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Merge pull request #55 from glycojones/privateerpython
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Merge privateerpython(Harold's Dev PhD branch) into main
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@GABRAH
GABRAH authored Oct 15, 2023
2 parents f626d04 + 53e2ee8 commit d977ba8
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17 changes: 12 additions & 5 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -77,11 +77,18 @@ else()
${PRIVATEER_SOURCE_DIR}/cpp/pybind11)
endif()

file(COPY ${PRIVATEERDATA}/glycomics/privateer_glycomics_database.json
DESTINATION ${CLIBDENV})

file(COPY ${PRIVATEERDATA}/linkage_torsions/privateer_torsion_database.json
DESTINATION ${CLIBDENV})
# file(COPY ${PRIVATEERDATA}/glycomics/privateer_glycomics_database.json
# DESTINATION ${CLIBDENV})

# file(COPY ${PRIVATEERDATA}/linkage_torsions/privateer_torsion_database.json
# DESTINATION ${CLIBDENV})

# Copy directories
add_custom_target(copy_resources ALL
COMMAND ${CMAKE_COMMAND} -E copy_directory
${CMAKE_SOURCE_DIR}/data
${CLIBDENV}/privateer_data
COMMENT "Copying Privateer Data files to ${CLIBDENV}/privateer_data")

add_library(privateer_lib
${PRIVATEER_SOURCE_DIR}/cpp/third-party/gemmi_compilation_unit.cpp
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15 changes: 10 additions & 5 deletions DependencyInstaller.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -124,15 +124,20 @@ echo "CCP4 (libccp4) installation ... falied. We can not continue the rest of th
exit 3
fi

if [[ ! -d share/ccp4srs ]]; then
cd $dependencyDir/share


if [[ -d share ]]; then
cd $dependencyDir/share
else
mkdir share
cd $dependencyDir/share
fi
if [[ -d ccp4srs ]]; then
rm -rf ccp4srs
rm -rf ccp4srs
fi
mkdir ccp4srs
cd ccp4srs
tar -zxvf $dependencyDir/ccp4srs-data-20180406.tar.gz --directory $dependencyDir/share/ccp4srs
fi
tar -zxvf $dependencyDir/ccp4srs-data-20180406.tar.gz
cd $dependencyDir

if [[ ! -d include/ccp4srs ]]; then
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176 changes: 176 additions & 0 deletions data/glycan_donor_repertoire/Complex/a2/cluster1.pdb
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Original file line number Diff line number Diff line change
@@ -0,0 +1,176 @@
ATOM 1 HO1 NAG 2 22.991 26.414 7.642 0.4450 0.2000 H
ATOM 2 O1 NAG 2 22.832 25.488 7.839 -0.6390 1.7210 O
