Merge pull request #59 from openforcefield/test_ncaa

Test ncaa
openforcefield · Feb 12, 2025 · 06719cf · 06719cf
2 parents 6c0a2b8 + 6a4aaea
commit 06719cf
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Showing 14 changed files with 64,583 additions and 345 deletions.
diff --git a/docs/tests.md b/docs/tests.md
@@ -31,6 +31,12 @@ Pablo has a (developing) PDB test suite.
     - NMR model direct from PDB, multi-model file, RNA and protein in same file
 *   - 1a45_samechain.pdb
     - RNA and protein in same file, missing TER record between incompatible polymers with same chain ID
+*   - 2MUM_blowup.pdb
+    - Strained conformation
+*   - 5eil_fixed.pdb
+    - Non-canonical amino acid from CCD, iron ion
+*   - 3ip9_dye_solvated.pdb
+    - Large system with water and NaCl, non-canonical amino acid not in CCD
 :::
 
 <script>

diff --git a/examples/prepare_jsontop.ipynb b/examples/prepare_jsontop.ipynb
diff --git a/examples/smiles_names.ipynb b/examples/smiles_names.ipynb
diff --git a/openff/pablo/_pdb_data.py b/openff/pablo/_pdb_data.py
@@ -348,8 +348,11 @@ def residue_indices(self) -> Iterator[tuple[int, ...]]:
             ),
         ):
             if alt_loc != "":
-                # TODO: Support alt locs
-                raise ValueError("Alt loc not supported")
+                warnings.warn(
+                    "Alt locs not supported; only empty or 'A' alt locs will be read",
+                )
+                if alt_loc != "A":
+                    continue
             if prev is not None and residue_info[0] != prev[0]:
                 # TODO: Support multi-model files
                 warnings.warn(
@@ -556,14 +559,20 @@ def get_residue_matches(
                         match.expect_prior_bond != neighbours_support_prior_bond
                     )
                     if prior_bond_mismatched:
-                        logging.debug("    Prior bond mismatched")
+                        logging.debug("    Match failed: Prior bond mismatched")
+                        logging.debug(
+                            f"    {match.expect_prior_bond=} but {neighbours_support_prior_bond=}",
+                        )
                         continue
 
                     posterior_bond_mismatched = (
                         match.expect_posterior_bond != neighbours_support_posterior_bond
                     )
                     if posterior_bond_mismatched:
-                        logging.debug("    Posterior bond mismatched")
+                        logging.debug("    Match failed: Posterior bond mismatched")
+                        logging.debug(
+                            f"    {match.expect_posterior_bond=} but {neighbours_support_posterior_bond=}",
+                        )
                         continue
 
                     this_filtered_matches.append(match)

diff --git a/openff/pablo/_tests/data/capped_arg_altresonance.pdb b/openff/pablo/_tests/data/capped_arg_altresonance.pdb
@@ -0,0 +1,37 @@
+ATOM      1  C   ACE     1      -1.029  -4.440   2.368  1.00  0.00           C  
+ATOM      2  O   ACE     1      -1.515  -4.609   1.242  1.00  0.00           O  
+ATOM      3  CH3 ACE     1      -1.599  -5.150   3.577  1.00  0.00           C  
+ATOM      4 1HH3 ACE     1      -1.537  -6.220   3.442  1.00  0.00           H  
+ATOM      5 2HH3 ACE     1      -1.044  -4.876   4.463  1.00  0.00           H  
+ATOM      6 3HH3 ACE     1      -2.635  -4.874   3.714  1.00  0.00           H  
+ATOM      7  N   ARG     2      -0.022  -3.647   2.514  1.00  0.00           N  
+ATOM      8  CA  ARG     2       0.519  -2.968   1.340  1.00  0.00           C  
+ATOM      9  C   ARG     2       2.029  -2.951   1.374  1.00  0.00           C  
+ATOM     10  O   ARG     2       2.654  -2.667   2.392  1.00  0.00           O  
+ATOM     11  CB  ARG     2      -0.063  -1.527   1.282  1.00  0.00           C  
+ATOM     12  CG  ARG     2       0.188  -0.757  -0.045  1.00  0.00           C  
+ATOM     13  CD  ARG     2      -0.388   0.668  -0.004  1.00  0.00           C  
+ATOM     14  NE  ARG     2      -0.136   1.349  -1.308  1.00  0.00           N  
+ATOM     15  CZ  ARG     2      -0.497   2.593  -1.608  1.00  0.00           C  
+ATOM     16  NH1 ARG     2      -1.121   3.383  -0.780  1.00  0.00           N  
+ATOM     17  NH2 ARG     2      -0.215   3.048  -2.788  1.00  0.00           N1+
+ATOM     18  H   ARG     2       0.386  -3.498   3.425  1.00  0.00           H  
+ATOM     19  HA  ARG     2       0.211  -3.538   0.443  1.00  0.00           H  
+ATOM     20 2HB  ARG     2       0.336  -0.947   2.140  1.00  0.00           H  
+ATOM     21 3HB  ARG     2      -1.156  -1.569   1.465  1.00  0.00           H  
+ATOM     22 2HG  ARG     2      -0.252  -1.330  -0.887  1.00  0.00           H  
+ATOM     23 3HG  ARG     2       1.276  -0.706  -0.255  1.00  0.00           H  
+ATOM     24 2HD  ARG     2       0.080   1.230   0.834  1.00  0.00           H  
+ATOM     25 3HD  ARG     2      -1.476   0.622   0.217  1.00  0.00           H  
+ATOM     26  HE  ARG     2       0.348   0.865  -2.071  1.00  0.00           H  
+ATOM     27 1HH1 ARG     2      -1.312   2.964   0.133  1.00  0.00           H  
+ATOM     28 2HH1 ARG     2      -1.365   4.326  -1.087  1.00  0.00           H  
+ATOM     29 1HH2 ARG     2       0.275   2.415  -3.423  1.00  0.00           H  
+ATOM     30 2HH2 ARG     2      -0.502   4.005  -3.000  1.00  0.00           H  
+ATOM     31  N   NME     3       2.682  -3.244   0.300  1.00  0.00           N  
+ATOM     32  CH3 NME     3       4.134  -3.234   0.309  1.00  0.00           C  
+ATOM     33  H   NME     3       2.183  -3.480  -0.546  1.00  0.00           H  
+ATOM     34 1HH3 NME     3       4.498  -2.228   0.165  1.00  0.00           H  
+ATOM     35 2HH3 NME     3       4.501  -3.607   1.254  1.00  0.00           H  
+ATOM     36 3HH3 NME     3       4.512  -3.861  -0.486  1.00  0.00           H  
+END