Support multi-residue molecules in template generator and improve performance

.github/workflows/test_charmm.yaml

@@ -25,7 +25,7 @@ jobs:
       matrix:
         os: [ubuntu-latest]
         python-version: ["3.13"]
-        openmm-version: ["8.4.0"]
+        openmm-version: ["8.5.0beta"]
 
     steps:
     - uses: actions/checkout@v6

charmm/convert_charmm_anisotropy_script.txt

@@ -23,13 +23,11 @@ def extract_atom_name(raw_atom_name, templates):
 
 residue_data = []
 
-for residue_index, residue in enumerate(topology.residues()):
+for residue in topology.residues():
     # Extract the residue or patch names and atom names.
-    template_data = templateForResidue[residue_index]
     templates = set()
-    if template_data is None:
-        # Multi-residue patch; fall back to parsing atom names because OpenMM
-        # leaves None in templateForResidue in this case.
+    if residue not in templateForResidue:
+        # Multi-residue patch; fall back to parsing atom names.
         atom_names = []
         skip_residue = False
         for atom in residue.atoms():
@@ -45,6 +43,7 @@ for residue_index, residue in enumerate(topology.residues()):
             continue
     else:
         # Extract names from template name.
+        template_data = templateForResidue[residue]
         for template_index, template_name in enumerate(template_data.name.split("-")):
             if template_index:
                 # Patch name.

charmm/convert_charmm_improper_script.txt

@@ -48,13 +48,11 @@ def find_improper(improper_types, atom_classes):
 
 residue_data = []
 
-for residue_index, residue in enumerate(topology.residues()):
+for residue in topology.residues():
     # Extract the residue or patch names and atom names.
-    template_data = templateForResidue[residue_index]
     templates = set()
-    if template_data is None:
-        # Multi-residue patch; fall back to parsing atom names because OpenMM
-        # leaves None in templateForResidue in this case.
+    if residue not in templateForResidue:
+        # Multi-residue patch; fall back to parsing atom names.
         atom_names = []
         skip_residue = False
         for atom in residue.atoms():
@@ -70,6 +68,7 @@ for residue_index, residue in enumerate(topology.residues()):
             continue
     else:
         # Extract names from template name.
+        template_data = templateForResidue[residue]
         for template_index, template_name in enumerate(template_data.name.split("-")):
             if template_index:
                 # Patch name.

devtools/conda-envs/test_charmm_env.yaml

@@ -1,5 +1,6 @@
 name: openmmforcefields-test-charmm
 channels:
+  - conda-forge/label/openmm_rc
   - conda-forge
 dependencies:
   - numpy <2.3

devtools/conda-envs/test_env.yaml

@@ -5,7 +5,6 @@ channels:
 dependencies:
   - ambertools >=24
   - lxml
-  - networkx
   - numpy <2.3
   - openff-toolkit >=0.11
   - openmm