ATOM 3 C1 NAG 2 23.001 25.393 9.265 0.2870 1.9080 C
ATOM 4 H1 NAG 2 23.688 26.159 9.624 0.0000 1.2870 H
ATOM 5 O5 NAG 2 23.448 24.046 9.566 -0.4330 1.6837 O
ATOM 6 C5 NAG 2 23.588 23.664 11.022 0.2080 1.9080 C
ATOM 7 H5 NAG 2 24.364 24.219 11.548 0.0000 1.3870 H
ATOM 8 C6 NAG 2 23.983 22.170 11.141 0.2890 1.9080 C
ATOM 9 H62 NAG 2 23.234 21.551 10.647 0.0000 1.3870 H
ATOM 10 H61 NAG 2 24.094 21.688 12.112 0.0000 1.3870 H
ATOM 11 O6 NAG 2 25.207 21.932 10.310 -0.6890 1.7210 O
ATOM 12 HO6 NAG 2 25.402 20.991 10.316 0.4240 0.2000 H
ATOM 13 C4 NAG 2 22.225 23.860 11.686 0.3020 1.9080 C
ATOM 14 H4 NAG 2 21.509 23.215 11.176 0.0000 1.3870 H
ATOM 15 C3 NAG 2 21.619 25.264 11.484 0.1800 1.9080 C
ATOM 16 H3 NAG 2 22.131 25.967 12.142 0.0000 1.3870 H
ATOM 17 O3 NAG 2 20.296 25.228 12.034 -0.6810 1.7210 O
ATOM 18 HO3 NAG 2 20.305 25.151 12.991 0.4230 0.2000 H
ATOM 19 C2 NAG 2 21.720 25.754 10.003 0.4800 1.9080 C
ATOM 20 H2 NAG 2 20.914 25.229 9.490 0.0000 1.3870 H
ATOM 21 N2 NAG 2 21.451 27.213 9.988 -0.7220 1.8240 N
ATOM 22 HN2 NAG 2 21.598 27.850 10.758 0.3000 0.6000 H
ATOM 23 C7 NAG 2 20.631 27.758 9.133 0.6480 1.9080 C
ATOM 24 O7 NAG 2 20.230 27.188 8.146 -0.5760 1.6612 O
ATOM 25 C8 NAG 2 20.021 29.139 9.544 0.0340 1.9080 C
ATOM 26 H83 NAG 2 20.706 29.757 10.125 0.0000 1.4870 H
ATOM 27 H82 NAG 2 19.677 29.622 8.629 0.0000 1.4870 H
ATOM 28 H81 NAG 2 19.155 28.946 10.177 0.0000 1.4870 H
ATOM 29 O4 NAG 2 22.330 23.587 13.157 -0.4740 1.6837 O
ATOM 30 C1 NAG 3 21.543 22.446 13.641 0.2870 1.9080 C
ATOM 31 H1 NAG 3 21.569 21.615 12.937 0.0000 1.2870 H
ATOM 32 O5 NAG 3 20.171 22.894 13.875 -0.4330 1.6837 O
ATOM 33 C5 NAG 3 19.252 21.883 14.409 0.2080 1.9080 C
ATOM 34 H5 NAG 3 19.121 21.111 13.652 0.0000 1.3870 H
ATOM 35 C6 NAG 3 17.863 22.513 14.333 0.2890 1.9080 C
ATOM 36 H62 NAG 3 17.034 21.810 14.413 0.0000 1.3870 H
ATOM 37 H61 NAG 3 17.836 22.952 13.335 0.0000 1.3870 H
ATOM 38 O6 NAG 3 17.652 23.610 15.229 -0.6890 1.7210 O
ATOM 39 HO6 NAG 3 16.815 23.474 15.679 0.4240 0.2000 H
ATOM 40 C4 NAG 3 19.739 21.190 15.694 0.3020 1.9080 C
ATOM 41 H4 NAG 3 19.724 21.947 16.478 0.0000 1.3870 H
ATOM 42 C3 NAG 3 21.225 20.745 15.534 0.1800 1.9080 C
ATOM 43 H3 NAG 3 21.249 19.900 14.846 0.0000 1.3870 H
ATOM 44 O3 NAG 3 21.707 20.270 16.807 -0.6810 1.7210 O
ATOM 45 HO3 NAG 3 21.394 19.405 17.084 0.4230 0.2000 H
ATOM 46 C2 NAG 3 22.188 21.906 14.979 0.4800 1.9080 C
