1# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- 2# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 3# 4# MDAnalysis --- https://www.mdanalysis.org 5# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors 6# (see the file AUTHORS for the full list of names) 7# 8# Released under the GNU Public Licence, v2 or any higher version 9# 10# Please cite your use of MDAnalysis in published work: 11# 12# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, 13# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. 14# MDAnalysis: A Python package for the rapid analysis of molecular dynamics 15# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th 16# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. 17# 18# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. 19# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. 20# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 21# 22 23""" 24Location of data files for the MDAnalysis unit tests 25==================================================== 26 27Real MD simulation data are stored in the ``data/`` sub 28directory. Use as :: 29 30 from MDAnalysis.tests.datafiles import * 31 32Note that the files are actually located in a separate package, 33:mod:`MDAnalysisTestData` from where they are initially imported as :: 34 35 from MDAnalysisTestData.datafiles import * 36""" 37from __future__ import absolute_import 38 39__all__ = [ 40 "PSF", "DCD", "CRD", # CHARMM (AdK example, DIMS trajectory from JMB 2009 paper) 41 "DCD2", # CHARMM (AdK example, DIMS trajectory from PLOS Comput Biol paper) 42 "PSF_notop", "PSF_BAD", # Same as PSF but no bonds etc, malformed version of previous 43 "DCD_empty", 44 "PSF_TRICLINIC", "DCD_TRICLINIC", # CHARMM c36 new unitcell, NPT 125 TIP3P (box vectors, see Issue 187 for details) 45 "PSF_NAMD", "PDB_NAMD", # NAMD 46 "PSF_NAMD_TRICLINIC", "DCD_NAMD_TRICLINIC", # NAMD, triclinic unitcell (Issue 187) 47 "PSF_NAMD_GBIS", "DCD_NAMD_GBIS", # NAMD, implicit solvent, 100 steps, #1819 48 "PSF_nosegid", # psf without a segid, Issue 121 49 "PDB_small", # PDB 50 "PDB_closed", 51 "PDB_multiframe", 52 "PDB_helix", 53 "PDB_conect", 54 "PDB_conect2TER", # Conect record to a TER entry (Issue 936) 55 "PDB_singleconect", # Conect record with one entry (Issue 937) 56 "PDB_icodes", # stripped down version of 1osm, has icodes! 57 "XPDB_small", 58 "PDB_full", # PDB 4E43 (full HEADER, TITLE, COMPND, REMARK, altloc) 59 "ALIGN", # Various way to align atom names in PDB files 60 "NUCL", # nucleic acid (PDB) 61 "INC_PDB", # incomplete PDB file (Issue #396) 62 # for testing cryst before/after model headers 63 "PDB_cm", "PDB_cm_bz2", "PDB_cm_gz", 64 "PDB_mc", "PDB_mc_bz2", "PDB_mc_gz", 65 "PDB_chainidnewres", # Issue 1110 66 "PDB_sameresid_diffresname", #Case where two residues share the same resid 67 "PDB_chainidrepeat", # Issue #1107 68 "PDB", "GRO", "XTC", "TRR", "TPR", "GRO_velocity", # Gromacs (AdK) 69 "GRO_incomplete_vels", 70 "COORDINATES_GRO_BZ2", 71 "GRO_large", #atom number truncation at > 100,000 particles, Issue 550 72 "GRO_residwrap", # resids wrapping because of 5 digit field (Issue #728) 73 "GRO_residwrap_0base", # corner case of #728 with resid=0 for first atom 74 "GRO_sameresid_diffresname", # Case where two residues share the same resid 75 "PDB_xvf", "TPR_xvf", "TRR_xvf", # Gromacs coords/veloc/forces (cobrotoxin, OPLS-AA, Gromacs 4.5.5 tpr) 76 "XVG_BZ2", # Compressed xvg file about cobrotoxin 77 "PDB_xlserial", 78 "TPR400", "TPR402", "TPR403", "TPR404", "TPR405", "TPR406", "TPR407", 79 "TPR450", "TPR451", "TPR452", "TPR453", "TPR454", "TPR455", "TPR455Double", 80 "TPR460", "TPR461", "TPR502", "TPR504", "TPR505", "TPR510", "TPR2016", 81 "TPR2018", 82 "TPR510_bonded", "TPR2016_bonded", "TPR2018_bonded", 83 "PDB_sub_sol", "PDB_sub_dry", # TRRReader sub selection 84 "TRR_sub_sol", 85 "XTC_sub_sol", 86 "XYZ", "XYZ_psf", "XYZ_bz2", 87 "XYZ_mini", "XYZ_five", # 3 and 5 atoms xyzs for an easy topology 88 "TXYZ", "ARC", "ARC_PBC", # Tinker files 89 "PRM", "TRJ", "TRJ_bz2", # Amber (no periodic box) 90 "INPCRD", 91 "PRMpbc", "TRJpbc_bz2", # Amber (periodic box) 92 "PRM7", "NCDFtruncoct", # Amber (cpptrj test trajectory, see Issue 488) 93 "PRM12", "TRJ12_bz2", # Amber (v12 format, Issue 100) 94 "PRMncdf", "TRJncdf", "NCDF", # Amber (netcdf) 95 "PFncdf_Top", "PFncdf_Trj", # Amber ncdf with Positions and Forces 96 "PRMcs", # Amber (format, Issue 1331) 97 "PRMNCRST", # Amber ncrst with positions/forces/velocities 98 "PRMErr1", "PRMErr2", "PRMErr3", # Amber TOP files to check raised errors 99 "PQR", # PQR v1 100 "PQR_icodes", # PQR v2 with icodes 101 "PDBQT_input", # PDBQT 102 "PDBQT_querypdb", 103 "FASTA", # sequence alignment, Issue 112 + 113 104 "HELANAL_BENDING_MATRIX", # HELANAL test (from PSF+DCD (AdK) helix 8) 105 "PDB_HOLE", # gramicidin A 106 "MULTIPDB_HOLE", # gramicidin A, normal mode 7 from ElNemo 107 "DMS", 108 "CONECT", # HIV Reverse Transcriptase with inhibitor 109 "TRZ", "TRZ_psf", 110 "TRIC", 111 "XTC_multi_frame", 112 "TRR_multi_frame", 113 "merge_protein", "merge_ligand", "merge_water", 114 "mol2_molecules", "mol2_molecule", "mol2_broken_molecule", 115 "mol2_zinc", 116 "capping_input", "capping_output", "capping_ace", "capping_nma", 117 "contacts_villin_folded", "contacts_villin_unfolded", "contacts_file", 118 "LAMMPSdata", "trz4data", "LAMMPSdata_mini", 119 "LAMMPSdata2", "LAMMPSdcd2", 120 "LAMMPScnt", "LAMMPScnt2", # triclinic box 121 "LAMMPShyd", "LAMMPShyd2", 122 "LAMMPSdata_deletedatoms", # with deleted atoms 123 "LAMMPSDUMP", 124 "unordered_res", # pdb file with resids non sequential 125 "GMS_ASYMOPT", # GAMESS C1 optimization 126 "GMS_SYMOPT", # GAMESS D4h optimization 127 "GMS_ASYMSURF", # GAMESS C1 surface 128 "two_water_gro", "two_water_gro_nonames", # for bond guessing, 2 water molecules, one with weird names 129 "two_water_gro_widebox", # Issue #548 130 "DLP_CONFIG", "DLP_CONFIG_order", "DLP_CONFIG_minimal", # dl_poly 4 config file 131 "DLP_HISTORY", "DLP_HISTORY_order", "DLP_HISTORY_minimal", # dl_poly 4 