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Fix issue with chain endings in cyclic peptide PDB reading. #150

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Fix issue with chain endings in cyclic peptide PDB reading. #150

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68a6d81
Fix issue with chain endings.
roccomoretti Sep 5, 2024
3c2e5be
Fix offset condition
roccomoretti Sep 5, 2024
b613cc4
Merge remote-tracking branch 'origin/main' into fix_cycle_chain_settings
roccomoretti Apr 25, 2025
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8 changes: 4 additions & 4 deletions source/src/core/io/pose_from_sfr/PoseFromSFRBuilder.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -1182,6 +1182,9 @@ void PoseFromSFRBuilder::build_initial_pose( pose::Pose & pose )

residues.push_back( ii_rsd );
jump_connections.push_back( root_index );
if ( residues.size() > 1 ) {
chain_endings.push_back( residues.size() - 1 );
}

} else { // Append residue to current chain dependent on bond length.
if ( ! options_.missing_dens_as_jump() ) {
Expand Down Expand Up @@ -1231,6 +1234,7 @@ void PoseFromSFRBuilder::build_initial_pose( pose::Pose & pose )

residues.push_back( ii_rsd );
jump_connections.push_back( old_nres );
// Keep this in the same chain -- no chain ending.


} else {
Expand Down Expand Up @@ -1263,10 +1267,6 @@ void PoseFromSFRBuilder::build_initial_pose( pose::Pose & pose )
pose_to_rinfo_.push_back( ii );
pose_temps_.push_back( rinfos_[ ii ].temps() );

// Update the pose-internal chain label if necessary.
if ( ( is_lower_terminus_[ ii ] || ! determine_check_Ntermini_for_this_chain( rinfos_[ ii ].chainID() ) ) && residues.size() > 1 ) {
chain_endings.push_back( residues.size() - 1 );
}
}

// Now actually append all the residues
Expand Down
1 change: 1 addition & 0 deletions source/test/core.test.settings
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Original file line number Diff line number Diff line change
Expand Up @@ -1084,6 +1084,7 @@ testinputfiles = [
"io/pose_from_sfr/ace_from_1VDN.pdb",
"io/pose_from_sfr/acetylated_and_methylated_alanine.pdb",
"io/pose_from_sfr/cyclic_pep_with_link.pdb",
"io/pose_from_sfr/cycle_chain_test.pdb",
"io/pose_from_sfr/1rgr_apo.pdb",
"io/pose_from_sfr/1IJ3_cleaned.pdb",
"io/pose_to_sfr/2_peptides_2_glycan_ligands.pdb",
Expand Down
15 changes: 15 additions & 0 deletions source/test/core/io/pose_from_sfr/PoseFromSFRBuilder.cxxtest.hh
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Original file line number Diff line number Diff line change
Expand Up @@ -234,6 +234,21 @@ public:
TS_ASSERT( pose->residue(pose->total_residue()).connected_residue_at_upper() == 1 );
}

/// @brief This tests for proper chain separation when you have a cyclic peptide after a regular one.
/// There was a bug where the peptide cycle was counted as "part of" the previous chain,
/// due to the lack of being "terminal"
void test_read_cyclic_peptide_chain_ending() {
core::pose::PoseOP pose( core::import_pose::pose_from_file( "core/io/pose_from_sfr/cycle_chain_test.pdb", false ) );
TS_ASSERT_EQUALS( pose->size(), 5 );
TR << "cycle_chain_test.pdb sequence: " << pose->annotated_sequence() << std::endl;
TS_ASSERT( pose->residue(2).is_upper_terminus() );
TS_ASSERT( !pose->residue(3).is_lower_terminus() );
TS_ASSERT( !pose->residue(5).is_upper_terminus() );
TS_ASSERT_EQUALS( pose->residue(3).connected_residue_at_lower(), 5 );
TS_ASSERT_EQUALS( pose->residue(5).connected_residue_at_upper(), 3 );
TS_ASSERT_EQUALS( pose->num_chains(), 2 );
}

