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HaotianZhangAI4Science / SurfGen

SurfGen: Learning on Topological Surface and Geometric Structure for 3D Molecular Generation
MIT License
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Generating surface data .ply File: property float charge column is missing only getting 9 columns not all 10 columns in .ply file #7

Open Pul45 opened 10 months ago

Pul45 commented 10 months ago

Hello, I appreciate your effort on Surfgen model. May you please help me this surface generation data that I am facing with APBS-3.0.0.Linux software. As every other parameters are coming in the output.ply file except the 'property float charge column' ##################################################### The Output (.ply file) that I'm getting while running surface_maker_test.py is like ##################################################### ply format ascii 1.0 comment Generated by PyMesh element vertex 446 property float x property float y property float z property float hbond property float hphob property float nx property float ny property float nz property float si element face 805 property list uchar int vertex_indices end_header -13.074 5.661 68.274 0 3.8 -0.971364 -0.222983 -0.0820393 0.999941 -1.892 16.077 73.411 0 -0.8 0.102763 0.174101 0.979351 -0.999975 -3.997 26.27 72.8665 0 -0.7 0.17659 0.186627 -0.96643 0.99989 -6.324 26.448 72.974 -0.807497 2.5 -0.190969 0.395765 -0.898277 0.999943 -13.172 14.9345 66.835 0 3.7237 -0.102213 0.350881 0.930825 0.697774 -6.111 22.691 65.0005 0 -0.7 -0.183088 0.979426 -0.0848715 -0.870389 -3.1055 28.31 69.301 -0.661166 -0.440122 -0.646251 -0.130766 0.751838 -0.999944 -14.147 14.717 56.098 -0.385374 -0.8 -0.0729836 -0.315923 0.945974 -0.999921 -15.002 6.21 60.441 -0.425088 -0.4 -0.496207 0.191318 0.846862 -0.213993 -3.9075 28.8505 68.754 -0.338156 -0.4 -0.72349 -0.206511 0.658723 0.999931 -10.567 5.969 63.595 -0.103339 -3.5 -0.646433 0.762787 -0.0167127 -0.999922 -0.146 26.116 69.607 0 -0.7 -0.30578 0.0822124 0.948546 -0.999933 -3.918 15.874 73.752 0 -0.8 0.327149 0.735182 0.593702 -0.9999 -8.117 17.7245 70.5845 0 1.9 -0.418765 0.0400892 0.907209 -0.842707 -7.8235 12.1365 67.687 0 4.2 -0.93187 -0.349319 0.0979471 -0.616382 -2.9085 16.2475 72.694 -0.719027 -0.8 -0.0175192 0.762239 0.647059 -0.583525 -7.554 22.786 66.249 -0.731165 -0.7 -0.374656 0.916643 -0.139276 0.201191 -12.874 4.462 62.3385 0 -0.4 -0.91739 -0.035228 0.396427 -0.999918 -7.85525 17.3507 59.315 -0.201146 -3.5 -0.913898 0.0700748 0.399849 0.632203 -7.4635 15.8135 64.468 0 -3.5 0.316005 -0.381916 -0.868493 -0.246186 -7.481 8.985 69.47 0 4.2 -0.973392 -0.00843771 -0.228991 -0.91981 -12.3378 19.0742 68.4778 -0.574713 -3.2 -0.904732 0.0972451 0.414733 0.179319 -8.7745 22.39 68.0605 0 -0.7 -0.058458 0.905261 0.420815 -0.0250776 -9.05212 7.93113 67.4796 0 4.2 -0.185931 0.504736 0.843013 -0.999867 ################################## While the output given with the code is below ##################################

ply format ascii 1.0 comment Generated by PyMesh element vertex 199 property float x property float y property float z property float charge property float hbond property float hphob property float nx property float ny property float nz property float si element face 346 property list uchar int vertex_indices end_header -10.415 6.95275 64.3453 -2.16407 -0.0888736 -3.5 -0.923633 0.323771 -0.205121 0.931742 -6.6575 17.7568 60.8273 -1.33331 -0.0282742 -3.5 -0.884894 -0.290329 0.364241 0.899322 -8.4695 20.4433 58.41 -0.00652805 0 -1.3 -0.955293 -0.148286 -0.255786 -0.999889 -15.2743 7.72125 57.5687 -1.24086 -0.61186 -0.4 -0.724413 0.561455 -0.399993 0.999912 -4.625 28.9982 67.7288 -0.360583 0 -0.7 -0.743594 0.310221 0.59231 -0.999917 -8.856 11.8562 56.0057 -0.0709853 0 3.8 0.107735 0.400098 0.910118 0.99987 -6.76775 26.269 73.0192 -1.35348 -0.400939 2.5 -0.233298 0.216453 -0.948009 -0.99993 -4.3535 15.9235 74.0175 -0.10814 0 -0.8 0.167714 0.725867 0.667075 -0.999925 -13.1435 6.16525 68.4287 0.252828 0 3.8 -0.983114 0.181715 0.0216044 -0.999907 -3.5065 28.5802 69.0275 -1.73075 -0.67497 -0.4 -0.556177 0.150855 0.817258 -0.999916 -12.9268 10.296 55.781 1.29658 -0.686359 -0.8 -0.805174 0.592306 -0.0294462 0.999921 -7.949 23.6863 74.315 -1.34833 -0.00673767 2.5 -0.269311 -0.756573 -0.595877 -0.999895 -8.77675 19.4382 60.1401 -0.0908766 -0.241443 -1.68887 -0.944851 -0.327159 0.0149781 -0.918154 -12.4091 13.3356 56.6625 -0.0437815 -0.599893 -1.1862 -0.0852623 -0.137972 0.986759 -0.90168 -6.4865 23.256 66.352 2.00684 0 -0.7 -0.411005 0.895826 -0.169026 -0.539646 -4.12075 22.913 68.472 -1.39125 -0.327394 -0.7 -0.310857 0.892814 0.325961 0.999877 -7.746 22.675 68.1035 1.31147 0 -0.7 -0.329026 0.902094 0.279226 -0.286345 -5.65112 12.9495 64.9967 0.137093 -0.28802 -3.5 -0.185774 0.883338 -0.43035 0.999892 -9.88387 12.3439 61.1232 -0.582409 0 3.8 -0.249049 0.685065 -0.684588 0.0113594 -8.4715 9.23475 70.5045 -0.107273 0 4.2 -0.821646 0.363744 -0.438848 0.310675 -6.99525 12.4408 63.2445 -1.61923 0 -3.5 0.0136195 0.999815 -0.0135723 0.999892 -12.1053 14.8097 56.2865 -1.01349 -0.877666 -1.3 -0.0141837 0.249873 0.968175 -0.999923 -2.51975 26.1318 72.6135 0.462894 -0.189056 -0.7 -0.0392867 0.0907302 -0.9951 -0.999899 -12.6027 17.3717 67.7795 -1.85343 -0.232191 -0.0712914 -0.946846 -0.288106 0.143099 -0.47367 -0.391 24.3805 71.224 -0.387783 0 -0.7 -0.579371 0.79828 0.164556 0.999882

Then, how we will get property float charge column in the final .ply file? is there any way to get it? Please explain with an example? Thanks

HaotianZhangAI4Science commented 9 months ago

You can decompose the code from the read_ply (./utils/surface). Like: from plyfile import PlyData ply_file = './data/crosssdock_test/4tos_A_rec_4tos_355_lig_tt_min_0/4tos_A_rec_4tos_355_lig_tt_min_0_pocket_8.0_res_1.5.ply' with open(ply_file, 'rb') as f: data = PlyData.read(f) print(data['vertex'].properties)