history file 132 "waterPSF","waterDCD","rmsfArray", 133 "HoomdXMLdata", 134 "Make_Whole", # for testing the function lib.mdamath.make_whole, has 9 atoms 135 "fullerene", # for make_whole, a nice friendly C60 with bonds 136 "Plength", 137 "COORDINATES_XYZ", 138 "COORDINATES_XYZ_BZ2", 139 "COORDINATES_GRO", 140 "COORDINATES_GRO_INCOMPLETE_VELOCITY", 141 "Martini_membrane_gro", # for testing the leaflet finder 142 "COORDINATES_XTC", 143 "COORDINATES_TRR", 144 "COORDINATES_DCD", 145 "COORDINATES_TOPOLOGY", 146 "NUCLsel", 147 "GRO_empty_atom", "GRO_missing_atomname", # for testing GROParser exception raise 148 "ENT", #for testing ENT file extension 149 "RANDOM_WALK", 150 "RANDOM_WALK_TOPO", # garbage topology to go along with XTC positions above 151 "AUX_XVG", "XVG_BAD_NCOL", #for testing .xvg auxiliary reader 152 "AUX_XVG_LOWF", "AUX_XVG_HIGHF", 153 "MMTF", "MMTF_gz", 154 "ALIGN_BOUND", # two component bound system 155 "ALIGN_UNBOUND", # two component unbound system 156 "legacy_DCD_ADK_coords", # frames 5 and 29 read in for adk_dims.dcd using legacy DCD reader 157 "legacy_DCD_NAMD_coords", # frame 0 read in for SiN_tric_namd.dcd using legacy DCD reader 158 "legacy_DCD_c36_coords", # frames 1 and 4 read in for tip125_tric_C36.dcd using legacy DCD reader 159 "GSD", 160 "GRO_MEMPROT", "XTC_MEMPROT", # YiiP transporter in POPE:POPG lipids with Na+, Cl-, Zn2+ dummy model without water 161 "DihedralArray", "DihedralsArray", # time series of single dihedral 162 "RamaArray", "GLYRamaArray", # time series of phi/psi angles 163 "JaninArray", "LYSJaninArray", # time series of chi1/chi2 angles 164 "PDB_rama", "PDB_janin", # for testing failures of Ramachandran and Janin classes 165 166 # DOS line endings 167 "WIN_PDB_multiframe", "WIN_DLP_HISTORY", "WIN_TRJ", "WIN_LAMMPSDUMP", "WIN_ARC", 168] 169 170from pkg_resources import resource_filename 171 172WIN_PDB_multiframe = resource_filename(__name__, 173 'data/windows/WIN_nmr_neopetrosiamide.pdb') 174WIN_DLP_HISTORY = resource_filename(__name__, 175 'data/windows/WIN_HISTORY') 176WIN_TRJ = resource_filename(__name__, 177 'data/windows/WIN_ache.mdcrd') 178WIN_ARC = resource_filename(__name__, 179 'data/windows/WIN_test.arc') 180WIN_LAMMPSDUMP = resource_filename(__name__, 181 'data/windows/WIN_wat.lammpstrj') 182 183legacy_DCD_NAMD_coords = resource_filename(__name__, 184'data/legacy_DCD_NAMD_coords.npy') 185legacy_DCD_ADK_coords = resource_filename(__name__, 186'data/legacy_DCD_adk_coords.npy') 187legacy_DCD_c36_coords = resource_filename(__name__, 188'data/legacy_DCD_c36_coords.npy') 189AUX_XVG_LOWF = resource_filename(__name__, 'data/test_lowf.xvg') 190AUX_XVG_HIGHF = resource_filename(__name__, 'data/test_highf.xvg') 191XVG_BAD_NCOL = resource_filename(__name__, 'data/bad_num_col.xvg') 192AUX_XVG = resource_filename(__name__, 'data/test.xvg') 193ENT = resource_filename(__name__, 'data/testENT.ent') 194GRO_missing_atomname = resource_filename(__name__, 'data/missing_atomname.gro') 195GRO_empty_atom = resource_filename(__name__, 