2" - -capping_input = data_ref / "capping/aaqaa.gro" -capping_output = data_ref / "capping/maestro_aaqaa_capped.pdb" -capping_ace = data_ref / "capping/ace.pdb" -capping_nma = data_ref / "capping/nma.pdb" - -contacts_villin_folded = data_ref / "contacts/villin_folded.gro.bz2" -contacts_villin_unfolded = data_ref / "contacts/villin_unfolded.gro.bz2" -contacts_file = data_ref / "contacts/2F4K_qlist5_remap.dat" - -trz4data = data_ref / "lammps/datatest.trz" -LAMMPSdata = data_ref / "lammps/datatest.data" -LAMMPSdata_mini = data_ref / "lammps/mini.data" -LAMMPSdata2 = data_ref / "lammps/ifabp_apo_100mM.data.bz2" -LAMMPSdcd2 = data_ref / "lammps/ifabp_apo_100mM.dcd" -LAMMPScnt = data_ref / "lammps/cnt-hexagonal-class1.data" -LAMMPScnt2 = data_ref / "lammps/cnt-hexagonal-class1.data2" -LAMMPShyd = data_ref / "lammps/hydrogen-class1.data" -LAMMPShyd2 = data_ref / "lammps/hydrogen-class1.data2" -LAMMPSdata_deletedatoms = data_ref / 'lammps/deletedatoms.data' -LAMMPSdata_triclinic = data_ref / "lammps/albite_triclinic.data" -LAMMPSdata_PairIJ = data_ref / "lammps/pairij_coeffs.data.bz2" -LAMMPSDUMP = data_ref / "lammps/wat.lammpstrj.bz2" -LAMMPSDUMP_long = data_ref / "lammps/wat.lammpstrj_long.bz2" -LAMMPSDUMP_allcoords = data_ref / "lammps/spce_all_coords.lammpstrj.bz2" -LAMMPSDUMP_nocoords = data_ref / "lammps/spce_no_coords.lammpstrj.bz2" -LAMMPSDUMP_triclinic = data_ref / "lammps/albite_triclinic.dump" -LAMMPSDUMP_image_vf = data_ref / "lammps/image_vf.lammpstrj" -LAMMPS_image_vf = data_ref / "lammps/image_vf.data" - -unordered_res = data_ref / "unordered_res.pdb" - -GMS_ASYMOPT = data_ref / "gms/c1opt.gms.gz" -GMS_SYMOPT = data_ref / "gms/symopt.gms" -GMS_ASYMSURF = data_ref / "gms/surf2wat.gms" - -two_water_gro = data_ref / "two_water_gro.gro" -two_water_gro_multiframe = data_ref / "two_water_gro_multiframe.gro" -two_water_gro_nonames = data_ref / "two_water_gro_nonames.gro" -two_water_gro_widebox = data_ref / "two_water_gro_widebox.gro" - -DLP_CONFIG = data_ref / "dlpoly/CONFIG" -DLP_CONFIG_order = data_ref / "dlpoly/CONFIG_order" -DLP_CONFIG_minimal = data_ref / "dlpoly/CONFIG_minimal" -DLP_HISTORY = data_ref / "dlpoly/HISTORY" -DLP_HISTORY_order = data_ref / "dlpoly/HISTORY_order" -DLP_HISTORY_minimal = data_ref / "dlpoly/HISTORY_minimal" -DLP_HISTORY_minimal_cell = data_ref / "dlpoly/HISTORY_minimal_cell" -DLP_HISTORY_classic = data_ref / "dlpoly/HISTORY_classic" - -waterPSF = data_ref / 'watdyn.psf' -waterDCD = data_ref / 'watdyn.dcd' - -rmsfArray = data_ref / 'adk_oplsaa_CA_rmsf.npy' - -HoomdXMLdata = data_ref / 'C12x64.xml.bz2' - -Make_Whole = data_ref / 'make_whole.gro' -fullerene = data_ref / 'fullerene.pdb.gz' - -Plength = data_ref / 'plength.gro' -Martini_membrane_gro = data_ref / 'martini_dppc_chol_bilayer.gro' +mol2_sodium_ion = str(data_ref / "mol2/sodium_ion.mol2") + +capping_input = str(data_ref / "capping/aaqaa.gro") +capping_output = str(data_ref / "capping/maestro_aaqaa_capped.pdb") +capping_ace = str(data_ref / "capping/ace.pdb") +capping_nma = str(data_ref / "capping/nma.pdb") + +contacts_villin_folded = str(data_ref / "contacts/villin_folded.gro.bz2") +contacts_villin_unfolded = str(data_ref / "contacts/villin_unfolded.gro.bz2") +contacts_file = str(data_ref / "contacts/2F4K_qlist5_remap.dat") + +trz4data = str(data_ref / "lammps/datatest.trz") +LAMMPSdata = str(data_ref / "lammps/datatest.data") +LAMMPSdata_mini = str(data_ref / "lammps/mini.data") +LAMMPSdata2 = str(data_ref / "lammps/ifabp_apo_100mM.data.bz2") +LAMMPSdcd2 = str(data_ref / "lammps/ifabp_apo_100mM.dcd") +LAMMPScnt = str(data_ref / "lammps/cnt-hexagonal-class1.data") +LAMMPScnt2 = str(data_ref / "lammps/cnt-hexagonal-class1.data2") +LAMMPShyd = str(data_ref / "lammps/hydrogen-class1.data") +LAMMPShyd2 = str(data_ref / "lammps/hydrogen-class1.data2") +LAMMPSdata_deletedatoms = str(data_ref / 'lammps/deletedatoms.data') +LAMMPSdata_triclinic = str(data_ref / "lammps/albite_triclinic.data") +LAMMPSdata_PairIJ = str(data_ref / "lammps/pairij_coeffs.data.bz2") +LAMMPSDUMP = str(data_ref / "lammps/wat.lammpstrj.bz2") +LAMMPSDUMP_long = str(data_ref / "lammps/wat.lammpstrj_long.bz2") +LAMMPSDUMP_allcoords = str(data_ref / "lammps/spce_all_coords.lammpstrj.bz2") +LAMMPSDUMP_nocoords = str(data_ref / "lammps/spce_no_coords.lammpstrj.bz2") +LAMMPSDUMP_triclinic = str(data_ref / "lammps/albite_triclinic.dump") +LAMMPSDUMP_image_vf = str(data_ref / "lammps/image_vf.lammpstrj") +LAMMPS_image_vf = str(data_ref / "lammps/image_vf.data") + +unordered_res = str(data_ref / "unordered_res.pdb") + +GMS_ASYMOPT = str(data_ref / "gms/c1opt.gms.gz") +GMS_SYMOPT = str(data_ref / "gms/symopt.gms") +GMS_ASYMSURF = str(data_ref / "gms/surf2wat.gms") + +two_water_gro = str(data_ref / "two_water_gro.gro") +two_water_gro_multiframe = str(data_ref / "two_water_gro_multiframe.gro") +two_water_gro_nonames = str(data_ref / "two_water_gro_nonames.gro") +two_water_gro_widebox = str(data_ref / "two_water_gro_widebox.gro") + +DLP_CONFIG = str(data_ref / "dlpoly/CONFIG") +DLP_CONFIG_order = str(data_ref / "dlpoly/CONFIG_order") +DLP_CONFIG_minimal = str(data_ref / "dlpoly/CONFIG_minimal") +DLP_HISTORY = str(data_ref / "dlpoly/HISTORY") +DLP_HISTORY_order = str(data_ref / "dlpoly/HISTORY_order") +DLP_HISTORY_minimal = str(data_ref / "dlpoly/HISTORY_minimal") +DLP_HISTORY_minimal_cell = str(data_ref / "dlpoly/HISTORY_minimal_cell") +DLP_HISTORY_classic = str(data_ref / "dlpoly/HISTORY_classic") + +waterPSF = str(data_ref / 'watdyn.psf') +waterDCD = str(data_ref / 'watdyn.dcd') + +rmsfArray = str(data_ref / 'adk_oplsaa_CA_rmsf.npy') + +HoomdXMLdata = str(data_ref / 'C12x64.xml.bz2') + +Make_Whole = str(data_ref / 'make_whole.gro') +fullerene = str(data_ref / 'fullerene.pdb.gz') + +Plength = str(data_ref / 'plength.gro') +Martini_membrane_gro = str(data_ref / 'martini_dppc_chol_bilayer.gro') # Contains one of each residue in 'nucleic' selections -NUCLsel = data_ref / 'nucl_res.pdb' +NUCLsel = str(data_ref / 'nucl_res.pdb') -RANDOM_WALK = data_ref / 'xyz_random_walk.xtc' -RANDOM_WALK_TOPO = data_ref / 'RANDOM_WALK_TOPO.pdb' +RANDOM_WALK = str(data_ref / 'xyz_random_walk.xtc') +RANDOM_WALK_TOPO = str(data_ref / 'RANDOM_WALK_TOPO.pdb') -MMTF = data_ref / '173D.mmtf' -MMTF_gz = data_ref / '5KIH.mmtf.gz' -MMTF_skinny = data_ref / '1ubq-less-optional.mmtf' -MMTF_skinny2 = data_ref / '3NJW-onlyrequired.mmtf' -MMTF_NOCRYST = data_ref / "6QYR.mmtf.gz" +MMTF = str(data_ref / '173D.mmtf') +MMTF_gz = str(data_ref / '5KIH.mmtf.gz') +MMTF_skinny = str(data_ref / '1ubq-less-optional.mmtf') +MMTF_skinny2 = str(data_ref / '3NJW-onlyrequired.mmtf') +MMTF_NOCRYST = str(data_ref / "6QYR.mmtf.gz") -ALIGN_BOUND = data_ref / 'analysis/align_bound.pdb.gz' -ALIGN_UNBOUND = data_ref / 'analysis/align_unbound.pdb.gz' +ALIGN_BOUND = str(data_ref / 'analysis/align_bound.pdb.gz') +ALIGN_UNBOUND = str(data_ref / 'analysis/align_unbound.pdb.gz') -GSD = data_ref / 'example.gsd' -GSD_bonds = data_ref / 'example_bonds.gsd' -GSD_long = data_ref / 'example_longer.gsd' +GSD = str(data_ref / 'example.gsd') +GSD_bonds = str(data_ref / 'example_bonds.gsd') +GSD_long = str(data_ref / 'example_longer.gsd') -DihedralArray = data_ref / 'adk_oplsaa_dihedral.npy' -DihedralsArray = data_ref / 'adk_oplsaa_dihedral_list.npy' -RamaArray = data_ref / 'adk_oplsaa_rama.npy' -GLYRamaArray = data_ref / 'adk_oplsaa_GLY_rama.npy' -JaninArray = data_ref / 'adk_oplsaa_janin.npy' -LYSJaninArray = data_ref / 'adk_oplsaa_LYS_janin.npy' -PDB_rama = data_ref / '19hc.pdb.gz' -PDB_janin = data_ref / '1a28.pdb.gz' +DihedralArray = str(data_ref / 'adk_oplsaa_dihedral.npy') +DihedralsArray = str(data_ref / 'adk_oplsaa_dihedral_list.npy') +RamaArray = str(data_ref / 'adk_oplsaa_rama.npy') +GLYRamaArray = str(data_ref / 'adk_oplsaa_GLY_rama.npy') +JaninArray = str(data_ref / 'adk_oplsaa_janin.npy') +LYSJaninArray = str(data_ref / 'adk_oplsaa_LYS_janin.npy') +PDB_rama = str(data_ref / '19hc.pdb.gz') +PDB_janin = str(data_ref / '1a28.pdb.gz') -BATArray = data_ref / 'mol2_comments_header_bat.npy' +BATArray = str(data_ref / 'mol2_comments_header_bat.npy') -ITP = data_ref / 'gromacs_ala10.itp' -ITP_nomass = data_ref / 'itp_nomass.itp' -ITP_atomtypes = data_ref / 'atomtypes.itp' -ITP_charges = data_ref / 'atomtypes_charge.itp' -ITP_edited = data_ref / 'edited_itp.itp' -ITP_tip5p = data_ref / "tip5p.itp" -ITP_spce = data_ref / 'spce.itp' +ITP = str(data_ref / 'gromacs_ala10.itp') +ITP_nomass = str(data_ref / 'itp_nomass.itp') +ITP_atomtypes = str(data_ref / 'atomtypes.itp') +ITP_charges = str(data_ref / 'atomtypes_charge.itp') +ITP_edited = str(data_ref / 'edited_itp.itp') +ITP_tip5p = str(data_ref / "tip5p.itp") +ITP_spce = str(data_ref / 'spce.itp') -GMX_TOP = data_ref / 'gromacs_ala10.top' -GMX_DIR = data_ref / 'gromacs/' -GMX_TOP_BAD = data_ref / 'bad_top.top' -ITP_no_endif = data_ref / 'no_endif_spc.itp' +GMX_TOP = str(data_ref / 'gromacs_ala10.top') +GMX_DIR = str(data_ref / 'gromacs/') +GMX_TOP_BAD = str(data_ref / 'bad_top.top') +ITP_no_endif = str(data_ref / 'no_endif_spc.itp') -NAMDBIN = data_ref / 'adk_open.coor' +NAMDBIN = str(data_ref / 'adk_open.coor') -SDF_molecule = data_ref / 'molecule.sdf' +SDF_molecule = str(data_ref / 'molecule.sdf') -PDB_elements = data_ref / 'elements.pdb' -PDB_charges = data_ref / 'charges.pdb' +PDB_elements = str(data_ref / 'elements.pdb') +PDB_charges = str(data_ref / 'charges.pdb') -PDBX = data_ref / "4x8u.pdbx" +PDBX = str(data_ref / "4x8u.pdbx") -SURFACE_PDB = data_ref / 'surface.pdb.bz2' -SURFACE_TRR = data_ref / 'surface.trr' +SURFACE_PDB = str(data_ref / 'surface.pdb.bz2') +SURFACE_TRR = str(data_ref / 'surface.trr') # This should be the last line: clean up namespace From 956b7c10ce04a9e2bd4b83efd84f1e61544dd2b7 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Mon, 6 Mar 2023 21:23:12 +0000 Subject: [PATCH 3/8] sed did too good a job --- testsuite/MDAnalysisTests/datafiles.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/testsuite/MDAnalysisTests/datafiles.py b/testsuite/MDAnalysisTests/datafiles.py index c988330bbc2..753b100e3fb 100644 --- a/testsuite/MDAnalysisTests/datafiles.py +++ b/testsuite/MDAnalysisTests/datafiles.py @@ -25,7 +25,7 @@ Location of data files for the MDAnalysis unit tests ==================================================== -Real MD simulation data are stored in the ```` sub +Real MD simulation data are stored in the ``data/`` sub directory. Use as :: from MDAnalysis.tests.datafiles import * From 9ad25f06d3bf7b668ecb371dd581b7fa3e8775ca Mon Sep 17 00:00:00 2001 From: IAlibay Date: Thu, 20 Apr 2023 04:54:43 +0100 Subject: [PATCH 4/8] typo --- testsuite/MDAnalysisTests/datafiles.