ATOM 47 H2 NAG 3 22.123 22.623 15.797 0.0000 1.3870 H
ATOM 48 N2 NAG 3 23.587 21.373 14.777 -0.7220 1.8240 N
ATOM 49 HN2 NAG 3 23.830 20.556 14.236 0.3000 0.6000 H
ATOM 50 C7 NAG 3 24.617 21.931 15.494 0.6480 1.9080 C
ATOM 51 O7 NAG 3 24.486 22.839 16.247 -0.5760 1.6612 O
ATOM 52 C8 NAG 3 26.052 21.281 15.218 0.0340 1.9080 C
ATOM 53 H83 NAG 3 26.166 20.356 15.783 0.0000 1.4870 H
ATOM 54 H82 NAG 3 26.270 21.034 14.179 0.0000 1.4870 H
ATOM 55 H81 NAG 3 26.743 22.068 15.522 0.0000 1.4870 H
ATOM 56 O4 NAG 3 18.774 20.100 15.873 -0.4740 1.6837 O
ATOM 57 C1 BMA 4 18.623 19.603 17.252 0.3140 1.9080 C
ATOM 58 H1 BMA 4 18.873 20.484 17.843 0.0000 1.2870 H
ATOM 59 O5 BMA 4 19.608 18.548 17.513 -0.3930 1.6837 O
ATOM 60 C5 BMA 4 19.565 17.876 18.824 0.2060 1.9080 C
ATOM 61 H5 BMA 4 19.992 18.526 19.588 0.0000 1.3870 H
ATOM 62 C6 BMA 4 20.497 16.632 18.753 0.2730 1.9080 C
ATOM 63 H62 BMA 4 20.161 15.939 17.982 0.0000 1.3870 H
ATOM 64 H61 BMA 4 20.310 16.044 19.651 0.0000 1.3870 H
ATOM 65 O6 BMA 4 21.895 16.991 18.442 -0.4550 1.6837 O
ATOM 66 C4 BMA 4 18.078 17.408 19.133 0.3490 1.9080 C
ATOM 67 H4 BMA 4 17.835 16.539 18.523 0.0000 1.3870 H
ATOM 68 O4 BMA 4 18.131 16.985 20.443 -0.7460 1.7210 O
ATOM 69 HO4 BMA 4 17.830 16.076 20.502 0.4430 0.2000 H
ATOM 70 C3 BMA 4 17.027 18.512 18.936 0.2630 1.9080 C
ATOM 71 H3 BMA 4 17.337 19.169 19.749 0.0000 1.3870 H
ATOM 72 C2 BMA 4 17.193 19.119 17.510 0.2410 1.9080 C
ATOM 73 H2 BMA 4 16.497 19.956 17.447 0.0000 1.3870 H
ATOM 74 O2 BMA 4 16.923 18.083 16.478 -0.6640 1.7210 O
ATOM 75 HO2 BMA 4 16.720 18.585 15.685 0.4310 0.2000 H
ATOM 76 O3 BMA 4 15.744 17.806 19.288 -0.4560 1.6837 O
ATOM 77 C1 MAN 5 22.726 17.803 19.431 0.4330 1.9080 C
ATOM 78 H1 MAN 5 22.250 18.689 19.850 0.0000 1.2870 H
ATOM 79 C2 MAN 5 23.963 18.317 18.689 0.2450 1.9080 C
ATOM 80 H2 MAN 5 23.633 18.790 17.763 0.0000 1.3870 H
ATOM 81 C3 MAN 5 24.868 17.063 18.445 0.2520 1.9080 C
ATOM 82 H3 MAN 5 24.318 16.300 17.893 0.0000 1.3870 H
ATOM 83 C4 MAN 5 25.288 16.343 19.735 0.3260 1.9080 C
ATOM 84 H4 MAN 5 25.754 17.066 20.404 0.0000 1.3870 H
ATOM 85 C5 MAN 5 24.017 15.823 20.523 0.2760 1.9080 C
ATOM 86 H5 MAN 5 23.523 14.958 20.082 0.0000 1.3870 H
ATOM 87 C6 MAN 5 24.370 15.212 21.928 0.2660 1.9080 C
ATOM 88 H62 MAN 5 23.412 14.797 22.244 0.0000 1.3870 H
ATOM 89 H61 MAN 5 25.061 14.369 21.953 0.0000 1.3870 H
ATOM 90 O6 MAN 5 24.829 16.230 22.848 -0.6880 1.7210 O