'data/empty_atom.gro') 196 197COORDINATES_GRO = resource_filename(__name__, 'data/coordinates/test.gro') 198COORDINATES_GRO_INCOMPLETE_VELOCITY = resource_filename(__name__, 'data/coordinates/test_incomplete_vel.gro') 199COORDINATES_GRO_BZ2 = resource_filename(__name__, 'data/coordinates/test.gro.bz2') 200COORDINATES_XYZ = resource_filename(__name__, 'data/coordinates/test.xyz') 201COORDINATES_XYZ_BZ2 = resource_filename( 202 __name__, 'data/coordinates/test.xyz.bz2') 203COORDINATES_XTC = resource_filename(__name__, 'data/coordinates/test.xtc') 204COORDINATES_TRR = resource_filename(__name__, 'data/coordinates/test.trr') 205COORDINATES_DCD = resource_filename(__name__, 'data/coordinates/test.dcd') 206COORDINATES_TOPOLOGY = resource_filename(__name__, 'data/coordinates/test_topology.pdb') 207 208PSF = resource_filename(__name__, 'data/adk.psf') 209PSF_notop = resource_filename(__name__, 'data/adk_notop.psf') 210PSF_BAD = resource_filename(__name__, 'data/adk_notop_BAD.psf') 211DCD = resource_filename(__name__, 'data/adk_dims.dcd') 212DCD_empty = resource_filename(__name__, 'data/empty.dcd') 213CRD = resource_filename(__name__, 'data/adk_open.crd') 214PSF_TRICLINIC = resource_filename(__name__, 'data/tip125_tric_C36.psf') 215DCD_TRICLINIC = resource_filename(__name__, 'data/tip125_tric_C36.dcd') 216DCD2 = resource_filename(__name__, 'data/adk_dims2.dcd') 217 218PSF_NAMD = resource_filename(__name__, 'data/namd_cgenff.psf') 219PDB_NAMD = resource_filename(__name__, 'data/namd_cgenff.pdb') 220PSF_NAMD_TRICLINIC = resource_filename(__name__, 'data/SiN_tric_namd.psf') 221DCD_NAMD_TRICLINIC = resource_filename(__name__, 'data/SiN_tric_namd.dcd') 222PSF_NAMD_GBIS = resource_filename(__name__, 'data/adk_closed_NAMD.psf') 223DCD_NAMD_GBIS = resource_filename(__name__, 'data/adk_gbis_tmd-fast1_NAMD.dcd') 224 225PSF_nosegid = resource_filename(__name__, 'data/nosegid.psf') 226 227PDB_small = resource_filename(__name__, 'data/adk_open.pdb') 228PDB_closed = resource_filename(__name__, 'data/adk_closed.pdb') 229 230ALIGN = resource_filename(__name__, 'data/align.pdb') 231NUCL = resource_filename(__name__, 'data/1k5i.pdb') 232INC_PDB = resource_filename(__name__, 'data/incomplete.pdb') 233PDB_cm = resource_filename(__name__, 'data/cryst_then_model.pdb') 234PDB_cm_gz = resource_filename(__name__, 'data/cryst_then_model.pdb.gz') 235PDB_cm_bz2 = resource_filename(__name__, 'data/cryst_then_model.pdb.bz2') 236PDB_mc = resource_filename(__name__, 'data/model_then_cryst.pdb') 237PDB_mc_gz = resource_filename(__name__, 'data/model_then_cryst.pdb.gz') 238PDB_mc_bz2 = resource_filename(__name__, 'data/model_then_cryst.pdb.bz2') 239PDB_chainidnewres = resource_filename(__name__, 'data/chainIDnewres.pdb.gz') 240PDB_sameresid_diffresname = resource_filename(__name__, 'data/sameresid_diffresname.pdb') 241PDB_chainidrepeat = resource_filename(__name__, 'data/chainIDrepeat.pdb.gz') 242PDB_multiframe = resource_filename(__name__, 'data/nmr_neopetrosiamide.pdb') 243PDB_helix = resource_filename(__name__, 'data/A6PA6_alpha.pdb') 244PDB_conect = resource_filename(__name__, 'data/conect_parsing.pdb') 245PDB_conect2TER = resource_filename(__name__, 'data/CONECT2TER.pdb') 246PDB_singleconect = resource_filename(__name__, 'data/SINGLECONECT.pdb') 247PDB_icodes = resource_filename(__name__, 'data/1osm.pdb.gz') 248 249GRO = resource_filename(__name__, 'data/adk_oplsaa.gro') 250GRO_velocity = resource_filename(__name__, 'data/sample_velocity_file.gro') 251GRO_incomplete_vels = resource_filename(__name__, 'data/grovels.gro') 252GRO_large = resource_filename(__name__, 'data/bigbox.gro.bz2') 253GRO_residwrap = resource_filename(__name__, 'data/residwrap.gro') 254GRO_residwrap_0base = resource_filename(__name__, 'data/residwrap_0base.gro') 255GRO_sameresid_diffresname = resource_filename(__name__, 'data/sameresid_diffresname.gro') 256PDB = resource_filename(__name__, 'data/adk_oplsaa.pdb') 257XTC = resource_filename(__name__, 'data/adk_oplsaa.xtc') 258TRR = resource_filename(__name__, 'data/adk_oplsaa.trr') 259TPR = resource_filename(__name__, 'data/adk_oplsaa.tpr') 260PDB_sub_dry = resource_filename(__name__, 'data/cobrotoxin_dry_neutral_0.pdb') 261TRR_sub_sol = resource_filename(__name__, 'data/cobrotoxin.trr') 262XTC_sub_sol = resource_filename(__name__, 'data/cobrotoxin.xtc') 263PDB_sub_sol = resource_filename(__name__, 'data/cobrotoxin.pdb') 264PDB_xlserial = resource_filename(__name__, 'data/xl_serial.pdb') 265GRO_MEMPROT = resource_filename(__name__, 'data/analysis/YiiP_lipids.gro.gz') 266XTC_MEMPROT = resource_filename(__name__, 'data/analysis/YiiP_lipids.xtc') 267XTC_multi_frame = resource_filename( 268 __name__, 'data/xtc_test_only_10_frame_10_atoms.xtc' 269) 270TRR_multi_frame = resource_filename( 271 __name__, 'data/trr_test_only_10_frame_10_atoms.trr' 272) 273 274PDB_xvf = resource_filename(__name__, 'data/cobrotoxin.pdb') 275TPR_xvf = resource_filename(__name__, 'data/cobrotoxin.tpr') 276TRR_xvf = resource_filename(__name__, 'data/cobrotoxin.trr') 277XVG_BZ2 = resource_filename(__name__, 'data/cobrotoxin_protein_forces.xvg.bz2') 278 279XPDB_small = resource_filename(__name__, 'data/5digitResid.pdb') 280# number is the gromacs version 281TPR400 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.0.tpr') 282TPR402 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.0.2.tpr') 283TPR403 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.0.3.tpr') 284TPR404 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.0.4.tpr') 285TPR405 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.0.5.tpr') 286TPR406 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.0.6.tpr') 287TPR407 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.0.7.tpr') 288TPR450 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.5.tpr') 289TPR451 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.5.1.tpr') 290TPR452 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.5.2.tpr') 291TPR453 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.5.3.tpr') 