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/testsuite/MDAnalysisTests/datafiles.py b/testsuite/MDAnalysisTests/datafiles.py index 324d8e1263f..bc9c112fe14 100644 --- a/testsuite/MDAnalysisTests/datafiles.py +++ b/testsuite/MDAnalysisTests/datafiles.py @@ -426,9 +426,6 @@ PRMpbc = str(data_ref / 'Amber/capped-ala.prmtop') TRJpbc_bz2 = str(data_ref / 'Amber/capped-ala.mdcrd.bz2') -PRMpbc = resource_filename(__name__, 'data/Amber/capped-ala.prmtop') -TRJpbc_bz2 = resource_filename(__name__, 'data/Amber/capped-ala.mdcrd.bz2') - PRMncdf = str(data_ref / 'Amber/bala.prmtop') TRJncdf = str(data_ref / 'Amber/bala.trj') NCDF = str(data_ref / 'Amber/bala.ncdf') From b73c7504cc305115479fecbcd8a508d2013bc0bc Mon Sep 17 00:00:00 2001 From: IAlibay Date: Wed, 24 May 2023 07:21:03 +0100 Subject: [PATCH 5/8] fix test_datafiles --- testsuite/MDAnalysisTests/datafiles.py | 664 +++++++++--------- .../MDAnalysisTests/utils/test_datafiles.py | 2 +- 2 files changed, 333 insertions(+), 333 deletions(-) diff --git a/testsuite/MDAnalysisTests/datafiles.py b/testsuite/MDAnalysisTests/datafiles.py index bc9c112fe14..28c5f09477a 100644 --- a/testsuite/MDAnalysisTests/datafiles.py +++ b/testsuite/MDAnalysisTests/datafiles.py @@ -234,384 +234,384 @@ from importlib import resources import MDAnalysisTests.data -data_ref = resources.files('MDAnalysisTests.data') - -WIN_PDB_multiframe = str(data_ref / 'windows/WIN_nmr_neopetrosiamide.pdb') -WIN_DLP_HISTORY = str(data_ref / 'windows/WIN_HISTORY') -WIN_TRJ = str(data_ref / 'windows/WIN_ache.mdcrd') -WIN_ARC = str(data_ref / 'windows/WIN_test.arc') -WIN_LAMMPSDUMP = str(data_ref / 'windows/WIN_wat.lammpstrj') - -legacy_DCD_NAMD_coords = str(data_ref / 'legacy_DCD_NAMD_coords.npy') -legacy_DCD_ADK_coords = str(data_ref / 'legacy_DCD_adk_coords.npy') -legacy_DCD_c36_coords = str(data_ref / 'legacy_DCD_c36_coords.npy') -AUX_XVG_LOWF = str(data_ref / 'test_lowf.xvg') -AUX_XVG_HIGHF = str(data_ref / 'test_highf.xvg') -XVG_BAD_NCOL = str(data_ref / 'bad_num_col.xvg') -AUX_XVG = str(data_ref / 'test.xvg') -AUX_EDR = str(data_ref / 'test.edr') -AUX_EDR_RAW = str(data_ref / 'aux_edr_raw.txt') -AUX_EDR_TPR = str(data_ref / 'aux_edr.tpr') -AUX_EDR_XTC = str(data_ref / 'aux_edr.xtc') -AUX_EDR_SINGLE_FRAME = str(data_ref / 'single_frame.edr') -ENT = str(data_ref / 'testENT.ent') -GRO_missing_atomname = str(data_ref / 'missing_atomname.gro') -GRO_empty_atom = str(data_ref / 'empty_atom.gro') -GRO_huge_box = str(data_ref / 'huge_box.gro') - -COORDINATES_GRO = str(data_ref / 'coordinates/test.gro') -COORDINATES_GRO_INCOMPLETE_VELOCITY = str(data_ref / 'coordinates/test_incomplete_vel.gro') -COORDINATES_GRO_BZ2 = str(data_ref / 'coordinates/test.gro.bz2') -COORDINATES_XYZ = str(data_ref / 'coordinates/test.xyz') -COORDINATES_XYZ_BZ2 = str(data_ref / 'coordinates/test.xyz.bz2') -COORDINATES_XTC = str(data_ref / 'coordinates/test.xtc') -COORDINATES_TRR = str(data_ref / 'coordinates/test.trr') -COORDINATES_TNG = str(data_ref / 'coordinates/test.tng') -COORDINATES_H5MD = str(data_ref / 'coordinates/test.h5md') -COORDINATES_DCD = str(data_ref / 'coordinates/test.dcd') -COORDINATES_TOPOLOGY = str(data_ref / 'coordinates/test_topology.pdb') - -PSF = str(data_ref / 'adk.psf') -PSF_notop = str(data_ref / 'adk_notop.psf') -PSF_BAD = str(data_ref / 'adk_notop_BAD.psf') -DCD = str(data_ref / 'adk_dims.dcd') -DCD_empty = str(data_ref / 'empty.dcd') -CRD = str(data_ref / 'adk_open.crd') -PSF_TRICLINIC = str(data_ref / 'tip125_tric_C36.psf') -DCD_TRICLINIC = str(data_ref / 'tip125_tric_C36.dcd') -DCD2 = str(data_ref / 'adk_dims2.dcd') - -PSF_NAMD = str(data_ref / 'namd_cgenff.psf') -PDB_NAMD = str(data_ref / 'namd_cgenff.pdb') -PDB_multipole = str(data_ref / 'water_methane_acetic-acid_ammonia.pdb') -PSF_NAMD_TRICLINIC = str(data_ref / 'SiN_tric_namd.psf') -DCD_NAMD_TRICLINIC = str(data_ref / 'SiN_tric_namd.dcd') -PSF_NAMD_GBIS = str(data_ref / 'adk_closed_NAMD.psf') -DCD_NAMD_GBIS = str(data_ref / 'adk_gbis_tmd-fast1_NAMD.dcd') - -PSF_nosegid = str(data_ref / 'nosegid.psf') - -PSF_cmap = str(data_ref / 'parmed_ala3.psf') - -PDB_small = str(data_ref / 'adk_open.pdb') -PDB_closed = str(data_ref / 'adk_closed.pdb') - -ALIGN = str(data_ref / 'align.pdb') -RNA_PSF = str(data_ref / 'analysis/1k5i_c36.psf.gz') -RNA_PDB = str(data_ref / 'analysis/1k5i_c36.pdb.gz') -INC_PDB = str(data_ref / 'incomplete.pdb') -PDB_cm = str(data_ref / 'cryst_then_model.pdb') -PDB_cm_gz = str(data_ref / 'cryst_then_model.pdb.gz') -PDB_cm_bz2 = str(data_ref / 'cryst_then_model.pdb.bz2') -PDB_mc = str(data_ref / 'model_then_cryst.pdb') -PDB_mc_gz = str(data_ref / 'model_then_cryst.pdb.gz') -PDB_mc_bz2 = str(data_ref / 'model_then_cryst.pdb.bz2') -PDB_chainidnewres = str(data_ref / 'chainIDnewres.pdb.gz') -PDB_sameresid_diffresname = str(data_ref / 'sameresid_diffresname.pdb') -PDB_chainidrepeat = str(data_ref / 'chainIDrepeat.pdb.gz') -PDB_multiframe = str(data_ref / 'nmr_neopetrosiamide.pdb') -PDB_helix = str(data_ref / 'A6PA6_alpha.pdb') -PDB_conect = str(data_ref / 'conect_parsing.pdb') -PDB_conect2TER = str(data_ref / 'CONECT2TER.pdb') -PDB_singleconect = str(data_ref / 'SINGLECONECT.pdb') -PDB_icodes = str(data_ref / '1osm.pdb.gz') -PDB_CRYOEM_BOX = str(data_ref / '5a7u.pdb') -PDB_CHECK_RIGHTHAND_PA = str(data_ref / '6msm.pdb.bz2') -FHIAIMS = str(data_ref / 'fhiaims.in') - -GRO = str(data_ref / 'adk_oplsaa.gro') -GRO_velocity = str(data_ref / 'sample_velocity_file.gro') -GRO_incomplete_vels = str(data_ref / 'grovels.gro') -GRO_large = str(data_ref / 'bigbox.gro.bz2') -GRO_residwrap = str(data_ref / 'residwrap.gro') -GRO_residwrap_0base = str(data_ref / 'residwrap_0base.gro') -GRO_sameresid_diffresname = str(data_ref / 'sameresid_diffresname.gro') -PDB = str(data_ref / 'adk_oplsaa.pdb') -XTC = str(data_ref / 'adk_oplsaa.xtc') -TRR = str(data_ref / 'adk_oplsaa.trr') -TPR = str(data_ref / 'adk_oplsaa.tpr') -PDB_sub_dry = str(data_ref / 'cobrotoxin_dry_neutral_0.pdb') -TRR_sub_sol = str(data_ref / 'cobrotoxin.trr') -XTC_sub_sol = str(data_ref / 'cobrotoxin.xtc') -PDB_sub_sol = str(data_ref / 'cobrotoxin.pdb') -PDB_xlserial = str(data_ref / 'xl_serial.pdb') -GRO_MEMPROT = str(data_ref / 'analysis/YiiP_lipids.gro.gz') -XTC_MEMPROT = str(data_ref / 'analysis/YiiP_lipids.xtc') -XTC_multi_frame = str(data_ref / 'xtc_test_only_10_frame_10_atoms.xtc') -TRR_multi_frame = str(data_ref / 'trr_test_only_10_frame_10_atoms.trr') -TNG_traj = str(data_ref / 'argon_npt_compressed.tng') -TNG_traj_gro = str(data_ref / 'argon_npt_compressed.gro.gz') -TNG_traj_uneven_blocks = str(data_ref / 'argon_npt_compressed_uneven.tng') -TNG_traj_vels_forces = str(data_ref / 'argon_npt_compressed_vels_forces.tng') -PDB_xvf = str(data_ref / 'cobrotoxin.pdb') -TPR_xvf = str(data_ref / 'cobrotoxin.tpr') -TRR_xvf = str(data_ref / 'cobrotoxin.trr') -H5MD_xvf = str(data_ref / 'cobrotoxin.h5md') -XVG_BZ2 = str(data_ref / 'cobrotoxin_protein_forces.xvg.bz2') - -XPDB_small = str(data_ref / '5digitResid.pdb') +_data_ref = resources.files('MDAnalysisTests.data') + +WIN_PDB_multiframe = str(_data_ref / 'windows/WIN_nmr_neopetrosiamide.pdb') +WIN_DLP_HISTORY = str(_data_ref / 'windows/WIN_HISTORY') +WIN_TRJ = str(_data_ref / 'windows/WIN_ache.mdcrd') +WIN_ARC = str(_data_ref / 'windows/WIN_test.arc') +WIN_LAMMPSDUMP = str(_data_ref / 'windows/WIN_wat.lammpstrj') + +legacy_DCD_NAMD_coords = str(_data_ref / 'legacy_DCD_NAMD_coords.npy') +legacy_DCD_ADK_coords = str(_data_ref / 'legacy_DCD_adk_coords.npy') +legacy_DCD_c36_coords = str(_data_ref / 'legacy_DCD_c36_coords.npy') +AUX_XVG_LOWF = str(_data_ref / 'test_lowf.xvg') +AUX_XVG_HIGHF = str(_data_ref / 'test_highf.xvg') +XVG_BAD_NCOL = str(_data_ref / 'bad_num_col.xvg') +AUX_XVG = str(_data_ref / 'test.xvg') +AUX_EDR = str(_data_ref / 'test.edr') +AUX_EDR_RAW = str(_data_ref / 'aux_edr_raw.txt') +AUX_EDR_TPR = str(_data_ref / 'aux_edr.tpr') +AUX_EDR_XTC = str(_data_ref / 'aux_edr.xtc') +AUX_EDR_SINGLE_FRAME = str(_data_ref / 'single_frame.edr') +ENT = str(_data_ref / 'testENT.ent') +GRO_missing_atomname = str(_data_ref / 'missing_atomname.gro') +GRO_empty_atom = str(_data_ref / 'empty_atom.gro') +GRO_huge_box = str(_data_ref / 'huge_box.gro') + +COORDINATES_GRO = str(_data_ref / 'coordinates/test.gro') +COORDINATES_GRO_INCOMPLETE_VELOCITY = str(_data_ref / 'coordinates/test_incomplete_vel.gro') +COORDINATES_GRO_BZ2 = str(_data_ref / 'coordinates/test.gro.bz2') +COORDINATES_XYZ = str(_data_ref / 'coordinates/test.xyz') +COORDINATES_XYZ_BZ2 = str(_data_ref / 'coordinates/test.xyz.bz2') +COORDINATES_XTC = str(_data_ref / 'coordinates/test.xtc') +COORDINATES_TRR = str(_data_ref / 'coordinates/test.trr') +COORDINATES_TNG = str(_data_ref / 'coordinates/test.tng') +COORDINATES_H5MD = str(_data_ref / 'coordinates/test.h5md') +COORDINATES_DCD = str(_data_ref / 'coordinates/test.dcd') +COORDINATES_TOPOLOGY = str(_data_ref / 'coordinates/test_topology.pdb') + +PSF = str(_data_ref / 'adk.psf') +PSF_notop = str(_data_ref / 'adk_notop.psf') +PSF_BAD = str(_data_ref / 'adk_notop_BAD.psf') +DCD = str(_data_ref / 'adk_dims.dcd') +DCD_empty = str(_data_ref / 'empty.dcd') +CRD = str(_data_ref / 'adk_open.crd') +PSF_TRICLINIC = str(_data_ref / 'tip125_tric_C36.psf') +DCD_TRICLINIC = str(_data_ref / 'tip125_tric_C36.dcd') +DCD2 = str(_data_ref / 'adk_dims2.dcd') + +PSF_NAMD = str(_data_ref / 'namd_cgenff.psf') +PDB_NAMD = str(_data_ref / 'namd_cgenff.pdb') +PDB_multipole = str(_data_ref / 'water_methane_acetic-acid_ammonia.pdb') +PSF_NAMD_TRICLINIC = str(_data_ref / 'SiN_tric_namd.psf') +DCD_NAMD_TRICLINIC = str(_data_ref / 'SiN_tric_namd.dcd') +PSF_NAMD_GBIS = str(_data_ref / 'adk_closed_NAMD.psf') +DCD_NAMD_GBIS = str(_data_ref / 'adk_gbis_tmd-fast1_NAMD.dcd') + +PSF_nosegid = str(_data_ref / 'nosegid.psf') + +PSF_cmap = str(_data_ref / 'parmed_ala3.psf') + +PDB_small = str(_data_ref / 'adk_open.pdb') +PDB_closed = str(_data_ref / 'adk_closed.pdb') + +ALIGN = str(_data_ref / 'align.pdb') +RNA_PSF = str(_data_ref / 'analysis/1k5i_c36.psf.gz') +RNA_PDB = str(_data_ref / 'analysis/1k5i_c36.pdb.gz') +INC_PDB = str(_data_ref / 'incomplete.pdb') +PDB_cm = str(_data_ref / 'cryst_then_model.pdb') +PDB_cm_gz = str(_data_ref / 'cryst_then_model.pdb.gz') +PDB_cm_bz2 = str(_data_ref / 'cryst_then_model.pdb.bz2') +PDB_mc = str(_data_ref / 'model_then_cryst.pdb') +PDB_mc_gz = str(_data_ref / 'model_then_cryst.pdb.gz') +PDB_mc_bz2 = str(_data_ref / 'model_then_cryst.pdb.bz2') +PDB_chainidnewres = str(_data_ref / 'chainIDnewres.pdb.gz') +PDB_sameresid_diffresname = str(_data_ref / 'sameresid_diffresname.pdb') +PDB_chainidrepeat = str(_data_ref / 'chainIDrepeat.pdb.gz') +PDB_multiframe = str(_data_ref / 'nmr_neopetrosiamide.pdb') +PDB_helix = str(_data_ref / 'A6PA6_alpha.pdb') +PDB_conect = str(_data_ref / 'conect_parsing.pdb') +PDB_conect2TER = str(_data_ref / 'CONECT2TER.pdb') +PDB_singleconect = str(_data_ref / 'SINGLECONECT.pdb') +PDB_icodes = str(_data_ref / '1osm.pdb.gz') +PDB_CRYOEM_BOX = str(_data_ref / '5a7u.pdb') +PDB_CHECK_RIGHTHAND_PA = str(_data_ref / '6msm.pdb.bz2') +FHIAIMS = str(_data_ref / 'fhiaims.in') + +GRO = str(_data_ref / 'adk_oplsaa.gro') +GRO_velocity = str(_data_ref / 'sample_velocity_file.gro') +GRO_incomplete_vels = str(_data_ref / 'grovels.gro') +GRO_large = str(_data_ref / 'bigbox.gro.bz2') +GRO_residwrap = str(_data_ref / 'residwrap.gro') +GRO_residwrap_0base = str(_data_ref / 'residwrap_0base.gro') +GRO_sameresid_diffresname = str(_data_ref / 'sameresid_diffresname.gro') +PDB = str(_data_ref / 'adk_oplsaa.pdb') +XTC = str(_data_ref / 'adk_oplsaa.xtc') +TRR = str(_data_ref / 'adk_oplsaa.trr') +TPR = str(_data_ref / 'adk_oplsaa.tpr') +PDB_sub_dry = str(_data_ref / 'cobrotoxin_dry_neutral_0.pdb') +TRR_sub_sol = str(_data_ref / 'cobrotoxin.trr') +XTC_sub_sol = str(_data_ref / 'cobrotoxin.xtc') +PDB_sub_sol = str(_data_ref / 'cobrotoxin.pdb') +PDB_xlserial = str(_data_ref / 'xl_serial.pdb') +GRO_MEMPROT = str(_data_ref / 'analysis/YiiP_lipids.gro.gz') +XTC_MEMPROT = str(_data_ref / 'analysis/YiiP_lipids.xtc') +XTC_multi_frame = str(_data_ref / 'xtc_test_only_10_frame_10_atoms.xtc') +TRR_multi_frame = str(_data_ref / 'trr_test_only_10_frame_10_atoms.trr') +TNG_traj = str(_data_ref / 'argon_npt_compressed.tng') +TNG_traj_gro = str(_data_ref / 'argon_npt_compressed.gro.gz') +TNG_traj_uneven_blocks = str(_data_ref / 'argon_npt_compressed_uneven.tng') +TNG_traj_vels_forces = str(_data_ref / 'argon_npt_compressed_vels_forces.tng') +PDB_xvf = str(_data_ref / 'cobrotoxin.pdb') +TPR_xvf = str(_data_ref / 'cobrotoxin.tpr') +TRR_xvf = str(_data_ref / 'cobrotoxin.trr') +H5MD_xvf = str(_data_ref / 'cobrotoxin.h5md') +XVG_BZ2 = str(_data_ref / 'cobrotoxin_protein_forces.xvg.bz2') + +XPDB_small = str(_data_ref / '5digitResid.pdb') # number is the gromacs version -TPR400 = str(data_ref / 'tprs/2lyz_gmx_4.0.tpr') -TPR402 = str(data_ref / 'tprs/2lyz_gmx_4.0.2.tpr') -TPR403 = str(data_ref / 'tprs/2lyz_gmx_4.0.3.tpr') -TPR404 = str(data_ref / 'tprs/2lyz_gmx_4.0.4.tpr') -TPR405 = str(data_ref / 'tprs/2lyz_gmx_4.0.5.tpr') -TPR406 = str(data_ref / 'tprs/2lyz_gmx_4.0.6.tpr') -TPR407 = str(data_ref / 'tprs/2lyz_gmx_4.0.7.tpr') -TPR450 = str(data_ref / 'tprs/2lyz_gmx_4.5.tpr') -TPR451 = str(data_ref / 'tprs/2lyz_gmx_4.5.1.tpr') -TPR452 = str(data_ref / 'tprs/2lyz_gmx_4.5.2.tpr') -TPR453 = str(data_ref / 'tprs/2lyz_gmx_4.5.3.tpr') -TPR454 = str(data_ref / 'tprs/2lyz_gmx_4.5.4.tpr') -TPR455 = str(data_ref / 'tprs/2lyz_gmx_4.5.5.tpr') -TPR502 = str(data_ref / 'tprs/2lyz_gmx_5.0.2.tpr') -TPR504 = str(data_ref / 'tprs/2lyz_gmx_5.0.4.tpr') -TPR505 = str(data_ref / 'tprs/2lyz_gmx_5.0.5.tpr') -TPR510 = str(data_ref / 'tprs/2lyz_gmx_5.1.tpr') -TPR2016 = str(data_ref / 'tprs/2lyz_gmx_2016.tpr') -TPR2018 = str(data_ref / 'tprs/2lyz_gmx_2018.tpr') -TPR2019B3 = str(data_ref / 'tprs/2lyz_gmx_2019-beta3.tpr') -TPR2020B2 = str(data_ref / 'tprs/2lyz_gmx_2020-beta2.tpr') -TPR2020 = str(data_ref / 'tprs/2lyz_gmx_2020.tpr') -TPR2021 = str(data_ref / 'tprs/2lyz_gmx_2021.tpr') -TPR2022RC1 = str(data_ref / 'tprs/2lyz_gmx_2022-rc1.tpr') -TPR2023 = str(data_ref / 'tprs/2lyz_gmx_2023.tpr') +TPR400 = str(_data_ref / 'tprs/2lyz_gmx_4.0.tpr') +TPR402 = str(_data_ref / 'tprs/2lyz_gmx_4.0.2.tpr') +TPR403 = str(_data_ref / 'tprs/2lyz_gmx_4.0.3.tpr') +TPR404 = str(_data_ref / 'tprs/2lyz_gmx_4.0.4.tpr') +TPR405 = str(_data_ref / 'tprs/2lyz_gmx_4.0.5.tpr') +TPR406 = str(_data_ref / 'tprs/2lyz_gmx_4.0.6.tpr') +TPR407 = str(_data_ref / 'tprs/2lyz_gmx_4.0.7.tpr') +TPR450 = str(_data_ref / 'tprs/2lyz_gmx_4.5.tpr') +TPR451 = str(_data_ref / 'tprs/2lyz_gmx_4.5.1.tpr') +TPR452 = str(_data_ref / 'tprs/2lyz_gmx_4.5.2.tpr') +TPR453 = str(_data_ref / 'tprs/2lyz_gmx_4.5.3.tpr') +TPR454 = str(_data_ref / 'tprs/2lyz_gmx_4.5.4.tpr') +TPR455 = str(_data_ref / 'tprs/2lyz_gmx_4.5.5.tpr') +TPR502 = str(_data_ref / 'tprs/2lyz_gmx_5.0.2.tpr') +TPR504 = str(_data_ref / 'tprs/2lyz_gmx_5.0.4.tpr') +TPR505 = str(_data_ref / 'tprs/2lyz_gmx_5.0.5.tpr') +TPR510 = str(_data_ref / 'tprs/2lyz_gmx_5.1.tpr') +TPR2016 = str(_data_ref / 'tprs/2lyz_gmx_2016.tpr') +TPR2018 = str(_data_ref / 'tprs/2lyz_gmx_2018.tpr') +TPR2019B3 = str(_data_ref / 'tprs/2lyz_gmx_2019-beta3.tpr') +TPR2020B2 = str(_data_ref / 'tprs/2lyz_gmx_2020-beta2.tpr') +TPR2020 = str(_data_ref / 'tprs/2lyz_gmx_2020.tpr') +TPR2021 = str(_data_ref / 'tprs/2lyz_gmx_2021.tpr') +TPR2022RC1 = str(_data_ref / 'tprs/2lyz_gmx_2022-rc1.tpr') +TPR2023 = str(_data_ref / 'tprs/2lyz_gmx_2023.tpr') # double precision -TPR455Double = str(data_ref / 'tprs/drew_gmx_4.5.5.double.tpr') -TPR460 = str(data_ref / 'tprs/ab42_gmx_4.6.tpr') -TPR461 = str(data_ref / 'tprs/ab42_gmx_4.6.1.tpr') -TPR2020Double = str(data_ref / 'tprs/2lyz_gmx_2020_double.tpr') -TPR2021Double = str(data_ref / 'tprs/2lyz_gmx_2021_double.tpr') +TPR455Double = str(_data_ref / 'tprs/drew_gmx_4.5.5.double.tpr') +TPR460 = str(_data_ref / 'tprs/ab42_gmx_4.6.tpr') +TPR461 = str(_data_ref / 'tprs/ab42_gmx_4.6.1.tpr') +TPR2020Double = str(_data_ref / 'tprs/2lyz_gmx_2020_double.tpr') +TPR2021Double = str(_data_ref / 'tprs/2lyz_gmx_2021_double.tpr') # all bonded interactions -TPR334_bonded = str(data_ref / 'tprs/all_bonded/dummy_3.3.4.tpr') -TPR510_bonded = str(data_ref / 'tprs/all_bonded/dummy_5.1.tpr') -TPR2016_bonded = str(data_ref / 'tprs/all_bonded/dummy_2016.tpr') -TPR2018_bonded = str(data_ref / 'tprs/all_bonded/dummy_2018.tpr') -TPR2019B3_bonded = str(data_ref / 'tprs/all_bonded/dummy_2019-beta3.tpr') -TPR2020B2_bonded = str(data_ref / 'tprs/all_bonded/dummy_2020-beta2.tpr') -TPR2020_bonded = str(data_ref / 'tprs/all_bonded/dummy_2020.tpr') -TPR2020_double_bonded = str(data_ref / 'tprs/all_bonded/dummy_2020_double.tpr') -TPR2021_bonded = str(data_ref / 'tprs/all_bonded/dummy_2021.tpr') -TPR2021_double_bonded = str(data_ref / 'tprs/all_bonded/dummy_2021_double.tpr') -TPR2022RC1_bonded = str(data_ref / 'tprs/all_bonded/dummy_2022-rc1.tpr') -TPR2023_bonded = str(data_ref / 'tprs/all_bonded/dummy_2023.tpr') +TPR334_bonded = str(_data_ref / 'tprs/all_bonded/dummy_3.3.4.tpr') +TPR510_bonded = str(_data_ref / 'tprs/all_bonded/dummy_5.1.tpr') +TPR2016_bonded = str(_data_ref / 'tprs/all_bonded/dummy_2016.tpr') +TPR2018_bonded = str(_data_ref / 'tprs/all_bonded/dummy_2018.tpr') +TPR2019B3_bonded = str(_data_ref / 'tprs/all_bonded/dummy_2019-beta3.tpr') +TPR2020B2_bonded = str(_data_ref / 'tprs/all_bonded/dummy_2020-beta2.tpr') +TPR2020_bonded = str(_data_ref / 'tprs/all_bonded/dummy_2020.tpr') +TPR2020_double_bonded = str(_data_ref / 'tprs/all_bonded/dummy_2020_double.tpr') +TPR2021_bonded = str(_data_ref / 'tprs/all_bonded/dummy_2021.tpr') +TPR2021_double_bonded = str(_data_ref / 'tprs/all_bonded/dummy_2021_double.tpr') +TPR2022RC1_bonded = str(_data_ref / 'tprs/all_bonded/dummy_2022-rc1.tpr') +TPR2023_bonded = str(_data_ref / 'tprs/all_bonded/dummy_2023.tpr') # all interactions -TPR_EXTRA_2023 = str(data_ref / 'tprs/virtual_sites/extra-interactions-2023.tpr') -TPR_EXTRA_2022RC1 = str(data_ref / 'tprs/virtual_sites/extra-interactions-2022-rc1.tpr') -TPR_EXTRA_2021 = str(data_ref / 'tprs/virtual_sites/extra-interactions-2021.tpr') -TPR_EXTRA_2020 = str(data_ref / 'tprs/virtual_sites/extra-interactions-2020.tpr') -TPR_EXTRA_2018 = str(data_ref / 'tprs/virtual_sites/extra-interactions-2018.tpr') -TPR_EXTRA_2016 = str(data_ref / 'tprs/virtual_sites/extra-interactions-2016.3.tpr') -TPR_EXTRA_407 = str(data_ref / 'tprs/virtual_sites/extra-interactions-4.0.7.tpr') +TPR_EXTRA_2023 = str(_data_ref / 'tprs/virtual_sites/extra-interactions-2023.tpr') +TPR_EXTRA_2022RC1 = str(_data_ref / 'tprs/virtual_sites/extra-interactions-2022-rc1.tpr') +TPR_EXTRA_2021 = str(_data_ref / 'tprs/virtual_sites/extra-interactions-2021.tpr') +TPR_EXTRA_2020 = str(_data_ref / 'tprs/virtual_sites/extra-interactions-2020.tpr') +TPR_EXTRA_2018 = str(_data_ref / 'tprs/virtual_sites/extra-interactions-2018.tpr') +TPR_EXTRA_2016 = str(_data_ref / 'tprs/virtual_sites/extra-interactions-2016.3.tpr') +TPR_EXTRA_407 = str(_data_ref / 'tprs/virtual_sites/extra-interactions-4.0.7.tpr') -XYZ_psf = str(data_ref / '2r9r-1b.psf') -XYZ_bz2 = str(data_ref / '2r9r-1b.xyz.bz2') -XYZ = str(data_ref / '2r9r-1b.xyz') -XYZ_mini = str(data_ref / 'mini.xyz') -XYZ_five = str(data_ref / 'five.xyz') -TXYZ = str(data_ref / 'coordinates/test.txyz') -ARC = str(data_ref / 'coordinates/test.arc') -ARC_PBC = str(data_ref / 'coordinates/new_hexane.arc') +XYZ_psf = str(_data_ref / '2r9r-1b.psf') +XYZ_bz2 = str(_data_ref / '2r9r-1b.xyz.bz2') +XYZ = str(_data_ref / '2r9r-1b.xyz') +XYZ_mini = str(_data_ref / 'mini.xyz') +XYZ_five = str(_data_ref / 'five.xyz') +TXYZ = str(_data_ref / 'coordinates/test.txyz') +ARC = str(_data_ref / 'coordinates/test.arc') +ARC_PBC = str(_data_ref / 'coordinates/new_hexane.arc') -PRM = str(data_ref / 'Amber/ache.prmtop') -TRJ = str(data_ref / 'Amber/ache.mdcrd') -INPCRD = str(data_ref / 'Amber/test.inpcrd') -TRJ_bz2 = str(data_ref / 'Amber/ache.mdcrd.bz2') -PFncdf_Top = str(data_ref / 'Amber/posfor.top') -PFncdf_Trj = str(data_ref / 'Amber/posfor.ncdf') +PRM = str(_data_ref / 'Amber/ache.prmtop') +TRJ = str(_data_ref / 'Amber/ache.mdcrd') +INPCRD = str(_data_ref / 'Amber/test.inpcrd') +TRJ_bz2 = str(_data_ref / 'Amber/ache.mdcrd.bz2') +PFncdf_Top = str(_data_ref / 'Amber/posfor.top') +PFncdf_Trj = str(_data_ref / 'Amber/posfor.ncdf') -CPPTRAJ_TRAJ_TOP = str(data_ref / 'data/Amber/cpptraj_traj.prmtop') -CPPTRAJ_TRAJ = str(data_ref / 'data/Amber/cpptraj_traj.nc') +CPPTRAJ_TRAJ_TOP = str(_data_ref / 'data/Amber/cpptraj_traj.prmtop') +CPPTRAJ_TRAJ = str(_data_ref / 'data/Amber/cpptraj_traj.nc') -PRMpbc = str(data_ref / 'Amber/capped-ala.prmtop') -TRJpbc_bz2 = str(data_ref / 'Amber/capped-ala.mdcrd.bz2') +PRMpbc = str(_data_ref / 'Amber/capped-ala.prmtop') +TRJpbc_bz2 = str(_data_ref / 'Amber/capped-ala.mdcrd.bz2') -PRMncdf = str(data_ref / 'Amber/bala.prmtop') -TRJncdf = str(data_ref / 'Amber/bala.trj') -NCDF = str(data_ref / 'Amber/bala.ncdf') +PRMncdf = str(_data_ref / 'Amber/bala.prmtop') +TRJncdf = str(_data_ref / 'Amber/bala.trj') +NCDF = str(_data_ref / 'Amber/bala.ncdf') -PRM12 = str(data_ref / 'Amber/anti.top') -TRJ12_bz2 = str(data_ref / 'Amber/anti_md1.mdcrd.bz2') +PRM12 = str(_data_ref / 'Amber/anti.top') +TRJ12_bz2 = str(_data_ref / 'Amber/anti_md1.mdcrd.bz2') -PRM7 = str(data_ref / 'Amber/tz2.truncoct.parm7.bz2') -NCDFtruncoct = str(data_ref / 'Amber/tz2.truncoct.nc') +PRM7 = str(_data_ref / 'Amber/tz2.truncoct.parm7.bz2') +NCDFtruncoct = str(_data_ref / 'Amber/tz2.truncoct.nc') -PRMcs = str(data_ref / 'Amber/chitosan.prmtop') +PRMcs = str(_data_ref / 'Amber/chitosan.prmtop') -PRMNCRST = str(data_ref / 'Amber/ace_mbondi3.parm7') +PRMNCRST = str(_data_ref / 'Amber/ace_mbondi3.parm7') -PRM_NCBOX = str(data_ref / 'Amber/ace_tip3p.parm7') -TRJ_NCBOX = str(data_ref / 'Amber/ace_tip3p.nc') +PRM_NCBOX = str(_data_ref / 'Amber/ace_tip3p.parm7') +TRJ_NCBOX = str(_data_ref / 'Amber/ace_tip3p.nc') -PRMNEGATIVE = str(data_ref / 'Amber/ace_mbondi3.negative.parm7') +PRMNEGATIVE = str(_data_ref / 'Amber/ace_mbondi3.negative.parm7') -PRMErr1 = str(data_ref / 'Amber/ace_mbondi3.error1.parm7') -PRMErr2 = str(data_ref / 