/// @brief Test that we can correctly read poses without adding termini to user-specified chains.
/// @author Vikram K. Mulligan ([email protected]).
void test_read_pose_without_terminal_variant_types() {
Expand Down
86 changes: 86 additions & 0 deletions source/test/core/io/pose_from_sfr/cycle_chain_test.pdb
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Original file line number Diff line number Diff line change
@@ -0,0 +1,86 @@
LINK N ARG B 304 C ALA B 306 1.35
ATOM 4888 N CYS A 302 124.240 127.763 155.412 1.00 0.00 N
ATOM 4889 CA CYS A 302 125.068 127.591 156.591 1.00 0.00 C
ATOM 4890 C CYS A 302 124.803 128.755 157.559 1.00 0.00 C
ATOM 4891 O CYS A 302 125.504 129.749 157.358 1.00 0.00 O
ATOM 4892 CB CYS A 302 126.549 127.545 156.217 1.00 0.00 C
ATOM 4893 SG CYS A 302 127.659 127.297 157.624 1.00 0.00 S
ATOM 4894 H CYS A 302 123.880 128.693 155.260 1.00 0.00 H
ATOM 4895 HA CYS A 302 124.828 126.637 157.048 1.00 0.00 H
ATOM 4896 1HB CYS A 302 126.721 126.737 155.506 1.00 0.00 H
ATOM 4897 2HB CYS A 302 126.830 128.477 155.727 1.00 0.00 H
ATOM 4898 HG CYS A 302 127.024 128.123 158.450 1.00 0.00 H
ATOM 4899 N GLN A 303 124.535 128.417 158.826 1.00 0.00 N
ATOM 4900 CA GLN A 303 124.536 127.021 159.280 1.00 0.00 C
ATOM 4901 C GLN A 303 123.267 126.269 158.883 1.00 0.00 C
ATOM 4902 O GLN A 303 122.182 126.566 159.381 1.00 0.00 O
ATOM 4903 OXT GLN A 303 123.362 125.266 158.177 1.00 0.00 O
ATOM 4904 CB GLN A 303 124.711 126.959 160.799 1.00 0.00 C
ATOM 4905 CG GLN A 303 124.855 125.552 161.353 1.00 0.00 C
ATOM 4906 CD GLN A 303 125.128 125.543 162.845 1.00 0.00 C
ATOM 4907 OE1 GLN A 303 125.018 126.571 163.518 1.00 0.00 O
ATOM 4908 NE2 GLN A 303 125.489 124.378 163.372 1.00 0.00 N
ATOM 4909 H GLN A 303 123.733 128.950 159.165 1.00 0.00 H
ATOM 4910 HA GLN A 303 125.386 126.514 158.824 1.00 0.00 H
ATOM 4911 1HB GLN A 303 125.595 127.526 161.087 1.00 0.00 H
ATOM 4912 2HB GLN A 303 123.852 127.425 161.284 1.00 0.00 H
ATOM 4913 1HG GLN A 303 123.930 125.004 161.173 1.00 0.00 H
ATOM 4914 2HG GLN A 303 125.686 125.058 160.851 1.00 0.00 H
ATOM 4915 1HE2 GLN A 303 125.681 124.309 164.352 1.00 0.00 H
ATOM 4916 2HE2 GLN A 303 125.566 123.567 162.791 1.00 0.00 H
TER
ATOM 4918 N ARG B 304 156.718 110.241 143.432 1.00 0.00 N
ATOM 4919 CA ARG B 304 155.819 109.548 142.520 1.00 0.00 C
ATOM 4920 C ARG B 304 155.287 108.243 143.101 1.00 0.00 C
ATOM 4921 O ARG B 304 154.079 108.074 143.270 1.00 0.00 O
ATOM 4922 CB ARG B 304 156.529 109.252 141.208 1.00 0.00 C
ATOM 4923 CG ARG B 304 155.803 108.279 140.292 1.00 0.00 C
ATOM 4924 CD ARG B 304 156.693 107.764 139.221 1.00 0.00 C
ATOM 4925 NE ARG B 304 157.739 106.905 139.751 1.00 0.00 N