openmmforcefields/data/test-ala-3.pdb

@@ -0,0 +1,36 @@
+REMARK   1 CREATED WITH OPENMM 8.4, 2026-02-10
+ATOM      1  N   ALA A   1       0.024  -0.103  -0.101  1.00  0.00           N  
+ATOM      2  H   ALA A   1       0.027  -1.132  -0.239  1.00  0.00           H  
+ATOM      3  H2  ALA A   1      -0.805   0.163   0.471  1.00  0.00           H  
+ATOM      4  H3  ALA A   1      -0.059   0.384  -1.019  1.00  0.00           H  
+ATOM      5  CA  ALA A   1       1.247   0.375   0.636  1.00  0.00           C  
+ATOM      6  HA  ALA A   1       0.814   0.861   1.495  1.00  0.00           H  
+ATOM      7  CB  ALA A   1       2.057  -0.772   1.289  1.00  0.00           C  
+ATOM      8  HB1 ALA A   1       3.136  -0.752   1.032  1.00  0.00           H  
+ATOM      9  HB2 ALA A   1       1.990  -0.641   2.395  1.00  0.00           H  
+ATOM     10  HB3 ALA A   1       1.656  -1.782   1.063  1.00  0.00           H  
+ATOM     11  C   ALA A   1       1.956   1.579   0.036  1.00  0.00           C  
+ATOM     12  O   ALA A   1       1.219   2.525  -0.201  1.00  0.00           O  
+ATOM     13  N   ALA A   2       3.289   1.631  -0.202  1.00  0.00           N  
+ATOM     14  H   ALA A   2       3.939   0.868  -0.174  1.00  0.00           H  
+ATOM     15  CA  ALA A   2       3.990   2.909  -0.215  1.00  0.00           C  
+ATOM     16  HA  ALA A   2       3.742   3.440   0.695  1.00  0.00           H  
+ATOM     17  CB  ALA A   2       3.662   3.802  -1.434  1.00  0.00           C  
+ATOM     18  HB1 ALA A   2       4.192   4.778  -1.358  1.00  0.00           H  
+ATOM     19  HB2 ALA A   2       3.956   3.311  -2.382  1.00  0.00           H  
+ATOM     20  HB3 ALA A   2       2.577   4.027  -1.467  1.00  0.00           H  
+ATOM     21  C   ALA A   2       5.487   2.654  -0.128  1.00  0.00           C  
+ATOM     22  O   ALA A   2       5.889   1.489  -0.137  1.00  0.00           O  
+ATOM     23  C   ALA A   3       8.018   5.323   0.136  1.00  0.00           C  
+ATOM     24  O   ALA A   3       7.032   6.119   0.127  1.00  0.00           O  
+ATOM     25  OXT ALA A   3       9.219   5.692   0.188  1.00  0.00           O  
+ATOM     26  N   ALA A   3       6.275   3.733  -0.037  1.00  0.00           N  
+ATOM     27  H   ALA A   3       5.963   4.691  -0.028  1.00  0.00           H  
+ATOM     28  CA  ALA A   3       7.707   3.802   0.068  1.00  0.00           C  
+ATOM     29  HA  ALA A   3       8.160   3.418  -0.833  1.00  0.00           H  
+ATOM     30  CB  ALA A   3       8.233   3.093   1.333  1.00  0.00           C  
+ATOM     31  HB1 ALA A   3       9.342   3.149   1.356  1.00  0.00           H  
+ATOM     32  HB2 ALA A   3       7.835   3.593   2.240  1.00  0.00           H  
+ATOM     33  HB3 ALA A   3       7.923   2.030   1.332  1.00  0.00           H  
+TER      34      ALA A   3
+END

openmmforcefields/ffxml/charmm/charmm36_carb_imlab.xml

@@ -1,6 +1,6 @@
 <ForceField>
   <Info>
-    <DateGenerated>2025-02-27</DateGenerated>
+    <DateGenerated>2026-03-04</DateGenerated>
     <Source Source="toppar/top_all36_prot.rtf" md5hash="4e53dc8450d0533691e95e37c2648d20" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/top_all36_prot.rtf</Source>
     <Source Source="toppar/par_all36m_prot.prm" md5hash="ff62b63c74f62fde2e1a458c0eaa29c9" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/par_all36m_prot.prm</Source>
     <Source Source="toppar/top_all36_na.rtf" md5hash="ffd9d681ff73591157e2458e336ab4a3" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/top_all36_na.rtf</Source>

openmmforcefields/ffxml/charmm/charmm36_cgenff.xml

@@ -1,6 +1,6 @@
 <ForceField>
   <Info>
-    <DateGenerated>2025-06-23</DateGenerated>
+    <DateGenerated>2026-03-04</DateGenerated>
     <Source Source="toppar/top_all36_prot.rtf" md5hash="4e53dc8450d0533691e95e37c2648d20" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/top_all36_prot.rtf</Source>
     <Source Source="toppar/par_all36m_prot.prm" md5hash="ff62b63c74f62fde2e1a458c0eaa29c9" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/par_all36m_prot.prm</Source>
     <Source Source="toppar/top_all36_na.rtf" md5hash="ffd9d681ff73591157e2458e336ab4a3" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/top_all36_na.rtf</Source>

openmmforcefields/ffxml/charmm/charmm36_d_modified.xml

@@ -1,6 +1,6 @@
 <ForceField>
   <Info>
-    <DateGenerated>2025-06-23</DateGenerated>
+    <DateGenerated>2026-03-04</DateGenerated>
     <Source Source="toppar/top_all36_prot.rtf" md5hash="4e53dc8450d0533691e95e37c2648d20" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/top_all36_prot.rtf</Source>
     <Source Source="toppar/par_all36m_prot.prm" md5hash="ff62b63c74f62fde2e1a458c0eaa29c9" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/par_all36m_prot.prm</Source>
     <Source Source="toppar/top_all36_na.rtf" md5hash="ffd9d681ff73591157e2458e336ab4a3" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/top_all36_na.rtf</Source>