'Amber/ace_mbondi3.error2.parm7') -PRMErr3 = str(data_ref / 'Amber/ace_mbondi3.error3.parm7') +PRMErr1 = str(_data_ref / 'Amber/ace_mbondi3.error1.parm7') +PRMErr2 = str(_data_ref / 'Amber/ace_mbondi3.error2.parm7') +PRMErr3 = str(_data_ref / 'Amber/ace_mbondi3.error3.parm7') -PRM_UreyBradley = str(data_ref / 'Amber/parmed_fad.prmtop') -PRM7_ala2 = str(data_ref / 'Amber/parmed_ala2_solv.parm7') -RST7_ala2 = str(data_ref / 'Amber/parmed_ala2_solv.rst7') +PRM_UreyBradley = str(_data_ref / 'Amber/parmed_fad.prmtop') +PRM7_ala2 = str(_data_ref / 'Amber/parmed_ala2_solv.parm7') +RST7_ala2 = str(_data_ref / 'Amber/parmed_ala2_solv.rst7') -PRM19SBOPC = str(data_ref / 'Amber/ala.ff19SB.OPC.parm7.bz2') +PRM19SBOPC = str(_data_ref / 'Amber/ala.ff19SB.OPC.parm7.bz2') -PQR = str(data_ref / 'adk_open.pqr') -PQR_icodes = str(data_ref / '1A2C.pqr') +PQR = str(_data_ref / 'adk_open.pqr') +PQR_icodes = str(_data_ref / '1A2C.pqr') -PDBQT_input = str(data_ref / 'pdbqt_inputpdbqt.pdbqt') -PDBQT_querypdb = str(data_ref / 'pdbqt_querypdb.pdb') +PDBQT_input = str(_data_ref / 'pdbqt_inputpdbqt.pdbqt') +PDBQT_querypdb = str(_data_ref / 'pdbqt_querypdb.pdb') -FASTA = str(data_ref / 'test.fasta') -HELANAL_BENDING_MATRIX = str(data_ref / 'helanal_bending_matrix_AdK_DIMS_H8.dat') -HELANAL_BENDING_MATRIX_SUBSET = str(data_ref / 'helanal_bending_matrix_AdK_DIMS_H8_frames10to79.dat') +FASTA = str(_data_ref / 'test.fasta') +HELANAL_BENDING_MATRIX = str(_data_ref / 'helanal_bending_matrix_AdK_DIMS_H8.dat') +HELANAL_BENDING_MATRIX_SUBSET = str(_data_ref / 'helanal_bending_matrix_AdK_DIMS_H8_frames10to79.dat') -PDB_HOLE = str(data_ref / '1grm_single.pdb') -MULTIPDB_HOLE = str(data_ref / '1grm_elNemo_mode7.pdb.bz2') +PDB_HOLE = str(_data_ref / '1grm_single.pdb') +MULTIPDB_HOLE = str(_data_ref / '1grm_elNemo_mode7.pdb.bz2') -DMS = str(data_ref / 'adk_closed.dms') -DMS_DOMAINS = str(data_ref / 'adk_closed_domains.dms') -DMS_NO_SEGID = str(data_ref / 'adk_closed_no_segid.dms') +DMS = str(_data_ref / 'adk_closed.dms') +DMS_DOMAINS = str(_data_ref / 'adk_closed_domains.dms') +DMS_NO_SEGID = str(_data_ref / 'adk_closed_no_segid.dms') -CONECT = str(data_ref / '1hvr.pdb') -CONECT_ERROR = str(data_ref / 'conect_error.pdb') +CONECT = str(_data_ref / '1hvr.pdb') +CONECT_ERROR = str(_data_ref / 'conect_error.pdb') -TRZ = str(data_ref / 'trzfile.trz') -TRZ_psf = str(data_ref / 'trz_psf.psf') +TRZ = str(_data_ref / 'trzfile.trz') +TRZ_psf = str(_data_ref / 'trz_psf.psf') -TRIC = str(data_ref / 'dppc_vesicle_hg.gro') +TRIC = str(_data_ref / 'dppc_vesicle_hg.gro') -PDB_full = str(data_ref / "4E43.pdb") +PDB_full = str(_data_ref / "4E43.pdb") -merge_protein = str(data_ref / "merge/2zmm/protein.pdb") -merge_ligand = str(data_ref / "merge/2zmm/ligand.pdb") -merge_water = str(data_ref / "merge/2zmm/water.pdb") +merge_protein = str(_data_ref / "merge/2zmm/protein.pdb") +merge_ligand = str(_data_ref / "merge/2zmm/ligand.pdb") +merge_water = str(_data_ref / "merge/2zmm/water.pdb") -mol2_molecules = str(data_ref / "mol2/Molecules.mol2") -mol2_molecule = str(data_ref / "mol2/Molecule.mol2") -mol2_ligand = str(data_ref / "mol2/Ligand.mol2") -mol2_broken_molecule = str(data_ref / "mol2/BrokenMolecule.mol2") -mol2_comments_header = str(data_ref / "mol2/Molecule_comments_header.mol2") +mol2_molecules = str(_data_ref / "mol2/Molecules.mol2") +mol2_molecule = str(_data_ref / "mol2/Molecule.mol2") +mol2_ligand = str(_data_ref / "mol2/Ligand.mol2") +mol2_broken_molecule = str(_data_ref / "mol2/BrokenMolecule.mol2") +mol2_comments_header = str(_data_ref / "mol2/Molecule_comments_header.mol2") # MOL2 file without substructure field -mol2_zinc = str(data_ref / "mol2/zinc_856218.mol2") +mol2_zinc = str(_data_ref / "mol2/zinc_856218.mol2") # MOL2 file without bonds -mol2_sodium_ion = str(data_ref / "mol2/sodium_ion.mol2") - -capping_input = str(data_ref / "capping/aaqaa.gro") -capping_output = str(data_ref / "capping/maestro_aaqaa_capped.pdb") -capping_ace = str(data_ref / "capping/ace.pdb") -capping_nma = str(data_ref / "capping/nma.pdb") - -contacts_villin_folded = str(data_ref / "contacts/villin_folded.gro.bz2") -contacts_villin_unfolded = str(data_ref / "contacts/villin_unfolded.gro.bz2") -contacts_file = str(data_ref / "contacts/2F4K_qlist5_remap.dat") - -trz4data = str(data_ref / "lammps/datatest.trz") -LAMMPSdata = str(data_ref / "lammps/datatest.data") -LAMMPSdata_mini = str(data_ref / "lammps/mini.data") -LAMMPSdata2 = str(data_ref / "lammps/ifabp_apo_100mM.data.bz2") -LAMMPSdcd2 = str(data_ref / "lammps/ifabp_apo_100mM.dcd") -LAMMPScnt = str(data_ref / "lammps/cnt-hexagonal-class1.data") -LAMMPScnt2 = str(data_ref / "lammps/cnt-hexagonal-class1.data2") -LAMMPShyd = str(data_ref / "lammps/hydrogen-class1.data") -LAMMPShyd2 = str(data_ref / "lammps/hydrogen-class1.data2") -LAMMPSdata_deletedatoms = str(data_ref / 'lammps/deletedatoms.data') -LAMMPSdata_triclinic = str(data_ref / "lammps/albite_triclinic.data") -LAMMPSdata_PairIJ = str(data_ref / "lammps/pairij_coeffs.data.bz2") -LAMMPSDUMP = str(data_ref / "lammps/wat.lammpstrj.bz2") -LAMMPSDUMP_long = str(data_ref / "lammps/wat.lammpstrj_long.bz2") -LAMMPSDUMP_allcoords = str(data_ref / "lammps/spce_all_coords.lammpstrj.bz2") -LAMMPSDUMP_nocoords = str(data_ref / "lammps/spce_no_coords.lammpstrj.bz2") -LAMMPSDUMP_triclinic = str(data_ref / "lammps/albite_triclinic.dump") -LAMMPSDUMP_image_vf = str(data_ref / "lammps/image_vf.lammpstrj") -LAMMPS_image_vf = str(data_ref / "lammps/image_vf.data") - -unordered_res = str(data_ref / "unordered_res.pdb") - -GMS_ASYMOPT = str(data_ref / "gms/c1opt.gms.gz") -GMS_SYMOPT = str(data_ref / "gms/symopt.gms") -GMS_ASYMSURF = str(data_ref / "gms/surf2wat.gms") - -two_water_gro = str(data_ref / "two_water_gro.gro") -two_water_gro_multiframe = str(data_ref / "two_water_gro_multiframe.gro") -two_water_gro_nonames = str(data_ref / "two_water_gro_nonames.gro") -two_water_gro_widebox = str(data_ref / "two_water_gro_widebox.gro") - -DLP_CONFIG = str(data_ref / "dlpoly/CONFIG") -DLP_CONFIG_order = str(data_ref / "dlpoly/CONFIG_order") -DLP_CONFIG_minimal = str(data_ref / "dlpoly/CONFIG_minimal") -DLP_HISTORY = str(data_ref / "dlpoly/HISTORY") -DLP_HISTORY_order = str(data_ref / "dlpoly/HISTORY_order") -DLP_HISTORY_minimal = str(data_ref / "dlpoly/HISTORY_minimal") -DLP_HISTORY_minimal_cell = str(data_ref / "dlpoly/HISTORY_minimal_cell") -DLP_HISTORY_classic = str(data_ref / "dlpoly/HISTORY_classic") - -waterPSF = str(data_ref / 'watdyn.psf') -waterDCD = str(data_ref / 'watdyn.dcd') - -rmsfArray = str(data_ref / 'adk_oplsaa_CA_rmsf.npy') - -HoomdXMLdata = str(data_ref / 'C12x64.xml.bz2') - -Make_Whole = str(data_ref / 'make_whole.gro') -fullerene = str(data_ref / 'fullerene.pdb.gz') - -Plength = str(data_ref / 'plength.gro') -Martini_membrane_gro = str(data_ref / 'martini_dppc_chol_bilayer.gro') +mol2_sodium_ion = str(_data_ref / "mol2/sodium_ion.mol2") + +capping_input = str(_data_ref / "capping/aaqaa.gro") +capping_output = str(_data_ref / "capping/maestro_aaqaa_capped.pdb") +capping_ace = str(_data_ref / "capping/ace.pdb") +capping_nma = str(_data_ref / "capping/nma.pdb") + +contacts_villin_folded = str(_data_ref / "contacts/villin_folded.gro.bz2") +contacts_villin_unfolded = str(_data_ref / "contacts/villin_unfolded.gro.bz2") +contacts_file = str(_data_ref / "contacts/2F4K_qlist5_remap.dat") + +trz4data = str(_data_ref / "lammps/datatest.trz") +LAMMPSdata = str(_data_ref / "lammps/datatest.data") +LAMMPSdata_mini = str(_data_ref / "lammps/mini.data") +LAMMPSdata2 = str(_data_ref / "lammps/ifabp_apo_100mM.data.bz2") +LAMMPSdcd2 = str(_data_ref / "lammps/ifabp_apo_100mM.dcd") +LAMMPScnt = str(_data_ref / "lammps/cnt-hexagonal-class1.data") +LAMMPScnt2 = str(_data_ref / "lammps/cnt-hexagonal-class1.data2") +LAMMPShyd = str(_data_ref / "lammps/hydrogen-class1.data") +LAMMPShyd2 = str(_data_ref / "lammps/hydrogen-class1.data2") +LAMMPSdata_deletedatoms = str(_data_ref / 'lammps/deletedatoms.data') +LAMMPSdata_triclinic = str(_data_ref / "lammps/albite_triclinic.data") +LAMMPSdata_PairIJ = str(_data_ref / "lammps/pairij_coeffs.data.bz2") +LAMMPSDUMP = str(_data_ref / "lammps/wat.lammpstrj.bz2") +LAMMPSDUMP_long = str(_data_ref / "lammps/wat.lammpstrj_long.bz2") +LAMMPSDUMP_allcoords = str(_data_ref / "lammps/spce_all_coords.lammpstrj.bz2") +LAMMPSDUMP_nocoords = str(_data_ref / "lammps/spce_no_coords.lammpstrj.bz2") +LAMMPSDUMP_triclinic = str(_data_ref / "lammps/albite_triclinic.dump") +LAMMPSDUMP_image_vf = str(_data_ref / "lammps/image_vf.lammpstrj") +LAMMPS_image_vf = str(_data_ref / "lammps/image_vf.data") + +unordered_res = str(_data_ref / "unordered_res.pdb") + +GMS_ASYMOPT = str(_data_ref / "gms/c1opt.gms.gz") +GMS_SYMOPT = str(_data_ref / "gms/symopt.gms") +GMS_ASYMSURF = str(_data_ref / "gms/surf2wat.gms") + +two_water_gro = str(_data_ref / "two_water_gro.gro") +two_water_gro_multiframe = str(_data_ref / "two_water_gro_multiframe.gro") +two_water_gro_nonames = str(_data_ref / "two_water_gro_nonames.gro") +two_water_gro_widebox = str(_data_ref / "two_water_gro_widebox.gro") + +DLP_CONFIG = str(_data_ref / "dlpoly/CONFIG") +DLP_CONFIG_order = str(_data_ref / "dlpoly/CONFIG_order") +DLP_CONFIG_minimal = str(_data_ref / "dlpoly/CONFIG_minimal") +DLP_HISTORY = str(_data_ref / "dlpoly/HISTORY") +DLP_HISTORY_order = str(_data_ref / "dlpoly/HISTORY_order") +DLP_HISTORY_minimal = str(_data_ref / "dlpoly/HISTORY_minimal") +DLP_HISTORY_minimal_cell = str(_data_ref / "dlpoly/HISTORY_minimal_cell") +DLP_HISTORY_classic = str(_data_ref / "dlpoly/HISTORY_classic") + +waterPSF = str(_data_ref / 'watdyn.psf') +waterDCD = str(_data_ref / 'watdyn.dcd') + +rmsfArray = str(_data_ref / 'adk_oplsaa_CA_rmsf.npy') + +HoomdXMLdata = str(_data_ref / 'C12x64.xml.bz2') + +Make_Whole = str(_data_ref / 'make_whole.gro') +fullerene = str(_data_ref / 'fullerene.pdb.gz') + +Plength = str(_data_ref / 'plength.gro') +Martini_membrane_gro = str(_data_ref / 'martini_dppc_chol_bilayer.gro') # Contains one of each residue in 'nucleic' selections -NUCLsel = str(data_ref / 'nucl_res.pdb') +NUCLsel = str(_data_ref / 'nucl_res.pdb') -RANDOM_WALK = str(data_ref / 'xyz_random_walk.xtc') -RANDOM_WALK_TOPO = str(data_ref / 'RANDOM_WALK_TOPO.pdb') +RANDOM_WALK = str(_data_ref / 'xyz_random_walk.xtc') +RANDOM_WALK_TOPO = str(_data_ref / 'RANDOM_WALK_TOPO.pdb') -MMTF = str(data_ref / '173D.mmtf') -MMTF_gz = str(data_ref / '5KIH.mmtf.gz') -MMTF_skinny = str(data_ref / '1ubq-less-optional.mmtf') -MMTF_skinny2 = str(data_ref / '3NJW-onlyrequired.mmtf') -MMTF_NOCRYST = str(data_ref / "6QYR.mmtf.gz") +MMTF = str(_data_ref / '173D.mmtf') +MMTF_gz = str(_data_ref / '5KIH.mmtf.gz') +MMTF_skinny = str(_data_ref / '1ubq-less-optional.mmtf') +MMTF_skinny2 = str(_data_ref / '3NJW-onlyrequired.mmtf') +MMTF_NOCRYST = str(_data_ref / "6QYR.mmtf.gz") -ALIGN_BOUND = str(data_ref / 'analysis/align_bound.pdb.gz') -ALIGN_UNBOUND = str(data_ref / 