292TPR454 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.5.4.tpr') 293TPR455 = resource_filename(__name__, 'data/tprs/2lyz_gmx_4.5.5.tpr') 294TPR502 = resource_filename(__name__, 'data/tprs/2lyz_gmx_5.0.2.tpr') 295TPR504 = resource_filename(__name__, 'data/tprs/2lyz_gmx_5.0.4.tpr') 296TPR505 = resource_filename(__name__, 'data/tprs/2lyz_gmx_5.0.5.tpr') 297TPR510 = resource_filename(__name__, 'data/tprs/2lyz_gmx_5.1.tpr') 298TPR2016 = resource_filename(__name__, 'data/tprs/2lyz_gmx_2016.tpr') 299TPR2018 = resource_filename(__name__, 'data/tprs/2lyz_gmx_2018.tpr') 300# double precision 301TPR455Double = resource_filename(__name__, 'data/tprs/drew_gmx_4.5.5.double.tpr') 302TPR460 = resource_filename(__name__, 'data/tprs/ab42_gmx_4.6.tpr') 303TPR461 = resource_filename(__name__, 'data/tprs/ab42_gmx_4.6.1.tpr') 304# all bonded interactions 305TPR510_bonded = resource_filename(__name__, 'data/tprs/all_bonded/dummy_5.1.tpr') 306TPR2016_bonded = resource_filename(__name__, 'data/tprs/all_bonded/dummy_2016.tpr') 307TPR2018_bonded = resource_filename(__name__, 'data/tprs/all_bonded/dummy_2018.tpr') 308 309XYZ_psf = resource_filename(__name__, 'data/2r9r-1b.psf') 310XYZ_bz2 = resource_filename(__name__, 'data/2r9r-1b.xyz.bz2') 311XYZ = resource_filename(__name__, 'data/2r9r-1b.xyz') 312XYZ_mini = resource_filename(__name__, 'data/mini.xyz') 313XYZ_five = resource_filename(__name__, 'data/five.xyz') 314TXYZ = resource_filename(__name__, 'data/coordinates/test.txyz') 315ARC = resource_filename(__name__, 'data/coordinates/test.arc') 316ARC_PBC = resource_filename(__name__, 'data/coordinates/new_hexane.arc') 317 318PRM = resource_filename(__name__, 'data/Amber/ache.prmtop') 319TRJ = resource_filename(__name__, 'data/Amber/ache.mdcrd') 320INPCRD = resource_filename(__name__, 'data/Amber/test.inpcrd') 321TRJ_bz2 = resource_filename(__name__, 'data/Amber/ache.mdcrd.bz2') 322PFncdf_Top = resource_filename(__name__, 'data/Amber/posfor.top') 323PFncdf_Trj = resource_filename(__name__, 'data/Amber/posfor.ncdf') 324 325PRMpbc = resource_filename(__name__, 'data/Amber/capped-ala.prmtop') 326TRJpbc_bz2 = resource_filename(__name__, 'data/Amber/capped-ala.mdcrd.bz2') 327 328PRMncdf = resource_filename(__name__, 'data/Amber/bala.prmtop') 329TRJncdf = resource_filename(__name__, 'data/Amber/bala.trj') 330NCDF = resource_filename(__name__, 'data/Amber/bala.ncdf') 331 332PRM12 = resource_filename(__name__, 'data/Amber/anti.top') 333TRJ12_bz2 = resource_filename(__name__, 'data/Amber/anti_md1.mdcrd.bz2') 334 335PRM7 = resource_filename(__name__, 'data/Amber/tz2.truncoct.parm7.bz2') 336NCDFtruncoct = resource_filename(__name__, 'data/Amber/tz2.truncoct.nc') 337 338PRMcs = resource_filename(__name__, 'data/Amber/chitosan.prmtop') 339 340PRMNCRST = resource_filename(__name__, 'data/Amber/ace_mbondi3.parm7') 341 342PRMErr1 = resource_filename(__name__, 'data/Amber/ace_mbondi3.error1.parm7') 343PRMErr2 = resource_filename(__name__, 'data/Amber/ace_mbondi3.error2.parm7') 