openmmforcefields/ffxml/charmm/charmm36_nowaters.xml

@@ -1,6 +1,6 @@
 <ForceField>
   <Info>
-    <DateGenerated>2025-06-23</DateGenerated>
+    <DateGenerated>2026-03-04</DateGenerated>
     <Source Source="toppar/top_all36_prot.rtf" md5hash="4e53dc8450d0533691e95e37c2648d20" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/top_all36_prot.rtf</Source>
     <Source Source="toppar/par_all36m_prot.prm" md5hash="ff62b63c74f62fde2e1a458c0eaa29c9" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/par_all36m_prot.prm</Source>
     <Source Source="toppar/top_all36_na.rtf" md5hash="ffd9d681ff73591157e2458e336ab4a3" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/top_all36_na.rtf</Source>
@@ -259286,13 +259286,11 @@ def find_improper(improper_types, atom_classes):
 
 residue_data = []
 
-for residue_index, residue in enumerate(topology.residues()):
+for residue in topology.residues():
     # Extract the residue or patch names and atom names.
-    template_data = templateForResidue[residue_index]
     templates = set()
-    if template_data is None:
-        # Multi-residue patch; fall back to parsing atom names because OpenMM
-        # leaves None in templateForResidue in this case.
+    if residue not in templateForResidue:
+        # Multi-residue patch; fall back to parsing atom names.
         atom_names = []
         skip_residue = False
         for atom in residue.atoms():
@@ -259308,6 +259306,7 @@ for residue_index, residue in enumerate(topology.residues()):
             continue
     else:
         # Extract names from template name.
+        template_data = templateForResidue[residue]
         for template_index, template_name in enumerate(template_data.name.split("-")):
             if template_index:
                 # Patch name.

openmmforcefields/ffxml/charmm/charmm36_protein.xml

@@ -1,6 +1,6 @@
 <ForceField>
   <Info>
-    <DateGenerated>2025-06-23</DateGenerated>
+    <DateGenerated>2026-03-04</DateGenerated>
     <Source Source="toppar/top_all36_prot.rtf" md5hash="4e53dc8450d0533691e95e37c2648d20" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/top_all36_prot.rtf</Source>
     <Source Source="toppar/par_all36m_prot.prm" md5hash="ff62b63c74f62fde2e1a458c0eaa29c9" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/par_all36m_prot.prm</Source>
     <Source Source="toppar/stream/prot/toppar_all36_prot_aldehydes.str" md5hash="dda2e0968eb30c1b8689e6f06b8502f7" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/stream/prot/toppar_all36_prot_aldehydes.str</Source>
@@ -8760,13 +8760,11 @@ def find_improper(improper_types, atom_classes):
 
 residue_data = []
 
-for residue_index, residue in enumerate(topology.residues()):
+for residue in topology.residues():
     # Extract the residue or patch names and atom names.
-    template_data = templateForResidue[residue_index]
     templates = set()
-    if template_data is None:
-        # Multi-residue patch; fall back to parsing atom names because OpenMM
-        # leaves None in templateForResidue in this case.
+    if residue not in templateForResidue:
+        # Multi-residue patch; fall back to parsing atom names.
         atom_names = []
         skip_residue = False
         for atom in residue.atoms():
@@ -8782,6 +8780,7 @@ for residue_index, residue in enumerate(topology.residues()):
             continue
     else:
         # Extract names from template name.
+        template_data = templateForResidue[residue]
         for template_index, template_name in enumerate(template_data.name.split("-")):
             if template_index:
                 # Patch name.

openmmforcefields/ffxml/charmm/charmm36_protein_d.xml

@@ -1,6 +1,6 @@
 <ForceField>
   <Info>
-    <DateGenerated>2025-02-27</DateGenerated>
+    <DateGenerated>2026-03-04</DateGenerated>
     <Source Source="toppar/top_all36_prot.rtf" md5hash="4e53dc8450d0533691e95e37c2648d20" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/top_all36_prot.rtf</Source>
     <Source Source="toppar/par_all36m_prot.prm" md5hash="ff62b63c74f62fde2e1a458c0eaa29c9" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/par_all36m_prot.prm</Source>
     <Source Source="toppar/stream/prot/toppar_all36_prot_aldehydes.str" md5hash="dda2e0968eb30c1b8689e6f06b8502f7" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/stream/prot/toppar_all36_prot_aldehydes.str</Source>

