Fix the local frame axis setting in ADMP to be consistent with MPID

dmff/admp/qeq.py

@@ -24,11 +24,13 @@
         JAXOPT_OLD = False
     except ImportError:
         JAXOPT_OLD = True
-        print(
+        import warnings
+        warnings.warn(
             "jaxopt is too old. The QEQ potential function cannot be jitted. Please update jaxopt to the latest version for speed concern."
         )
 except ImportError:
-    print("jaxopt not found, QEQ cannot be used.")
+    import warnings
+    warnings.warn("jaxopt not found, QEQ cannot be used.")
 import jax
 
 from jax.scipy.special import erf, erfc

dmff/api/graph.py

@@ -104,7 +104,7 @@ def graph2top(graph: nx.Graph) -> app.Topology:
     return top
 
 
-def top2rdmol(top: app.Topology, indices: List[int]) -> Chem.rdchem.Mol:
+def top2rdmol(top: app.Topology, indices: List[int]):
     rdmol = Chem.Mol()
     emol = Chem.EditableMol(rdmol)
     idx2ridx = {}

dmff/api/topology.py

@@ -346,7 +346,7 @@ def vsites(self):
         return iter(self._vsites)
 
     @classmethod
-    def regularize_aromaticity(cls, mol: Chem.Mol) -> bool:
+    def regularize_aromaticity(cls, mol) -> bool:
         """
         Regularize Aromaticity for a rdkit.Mol object. Rings with exocyclic double bonds will not be set aromatic.
         """
@@ -681,7 +681,7 @@ def decomptop(top) -> List[List[int]]:
     return indices
 
 
-def top2rdmol(top, indices) -> Chem.rdchem.Mol:
+def top2rdmol(top, indices):
     rdmol = Chem.Mol()
     emol = Chem.EditableMol(rdmol)
     idx2ridx = {}

dmff/generators/admp.py

@@ -962,15 +962,9 @@ def __init__(self, ffinfo: dict, paramset: ParamSet):
             self.multipole_types.append(attribs[self.key_type])
             # record local coords as kz kx ky
             # None if not occur
-            kx = attribs.get("kx", None)
-            ky = attribs.get("ky", None)
-            kz = attribs.get("kz", None)
-            if kx == "-1":
-                kx = None
-            if ky == "-1":
-                ky = None
-            if kz == "-1":
-                kz = None
+            kx = attribs.get("kx", "")
+            ky = attribs.get("ky", "")
+            kz = attribs.get("kz", "")
             kxs.append(kx)
             kys.append(ky)
             kzs.append(kz)
@@ -1124,6 +1118,51 @@ def _find_polarize_key_index(self, atype: str):
             if i == atype:
                 return n
         return None
+
+    @staticmethod
+    def setAxisType(kIndices):
+        # setting up axis_indices and axis_type
+        ZThenX = 0
+        Bisector = 1
+        ZBisect = 2
+        ThreeFold = 3
+        ZOnly = 4  # typo fix
+        NoAxisType = 5
+        LastAxisTypeIndex = 6
+
+        # set axis type
+
+        ky = kIndices[2]
+        kyNegative = False
+        if ky.startswith('-'):
+            ky = ky[1:]
+            kyNegative = True
+
+        kx = kIndices[1]
+        kxNegative = False
+        if kx.startswith('-'):
+            kx = kx[1:]
+            kxNegative = True
+
+        kz = kIndices[0]
+        kzNegative = False
+        if kz.startswith('-'):
+            kz = kz[1:]
+            kzNegative = True
+
+        axisType = ZThenX
+        if (not kz):
+            axisType = NoAxisType
+        if (kz and not kx):
+            axisType = ZOnly
+        if (kz and kzNegative or kx and kxNegative):
+            axisType = Bisector
+        if (kx and kxNegative and ky and kyNegative):
+            axisType = ZBisect
+        if (kz and kzNegative and kx and kxNegative and ky and kyNegative):
+            axisType = ThreeFold
+
+        return axisType, [kz, kx, ky]
 