'analysis/align_unbound.pdb.gz') +ALIGN_BOUND = str(_data_ref / 'analysis/align_bound.pdb.gz') +ALIGN_UNBOUND = str(_data_ref / 'analysis/align_unbound.pdb.gz') -GSD = str(data_ref / 'example.gsd') -GSD_bonds = str(data_ref / 'example_bonds.gsd') -GSD_long = str(data_ref / 'example_longer.gsd') +GSD = str(_data_ref / 'example.gsd') +GSD_bonds = str(_data_ref / 'example_bonds.gsd') +GSD_long = str(_data_ref / 'example_longer.gsd') -DihedralArray = str(data_ref / 'adk_oplsaa_dihedral.npy') -DihedralsArray = str(data_ref / 'adk_oplsaa_dihedral_list.npy') -RamaArray = str(data_ref / 'adk_oplsaa_rama.npy') -GLYRamaArray = str(data_ref / 'adk_oplsaa_GLY_rama.npy') -JaninArray = str(data_ref / 'adk_oplsaa_janin.npy') -LYSJaninArray = str(data_ref / 'adk_oplsaa_LYS_janin.npy') -PDB_rama = str(data_ref / '19hc.pdb.gz') -PDB_janin = str(data_ref / '1a28.pdb.gz') +DihedralArray = str(_data_ref / 'adk_oplsaa_dihedral.npy') +DihedralsArray = str(_data_ref / 'adk_oplsaa_dihedral_list.npy') +RamaArray = str(_data_ref / 'adk_oplsaa_rama.npy') +GLYRamaArray = str(_data_ref / 'adk_oplsaa_GLY_rama.npy') +JaninArray = str(_data_ref / 'adk_oplsaa_janin.npy') +LYSJaninArray = str(_data_ref / 'adk_oplsaa_LYS_janin.npy') +PDB_rama = str(_data_ref / '19hc.pdb.gz') +PDB_janin = str(_data_ref / '1a28.pdb.gz') -BATArray = str(data_ref / 'mol2_comments_header_bat.npy') +BATArray = str(_data_ref / 'mol2_comments_header_bat.npy') -ITP = str(data_ref / 'gromacs_ala10.itp') -ITP_nomass = str(data_ref / 'itp_nomass.itp') -ITP_atomtypes = str(data_ref / 'atomtypes.itp') -ITP_charges = str(data_ref / 'atomtypes_charge.itp') -ITP_edited = str(data_ref / 'edited_itp.itp') -ITP_tip5p = str(data_ref / "tip5p.itp") -ITP_spce = str(data_ref / 'spce.itp') +ITP = str(_data_ref / 'gromacs_ala10.itp') +ITP_nomass = str(_data_ref / 'itp_nomass.itp') +ITP_atomtypes = str(_data_ref / 'atomtypes.itp') +ITP_charges = str(_data_ref / 'atomtypes_charge.itp') +ITP_edited = str(_data_ref / 'edited_itp.itp') +ITP_tip5p = str(_data_ref / "tip5p.itp") +ITP_spce = str(_data_ref / 'spce.itp') -GMX_TOP = str(data_ref / 'gromacs_ala10.top') -GMX_DIR = str(data_ref / 'gromacs/') -GMX_TOP_BAD = str(data_ref / 'bad_top.top') -ITP_no_endif = str(data_ref / 'no_endif_spc.itp') +GMX_TOP = str(_data_ref / 'gromacs_ala10.top') +GMX_DIR = str(_data_ref / 'gromacs/') +GMX_TOP_BAD = str(_data_ref / 'bad_top.top') +ITP_no_endif = str(_data_ref / 'no_endif_spc.itp') -NAMDBIN = str(data_ref / 'adk_open.coor') +NAMDBIN = str(_data_ref / 'adk_open.coor') -SDF_molecule = str(data_ref / 'molecule.sdf') +SDF_molecule = str(_data_ref / 'molecule.sdf') -PDB_elements = str(data_ref / 'elements.pdb') -PDB_charges = str(data_ref / 'charges.pdb') +PDB_elements = str(_data_ref / 'elements.pdb') +PDB_charges = str(_data_ref / 'charges.pdb') -PDBX = str(data_ref / "4x8u.pdbx") +PDBX = str(_data_ref / "4x8u.pdbx") -SURFACE_PDB = str(data_ref / 'surface.pdb.bz2') -SURFACE_TRR = str(data_ref / 'surface.trr') +SURFACE_PDB = str(_data_ref / 'surface.pdb.bz2') +SURFACE_TRR = str(_data_ref / 'surface.trr') # This should be the last line: clean up namespace diff --git a/testsuite/MDAnalysisTests/utils/test_datafiles.py b/testsuite/MDAnalysisTests/utils/test_datafiles.py index 110928f4645..7f2f1ec2e9f 100644 --- a/testsuite/MDAnalysisTests/utils/test_datafiles.py +++ b/testsuite/MDAnalysisTests/utils/test_datafiles.py @@ -49,7 +49,7 @@ def test_all_exports(): import MDAnalysisTests.datafiles missing = [name for name in dir(MDAnalysisTests.datafiles) if - not name.startswith('_') and name not in MDAnalysisTests.datafiles.__all__ and name != 'absolute_import'] + not name.startswith('_') and name not in MDAnalysisTests.datafiles.__all__ and name != 'MDAnalysisTests'] assert_equal(missing, [], err_msg="Variables need to be added to __all__.") From 04e2cc6bd0474be50e9d4fdc7427aec59a18a773 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Wed, 24 May 2023 07:23:27 +0100 Subject: [PATCH 6/8] fix cpptraj_traj.prmtop path --- testsuite/MDAnalysisTests/datafiles.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/testsuite/MDAnalysisTests/datafiles.py b/testsuite/MDAnalysisTests/datafiles.py index 28c5f09477a..eed5424d6d9 100644 --- a/testsuite/MDAnalysisTests/datafiles.py +++ b/testsuite/MDAnalysisTests/datafiles.py @@ -420,8 +420,8 @@ PFncdf_Top = str(_data_ref / 'Amber/posfor.top') PFncdf_Trj = str(_data_ref / 'Amber/posfor.ncdf') -CPPTRAJ_TRAJ_TOP = str(_data_ref / 'data/Amber/cpptraj_traj.prmtop') -CPPTRAJ_TRAJ = str(_data_ref / 'data/Amber/cpptraj_traj.nc') +CPPTRAJ_TRAJ_TOP = str(_data_ref / 'Amber/cpptraj_traj.prmtop') +CPPTRAJ_TRAJ = str(_data_ref / 'Amber/cpptraj_traj.nc') PRMpbc = str(_data_ref / 'Amber/capped-ala.prmtop') TRJpbc_bz2 = str(_data_ref / 'Amber/capped-ala.mdcrd.bz2') From 752e366583f1a7029cdb50141371c93b3f83c194 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Wed, 24 May 2023 07:55:58 +0100 Subject: [PATCH 7/8] try using as_posix() --- azure-pipelines.yml | 2 +- testsuite/MDAnalysisTests/datafiles.py | 660 ++++++++++++------------- 2 files changed, 331 insertions(+), 331 deletions(-) diff --git a/azure-pipelines.yml b/azure-pipelines.yml index a17f58052e6..a640136abcd 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -114,7 +114,7 @@ jobs: - script: >- python -m pip install biopython - chemfiles>=0.10 + chemfiles>=0.10,<0.10.4 duecredit gsd joblib diff --git a/testsuite/MDAnalysisTests/datafiles.py b/testsuite/MDAnalysisTests/datafiles.py index eed5424d6d9..6d070581882 100644 --- a/testsuite/MDAnalysisTests/datafiles.py +++ b/testsuite/MDAnalysisTests/datafiles.py @@ -236,382 +236,382 @@ _data_ref = resources.files('MDAnalysisTests.data') -WIN_PDB_multiframe = str(_data_ref / 'windows/WIN_nmr_neopetrosiamide.pdb') -WIN_DLP_HISTORY = str(_data_ref / 'windows/WIN_HISTORY') -WIN_TRJ = str(_data_ref / 'windows/WIN_ache.mdcrd') -WIN_ARC = str(_data_ref / 'windows/WIN_test.arc') -WIN_LAMMPSDUMP = str(_data_ref / 'windows/WIN_wat.lammpstrj') - -legacy_DCD_NAMD_coords = str(_data_ref / 'legacy_DCD_NAMD_coords.npy') -legacy_DCD_ADK_coords = str(_data_ref / 'legacy_DCD_adk_coords.npy') -legacy_DCD_c36_coords = str(_data_ref / 'legacy_DCD_c36_coords.npy') -AUX_XVG_LOWF = str(_data_ref / 'test_lowf.xvg') -AUX_XVG_HIGHF = str(_data_ref / 'test_highf.xvg') -XVG_BAD_NCOL = str(_data_ref / 'bad_num_col.xvg') -AUX_XVG = str(_data_ref / 'test.xvg') -AUX_EDR = str(_data_ref / 'test.edr') -AUX_EDR_RAW = str(_data_ref / 'aux_edr_raw.txt') -AUX_EDR_TPR = str(_data_ref / 'aux_edr.tpr') -AUX_EDR_XTC = str(_data_ref / 'aux_edr.xtc') -AUX_EDR_SINGLE_FRAME = str(_data_ref / 'single_frame.edr') -ENT = str(_data_ref / 'testENT.ent') -GRO_missing_atomname = str(_data_ref / 'missing_atomname.gro') -GRO_empty_atom = str(_data_ref / 'empty_atom.gro') -GRO_huge_box = str(_data_ref / 'huge_box.gro') - -COORDINATES_GRO = str(_data_ref / 'coordinates/test.gro') -COORDINATES_GRO_INCOMPLETE_VELOCITY = str(_data_ref / 'coordinates/test_incomplete_vel.gro') -COORDINATES_GRO_BZ2 = str(_data_ref / 'coordinates/test.gro.bz2') -COORDINATES_XYZ = str(_data_ref / 'coordinates/test.xyz') -COORDINATES_XYZ_BZ2 = str(_data_ref / 'coordinates/test.xyz.bz2') -COORDINATES_XTC = str(_data_ref / 'coordinates/test.xtc') -COORDINATES_TRR = str(_data_ref / 'coordinates/test.trr') -COORDINATES_TNG = str(_data_ref / 'coordinates/test.tng') -COORDINATES_H5MD = str(_data_ref / 'coordinates/test.h5md') -COORDINATES_DCD = str(_data_ref / 'coordinates/test.dcd') -COORDINATES_TOPOLOGY = str(_data_ref / 'coordinates/test_topology.pdb') - -PSF = str(_data_ref / 'adk.psf') -PSF_notop = str(_data_ref / 'adk_notop.psf') -PSF_BAD = str(_data_ref / 'adk_notop_BAD.psf') -DCD = str(_data_ref / 'adk_dims.dcd') -DCD_empty = str(_data_ref / 'empty.dcd') -CRD = str(_data_ref / 'adk_open.crd') -PSF_TRICLINIC = str(_data_ref / 'tip125_tric_C36.psf') -DCD_TRICLINIC = str(_data_ref / 'tip125_tric_C36.dcd') -DCD2 = str(_data_ref / 'adk_dims2.dcd') - -PSF_NAMD = str(_data_ref / 'namd_cgenff.psf') -PDB_NAMD = str(_data_ref / 'namd_cgenff.pdb') -PDB_multipole = str(_data_ref / 'water_methane_acetic-acid_ammonia.pdb') -PSF_NAMD_TRICLINIC = str(_data_ref / 'SiN_tric_namd.psf') -DCD_NAMD_TRICLINIC = str(_data_ref / 'SiN_tric_namd.dcd') -PSF_NAMD_GBIS = str(_data_ref / 'adk_closed_NAMD.psf') -DCD_NAMD_GBIS = str(_data_ref / 'adk_gbis_tmd-fast1_NAMD.dcd') - -PSF_nosegid = str(_data_ref / 'nosegid.psf') - -PSF_cmap = str(_data_ref / 'parmed_ala3.psf') - -PDB_small = str(_data_ref / 'adk_open.pdb') -PDB_closed = str(_data_ref / 'adk_closed.pdb') - -ALIGN = str(_data_ref / 'align.pdb') -RNA_PSF = str(_data_ref / 'analysis/1k5i_c36.psf.gz') -RNA_PDB = str(_data_ref / 'analysis/1k5i_c36.pdb.gz') -INC_PDB = str(_data_ref / 'incomplete.pdb') -PDB_cm = str(_data_ref / 'cryst_then_model.pdb') -PDB_cm_gz = str(_data_ref / 'cryst_then_model.pdb.gz') -PDB_cm_bz2 = str(_data_ref / 'cryst_then_model.pdb.bz2') -PDB_mc = str(_data_ref / 'model_then_cryst.pdb') -PDB_mc_gz = str(_data_ref / 'model_then_cryst.pdb.gz') -PDB_mc_bz2 = str(_data_ref / 'model_then_cryst.pdb.bz2') -PDB_chainidnewres = str(_data_ref / 'chainIDnewres.pdb.gz') -PDB_sameresid_diffresname = str(_data_ref / 'sameresid_diffresname.pdb') -PDB_chainidrepeat = str(_data_ref / 'chainIDrepeat.pdb.gz') -PDB_multiframe = str(_data_ref / 'nmr_neopetrosiamide.pdb') -PDB_helix = str(_data_ref / 'A6PA6_alpha.pdb') -PDB_conect = str(_data_ref / 'conect_parsing.pdb') -PDB_conect2TER = str(_data_ref / 'CONECT2TER.pdb') -PDB_singleconect = str(_data_ref / 'SINGLECONECT.pdb') -PDB_icodes = str(_data_ref / '1osm.pdb.gz') -PDB_CRYOEM_BOX = str(_data_ref / '5a7u.pdb') -PDB_CHECK_RIGHTHAND_PA = str(_data_ref / '6msm.pdb.bz2') -FHIAIMS = str(_data_ref / 'fhiaims.in') - -GRO = str(_data_ref / 'adk_oplsaa.gro') -GRO_velocity = str(_data_ref / 'sample_velocity_file.gro') -GRO_incomplete_vels = str(_data_ref / 'grovels.gro') -GRO_large = str(_data_ref / 'bigbox.gro.bz2') -GRO_residwrap = str(_data_ref / 'residwrap.gro') -GRO_residwrap_0base = str(_data_ref / 'residwrap_0base.gro') -GRO_sameresid_diffresname = str(_data_ref / 'sameresid_diffresname.gro') -PDB = str(_data_ref / 'adk_oplsaa.pdb') -XTC = str(_data_ref / 'adk_oplsaa.xtc') -TRR = str(_data_ref / 'adk_oplsaa.trr') -TPR = str(_data_ref / 'adk_oplsaa.tpr') -PDB_sub_dry = str(_data_ref / 'cobrotoxin_dry_neutral_0.pdb') -TRR_sub_sol = str(_data_ref / 'cobrotoxin.trr') -XTC_sub_sol = str(_data_ref / 'cobrotoxin.xtc') -PDB_sub_sol = str(_data_ref / 'cobrotoxin.pdb') -PDB_xlserial = str(_data_ref / 'xl_serial.pdb') -GRO_MEMPROT = str(_data_ref / 'analysis/YiiP_lipids.gro.gz') -XTC_MEMPROT = str(_data_ref / 'analysis/YiiP_lipids.xtc') -XTC_multi_frame = str(_data_ref / 'xtc_test_only_10_frame_10_atoms.xtc') -TRR_multi_frame = str(_data_ref / 'trr_test_only_10_frame_10_atoms.trr') -TNG_traj = str(_data_ref / 'argon_npt_compressed.tng') -TNG_traj_gro = str(_data_ref / 