344PRMErr3 = resource_filename(__name__, 'data/Amber/ace_mbondi3.error3.parm7') 345 346PQR = resource_filename(__name__, 'data/adk_open.pqr') 347PQR_icodes = resource_filename(__name__, 'data/1A2C.pqr') 348 349PDBQT_input = resource_filename(__name__, 'data/pdbqt_inputpdbqt.pdbqt') 350PDBQT_querypdb = resource_filename(__name__, 'data/pdbqt_querypdb.pdb') 351 352FASTA = resource_filename(__name__, 'data/test.fasta') 353HELANAL_BENDING_MATRIX = resource_filename(__name__, 'data/helanal_bending_matrix_AdK_DIMS_H8.dat') 354 355 356PDB_HOLE = resource_filename(__name__, 'data/1grm_single.pdb') 357MULTIPDB_HOLE = resource_filename(__name__, 'data/1grm_elNemo_mode7.pdb.bz2') 358 359DMS = resource_filename(__name__, 'data/adk_closed.dms') 360 361CONECT = resource_filename(__name__, 'data/1hvr.pdb') 362 363TRZ = resource_filename(__name__, 'data/trzfile.trz') 364TRZ_psf = resource_filename(__name__, 'data/trz_psf.psf') 365 366TRIC = resource_filename(__name__, 'data/dppc_vesicle_hg.gro') 367 368PDB_full = resource_filename(__name__, "data/4E43.pdb") 369 370merge_protein = resource_filename(__name__, "data/merge/2zmm/protein.pdb") 371merge_ligand = resource_filename(__name__, "data/merge/2zmm/ligand.pdb") 372merge_water = resource_filename(__name__, "data/merge/2zmm/water.pdb") 373 374mol2_molecules = resource_filename(__name__, "data/mol2/Molecules.mol2") 375mol2_molecule = resource_filename(__name__, "data/mol2/Molecule.mol2") 376mol2_broken_molecule = resource_filename(__name__, "data/mol2/BrokenMolecule.mol2") 377# MOL2 file without substructure field 378mol2_zinc = resource_filename(__name__, "data/mol2/zinc_856218.mol2") 379 380capping_input = resource_filename(__name__, "data/capping/aaqaa.gro") 381capping_output = resource_filename(__name__, "data/capping/maestro_aaqaa_capped.pdb") 382capping_ace = resource_filename(__name__, "data/capping/ace.pdb") 383capping_nma = resource_filename(__name__, "data/capping/nma.pdb") 384 385contacts_villin_folded = resource_filename(__name__, "data/contacts/villin_folded.gro.bz2") 386contacts_villin_unfolded = resource_filename(__name__, "data/contacts/villin_unfolded.gro.bz2") 387contacts_file = resource_filename(__name__, "data/contacts/2F4K_qlist5_remap.dat") 388 389trz4data = resource_filename(__name__, "data/lammps/datatest.trz") 390LAMMPSdata = resource_filename(__name__, "data/lammps/datatest.data") 391LAMMPSdata_mini = resource_filename(__name__, "data/lammps/mini.data") 392LAMMPSdata2 = resource_filename(__name__, "data/lammps/ifabp_apo_100mM.data.bz2") 393LAMMPSdcd2 = resource_filename(__name__, "data/lammps/ifabp_apo_100mM.dcd") 394LAMMPScnt = resource_filename(__name__, "data/lammps/cnt-hexagonal-class1.data") 395LAMMPScnt2 = resource_filename(__name__, "data/lammps/cnt-hexagonal-class1.data2") 396LAMMPShyd = resource_filename(__name__, "data/lammps/hydrogen-class1.data") 397LAMMPShyd2 = resource_filename(__name__, "data/lammps/hydrogen-class1.data2") 398LAMMPSdata_deletedatoms = resource_filename(__name__, 