openmmforcefields/ffxml/charmm/charmm_polar_2023.xml

@@ -1,6 +1,6 @@
 <ForceField>
   <Info>
-    <DateGenerated>2025-06-23</DateGenerated>
+    <DateGenerated>2026-03-04</DateGenerated>
     <Source Source="toppar/drude/drude_toppar_2023/toppar_drude_main_protein_2023a.str" md5hash="f3c4caab3ff08e7b822f7b944db3f197" sourcePackage="drude" sourcePackageVersion="drude_toppar_2023.tgz">toppar/drude/drude_toppar_2023/toppar_drude_main_protein_2023a.str</Source>
     <Source Source="toppar/drude/drude_toppar_2023/toppar_drude_d_aminoacids_2023a.str" md5hash="192af93e684f3891df130182b8302c58" sourcePackage="drude" sourcePackageVersion="drude_toppar_2023.tgz">toppar/drude/drude_toppar_2023/toppar_drude_d_aminoacids_2023a.str</Source>
     <Source Source="toppar/drude/drude_toppar_2023/toppar_drude_carbohydrate_2023a.str" md5hash="6d8a686b8b5ecf19de7e598d928a7c1a" sourcePackage="drude" sourcePackageVersion="drude_toppar_2023.tgz">toppar/drude/drude_toppar_2023/toppar_drude_carbohydrate_2023a.str</Source>
@@ -30887,13 +30887,11 @@ def find_improper(improper_types, atom_classes):
 
 residue_data = []
 
-for residue_index, residue in enumerate(topology.residues()):
+for residue in topology.residues():
     # Extract the residue or patch names and atom names.
-    template_data = templateForResidue[residue_index]
     templates = set()
-    if template_data is None:
-        # Multi-residue patch; fall back to parsing atom names because OpenMM
-        # leaves None in templateForResidue in this case.
+    if residue not in templateForResidue:
+        # Multi-residue patch; fall back to parsing atom names.
         atom_names = []
         skip_residue = False
         for atom in residue.atoms():
@@ -30909,6 +30907,7 @@ for residue_index, residue in enumerate(topology.residues()):
             continue
     else:
         # Extract names from template name.
+        template_data = templateForResidue[residue]
         for template_index, template_name in enumerate(template_data.name.split("-")):
             if template_index:
                 # Patch name.
@@ -31531,13 +31530,11 @@ def extract_atom_name(raw_atom_name, templates):
 
 residue_data = []
 
-for residue_index, residue in enumerate(topology.residues()):
+for residue in topology.residues():
     # Extract the residue or patch names and atom names.
-    template_data = templateForResidue[residue_index]
     templates = set()
-    if template_data is None:
-        # Multi-residue patch; fall back to parsing atom names because OpenMM
-        # leaves None in templateForResidue in this case.
+    if residue not in templateForResidue:
+        # Multi-residue patch; fall back to parsing atom names.
         atom_names = []
         skip_residue = False
         for atom in residue.atoms():
@@ -31553,6 +31550,7 @@ for residue_index, residue in enumerate(topology.residues()):
             continue
     else:
         # Extract names from template name.
+        template_data = templateForResidue[residue]
         for template_index, template_name in enumerate(template_data.name.split("-")):
             if template_index:
                 # Patch name.

openmmforcefields/ffxml/charmm/charmm_polar_2023_d.xml

@@ -1,6 +1,6 @@
 <ForceField>
   <Info>
-    <DateGenerated>2025-06-23</DateGenerated>
+    <DateGenerated>2026-03-04</DateGenerated>
     <Source Source="toppar/drude/drude_toppar_2023/toppar_drude_main_protein_2023a.str" md5hash="f3c4caab3ff08e7b822f7b944db3f197" sourcePackage="drude" sourcePackageVersion="drude_toppar_2023.tgz">toppar/drude/drude_toppar_2023/toppar_drude_main_protein_2023a.str</Source>
     <Source Source="toppar/drude/drude_toppar_2023/toppar_drude_d_aminoacids_2023a.str" md5hash="192af93e684f3891df130182b8302c58" sourcePackage="drude" sourcePackageVersion="drude_toppar_2023.tgz">toppar/drude/drude_toppar_2023/toppar_drude_d_aminoacids_2023a.str</Source>
     <Source Source="toppar/drude/drude_toppar_2023/toppar_drude_carbohydrate_2023a.str" md5hash="6d8a686b8b5ecf19de7e598d928a7c1a" sourcePackage="drude" sourcePackageVersion="drude_toppar_2023.tgz">toppar/drude/drude_toppar_2023/toppar_drude_carbohydrate_2023a.str</Source>