'argon_npt_compressed.gro.gz') -TNG_traj_uneven_blocks = str(_data_ref / 'argon_npt_compressed_uneven.tng') -TNG_traj_vels_forces = str(_data_ref / 'argon_npt_compressed_vels_forces.tng') -PDB_xvf = str(_data_ref / 'cobrotoxin.pdb') -TPR_xvf = str(_data_ref / 'cobrotoxin.tpr') -TRR_xvf = str(_data_ref / 'cobrotoxin.trr') -H5MD_xvf = str(_data_ref / 'cobrotoxin.h5md') -XVG_BZ2 = str(_data_ref / 'cobrotoxin_protein_forces.xvg.bz2') - -XPDB_small = str(_data_ref / '5digitResid.pdb') +WIN_PDB_multiframe = (_data_ref / 'windows/WIN_nmr_neopetrosiamide.pdb').as_posix() +WIN_DLP_HISTORY = (_data_ref / 'windows/WIN_HISTORY').as_posix() +WIN_TRJ = (_data_ref / 'windows/WIN_ache.mdcrd').as_posix() +WIN_ARC = (_data_ref / 'windows/WIN_test.arc').as_posix() +WIN_LAMMPSDUMP = (_data_ref / 'windows/WIN_wat.lammpstrj').as_posix() + +legacy_DCD_NAMD_coords = (_data_ref / 'legacy_DCD_NAMD_coords.npy').as_posix() +legacy_DCD_ADK_coords = (_data_ref / 'legacy_DCD_adk_coords.npy').as_posix() +legacy_DCD_c36_coords = (_data_ref / 'legacy_DCD_c36_coords.npy').as_posix() +AUX_XVG_LOWF = (_data_ref / 'test_lowf.xvg').as_posix() +AUX_XVG_HIGHF = (_data_ref / 'test_highf.xvg').as_posix() +XVG_BAD_NCOL = (_data_ref / 'bad_num_col.xvg').as_posix() +AUX_XVG = (_data_ref / 'test.xvg').as_posix() +AUX_EDR = (_data_ref / 'test.edr').as_posix() +AUX_EDR_RAW = (_data_ref / 'aux_edr_raw.txt').as_posix() +AUX_EDR_TPR = (_data_ref / 'aux_edr.tpr').as_posix() +AUX_EDR_XTC = (_data_ref / 'aux_edr.xtc').as_posix() +AUX_EDR_SINGLE_FRAME = (_data_ref / 'single_frame.edr').as_posix() +ENT = (_data_ref / 'testENT.ent').as_posix() +GRO_missing_atomname = (_data_ref / 'missing_atomname.gro').as_posix() +GRO_empty_atom = (_data_ref / 'empty_atom.gro').as_posix() +GRO_huge_box = (_data_ref / 'huge_box.gro').as_posix() + +COORDINATES_GRO = (_data_ref / 'coordinates/test.gro').as_posix() +COORDINATES_GRO_INCOMPLETE_VELOCITY = (_data_ref / 'coordinates/test_incomplete_vel.gro').as_posix() +COORDINATES_GRO_BZ2 = (_data_ref / 'coordinates/test.gro.bz2').as_posix() +COORDINATES_XYZ = (_data_ref / 'coordinates/test.xyz').as_posix() +COORDINATES_XYZ_BZ2 = (_data_ref / 'coordinates/test.xyz.bz2').as_posix() +COORDINATES_XTC = (_data_ref / 'coordinates/test.xtc').as_posix() +COORDINATES_TRR = (_data_ref / 'coordinates/test.trr').as_posix() +COORDINATES_TNG = (_data_ref / 'coordinates/test.tng').as_posix() +COORDINATES_H5MD = (_data_ref / 'coordinates/test.h5md').as_posix() +COORDINATES_DCD = (_data_ref / 'coordinates/test.dcd').as_posix() +COORDINATES_TOPOLOGY = (_data_ref / 'coordinates/test_topology.pdb').as_posix() + +PSF = (_data_ref / 'adk.psf').as_posix() +PSF_notop = (_data_ref / 'adk_notop.psf').as_posix() +PSF_BAD = (_data_ref / 'adk_notop_BAD.psf').as_posix() +DCD = (_data_ref / 'adk_dims.dcd').as_posix() +DCD_empty = (_data_ref / 'empty.dcd').as_posix() +CRD = (_data_ref / 'adk_open.crd').as_posix() +PSF_TRICLINIC = (_data_ref / 'tip125_tric_C36.psf').as_posix() +DCD_TRICLINIC = (_data_ref / 'tip125_tric_C36.dcd').as_posix() +DCD2 = (_data_ref / 'adk_dims2.dcd').as_posix() + +PSF_NAMD = (_data_ref / 'namd_cgenff.psf').as_posix() +PDB_NAMD = (_data_ref / 'namd_cgenff.pdb').as_posix() +PDB_multipole = (_data_ref / 'water_methane_acetic-acid_ammonia.pdb').as_posix() +PSF_NAMD_TRICLINIC = (_data_ref / 'SiN_tric_namd.psf').as_posix() +DCD_NAMD_TRICLINIC = (_data_ref / 'SiN_tric_namd.dcd').as_posix() +PSF_NAMD_GBIS = (_data_ref / 'adk_closed_NAMD.psf').as_posix() +DCD_NAMD_GBIS = (_data_ref / 'adk_gbis_tmd-fast1_NAMD.dcd').as_posix() + +PSF_nosegid = (_data_ref / 'nosegid.psf').as_posix() + +PSF_cmap = (_data_ref / 'parmed_ala3.psf').as_posix() + +PDB_small = (_data_ref / 'adk_open.pdb').as_posix() +PDB_closed = (_data_ref / 'adk_closed.pdb').as_posix() + +ALIGN = (_data_ref / 'align.pdb').as_posix() +RNA_PSF = (_data_ref / 'analysis/1k5i_c36.psf.gz').as_posix() +RNA_PDB = (_data_ref / 'analysis/1k5i_c36.pdb.gz').as_posix() +INC_PDB = (_data_ref / 'incomplete.pdb').as_posix() +PDB_cm = (_data_ref / 'cryst_then_model.pdb').as_posix() +PDB_cm_gz = (_data_ref / 'cryst_then_model.pdb.gz').as_posix() +PDB_cm_bz2 = (_data_ref / 'cryst_then_model.pdb.bz2').as_posix() +PDB_mc = (_data_ref / 'model_then_cryst.pdb').as_posix() +PDB_mc_gz = (_data_ref / 'model_then_cryst.pdb.gz').as_posix() +PDB_mc_bz2 = (_data_ref / 'model_then_cryst.pdb.bz2').as_posix() +PDB_chainidnewres = (_data_ref / 'chainIDnewres.pdb.gz').as_posix() +PDB_sameresid_diffresname = (_data_ref / 'sameresid_diffresname.pdb').as_posix() +PDB_chainidrepeat = (_data_ref / 'chainIDrepeat.pdb.gz').as_posix() +PDB_multiframe = (_data_ref / 'nmr_neopetrosiamide.pdb').as_posix() +PDB_helix = (_data_ref / 'A6PA6_alpha.pdb').as_posix() +PDB_conect = (_data_ref / 'conect_parsing.pdb').as_posix() +PDB_conect2TER = (_data_ref / 'CONECT2TER.pdb').as_posix() +PDB_singleconect = (_data_ref / 'SINGLECONECT.pdb').as_posix() +PDB_icodes = (_data_ref / '1osm.pdb.gz').as_posix() +PDB_CRYOEM_BOX = (_data_ref / '5a7u.pdb').as_posix() +PDB_CHECK_RIGHTHAND_PA = (_data_ref / '6msm.pdb.bz2').as_posix() +FHIAIMS = (_data_ref / 'fhiaims.in').as_posix() + +GRO = (_data_ref / 'adk_oplsaa.gro').as_posix() +GRO_velocity = (_data_ref / 'sample_velocity_file.gro').as_posix() +GRO_incomplete_vels = (_data_ref / 'grovels.gro').as_posix() +GRO_large = (_data_ref / 'bigbox.gro.bz2').as_posix() +GRO_residwrap = (_data_ref / 'residwrap.gro').as_posix() +GRO_residwrap_0base = (_data_ref / 'residwrap_0base.gro').as_posix() +GRO_sameresid_diffresname = (_data_ref / 'sameresid_diffresname.gro').as_posix() +PDB = (_data_ref / 'adk_oplsaa.pdb').as_posix() +XTC = (_data_ref / 'adk_oplsaa.xtc').as_posix() +TRR = (_data_ref / 'adk_oplsaa.trr').as_posix() +TPR = (_data_ref / 'adk_oplsaa.tpr').as_posix() +PDB_sub_dry = (_data_ref / 'cobrotoxin_dry_neutral_0.pdb').as_posix() +TRR_sub_sol = (_data_ref / 'cobrotoxin.trr').as_posix() +XTC_sub_sol = (_data_ref / 'cobrotoxin.xtc').as_posix() +PDB_sub_sol = (_data_ref / 'cobrotoxin.pdb').as_posix() +PDB_xlserial = (_data_ref / 'xl_serial.pdb').as_posix() +GRO_MEMPROT = (_data_ref / 'analysis/YiiP_lipids.gro.gz').as_posix() +XTC_MEMPROT = (_data_ref / 'analysis/YiiP_lipids.xtc').as_posix() +XTC_multi_frame = (_data_ref / 'xtc_test_only_10_frame_10_atoms.xtc').as_posix() +TRR_multi_frame = (_data_ref / 'trr_test_only_10_frame_10_atoms.trr').as_posix() +TNG_traj = (_data_ref / 'argon_npt_compressed.tng').as_posix() +TNG_traj_gro = (_data_ref / 'argon_npt_compressed.gro.gz').as_posix() +TNG_traj_uneven_blocks = (_data_ref / 'argon_npt_compressed_uneven.tng').as_posix() +TNG_traj_vels_forces = (_data_ref / 'argon_npt_compressed_vels_forces.tng').as_posix() +PDB_xvf = (_data_ref / 'cobrotoxin.pdb').as_posix() +TPR_xvf = (_data_ref / 'cobrotoxin.tpr').as_posix() +TRR_xvf = (_data_ref / 'cobrotoxin.trr').as_posix() +H5MD_xvf = (_data_ref / 'cobrotoxin.h5md').as_posix() +XVG_BZ2 = (_data_ref / 'cobrotoxin_protein_forces.xvg.bz2').as_posix() + +XPDB_small = (_data_ref / '5digitResid.pdb').as_posix() # number is the gromacs version -TPR400 = str(_data_ref / 'tprs/2lyz_gmx_4.0.tpr') -TPR402 = str(_data_ref / 'tprs/2lyz_gmx_4.0.2.tpr') -TPR403 = str(_data_ref / 'tprs/2lyz_gmx_4.0.3.tpr') -TPR404 = str(_data_ref / 'tprs/2lyz_gmx_4.0.4.tpr') -TPR405 = str(_data_ref / 'tprs/2lyz_gmx_4.0.5.tpr') -TPR406 = str(_data_ref / 'tprs/2lyz_gmx_4.0.6.tpr') -TPR407 = str(_data_ref / 'tprs/2lyz_gmx_4.0.7.tpr') -TPR450 = str(_data_ref / 'tprs/2lyz_gmx_4.5.tpr') -TPR451 = str(_data_ref / 'tprs/2lyz_gmx_4.5.1.tpr') -TPR452 = str(_data_ref / 'tprs/2lyz_gmx_4.5.2.tpr') -TPR453 = str(_data_ref / 'tprs/2lyz_gmx_4.5.3.tpr') -TPR454 = str(_data_ref / 'tprs/2lyz_gmx_4.5.4.tpr') -TPR455 = str(_data_ref / 'tprs/2lyz_gmx_4.5.5.tpr') -TPR502 = str(_data_ref / 'tprs/2lyz_gmx_5.0.2.tpr') -TPR504 = str(_data_ref / 'tprs/2lyz_gmx_5.0.4.tpr') -TPR505 = str(_data_ref / 'tprs/2lyz_gmx_5.0.5.tpr') -TPR510 = str(_data_ref / 'tprs/2lyz_gmx_5.1.tpr') -TPR2016 = str(_data_ref / 'tprs/2lyz_gmx_2016.tpr') -TPR2018 = str(_data_ref / 'tprs/2lyz_gmx_2018.tpr') -TPR2019B3 = str(_data_ref / 'tprs/2lyz_gmx_2019-beta3.tpr') -TPR2020B2 = str(_data_ref / 'tprs/2lyz_gmx_2020-beta2.tpr') -TPR2020 = str(_data_ref / 'tprs/2lyz_gmx_2020.tpr') -TPR2021 = str(_data_ref / 'tprs/2lyz_gmx_2021.tpr') -TPR2022RC1 = str(_data_ref / 'tprs/2lyz_gmx_2022-rc1.tpr') -TPR2023 = str(_data_ref / 'tprs/2lyz_gmx_2023.tpr') +TPR400 = (_data_ref / 'tprs/2lyz_gmx_4.0.tpr').as_posix() +TPR402 = (_data_ref / 'tprs/2lyz_gmx_4.0.2.tpr').as_posix() +TPR403 = (_data_ref / 'tprs/2lyz_gmx_4.0.3.tpr').as_posix() +TPR404 = (_data_ref / 'tprs/2lyz_gmx_4.0.4.tpr').as_posix() +TPR405 = (_data_ref / 'tprs/2lyz_gmx_4.0.5.tpr').as_posix() +TPR406 = (_data_ref / 'tprs/2lyz_gmx_4.0.6.tpr').as_posix() +TPR407 = (_data_ref / 'tprs/2lyz_gmx_4.0.7.tpr').as_posix() +TPR450 = (_data_ref / 'tprs/2lyz_gmx_4.5.tpr').as_posix() +TPR451 = (_data_ref / 'tprs/2lyz_gmx_4.5.1.tpr').as_posix() +TPR452 = (_data_ref / 'tprs/2lyz_gmx_4.5.2.tpr').as_posix() +TPR453 = (_data_ref / 'tprs/2lyz_gmx_4.5.3.tpr').as_posix() +TPR454 = (_data_ref / 'tprs/2lyz_gmx_4.5.4.tpr').as_posix() +TPR455 = (_data_ref / 'tprs/2lyz_gmx_4.5.5.tpr').as_posix() +TPR502 = (_data_ref / 'tprs/2lyz_gmx_5.0.2.tpr').as_posix() +TPR504 = (_data_ref / 'tprs/2lyz_gmx_5.0.4.tpr').as_posix() +TPR505 = (_data_ref / 'tprs/2lyz_gmx_5.0.5.tpr').as_posix() +TPR510 = (_data_ref / 'tprs/2lyz_gmx_5.1.tpr').as_posix() +TPR2016 = (_data_ref / 'tprs/2lyz_gmx_2016.tpr').as_posix() +TPR2018 = (_data_ref / 'tprs/2lyz_gmx_2018.tpr').as_posix() +TPR2019B3 = (_data_ref / 'tprs/2lyz_gmx_2019-beta3.tpr').as_posix() +TPR2020B2 = (_data_ref / 'tprs/2lyz_gmx_2020-beta2.tpr').as_posix() +TPR2020 = (_data_ref / 'tprs/2lyz_gmx_2020.tpr').as_posix() +TPR2021 = (_data_ref / 'tprs/2lyz_gmx_2021.tpr').as_posix() +TPR2022RC1 = (_data_ref / 'tprs/2lyz_gmx_2022-rc1.tpr').as_posix() +TPR2023 = (_data_ref / 'tprs/2lyz_gmx_2023.tpr').as_posix() # double precision -TPR455Double = str(_data_ref / 'tprs/drew_gmx_4.5.5.double.tpr') -TPR460 = str(_data_ref / 'tprs/ab42_gmx_4.6.tpr') -TPR461 = str(_data_ref / 'tprs/ab42_gmx_4.6.1.tpr') -TPR2020Double = str(_data_ref / 'tprs/2lyz_gmx_2020_double.tpr') -TPR2021Double = str(_data_ref / 'tprs/2lyz_gmx_2021_double.tpr') +TPR455Double = (_data_ref / 'tprs/drew_gmx_4.5.5.double.tpr').as_posix() +TPR460 = (_data_ref / 'tprs/ab42_gmx_4.6.tpr').as_posix() +TPR461 = (_data_ref / 'tprs/ab42_gmx_4.6.1.tpr').as_posix() +TPR2020Double = (_data_ref / 'tprs/2lyz_gmx_2020_double.tpr').as_posix() +TPR2021Double = (_data_ref / 'tprs/2lyz_gmx_2021_double.tpr').as_posix() # all bonded interactions -TPR334_bonded = str(_data_ref / 'tprs/all_bonded/dummy_3.3.4.tpr') -TPR510_bonded = str(_data_ref / 'tprs/all_bonded/dummy_5.1.tpr') -TPR2016_bonded = str(_data_ref / 'tprs/all_bonded/dummy_2016.tpr') -TPR2018_bonded = str(_data_ref / 'tprs/all_bonded/dummy_2018.tpr') -TPR2019B3_bonded = str(_data_ref / 'tprs/all_bonded/dummy_2019-beta3.tpr') -TPR2020B2_bonded = str(_data_ref / 'tprs/all_bonded/dummy_2020-beta2.tpr') -TPR2020_bonded = str(_data_ref / 'tprs/all_bonded/dummy_2020.tpr') -TPR2020_double_bonded = str(_data_ref / 'tprs/all_bonded/dummy_2020_double.tpr') -TPR2021_bonded = str(_data_ref / 'tprs/all_bonded/dummy_2021.tpr') -TPR2021_double_bonded = str(_data_ref / 'tprs/all_bonded/dummy_2021_double.tpr') -TPR2022RC1_bonded = str(_data_ref / 'tprs/all_bonded/dummy_2022-rc1.tpr') -TPR2023_bonded = str(_data_ref / 'tprs/all_bonded/dummy_2023.tpr') +TPR334_bonded = (_data_ref / 'tprs/all_bonded/dummy_3.3.4.tpr').as_posix() +TPR510_bonded = (_data_ref / 'tprs/all_bonded/dummy_5.1.tpr').as_posix() +TPR2016_bonded = (_data_ref / 'tprs/all_bonded/dummy_2016.tpr').as_posix() +TPR2018_bonded = (_data_ref / 'tprs/all_bonded/dummy_2018.tpr').as_posix() +TPR2019B3_bonded = (_data_ref / 'tprs/all_bonded/dummy_2019-beta3.tpr').as_posix() +TPR2020B2_bonded = (_data_ref / 'tprs/all_bonded/dummy_2020-beta2.tpr').as_posix() +TPR2020_bonded = (_data_ref / 'tprs/all_bonded/dummy_2020.tpr').as_posix() +TPR2020_double_bonded = (_data_ref / 'tprs/all_bonded/dummy_2020_double.tpr').as_posix() +TPR2021_bonded = (_data_ref / 'tprs/all_bonded/dummy_2021.tpr').as_posix() +TPR2021_double_bonded = (_data_ref / 'tprs/all_bonded/dummy_2021_double.tpr').as_posix() +TPR2022RC1_bonded = (_data_ref / 'tprs/all_bonded/dummy_2022-rc1.tpr').as_posix() +TPR2023_bonded = (_data_ref / 'tprs/all_bonded/dummy_2023.tpr').as_posix() # all interactions -TPR_EXTRA_2023 = str(_data_ref / 'tprs/virtual_sites/extra-interactions-2023.tpr') -TPR_EXTRA_2022RC1 = str(_data_ref / 'tprs/virtual_sites/extra-interactions-2022-rc1.tpr') -TPR_EXTRA_2021 = str(_data_ref / 'tprs/virtual_sites/extra-interactions-2021.tpr') -TPR_EXTRA_2020 = str(_data_ref / 'tprs/virtual_sites/extra-interactions-2020.tpr') -TPR_EXTRA_2018 = str(_data_ref / 'tprs/virtual_sites/extra-interactions-2018.tpr') -TPR_EXTRA_2016 = str(_data_ref / 'tprs/virtual_sites/extra-interactions-2016.3.tpr') -TPR_EXTRA_407 = str(_data_ref / 'tprs/virtual_sites/extra-interactions-4.0.7.tpr') +TPR_EXTRA_2023 = (_data_ref / 'tprs/virtual_sites/extra-interactions-2023.tpr').as_posix() +TPR_EXTRA_2022RC1 = (_data_ref / 'tprs/virtual_sites/extra-interactions-2022-rc1.tpr').as_posix() +TPR_EXTRA_2021 = (_data_ref / 'tprs/virtual_sites/extra-interactions-2021.tpr').as_posix() +TPR_EXTRA_2020 = (_data_ref / 'tprs/virtual_sites/extra-interactions-2020.tpr').as_posix() +TPR_EXTRA_2018 = (_data_ref / 'tprs/virtual_sites/extra-interactions-2018.tpr').as_posix() +TPR_EXTRA_2016 = (_data_ref / 'tprs/virtual_sites/extra-interactions-2016.3.tpr').as_posix() +TPR_EXTRA_407 = (_data_ref / 'tprs/virtual_sites/extra-interactions-4.0.7.tpr').as_posix() -XYZ_psf = str(_data_ref / '2r9r-1b.psf') -XYZ_bz2 = str(_data_ref / '2r9r-1b.xyz.bz2') -XYZ = str(_data_ref / '2r9r-1b.xyz') -XYZ_mini = str(_data_ref / 'mini.xyz') -XYZ_five = str(_data_ref / 'five.xyz') -TXYZ = str(_data_ref / 'coordinates/test.txyz') -ARC = str(_data_ref / 'coordinates/test.arc') -ARC_PBC = str(_data_ref / 'coordinates/new_hexane.arc') +XYZ_psf = (_data_ref / '2r9r-1b.psf').as_posix() +XYZ_bz2 = (_data_ref / '2r9r-1b.xyz.bz2').as_posix() +XYZ = (_data_ref / '2r9r-1b.xyz').as_posix() +XYZ_mini = (_data_ref / 'mini.xyz').as_posix() +XYZ_five = (_data_ref / 'five.xyz').as_posix() +TXYZ = (_data_ref / 'coordinates/test.txyz').as_posix() +ARC = (_data_ref / 'coordinates/test.arc').as_posix() +ARC_PBC = (_data_ref / 'coordinates/new_hexane.arc').as_posix() -PRM = str(_data_ref / 'Amber/ache.prmtop') -TRJ = str(_data_ref / 'Amber/ache.mdcrd') -INPCRD = str(_data_ref / 'Amber/test.inpcrd') -TRJ_bz2 = str(_data_ref / 'Amber/ache.mdcrd.bz2') -PFncdf_Top = str(_data_ref / 'Amber/posfor.top') -PFncdf_Trj = str(_data_ref / 'Amber/posfor.ncdf') +PRM = (_data_ref / 'Amber/ache.prmtop').as_posix() +TRJ = (_data_ref / 'Amber/ache.mdcrd').as_posix() +INPCRD = (_data_ref / 'Amber/test.inpcrd').as_posix() +TRJ_bz2 = (_data_ref / 'Amber/ache.mdcrd.bz2').as_posix() +PFncdf_Top = (_data_ref / 'Amber/posfor.top').as_posix() +PFncdf_Trj = (_data_ref / 'Amber/posfor.ncdf').as_posix() -CPPTRAJ_TRAJ_TOP = str(_data_ref / 'Amber/cpptraj_traj.prmtop') -CPPTRAJ_TRAJ = str(_data_ref / 'Amber/cpptraj_traj.nc') +CPPTRAJ_TRAJ_TOP = (_data_ref / 'Amber/cpptraj_traj.prmtop').as_posix() +CPPTRAJ_TRAJ = (_data_ref / 'Amber/cpptraj_traj.nc').as_posix() -PRMpbc = str(_data_ref / 'Amber/capped-ala.prmtop') -TRJpbc_bz2 = str(_data_ref / 'Amber/capped-ala.mdcrd.bz2') +PRMpbc = (_data_ref / 'Amber/capped-ala.prmtop').as_posix() +TRJpbc_bz2 = (_data_ref / 'Amber/capped-ala.mdcrd.bz2').as_posix() -PRMncdf = str(_data_ref / 'Amber/bala.prmtop') -TRJncdf = str(_data_ref / 'Amber/bala.trj') -NCDF = str(_data_ref / 'Amber/bala.ncdf') +PRMncdf = (_data_ref / 'Amber/bala.prmtop').as_posix() +TRJncdf = (_data_ref / 'Amber/bala.trj').as_posix() +NCDF = (_data_ref / 'Amber/bala.ncdf').as_posix() -PRM12 = str(_data_ref / 'Amber/anti.top') -TRJ12_bz2 = str(_data_ref / 'Amber/anti_md1.mdcrd.bz2') +PRM12 = (_data_ref / 'Amber/anti.top').as_posix() +TRJ12_bz2 = (_data_ref / 'Amber/anti_md1.mdcrd.bz2').as_posix() -PRM7 = str(_data_ref / 'Amber/tz2.truncoct.parm7.bz2') -NCDFtruncoct = str(_data_ref / 'Amber/tz2.truncoct.nc') +PRM7 = (_data_ref / 'Amber/tz2.truncoct.parm7.bz2').as_posix() +NCDFtruncoct = (_data_ref / 'Amber/tz2.truncoct.nc').as_posix() -PRMcs = str(_data_ref / 'Amber/chitosan.prmtop') +PRMcs = (_data_ref / 'Amber/chitosan.prmtop').as_posix() -PRMNCRST = str(_data_ref / 'Amber/ace_mbondi3.parm7') +PRMNCRST = (_data_ref / 'Amber/ace_mbondi3.parm7').as_posix() -PRM_NCBOX = str(_data_ref / 'Amber/ace_tip3p.parm7') -TRJ_NCBOX = str(_data_ref / 'Amber/ace_tip3p.nc') +PRM_NCBOX = (_data_ref / 'Amber/ace_tip3p.parm7').as_posix() +TRJ_NCBOX = (_data_ref / 'Amber/ace_tip3p.nc').as_posix() -PRMNEGATIVE = str(_data_ref / 'Amber/ace_mbondi3.negative.parm7') +PRMNEGATIVE = (_data_ref / 'Amber/ace_mbondi3.negative.parm7').as_posix() -PRMErr1 = str(_data_ref / 'Amber/ace_mbondi3.error1.parm7') -PRMErr2 = str(_data_ref / 'Amber/ace_mbondi3.error2.parm7') -PRMErr3 = str(_data_ref / 'Amber/ace_mbondi3.error3.parm7') +PRMErr1 = (_data_ref / 'Amber/ace_mbondi3.error1.parm7').as_posix() +PRMErr2 = (_data_ref / 'Amber/ace_mbondi3.error2.parm7').as_posix() +PRMErr3 = (_data_ref / 'Amber/ace_mbondi3.error3.parm7').as_posix() -PRM_UreyBradley = str(_data_ref / 'Amber/parmed_fad.prmtop') -PRM7_ala2 = str(_data_ref / 'Amber/parmed_ala2_solv.parm7') -RST7_ala2 = str(_data_ref / 'Amber/parmed_ala2_solv.rst7') +PRM_UreyBradley = (_data_ref / 'Amber/parmed_fad.prmtop').as_posix() +PRM7_ala2 = (_data_ref / 'Amber/parmed_ala2_solv.parm7').as_posix() +RST7_ala2 = (_data_ref / 'Amber/parmed_ala2_solv.rst7').as_posix() -PRM19SBOPC = str(_data_ref / 'Amber/ala.ff19SB.OPC.parm7.bz2') +PRM19SBOPC = (_data_ref / 'Amber/ala.ff19SB.OPC.parm7.bz2').as_posix() -PQR = str(_data_ref / 'adk_open.pqr') -PQR_icodes = str(_data_ref / '1A2C.pqr') +PQR = (_data_ref / 'adk_open.pqr').as_posix() +PQR_icodes = (_data_ref / '1A2C.pqr').as_posix() -PDBQT_input = str(_data_ref / 'pdbqt_inputpdbqt.pdbqt') -PDBQT_querypdb = str(_data_ref / 'pdbqt_querypdb.pdb') +PDBQT_input = (_data_ref / 'pdbqt_inputpdbqt.pdbqt').as_posix() +PDBQT_querypdb = (_data_ref / 'pdbqt_querypdb.pdb').as_posix() -FASTA = str(_data_ref / 'test.fasta') -HELANAL_BENDING_MATRIX = str(_data_ref / 'helanal_bending_matrix_AdK_DIMS_H8.dat') -HELANAL_BENDING_MATRIX_SUBSET = str(_data_ref / 'helanal_bending_matrix_AdK_DIMS_H8_frames10to79.dat') +FASTA = (_data_ref / 'test.fasta').as_posix() +HELANAL_BENDING_MATRIX = (_data_ref / 'helanal_bending_matrix_AdK_DIMS_H8.dat').as_posix() +HELANAL_BENDING_MATRIX_SUBSET = (_data_ref / 'helanal_bending_matrix_AdK_DIMS_H8_frames10to79.dat').as_posix() -PDB_HOLE = str(_data_ref / '1grm_single.pdb') -MULTIPDB_HOLE = str(_data_ref / '1grm_elNemo_mode7.pdb.bz2') +PDB_HOLE = (_data_ref / '1grm_single.pdb').as_posix() +MULTIPDB_HOLE = (_data_ref / '1grm_elNemo_mode7.pdb.bz2').as_posix() -DMS = str(_data_ref / 'adk_closed.dms') -DMS_DOMAINS = str(_data_ref / 'adk_closed_domains.dms') -DMS_NO_SEGID = str(_data_ref / 'adk_closed_no_segid.dms') +DMS = (_data_ref / 'adk_closed.dms').as_posix() +DMS_DOMAINS = (_data_ref / 'adk_closed_domains.dms').as_posix() +DMS_NO_SEGID = (_data_ref / 'adk_closed_no_segid.dms').as_posix() -CONECT = str(_data_ref / '1hvr.pdb') -CONECT_ERROR = str(_data_ref / 'conect_error.pdb') +CONECT = (_data_ref / '1hvr.pdb').as_posix() +CONECT_ERROR = (_data_ref / 'conect_error.pdb').as_posix() -TRZ = str(_data_ref / 'trzfile.trz') -TRZ_psf = str(_data_ref / 'trz_psf.psf') +TRZ = (_data_ref / 'trzfile.trz').as_posix() +TRZ_psf = (_data_ref / 'trz_psf.psf').as_posix() -TRIC = str(_data_ref / 'dppc_vesicle_hg.gro') +TRIC = (_data_ref / 'dppc_vesicle_hg.gro').as_posix() -PDB_full = str(_data_ref / "4E43.pdb") +PDB_full = (_data_ref / "4E43.pdb").as_posix() -merge_protein = str(_data_ref / "merge/2zmm/protein.pdb") -merge_ligand = str(_data_ref / "merge/2zmm/ligand.pdb") -merge_water = str(_data_ref / "merge/2zmm/water.pdb") +merge_protein = (_data_ref / "merge/2zmm/protein.pdb").as_posix() +merge_ligand = (_data_ref / "merge/2zmm/ligand.pdb").as_posix() +merge_water = (_data_ref / "merge/2zmm/water.pdb").as_posix() -mol2_molecules = str(_data_ref / "mol2/Molecules.mol2") -mol2_molecule = str(_data_ref / "mol2/Molecule.mol2") -mol2_ligand = str(_data_ref / "mol2/Ligand.mol2") -mol2_broken_molecule = str(_data_ref / "mol2/BrokenMolecule.mol2") -mol2_comments_header = str(_data_ref / "mol2/Molecule_comments_header.mol2") +mol2_molecules = (_data_ref / "mol2/Molecules.mol2").as_posix() +mol2_molecule = (_data_ref / "mol2/Molecule.mol2").as_posix() +mol2_ligand = (_data_ref / "mol2/Ligand.mol2").as_posix() +mol2_broken_molecule = (_data_ref / "mol2/BrokenMolecule.mol2").as_posix() +mol2_comments_header = (_data_ref / "mol2/Molecule_comments_header.mol2").as_posix() # MOL2 file without substructure field -mol2_zinc = str(_data_ref / "mol2/zinc_856218.mol2") +mol2_zinc = (_data_ref / "mol2/zinc_856218.mol2").as_posix() # MOL2 file without bonds -mol2_sodium_ion = str(_data_ref / "mol2/sodium_ion.mol2") - -capping_input = str(_data_ref / "capping/aaqaa.gro") -capping_output = str(_data_ref / "capping/maestro_aaqaa_capped.pdb") -capping_ace = str(_data_ref / "capping/ace.pdb") -capping_nma = str(_data_ref / "capping/nma.pdb") - -contacts_villin_folded = str(_data_ref / "contacts/villin_folded.gro.bz2") -contacts_villin_unfolded = str(_data_ref / "contacts/villin_unfolded.gro.bz2") -contacts_file = str(_data_ref / "contacts/2F4K_qlist5_remap.dat") - -trz4data = str(_data_ref / "lammps/datatest.trz") -LAMMPSdata = str(_data_ref / "lammps/datatest.data") -LAMMPSdata_mini = str(_data_ref / "lammps/mini.data") -LAMMPSdata2 = str(_data_ref / "lammps/ifabp_apo_100mM.data.bz2") -LAMMPSdcd2 = str(_data_ref / "lammps/ifabp_apo_100mM.dcd") -LAMMPScnt = str(_data_ref / "lammps/cnt-hexagonal-class1.data") -LAMMPScnt2 = str(_data_ref / "lammps/cnt-hexagonal-class1.data2") -LAMMPShyd = str(_data_ref / "lammps/hydrogen-class1.data") -LAMMPShyd2 = str(_data_ref / "lammps/hydrogen-class1.data2") -LAMMPSdata_deletedatoms = str(_data_ref / 'lammps/deletedatoms.data') -LAMMPSdata_triclinic = str(_data_ref / "lammps/albite_triclinic.data") -LAMMPSdata_PairIJ = str(_data_ref / "lammps/pairij_coeffs.data.bz2") -LAMMPSDUMP = str(_data_ref / "lammps/wat.lammpstrj.bz2") -LAMMPSDUMP_long = str(_data_ref / "lammps/wat.lammpstrj_long.bz2") -LAMMPSDUMP_allcoords = str(_data_ref / "lammps/spce_all_coords.lammpstrj.bz2") -LAMMPSDUMP_nocoords = str(_data_ref / "lammps/spce_no_coords.lammpstrj.bz2") -LAMMPSDUMP_triclinic = str(_data_ref / "lammps/albite_triclinic.dump") -LAMMPSDUMP_image_vf = str(_data_ref / "lammps/image_vf.lammpstrj") -LAMMPS_image_vf = str(_data_ref / "lammps/image_vf.data") - -unordered_res = str(_data_ref / "unordered_res.pdb") - -GMS_ASYMOPT = str(_data_ref / "gms/c1opt.gms.gz") -GMS_SYMOPT = str(_data_ref / "gms/symopt.gms") -GMS_ASYMSURF = str(_data_ref / "gms/surf2wat.gms") - -two_water_gro = str(_data_ref / "two_water_gro.gro") -two_water_gro_multiframe = str(_data_ref / "two_water_gro_multiframe.gro") -two_water_gro_nonames = str(_data_ref / "two_water_gro_nonames.gro") -two_water_gro_widebox = str(_data_ref / "two_water_gro_widebox.gro") - -DLP_CONFIG = str(_data_ref / "dlpoly/CONFIG") -DLP_CONFIG_order = str(_data_ref / "dlpoly/CONFIG_order") -DLP_CONFIG_minimal = str(_data_ref / "dlpoly/CONFIG_minimal") -DLP_HISTORY = str(_data_ref / "dlpoly/HISTORY") -DLP_HISTORY_order = str(_data_ref / "dlpoly/HISTORY_order") -DLP_HISTORY_minimal = str(_data_ref / "dlpoly/HISTORY_minimal") -DLP_HISTORY_minimal_cell = str(_data_ref / "dlpoly/HISTORY_minimal_cell") -DLP_HISTORY_classic = str(_data_ref / "dlpoly/HISTORY_classic") - -waterPSF = str(_data_ref / 'watdyn.psf') -waterDCD = str(_data_ref / 'watdyn.dcd') - -rmsfArray = str(_data_ref / 'adk_oplsaa_CA_rmsf.npy') - -HoomdXMLdata = str(_data_ref / 'C12x64.xml.bz2') - -Make_Whole = str(_data_ref / 'make_whole.gro') -fullerene = str(_data_ref / 'fullerene.pdb.gz') - -Plength = str(_data_ref / 'plength.gro') -Martini_membrane_gro = str(_data_ref / 'martini_dppc_chol_bilayer.gro') +mol2_sodium_ion = (_data_ref / "mol2/sodium_ion.mol2").as_posix() + +capping_input = (_data_ref / "capping/aaqaa.gro").as_posix() +capping_output = (_data_ref / "capping/maestro_aaqaa_capped.pdb").as_posix() +capping_ace = (_data_ref / "capping/ace.pdb").as_posix() +capping_nma = (_data_ref / "capping/nma.pdb").as_posix() + +contacts_villin_folded = (_data_ref / "contacts/villin_folded.gro.bz2").as_posix() +contacts_villin_unfolded = (_data_ref / "contacts/villin_unfolded.gro.bz2").as_posix() +contacts_file = (_data_ref / "contacts/2F4K_qlist5_remap.dat").as_posix() + +trz4data = (_data_ref / "lammps/datatest.trz").as_posix() +LAMMPSdata = (_data_ref / "lammps/datatest.data").as_posix() +LAMMPSdata_mini = (_data_ref / "lammps/mini.data").as_posix() +LAMMPSdata2 = (_data_ref / "lammps/ifabp_apo_100mM.data.bz2").as_posix() +LAMMPSdcd2 = (_data_ref / "lammps/ifabp_apo_100mM.dcd").as_posix() +LAMMPScnt = (_data_ref / "lammps/cnt-hexagonal-class1.data").as_posix() +LAMMPScnt2 = (_data_ref / "lammps/cnt-hexagonal-class1.data2").as_posix() +LAMMPShyd = (_data_ref / "lammps/hydrogen-class1.data").as_posix() +LAMMPShyd2 = (_data_ref / "lammps/hydrogen-class1.data2").as_posix() +LAMMPSdata_deletedatoms = (_data_ref / 'lammps/deletedatoms.data').as_posix() +LAMMPSdata_triclinic = (_data_ref / "lammps/albite_triclinic.data").as_posix() +LAMMPSdata_PairIJ = (_data_ref / "lammps/pairij_coeffs.data.bz2").as_posix() +LAMMPSDUMP = (_data_ref / "lammps/wat.lammpstrj.bz2").as_posix() +LAMMPSDUMP_long = (_data_ref / "lammps/wat.lammpstrj_long.bz2").as_posix() +LAMMPSDUMP_allcoords = (_data_ref / "lammps/spce_all_coords.lammpstrj.bz2").as_posix() +LAMMPSDUMP_nocoords = (_data_ref / "lammps/spce_no_coords.lammpstrj.bz2").as_posix() +LAMMPSDUMP_triclinic = (_data_ref / "lammps/albite_triclinic.dump").as_posix() +LAMMPSDUMP_image_vf = (_data_ref / "lammps/image_vf.lammpstrj").as_posix() +LAMMPS_image_vf = (_data_ref / "lammps/image_vf.data").as_posix() + +unordered_res = (_data_ref / "unordered_res.pdb").as_posix() + +GMS_ASYMOPT = (_data_ref / "gms/c1opt.gms.gz").as_posix() +GMS_SYMOPT = (_data_ref / "gms/symopt.gms").as_posix() +GMS_ASYMSURF = (_data_ref / "gms/surf2wat.gms").as_posix() + +two_water_gro = (_data_ref / "two_water_gro.gro").as_posix() +two_water_gro_multiframe = (_data_ref / "two_water_gro_multiframe.gro").as_posix() +two_water_gro_nonames = (_data_ref / "two_water_gro_nonames.gro").as_posix() +two_water_gro_widebox = (_data_ref / "two_water_gro_widebox.gro").as_posix() + +DLP_CONFIG = (_data_ref / "dlpoly/CONFIG").as_posix() +DLP_CONFIG_order = (_data_ref / "dlpoly/CONFIG_order").as_posix() +DLP_CONFIG_minimal = (_data_ref / "dlpoly/CONFIG_minimal").as_posix() +DLP_HISTORY = (_data_ref / "dlpoly/HISTORY").as_posix() +DLP_HISTORY_order = (_data_ref / "dlpoly/HISTORY_order").as_posix() +DLP_HISTORY_minimal = (_data_ref / "dlpoly/HISTORY_minimal").as_posix() +DLP_HISTORY_minimal_cell = (_data_ref / "dlpoly/HISTORY_minimal_cell").as_posix() +DLP_HISTORY_classic = (_data_ref / "dlpoly/HISTORY_classic").as_posix() + +waterPSF = (_data_ref / 'watdyn.psf').as_posix() +waterDCD = (_data_ref / 'watdyn.dcd').as_posix() + +rmsfArray = (_data_ref / 'adk_oplsaa_CA_rmsf.npy').as_posix() + +HoomdXMLdata = (_data_ref / 'C12x64.xml.bz2').as_posix() + +Make_Whole = (_data_ref / 'make_whole.gro').as_posix() +fullerene = (_data_ref / 'fullerene.pdb.gz').as_posix() + +Plength = (_data_ref / 'plength.gro').as_posix() +Martini_membrane_gro = (_data_ref / 'martini_dppc_chol_bilayer.gro').as_posix() # Contains one of each residue in 'nucleic' selections -NUCLsel = str(_data_ref / 'nucl_res.pdb') +NUCLsel = (_data_ref / 'nucl_res.pdb').as_posix() -RANDOM_WALK = str(_data_ref / 'xyz_random_walk.xtc') -RANDOM_WALK_TOPO = str(_data_ref / 'RANDOM_WALK_TOPO.pdb') +RANDOM_WALK = (_data_ref / 'xyz_random_walk.xtc').as_posix() +RANDOM_WALK_TOPO = (_data_ref / 'RANDOM_WALK_TOPO.pdb').as_posix() -MMTF = str(_data_ref / '173D.mmtf') -MMTF_gz = str(_data_ref / '5KIH.mmtf.gz') -MMTF_skinny = str(_data_ref / '1ubq-less-optional.mmtf') -MMTF_skinny2 = str(_data_ref / '3NJW-onlyrequired.mmtf') -MMTF_NOCRYST = str(_data_ref / "6QYR.mmtf.gz") +MMTF = (_data_ref / '173D.mmtf').as_posix() +MMTF_gz = (_data_ref / '5KIH.mmtf.gz').as_posix() +MMTF_skinny = (_data_ref / '1ubq-less-optional.mmtf').as_posix() +MMTF_skinny2 = (_data_ref / '3NJW-onlyrequired.mmtf').as_posix() +MMTF_NOCRYST = (_data_ref / "6QYR.mmtf.gz").as_posix() -ALIGN_BOUND = str(_data_ref / 'analysis/align_bound.pdb.gz') -ALIGN_UNBOUND = str(_data_ref / 'analysis/align_unbound.pdb.gz') +ALIGN_BOUND = (_data_ref / 'analysis/align_bound.pdb.gz').as_posix() +ALIGN_UNBOUND = (_data_ref / 'analysis/align_unbound.pdb.gz').as_posix() -GSD = str(_data_ref / 'example.gsd') -GSD_bonds = str(_data_ref / 'example_bonds.gsd') -GSD_long = str(_data_ref / 'example_longer.gsd') +GSD = (_data_ref / 'example.gsd').as_posix() +GSD_bonds = (_data_ref / 'example_bonds.gsd').as_posix() +GSD_long = (_data_ref / 'example_longer.gsd').as_posix() -DihedralArray = str(_data_ref / 'adk_oplsaa_dihedral.npy') -DihedralsArray = str(_data_ref / 'adk_oplsaa_dihedral_list.npy') -RamaArray = str(_data_ref / 'adk_oplsaa_rama.npy') -GLYRamaArray = str(_data_ref / 'adk_oplsaa_GLY_rama.npy') -JaninArray = str(_data_ref / 'adk_oplsaa_janin.npy') -LYSJaninArray = str(_data_ref / 'adk_oplsaa_LYS_janin.npy') -PDB_rama = str(_data_ref / '19hc.pdb.gz') -PDB_janin = str(_data_ref / '1a28.pdb.gz') +DihedralArray = (_data_ref / 'adk_oplsaa_dihedral.npy').as_posix() +DihedralsArray = (_data_ref / 'adk_oplsaa_dihedral_list.npy').as_posix() +RamaArray = (_data_ref / 'adk_oplsaa_rama.npy').as_posix() +GLYRamaArray = (_data_ref / 'adk_oplsaa_GLY_rama.npy').as_posix() +JaninArray = (_data_ref / 'adk_oplsaa_janin.npy').as_posix() +LYSJaninArray = (_data_ref / 'adk_oplsaa_LYS_janin.npy').as_posix() +PDB_rama = (_data_ref / '19hc.pdb.gz').as_posix() +PDB_janin = (_data_ref / '1a28.pdb.gz').as_posix() -BATArray = str(_data_ref / 'mol2_comments_header_bat.npy') +BATArray = (_data_ref / 'mol2_comments_header_bat.npy').as_posix() -ITP = str(_data_ref / 'gromacs_ala10.itp') -ITP_nomass = str(_data_ref / 'itp_nomass.itp') -ITP_atomtypes = str(_data_ref / 'atomtypes.itp') -ITP_charges = str(_data_ref / 'atomtypes_charge.itp') -ITP_edited = str(_data_ref / 'edited_itp.itp') -ITP_tip5p = str(_data_ref / "tip5p.itp") -ITP_spce = str(_data_ref / 'spce.itp') +ITP = (_data_ref / 'gromacs_ala10.itp').as_posix() +ITP_nomass = (_data_ref / 'itp_nomass.itp').as_posix() +ITP_atomtypes = (_data_ref / 'atomtypes.itp').as_posix() +ITP_charges = (_data_ref / 'atomtypes_charge.itp').as_posix() +ITP_edited = (_data_ref / 'edited_itp.itp').as_posix() +ITP_tip5p = (_data_ref / "tip5p.itp").as_posix() +ITP_spce = (_data_ref / 'spce.itp').as_posix() -GMX_TOP = str(_data_ref / 'gromacs_ala10.top') -GMX_DIR = str(_data_ref / 'gromacs/') -GMX_TOP_BAD = str(_data_ref / 'bad_top.top') -ITP_no_endif = str(_data_ref / 'no_endif_spc.itp') +GMX_TOP = (_data_ref / 'gromacs_ala10.top').as_posix() +GMX_DIR = (_data_ref / 'gromacs/').as_posix() +GMX_TOP_BAD = (_data_ref / 'bad_top.top').as_posix() +ITP_no_endif = (_data_ref / 'no_endif_spc.itp').as_posix() -NAMDBIN = str(_data_ref / 'adk_open.coor') +NAMDBIN = (_data_ref / 'adk_open.coor').as_posix() -SDF_molecule = str(_data_ref / 'molecule.sdf') +SDF_molecule = (_data_ref / 'molecule.sdf').as_posix() -PDB_elements = str(_data_ref / 'elements.pdb') -PDB_charges = str(_data_ref / 'charges.pdb') +PDB_elements = (_data_ref / 'elements.pdb').as_posix() +PDB_charges = (_data_ref / 'charges.pdb').as_posix() -PDBX = str(_data_ref / "4x8u.pdbx") +PDBX = (_data_ref / "4x8u.pdbx").as_posix() -SURFACE_PDB = str(_data_ref / 'surface.pdb.bz2') -SURFACE_TRR = str(_data_ref / 'surface.trr') +SURFACE_PDB = (_data_ref / 'surface.pdb.bz2').as_posix() +SURFACE_TRR = (_data_ref / 'surface.trr').as_posix() # This should be the last line: clean up namespace From b02b4f06bda73f4473686baf2a9df336dee0433c Mon Sep 17 00:00:00 2001 From: IAlibay Date: Wed, 24 May 2023 08:01:17 +0100 Subject: [PATCH 8/8] quote protect --- azure-pipelines.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/azure-pipelines.yml b/azure-pipelines.yml index a640136abcd..29673c14bb4 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -114,7 +114,7 @@ jobs: - script: >- python -m pip install biopython - chemfiles>=0.10,<0.10.4 + "chemfiles>=0.10,<0.10.4" duecredit gsd joblib