ATOM 91 HO6 MAN 5 23.955 16.514 23.126 0.4220 0.2000 H
ATOM 92 O5 MAN 5 23.046 16.963 20.595 -0.5070 1.6837 O
ATOM 93 O4 MAN 5 26.199 15.156 19.462 -0.7330 1.7210 O
ATOM 94 HO4 MAN 5 27.094 15.465 19.623 0.4380 0.2000 H
ATOM 95 O3 MAN 5 26.113 17.396 17.690 -0.6960 1.7210 O
ATOM 96 HO3 MAN 5 26.674 17.938 18.249 0.4310 0.2000 H
ATOM 97 O2 MAN 5 24.521 19.322 19.626 -0.4650 1.6837 O
ATOM 98 C1 NAG 6 25.644 20.160 19.186 0.2870 1.9080 C
ATOM 99 H1 NAG 6 25.610 20.284 18.104 0.0000 1.2870 H
ATOM 100 O5 NAG 6 26.872 19.501 19.405 -0.4330 1.6837 O
ATOM 101 C5 NAG 6 28.158 20.136 18.900 0.2080 1.9080 C
ATOM 102 H5 NAG 6 28.011 20.264 17.828 0.0000 1.3870 H
ATOM 103 C6 NAG 6 29.378 19.271 19.165 0.2890 1.9080 C
ATOM 104 H62 NAG 6 29.448 19.138 20.245 0.0000 1.3870 H
ATOM 105 H61 NAG 6 30.315 19.757 18.895 0.0000 1.3870 H
ATOM 106 O6 NAG 6 29.294 18.021 18.529 -0.6890 1.7210 O
ATOM 107 HO6 NAG 6 29.033 17.437 19.246 0.4240 0.2000 H
ATOM 108 C4 NAG 6 28.235 21.610 19.540 0.3020 1.9080 C
ATOM 109 H4 NAG 6 28.515 21.389 20.570 0.0000 1.3870 H
ATOM 110 O4 NAG 6 29.324 22.324 18.851 -0.7160 1.7210 O
ATOM 111 HO4 NAG 6 29.266 23.190 19.261 0.4360 0.2000 H
ATOM 112 C3 NAG 6 26.913 22.373 19.370 0.1800 1.9080 C
ATOM 113 H3 NAG 6 26.905 22.675 18.323 0.0000 1.3870 H
ATOM 114 O3 NAG 6 27.009 23.605 20.159 -0.6810 1.7210 O
ATOM 115 HO3 NAG 6 26.232 24.141 19.985 0.4230 0.2000 H
ATOM 116 C2 NAG 6 25.632 21.608 19.716 0.4800 1.9080 C
ATOM 117 H2 NAG 6 25.497 21.617 20.797 0.0000 1.3870 H
ATOM 118 N2 NAG 6 24.509 22.293 19.091 -0.7220 1.8240 N
ATOM 119 HN2 NAG 6 24.640 22.590 18.135 0.3000 0.6000 H
ATOM 120 C7 NAG 6 23.258 22.346 19.571 0.6480 1.9080 C
ATOM 121 O7 NAG 6 23.030 21.878 20.681 -0.5760 1.6612 O
ATOM 122 C8 NAG 6 22.179 23.184 18.860 0.0340 1.9080 C
ATOM 123 H83 NAG 6 22.105 24.156 19.347 0.0000 1.4870 H
ATOM 124 H82 NAG 6 22.381 23.252 17.791 0.0000 1.4870 H
ATOM 125 H81 NAG 6 21.182 22.753 18.947 0.0000 1.4870 H
ATOM 126 C1 MAN 7 14.747 18.691 19.773 0.4330 1.9080 C
ATOM 127 H1 MAN 7 15.125 19.240 20.636 0.0000 1.2870 H
ATOM 128 C2 MAN 7 13.634 17.769 20.284 0.2450 1.9080 C
ATOM 129 H2 MAN 7 14.120 17.040 20.932 0.0000 1.3870 H
ATOM 130 C3 MAN 7 12.977 17.007 19.134 0.2520 1.9080 C
ATOM 131 H3 MAN 7 13.768 16.506 18.576 0.0000 1.3870 H
ATOM 132 C4 MAN 7 12.373 18.008 18.138 0.3260 1.9080 C
ATOM 133 H4 MAN 7 11.545 18.474 18.672 0.0000 1.3870 H