'data/lammps/deletedatoms.data') 399LAMMPSDUMP = resource_filename(__name__, "data/lammps/wat.lammpstrj.bz2") 400 401unordered_res = resource_filename(__name__, "data/unordered_res.pdb") 402 403GMS_ASYMOPT = resource_filename(__name__, "data/gms/c1opt.gms.gz") 404GMS_SYMOPT = resource_filename(__name__, "data/gms/symopt.gms") 405GMS_ASYMSURF = resource_filename(__name__, "data/gms/surf2wat.gms") 406 407two_water_gro = resource_filename(__name__, "data/two_water_gro.gro") 408two_water_gro_nonames = resource_filename(__name__, "data/two_water_gro_nonames.gro") 409two_water_gro_widebox = resource_filename(__name__, "data/two_water_gro_widebox.gro") 410 411DLP_CONFIG = resource_filename(__name__, "data/dlpoly/CONFIG") 412DLP_CONFIG_order = resource_filename(__name__, "data/dlpoly/CONFIG_order") 413DLP_CONFIG_minimal = resource_filename(__name__, "data/dlpoly/CONFIG_minimal") 414DLP_HISTORY = resource_filename(__name__, "data/dlpoly/HISTORY") 415DLP_HISTORY_order = resource_filename(__name__, "data/dlpoly/HISTORY_order") 416DLP_HISTORY_minimal = resource_filename(__name__, "data/dlpoly/HISTORY_minimal") 417 418waterPSF = resource_filename(__name__, 'data/watdyn.psf') 419waterDCD = resource_filename(__name__, 'data/watdyn.dcd') 420 421rmsfArray = resource_filename(__name__, 'data/adk_oplsaa_CA_rmsf.npy') 422 423HoomdXMLdata = resource_filename(__name__, 'data/C12x64.xml.bz2') 424 425Make_Whole = resource_filename(__name__, 'data/make_whole.gro') 426fullerene = resource_filename(__name__, 'data/fullerene.pdb.gz') 427 428Plength = resource_filename(__name__, 'data/plength.gro') 429Martini_membrane_gro = resource_filename(__name__, 'data/martini_dppc_chol_bilayer.gro') 430 431# Contains one of each residue in 'nucleic' selections 432NUCLsel = resource_filename(__name__, 'data/nucl_res.pdb') 433 434RANDOM_WALK = resource_filename(__name__, 'data/xyz_random_walk.xtc') 435RANDOM_WALK_TOPO = resource_filename(__name__, 'data/RANDOM_WALK_TOPO.pdb') 436 437MMTF = resource_filename(__name__, 'data/173D.mmtf') 438MMTF_gz = resource_filename(__name__, 'data/5KIH.mmtf.gz') 439 440ALIGN_BOUND = resource_filename(__name__, 'data/analysis/align_bound.pdb.gz') 441ALIGN_UNBOUND = resource_filename(__name__, 'data/analysis/align_unbound.pdb.gz') 442 443GSD = resource_filename(__name__, 'data/example.gsd') 444 445DihedralArray = resource_filename(__name__, 'data/adk_oplsaa_dihedral.npy') 446DihedralsArray = resource_filename(__name__, 'data/adk_oplsaa_dihedral_list.npy') 447RamaArray = resource_filename(__name__, 'data/adk_oplsaa_rama.npy') 448GLYRamaArray = resource_filename(__name__, 'data/adk_oplsaa_GLY_rama.npy') 449JaninArray = resource_filename(__name__, 'data/adk_oplsaa_janin.npy') 450LYSJaninArray = resource_filename(__name__, 'data/adk_oplsaa_LYS_janin.npy') 451PDB_rama = resource_filename(__name__, 'data/19hc.pdb.gz') 452PDB_janin = resource_filename(__name__, 'data/1a28.pdb.gz') 453 454# This should be the last line: clean up namespace 455del resource_filename 456