ATOM 4926 CZ ARG B 304 158.802 106.470 139.047 1.00 0.00 C
ATOM 4927 NH1 ARG B 304 158.945 106.823 137.788 1.00 0.00 N
ATOM 4928 NH2 ARG B 304 159.701 105.690 139.621 1.00 0.00 N
ATOM 4929 HO ARG B 304 157.709 110.048 143.387 1.00 0.00 H
ATOM 4930 HA ARG B 304 154.968 110.201 142.327 1.00 0.00 H
ATOM 4931 1HB ARG B 304 156.671 110.180 140.655 1.00 0.00 H
ATOM 4932 2HB ARG B 304 157.516 108.838 141.412 1.00 0.00 H
ATOM 4933 1HG ARG B 304 155.442 107.431 140.876 1.00 0.00 H
ATOM 4934 2HG ARG B 304 154.956 108.783 139.823 1.00 0.00 H
ATOM 4935 1HD ARG B 304 156.107 107.186 138.507 1.00 0.00 H
ATOM 4936 2HD ARG B 304 157.165 108.601 138.708 1.00 0.00 H
ATOM 4937 HE ARG B 304 157.663 106.612 140.716 1.00 0.00 H
ATOM 4938 1HH1 ARG B 304 158.259 107.419 137.349 1.00 0.00 H
ATOM 4939 2HH1 ARG B 304 159.742 106.498 137.260 1.00 0.00 H
ATOM 4940 1HH2 ARG B 304 159.591 105.419 140.589 1.00 0.00 H
ATOM 4941 2HH2 ARG B 304 160.497 105.365 139.094 1.00 0.00 H
ATOM 4942 N TRP B 305 156.166 107.296 143.419 1.00 0.00 N
ATOM 4943 CA TRP B 305 155.692 106.052 144.029 1.00 0.00 C
ATOM 4944 C TRP B 305 155.568 106.155 145.548 1.00 0.00 C
ATOM 4945 O TRP B 305 156.424 105.667 146.299 1.00 0.00 O
ATOM 4946 CB TRP B 305 156.636 104.901 143.677 1.00 0.00 C
ATOM 4947 CG TRP B 305 156.550 104.475 142.242 1.00 0.00 C
ATOM 4948 CD1 TRP B 305 155.611 104.859 141.332 1.00 0.00 C
ATOM 4949 CD2 TRP B 305 157.444 103.577 141.541 1.00 0.00 C
ATOM 4950 NE1 TRP B 305 155.856 104.264 140.120 1.00 0.00 N
ATOM 4951 CE2 TRP B 305 156.975 103.477 140.229 1.00 0.00 C
ATOM 4952 CE3 TRP B 305 158.588 102.861 141.917 1.00 0.00 C
ATOM 4953 CZ2 TRP B 305 157.607 102.686 139.282 1.00 0.00 C
ATOM 4954 CZ3 TRP B 305 159.223 102.070 140.967 1.00 0.00 C
ATOM 4955 CH2 TRP B 305 158.745 101.985 139.684 1.00 0.00 C
ATOM 4956 H TRP B 305 157.148 107.385 143.195 1.00 0.00 H
ATOM 4957 HA TRP B 305 154.702 105.833 143.627 1.00 0.00 H
ATOM 4958 1HB TRP B 305 157.664 105.197 143.886 1.00 0.00 H
ATOM 4959 2HB TRP B 305 156.409 104.040 144.304 1.00 0.00 H
ATOM 4960 HD1 TRP B 305 154.787 105.539 141.538 1.00 0.00 H
ATOM 4961 HE1 TRP B 305 155.304 104.384 139.283 1.00 0.00 H
ATOM 4962 HE3 TRP B 305 158.973 102.927 142.934 1.00 0.00 H
ATOM 4963 HZ2 TRP B 305 157.243 102.606 138.258 1.00 0.00 H
ATOM 4964 HZ3 TRP B 305 160.112 101.515 141.268 1.00 0.00 H
ATOM 4965 HH2 TRP B 305 159.267 101.355 138.964 1.00 0.00 H
ATOM 4966 N ALA B 306 154.516 106.832 145.982 1.00 0.00 N
ATOM 4967 CA ALA B 306 154.229 107.109 147.360 1.00 0.00 C
ATOM 4968 C ALA B 306 154.087 105.847 148.144 1.00 0.00 C
ATOM 4969 O ALA B 306 153.182 105.010 147.926 1.00 0.00 O
ATOM 4970 CB ALA B 306 153.055 107.999 147.601 1.00 0.00 C
TER
END