     def createPotential(
         self, topdata: DMFFTopology, nonbondedMethod, nonbondedCutoff, **kwargs
@@ -1198,25 +1237,7 @@ def createPotential(
                     kz = self.kStrings["kz"][i_type]
                     kx = self.kStrings["kx"][i_type]
                     ky = self.kStrings["ky"][i_type]
-                    axisType = ZThenX  # Z, X, -1
-                    if kz is None:
-                        axisType = NoAxisType  # -1, -1, -1
-                    if kz is not None and kx is None:
-                        axisType = ZOnly  # Z, -1, -1
-                    if (kz is not None and kz[0] == "-") or (
-                        kx is not None and kx[0] == "-"
-                    ):
-                        axisType = Bisector  # Z, X, -1
-                    if (kx is not None and kx[0] == "-") and (
-                        ky is not None and ky[0] == "-"
-                    ):
-                        axisType = ZBisect  # Z, Y, X
-                    if (
-                        (kz is not None and kz[0] == "-")
-                        and (kx is not None and kx[0] == "-")
-                        and (ky is not None and ky[0] == "-")
-                    ):
-                        axisType = ThreeFold  # Z, Y, X
+                    axisType, (kz, kx, ky) = self.setAxisType([kz, kx, ky])
 
                     zaxis = -1
                     xaxis = -1
@@ -1228,90 +1249,73 @@ def createPotential(
                     if axisType == ZThenX:
                         if kz is None or kx is None:
                             raise DMFFException("ZThenX axis requires both kz and kx!")
-                        kz_real = kz[1:] if kz[0] == "-" else kz
-                        kx_real = kx[1:] if kx[0] == "-" else kx
-                        # 1-2, 1-2
-                        if neighbors.shape[0] > 1:
-                            # find zaxis
-                            for i_neighbor in neighbors:
-                                if kz_real == atoms[i_neighbor].meta[self.key_type]:
-                                    zaxis = i_neighbor
-                                    break
-                            if zaxis < 0:
-                                continue
-                            # find xaxis
-                            for i_neighbor in neighbors:
-                                if i_neighbor == zaxis:
-                                    continue
-                                if kx_real == atoms[i_neighbor].meta[self.key_type]:
-                                    xaxis = i_neighbor
-                                    break
-                            if xaxis < 0:
-                                continue
-                        # 1-2, 1-3
-                        elif neighbors.shape[0] == 1:
-                            if kz_real == atoms[neighbors[0]].meta[self.key_type]:
-                                zaxis = neighbors[0]
-                            else:
+                        # find zaxis
+                        for i_neighbor in neighbors:
+                            if kz == atoms[i_neighbor].meta[self.key_type]:
+                                zaxis = i_neighbor
+                                break
+                        if zaxis < 0:
+                            continue
+                        # find xaxis on 1-2 pairs
+                        for i_neighbor in neighbors:
+                            if i_neighbor == zaxis:
                                 continue
-                            # find xaxis
+                            if kx == atoms[i_neighbor].meta[self.key_type]:
+                                xaxis = i_neighbor
+                                break
+                        if xaxis < 0:
+                            # find xaxis on 1-3 pairs
                             neighbors2 = np.where(covalent_map[zaxis] == 1)[0]
                             for j_neighbor in neighbors2:
                                 if j_neighbor == i_atom:
                                     continue
-                                if kx_real == atoms[j_neighbor].meta[self.key_type]:
+                                if kx == atoms[j_neighbor].meta[self.key_type]:
                                     xaxis = j_neighbor
                                     break
-                            if xaxis < 0:
-                                continue
+                        if xaxis < 0:
+                            continue
                     elif axisType == ZOnly:
-                        kz_real = kz[1:] if kz[0] == "-" else kz
                         # 1-2 only
                         for i_neighbor in neighbors:
-                            if kz_real == atoms[i_neighbor].meta[self.key_type]:
+                            if kz == atoms[i_neighbor].meta[self.key_type]:
                                 zaxis = i_neighbor
                                 break
                         if zaxis < 0:
                             continue
                     elif axisType == Bisector:
-                        kz_real = kz[1:] if kz[0] == "-" else kz
-                        kx_real = kx[1:] if kx[0] == "-" else kx
                         for i_neighbor in neighbors:
-                            if kz_real == atoms[i_neighbor].meta[self.key_type]:
+                            if kz == atoms[i_neighbor].meta[self.key_type]:
                                 zaxis = i_neighbor
                                 break
                         if zaxis < 0:
                             continue
                         for j_neighbor in neighbors:
                             if j_neighbor == zaxis:
                                 continue
-                            if kx_real == atoms[j_neighbor].meta[self.key_type]:
+                            if kx == atoms[j_neighbor].meta[self.key_type]:
                                 xaxis = j_neighbor
                                 break
                         if xaxis < 0:
                             continue
                     elif axisType in [ZBisect, ThreeFold]:
-                        kz_real = kz[1:] if kz[0] == "-" else kz
-                        kx_real = kx[1:] if kx[0] == "-" else kx
-                        ky_real = ky[1:] if ky[0] == "-" else ky
                         for i_neighbor in neighbors:
-                            if kz_real == atoms[i_neighbor].meta[self.key_type]:
+                            if kz == atoms[i_neighbor].meta[self.key_type]:
                                 zaxis = i_neighbor
                                 break
                         if zaxis < 0:
                             continue
                         for j_neighbor in neighbors:
                             if j_neighbor == zaxis:
                                 continue
-                            if kx_real == atoms[j_neighbor].meta[self.key_type]:
+                            if kx == atoms[j_neighbor].meta[self.key_type]:
                                 xaxis = j_neighbor
                                 break
                         if xaxis < 0:
                             continue
                         for k_neighbor in neighbors:
                             if k_neighbor == zaxis or k_neighbor == xaxis:
                                 continue
-                            if ky_real == atoms[k_neighbor].meta[self.key_type]:
+                            if ky == atoms[k_neighbor].meta[self.key_type]:
                                 yaxis = k_neighbor
                                 break
                         if yaxis < 0:

dmff/mbar.py

@@ -1,5 +1,9 @@
 import numpy as np
-import mdtraj as md
+try:
+    import mdtraj as md
+except ImportError:
+    import warnings
+    warnings.warn("MDTraj not installed. MBAREstimator is not available.")
 
 try:
     from pymbar import MBAR

dmff/operators/parmed.py

@@ -50,7 +50,7 @@ def renderLennardJonesXML(self, filename):
             f.write("</ForceField>\n")
 
     @classmethod
-    def overwriteLennardJones(cls, top: parmed.gromacs.GromacsTopologyFile, ffinfo: dict):
+    def overwriteLennardJones(cls, top, ffinfo: dict):
         nodes = [n for n in ffinfo["Forces"]["LennardJonesForce"]["node"]]
         prm = {}
         for node in nodes:

dmff/sgnn/graph.py

@@ -1,11 +1,13 @@
-#!/usr/bin/env python
 import sys
 from functools import partial
 from itertools import permutations, product
 
 import jax.numpy as jnp
 # import MDAnalysis as mda
-import mdtraj as md
+try:
+    import mdtraj as md
+except ImportError:
+    pass
 import numpy as np
 from ..admp.pairwise import distribute_scalar, distribute_v3
 from ..admp.spatial import pbc_shift