openmmforcefields/ffxml/charmm/waters_ions_default.xml

@@ -1,6 +1,6 @@
 <ForceField>
   <Info>
-    <DateGenerated>2025-02-27</DateGenerated>
+    <DateGenerated>2026-03-04</DateGenerated>
     <Source Source="toppar/toppar_water_ions.str" md5hash="1eba52cd9a244fa3df9a274a806d9128" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/toppar_water_ions.str</Source>
     <Source Source="toppar/stream/misc/toppar_ions_won.str" md5hash="f523f7727e7dfa25468cc75f9b880c5b" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/stream/misc/toppar_ions_won.str</Source>
     <Reference Reference="W.L. Jorgensen; J.Chandrasekhar; J.D. Madura; R.W. Impey; M.L. Klein; &quot;Comparison of simple potential functions for simulating liquid water&quot;, J. Chem. Phys. 79 926-935 (1983)." forcefield="tip3p">W.L. Jorgensen; J.Chandrasekhar; J.D. Madura; R.W. Impey; M.L. Klein; "Comparison of simple potential functions for simulating liquid water", J. Chem. Phys. 79 926-935 (1983).</Reference>

openmmforcefields/ffxml/charmm/waters_ions_spc.xml

@@ -1,6 +1,6 @@
 <ForceField>
   <Info>
-    <DateGenerated>2025-02-27</DateGenerated>
+    <DateGenerated>2026-03-04</DateGenerated>
     <Source Source="toppar/non_charmm/toppar_water_ions_spc.str" md5hash="56e9bad61beb634f3f68a0df8e03a917" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/non_charmm/toppar_water_ions_spc.str</Source>
     <Source Source="toppar/stream/misc/toppar_ions_won.str" md5hash="f523f7727e7dfa25468cc75f9b880c5b" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/stream/misc/toppar_ions_won.str</Source>
     <Reference Reference="H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, and J. Hermans. INTERACTION MODELS FOR WATER IN RELATION TO PROTEIN HYDRATION In Intermolecular Forces, edited by B. Pullman (Reidel, Dordrecht, 1981), p. 331" forcefield="spc">H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, and J. Hermans. INTERACTION MODELS FOR WATER IN RELATION TO PROTEIN HYDRATION In Intermolecular Forces, edited by B. Pullman (Reidel, Dordrecht, 1981), p. 331</Reference>

openmmforcefields/ffxml/charmm/waters_ions_spc_e.xml

@@ -1,6 +1,6 @@
 <ForceField>
   <Info>
-    <DateGenerated>2025-02-27</DateGenerated>
+    <DateGenerated>2026-03-04</DateGenerated>
     <Source Source="toppar/non_charmm/toppar_water_ions_spc_e.str" md5hash="5a43bf944d3d6bd537b50538ceb83560" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/non_charmm/toppar_water_ions_spc_e.str</Source>
     <Source Source="toppar/stream/misc/toppar_ions_won.str" md5hash="f523f7727e7dfa25468cc75f9b880c5b" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/stream/misc/toppar_ions_won.str</Source>
     <Reference Reference="H.J.C. Berendsen, J. R. Grigera, and T. P. Straatsma. The Missing Term in Effective Pair Potentials. J. Phys. Chem 91:6269-6271, 1987." forcefield="spc-e">H.J.C. Berendsen, J. R. Grigera, and T. P. Straatsma. The Missing Term in Effective Pair Potentials. J. Phys. Chem 91:6269-6271, 1987.</Reference>

openmmforcefields/ffxml/charmm/waters_ions_tip3p_pme_b.xml

@@ -1,6 +1,6 @@
 <ForceField>
   <Info>
-    <DateGenerated>2025-02-27</DateGenerated>
+    <DateGenerated>2026-03-04</DateGenerated>
     <Source Source="toppar/non_charmm/toppar_water_ions_tip3p_pme_b.str" md5hash="772b85f388766661707343bb1947dc1a" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/non_charmm/toppar_water_ions_tip3p_pme_b.str</Source>
     <Source Source="toppar/stream/misc/toppar_ions_won.str" md5hash="f523f7727e7dfa25468cc75f9b880c5b" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/stream/misc/toppar_ions_won.str</Source>
     <Reference Reference="D.J. Price and C.L. Brooks III. A modified TIP3P water potential for simulation with Ewald summation. J. Chem. Phys. 121:10096-10103, 2004." forcefield="tip3p-pme-b">D.J. Price and C.L. Brooks III. A modified TIP3P water potential for simulation with Ewald summation. J. Chem. Phys. 121:10096-10103, 2004.</Reference>