Example Codes Fail

[kylezhang1011]

I'm running Python 3.12.7 locally on my computer and using the latest version of chiLife (1.1.4). In Example 4, some lines of codes returned an error instead of the results presented in the example.

T109R3A = xl.SpinLabel('R3A', 109, T4L, rotlib='R3A_rotlib.npz')
T109NBA = xl.SpinLabel('NBA', 109, T4L, rotlib='NBA')
T109GD3 = xl.SpinLabel('GD3', 109, T4L, sample=5000)

The error returned is:

WARNING:py.warnings:/opt/anaconda3/lib/python3.12/site-packages/MDAnalysis/core/universe.py:743: UserWarning: Reader has no dt information, set to 1.0 ps
  dt=self.trajectory.ts.dt * step,

WARNING:py.warnings:/opt/anaconda3/lib/python3.12/site-packages/chilife/protein_utils.py:148: RuntimeWarning: invalid value encountered in divide
  b1 /= np.linalg.norm(b1, axis=-1)[:, None]

WARNING:py.warnings:/opt/anaconda3/lib/python3.12/site-packages/MDAnalysis/core/universe.py:743: UserWarning: Reader has no dt information, set to 1.0 ps
  dt=self.trajectory.ts.dt * step,

WARNING:py.warnings:/opt/anaconda3/lib/python3.12/site-packages/chilife/protein_utils.py:148: RuntimeWarning: invalid value encountered in divide
  b1 /= np.linalg.norm(b1, axis=-1)[:, None]

WARNING:py.warnings:/opt/anaconda3/lib/python3.12/site-packages/MDAnalysis/core/universe.py:743: UserWarning: Reader has no dt information, set to 1.0 ps
  dt=self.trajectory.ts.dt * step,

WARNING:py.warnings:/opt/anaconda3/lib/python3.12/site-packages/chilife/protein_utils.py:148: RuntimeWarning: invalid value encountered in divide
  b1 /= np.linalg.norm(b1, axis=-1)[:, None]

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
Cell In[3], line 35
     22 xl.create_library('GD3', 'GD3/GD3_Ensemble.pdb', 
     23                   dihedral_atoms=[['N', 'CA', 'CB', 'SG'],
     24                                   ['CA', 'CB', 'SG', 'C18'],
   (...)
     28                   spin_atoms='Gd1',
     29                   weights=weights)
     34 T4L = xl.fetch('2lzm')
---> 35 T109R3A = xl.SpinLabel('R3A', 109, T4L, rotlib='R3A_rotlib.npz')
     36 #T109NBA = xl.SpinLabel('NBA', 109, T4L, rotlib='NBA')
     37 #T109GD3 = xl.SpinLabel('GD3', 109, T4L, sample=5000)
     39 xl.save(T109R3A, T109NBA, T109GD3, T4L)

File /opt/anaconda3/lib/python3.12/site-packages/chilife/SpinLabel.py:33, in SpinLabel.__init__(self, label, site, protein, chain, rotlib, **kwargs)
     30 if not kwargs.get('minimize', False):
     31     kwargs.setdefault("eval_clash", True)
---> 33 super().__init__(label, site, protein=protein, chain=chain, rotlib=rotlib, **kwargs)
     35 self.label = label
     37 # Parse spin delocalization information

File /opt/anaconda3/lib/python3.12/site-packages/chilife/RotamerEnsemble.py:191, in RotamerEnsemble.__init__(self, res, site, protein, chain, rotlib, **kwargs)
    188 if self.chain not in ('A', None):
    189     self.name += f"_{self.chain}"
--> 191 self.update(no_lib=True)
    193 # Store atom information as atom objects
    194 self.atoms = [
    195     FreeAtom(name, atype, idx, self.res, self.site, coord)
    196     for idx, (coord, atype, name) in enumerate(
    197         zip(self._coords[0], self.atom_types, self.atom_names)
    198     )
    199 ]