ATOM 134 C5 MAN 7 13.446 18.930 17.559 0.2760 1.9080 C
ATOM 135 H5 MAN 7 14.191 18.308 17.064 0.0000 1.3870 H
ATOM 136 C6 MAN 7 12.792 19.949 16.602 0.2660 1.9080 C
ATOM 137 H62 MAN 7 12.289 19.515 15.739 0.0000 1.3870 H
ATOM 138 H61 MAN 7 12.180 20.504 17.313 0.0000 1.3870 H
ATOM 139 O6 MAN 7 13.815 20.912 16.104 -0.6880 1.7210 O
ATOM 140 HO6 MAN 7 13.317 21.659 15.765 0.4220 0.2000 H
ATOM 141 O5 MAN 7 14.216 19.588 18.676 -0.5070 1.6837 O
ATOM 142 O4 MAN 7 11.836 17.184 17.068 -0.7330 1.7210 O
ATOM 143 HO4 MAN 7 10.923 17.477 17.036 0.4380 0.2000 H
ATOM 144 O3 MAN 7 11.933 16.147 19.631 -0.6960 1.7210 O
ATOM 145 HO3 MAN 7 11.442 16.596 20.323 0.4310 0.2000 H
ATOM 146 O2 MAN 7 12.617 18.557 20.966 -0.4650 1.6837 O
ATOM 147 C1 NAG 8 12.792 18.889 22.425 0.2870 1.9080 C
ATOM 148 H1 NAG 8 13.803 18.686 22.778 0.0000 1.2870 H
ATOM 149 O5 NAG 8 11.838 18.035 23.154 -0.4330 1.6837 O
ATOM 150 C5 NAG 8 11.704 18.244 24.665 0.2080 1.9080 C
ATOM 151 H5 NAG 8 12.613 17.860 25.127 0.0000 1.3870 H
ATOM 152 C6 NAG 8 10.607 17.320 25.138 0.2890 1.9080 C
ATOM 153 H62 NAG 8 9.696 17.315 24.539 0.0000 1.3870 H
ATOM 154 H61 NAG 8 10.443 17.500 26.201 0.0000 1.3870 H
ATOM 155 O6 NAG 8 11.076 15.941 25.027 -0.6890 1.7210 O
ATOM 156 HO6 NAG 8 10.369 15.389 25.368 0.4240 0.2000 H
ATOM 157 C4 NAG 8 11.594 19.727 25.074 0.3020 1.9080 C
ATOM 158 H4 NAG 8 10.568 20.028 24.864 0.0000 1.3870 H
ATOM 159 O4 NAG 8 11.891 19.848 26.486 -0.7160 1.7210 O
ATOM 160 HO4 NAG 8 11.574 20.686 26.830 0.4360 0.2000 H
ATOM 161 C3 NAG 8 12.455 20.667 24.214 0.1800 1.9080 C
ATOM 162 H3 NAG 8 13.501 20.556 24.500 0.0000 1.3870 H
ATOM 163 O3 NAG 8 11.966 22.045 24.403 -0.6810 1.7210 O
ATOM 164 HO3 NAG 8 12.770 22.565 24.338 0.4230 0.2000 H
ATOM 165 C2 NAG 8 12.455 20.356 22.680 0.4800 1.9080 C
ATOM 166 H2 NAG 8 11.478 20.501 22.219 0.0000 1.3870 H
ATOM 167 N2 NAG 8 13.467 21.238 21.983 -0.7220 1.8240 N
ATOM 168 HN2 NAG 8 14.407 21.266 22.350 0.3000 0.6000 H
ATOM 169 C7 NAG 8 13.331 21.824 20.761 0.6480 1.9080 C
ATOM 170 O7 NAG 8 12.277 21.728 20.131 -0.5760 1.6612 O
ATOM 171 C8 NAG 8 14.534 22.609 20.251 0.0340 1.9080 C
ATOM 172 H83 NAG 8 14.133 23.428 19.654 0.0000 1.4870 H
ATOM 173 H82 NAG 8 15.088 23.019 21.095 0.0000 1.4870 H
ATOM 174 H81 NAG 8 15.186 21.982 19.641 0.0000 1.4870 H
TER 175 NAG 8
ENDMDL
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