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Commit 902116b1 authored by Giovanni Bussi's avatar Giovanni Bussi
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Merge branch 'v2.4' into v2.5

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CHANGES/v2.4.md
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......@@ -252,4 +252,5 @@ For users:
For users:
- Take into account `UNITS` when using MD codes that feeds one line at a time to PLUMED (e.g., OpenMM). See \issue{582}.
- Fix PDB parser for non justified atom numbers. See \issue{592}.
regtest/basic/rt65/AA.pdb
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......@@ -2,37 +2,37 @@ TITLE Great Red Owns Many ACres of Sand
REMARK THIS IS A SIMULATION BOX
CRYST1 6.958 11.030 10.714 90.00 90.00 90.00 P 1 1
MODEL 1
ATOM 1 H5T A 1 14.820 -3.670 5.260 1.00 0.00
ATOM 2 O5' A 1 15.280 -2.790 5.160 1.00 0.00
ATOM 3 C5' A 1 16.340 -2.690 6.140 1.00 0.00
ATOM 4 1H5' A 1 17.000 -3.430 5.990 1.00 0.00
ATOM 5 2H5' A 1 15.960 -2.760 7.060 1.00 0.00
ATOM 6 C4' A 1 16.940 -1.350 5.900 1.00 0.00
ATOM 7 H4' A 1 17.680 -1.280 6.580 1.00 0.00
ATOM 8 O4' A 1 17.430 -1.280 4.600 1.00 0.00
ATOM 9 C1' A 1 17.500 0.110 4.240 1.00 0.00
ATOM 10 H1' A 1 18.450 0.400 4.070 1.00 0.00
ATOM 11 N9 A 1 16.660 0.250 3.040 1.00 0.00
ATOM 12 C8 A 1 15.860 -0.690 2.450 1.00 0.00
ATOM 13 H8 A 1 15.740 -1.610 2.820 1.00 0.00
ATOM 14 N7 A 1 15.260 -0.280 1.380 1.00 0.00
ATOM 15 C5 A 1 15.710 1.020 1.230 1.00 0.00
ATOM 16 C6 A 1 15.450 2.020 0.250 1.00 0.00
ATOM 17 N6 A 1 14.640 1.860 -0.780 1.00 0.00
ATOM 18 H61 A 1 14.160 0.990 -0.910 1.00 0.00
ATOM 19 H62 A 1 14.510 2.600 -1.430 1.00 0.00
ATOM 20 N1 A 1 16.090 3.170 0.480 1.00 0.00
ATOM 21 C2 A 1 16.910 3.400 1.530 1.00 0.00
ATOM 22 H2 A 1 17.340 4.300 1.590 1.00 0.00
ATOM 23 N3 A 1 17.200 2.530 2.470 1.00 0.00
ATOM 24 C4 A 1 16.570 1.360 2.260 1.00 0.00
ATOM 25 C3' A 1 15.940 -0.160 5.930 1.00 0.00
ATOM 26 H3' A 1 15.040 -0.310 5.530 1.00 0.00
ATOM 27 C2' A 1 16.900 0.910 5.350 1.00 0.00
ATOM 28 1H2' A 1 16.600 1.820 5.060 1.00 0.00
ATOM 29 O2' A 1 17.840 1.060 6.410 1.00 0.00
ATOM 30 2HO' A 1 17.420 1.600 7.150 1.00 0.00
ATOM 31 O3' A 1 15.700 0.220 7.290 1.00 0.00
ATOM 1 H5T A 1 14.820 -3.670 5.260 1.00 0.00
ATOM 2 O5' A 1 15.280 -2.790 5.160 1.00 0.00
ATOM 3 C5' A 1 16.340 -2.690 6.140 1.00 0.00
ATOM 4 1H5' A 1 17.000 -3.430 5.990 1.00 0.00
ATOM 5 2H5' A 1 15.960 -2.760 7.060 1.00 0.00
ATOM 6 C4' A 1 16.940 -1.350 5.900 1.00 0.00
ATOM 7 H4' A 1 17.680 -1.280 6.580 1.00 0.00
ATOM 8 O4' A 1 17.430 -1.280 4.600 1.00 0.00
ATOM 9 C1' A 1 17.500 0.110 4.240 1.00 0.00
ATOM 10 H1' A 1 18.450 0.400 4.070 1.00 0.00
ATOM 11 N9 A 1 16.660 0.250 3.040 1.00 0.00
ATOM 12 C8 A 1 15.860 -0.690 2.450 1.00 0.00
ATOM 13 H8 A 1 15.740 -1.610 2.820 1.00 0.00
ATOM 14 N7 A 1 15.260 -0.280 1.380 1.00 0.00
ATOM 15 C5 A 1 15.710 1.020 1.230 1.00 0.00
ATOM 16 C6 A 1 15.450 2.020 0.250 1.00 0.00
ATOM 17 N6 A 1 14.640 1.860 -0.780 1.00 0.00
ATOM 18 H61 A 1 14.160 0.990 -0.910 1.00 0.00
ATOM 19 H62 A 1 14.510 2.600 -1.430 1.00 0.00
ATOM 20 N1 A 1 16.090 3.170 0.480 1.00 0.00
ATOM 21 C2 A 1 16.910 3.400 1.530 1.00 0.00
ATOM 22 H2 A 1 17.340 4.300 1.590 1.00 0.00
ATOM 23 N3 A 1 17.200 2.530 2.470 1.00 0.00
ATOM 24 C4 A 1 16.570 1.360 2.260 1.00 0.00
ATOM 25 C3' A 1 15.940 -0.160 5.930 1.00 0.00
ATOM 26 H3' A 1 15.040 -0.310 5.530 1.00 0.00
ATOM 27 C2' A 1 16.900 0.910 5.350 1.00 0.00
ATOM 28 1H2' A 1 16.600 1.820 5.060 1.00 0.00
ATOM 29 O2' A 1 17.840 1.060 6.410 1.00 0.00
ATOM 30 2HO' A 1 17.420 1.600 7.150 1.00 0.00
ATOM 31 O3' A 1 15.700 0.220 7.290 1.00 0.00
ATOM 32 P A 2 14.280 0.530 7.900 1.00 0.00
ATOM 33 O1P A 2 14.390 -0.010 9.290 1.00 0.00
ATOM 34 O2P A 2 13.160 -0.100 7.150 1.00 0.00
......
src/tools/PDB.cpp
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......@@ -333,6 +333,7 @@ bool PDB::readFromFilepointer(FILE *fp,bool naturalUnits,double scale) {
int result;
auto trimmed=serial;
Tools::trim(trimmed);
while(trimmed.length()<5) trimmed = std::string(" ") + trimmed;
const char* errmsg = h36::hy36decode(5, trimmed.c_str(),trimmed.length(), &result);
if(errmsg) {
std::string msg(errmsg);
......
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