File /opt/anaconda3/lib/python3.12/site-packages/chilife/RotamerEnsemble.py:435, in RotamerEnsemble.update(self, no_lib)
    432     self.weights = self._weights.copy()
    434 if self.protein is not None:
--> 435     self.protein_setup()
    436 else:
    437     self.ICs_to_site(self.origin, self.mx)

File /opt/anaconda3/lib/python3.12/site-packages/chilife/RotamerEnsemble.py:440, in RotamerEnsemble.protein_setup(self)
    439 def protein_setup(self):
--> 440     self.to_site()
    442     # Get weight of current or closest rotamer
    443     clash_ignore_idx = self.protein.select_atoms(f"resid {self.site} and segid {self.chain}").ix

File /opt/anaconda3/lib/python3.12/site-packages/chilife/RotamerEnsemble.py:622, in RotamerEnsemble.to_site(self, site_pos)
    619 cmx = ori_mx @ mx
    621 self._coords = np.einsum("ijk,kl->ijl", self._coords, cmx) + ori
--> 622 self.ICs_to_site(ori, mx)
    623 if self._match_backbone:
    624     self.backbone_to_site()

File /opt/anaconda3/lib/python3.12/site-packages/chilife/RotamerEnsemble.py:642, in RotamerEnsemble.ICs_to_site(self, cori, cmx)
    639 m2m3 = self.ic_mx @ self.mx
    640 op = {}
--> 642 new_mx = self.internal_coords.chain_operators[0]["mx"] @ m2m3
    643 new_ori = (self.internal_coords.chain_operators[0]["ori"] - self.ic_ori) @ m2m3 + self.origin
    644 op[0] = {"mx": new_mx, "ori": new_ori}

KeyError: 0

This issue was also found in Example 5:

SL1_repack = xl.SpinLabel.from_trajectory(traj, 124, burn_in=5000, spin_atoms=SL1.spin_atoms)
SL2_repack = xl.SpinLabel.from_trajectory(traj, 281, burn_in=5000, spin_atoms=SL2.spin_atoms)

The error returned is:

KeyError                                  Traceback (most recent call last)
Cell In[2], line 10
      3 SL2 = xl.SpinLabel('R1M', 281, mbp)
      5 traj, dE = xl.repack(mbp, SL1, SL2,
      6                      repetitions=10000, temp=298,
      7                      off_rotamer=True,
      8                      repack_radius=10)
---> 10 SL1_repack = xl.SpinLabel.from_trajectory(traj, 124, burn_in=5000, spin_atoms=SL1.spin_atoms)
     11 SL2_repack = xl.SpinLabel.from_trajectory(traj, 281, burn_in=5000, spin_atoms=SL2.spin_atoms)

File /opt/anaconda3/lib/python3.12/site-packages/chilife/RotamerEnsemble.py:406, in RotamerEnsemble.from_trajectory(cls, traj, site, chain, energy, burn_in, **kwargs)
    404 kwargs.setdefault('eval_clash', False)
    405 kwargs.setdefault('_match_backbone', False)
--> 406 return cls(resname, site, chain=chain, rotlib=lib, **kwargs)

File /opt/anaconda3/lib/python3.12/site-packages/chilife/SpinLabel.py:33, in SpinLabel.__init__(self, label, site, protein, chain, rotlib, **kwargs)
     30 if not kwargs.get('minimize', False):
     31     kwargs.setdefault("eval_clash", True)
---> 33 super().__init__(label, site, protein=protein, chain=chain, rotlib=rotlib, **kwargs)
     35 self.label = label
     37 # Parse spin delocalization information

File /opt/anaconda3/lib/python3.12/site-packages/chilife/RotamerEnsemble.py:191, in RotamerEnsemble.__init__(self, res, site, protein, chain, rotlib, **kwargs)
    188 if self.chain not in ('A', None):
    189     self.name += f"_{self.chain}"
--> 191 self.update(no_lib=True)
    193 # Store atom information as atom objects
    194 self.atoms = [
    195     FreeAtom(name, atype, idx, self.res, self.site, coord)
    196     for idx, (coord, atype, name) in enumerate(
    197         zip(self._coords[0], self.atom_types, self.atom_names)
    198     )
    199 ]