docs/user_guide/installation.md

@@ -6,18 +6,15 @@ conda create -n dmff python=3.9 --yes
 ```
 + Install [jax](https://github.com/google/jax) (select the correct cuda version, see more details in the Jax installation guide):
 ```bash
-pip install "jaxlib[cuda11_cudnn805]==0.3.15" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
-pip install jax==0.3.17
+# CPU version
+pip install "jax[cpu]==0.4.19"
+# GPU version
+pip install "jax[cuda11_local]==0.4.19" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
 ```
-+ Install [jax-md](https://github.com/google/jax-md):
-```bash
-pip install jax-md==0.2.0
-```
-+ Install [mdtraj](https://github.com/mdtraj/mdtraj), [optax](https://github.com/deepmind/optax) and [pymbar](https://github.com/choderalab/pymbar):
++ Install [mdtraj](https://github.com/mdtraj/mdtraj), [optax](https://github.com/deepmind/optax), [jaxopt](https://github.com/google/jaxopt) and [pymbar](https://github.com/choderalab/pymbar):
 ```bash
 conda install -c conda-forge mdtraj==1.9.7
-pip install optax==0.1.3
-pip install pymbar==4.0.1
+pip install optax==0.1.3 pymbar==4.0.1 jaxopt==0.8.1
 ```
 + Install [OpenMM](https://openmm.org/):
 ```bash

setup.py

@@ -24,6 +24,8 @@
     "freud-analysis",
     "networkx>=3.0",
     "optax>=0.1.4",
+    "jaxopt>=0.8.0",
+    "pymbar>=4.0.0",
     "tqdm"
 ]
 

tests/test_dimer/test_run_dimer_energy.py

@@ -8,7 +8,6 @@
 import jax
 import openmm.app as app
 import openmm.unit as unit
-from rdkit import Chem
 import numpy as np
 
 
@@ -45,6 +44,7 @@ def test_load_protein():
 
 
 def test_build_dimer():
+    from rdkit import Chem
     ffinfo = load_xml()
 
     mol_top = DMFFTopology(from_sdf="tests/data/dimer/ligand.mol")
@@ -88,6 +88,7 @@ def test_build_dimer():
     print(energy_func.getPotentialFunc()(pos, box, pairs, hamilt.paramset))
 
 def test_dimer_coul():
+    from rdkit import Chem
     ffinfo = load_xml()
 
     print("------- Jax Ener Func --------")
@@ -214,6 +215,7 @@ def test_dimer_coul():
 
 
 def test_dimer_lj():
+    from rdkit import Chem
     ffinfo = load_xml()
     paramset = ParamSet()
     lj_gen = LennardJonesGenerator(ffinfo, paramset)
@@ -358,6 +360,7 @@ def test_dimer_lj():
 
 
 def test_hamiltonian():
+    from rdkit import Chem
     hamilt = Hamiltonian("tests/data/dimer/forcefield.xml", "tests/data/dimer/gaff2.xml", "tests/data/dimer/amber14_prot.xml")
     smarts_type = SMARTSATypeOperator(hamilt.ffinfo)
     smarts_vsite = SMARTSVSiteOperator(hamilt.ffinfo)
@@ -434,6 +437,7 @@ def test_hamiltonian():
     hamilt.renderXML("test.xml")
 
 def test_optax():
+    from rdkit import Chem
     hamilt = Hamiltonian("tests/data/dimer/forcefield.xml", "tests/data/dimer/gaff2.xml", "tests/data/dimer/amber14_prot.xml")
     hamilt.renderXML("tests/data/dimer/test-init.xml")
     smarts_type = SMARTSATypeOperator(hamilt.ffinfo)

tests/test_mbar/test_mbar.py

@@ -8,8 +8,16 @@
 import openmm as mm
 import numpy as np
 import numpy.testing as npt
-import mdtraj as md
-from pymbar import MBAR
+try:
+    import mdtraj as md
+except ImportError as e:
+    import warnings
+    warnings.warn(f"mdtraj not found. Tests about MBAR would fail.")
+try:
+    from pymbar import MBAR
+except ImportError as e:
+    import warnings
+    warnings.warn(f"pymbar not found. Tests about MBAR would fail.")
 from dmff import Hamiltonian, NeighborListFreud
 from tqdm import tqdm