File /opt/anaconda3/lib/python3.12/site-packages/chilife/RotamerEnsemble.py:437, in RotamerEnsemble.update(self, no_lib)
    435     self.protein_setup()
    436 else:
--> 437     self.ICs_to_site(self.origin, self.mx)

File /opt/anaconda3/lib/python3.12/site-packages/chilife/RotamerEnsemble.py:642, in RotamerEnsemble.ICs_to_site(self, cori, cmx)
    639 m2m3 = self.ic_mx @ self.mx
    640 op = {}
--> 642 new_mx = self.internal_coords.chain_operators[0]["mx"] @ m2m3
    643 new_ori = (self.internal_coords.chain_operators[0]["ori"] - self.ic_ori) @ m2m3 + self.origin
    644 op[0] = {"mx": new_mx, "ori": new_ori}

KeyError: 0

neighbors = [xl.RotamerEnsemble.from_trajectory(traj, resi, burn_in=5000) for resi in resis]
neighbors = [resi for resi in neighbors if len(resi) > 1]

The error returned is:

WARNING:py.warnings:/opt/anaconda3/lib/python3.12/site-packages/chilife/protein_utils.py:148: RuntimeWarning: invalid value encountered in divide
  b1 /= np.linalg.norm(b1, axis=-1)[:, None]

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
Cell In[5], line 4
      1 resis = [res.resnum for res in mbp.select_atoms('(not resname ALA GLY HOH) and around 14 resnum 124').residues] + \
      2         [res.resnum for res in mbp.select_atoms('(not resname ALA GLY HOH) and around 14 resnum 281').residues]
----> 4 neighbors = [xl.RotamerEnsemble.from_trajectory(traj, resi, burn_in=5000) for resi in resis]
      5 neighbors = [resi for resi in neighbors if len(resi) > 1]

File /opt/anaconda3/lib/python3.12/site-packages/chilife/RotamerEnsemble.py:406, in RotamerEnsemble.from_trajectory(cls, traj, site, chain, energy, burn_in, **kwargs)
    404 kwargs.setdefault('eval_clash', False)
    405 kwargs.setdefault('_match_backbone', False)
--> 406 return cls(resname, site, chain=chain, rotlib=lib, **kwargs)

File /opt/anaconda3/lib/python3.12/site-packages/chilife/RotamerEnsemble.py:191, in RotamerEnsemble.__init__(self, res, site, protein, chain, rotlib, **kwargs)
    188 if self.chain not in ('A', None):
    189     self.name += f"_{self.chain}"
--> 191 self.update(no_lib=True)
    193 # Store atom information as atom objects
    194 self.atoms = [
    195     FreeAtom(name, atype, idx, self.res, self.site, coord)
    196     for idx, (coord, atype, name) in enumerate(
    197         zip(self._coords[0], self.atom_types, self.atom_names)
    198     )
    199 ]

File /opt/anaconda3/lib/python3.12/site-packages/chilife/RotamerEnsemble.py:437, in RotamerEnsemble.update(self, no_lib)
    435     self.protein_setup()
    436 else:
--> 437     self.ICs_to_site(self.origin, self.mx)

File /opt/anaconda3/lib/python3.12/site-packages/chilife/RotamerEnsemble.py:642, in RotamerEnsemble.ICs_to_site(self, cori, cmx)
    639 m2m3 = self.ic_mx @ self.mx
    640 op = {}
--> 642 new_mx = self.internal_coords.chain_operators[0]["mx"] @ m2m3
    643 new_ori = (self.internal_coords.chain_operators[0]["ori"] - self.ic_ori) @ m2m3 + self.origin
    644 op[0] = {"mx": new_mx, "ori": new_ori}

KeyError: 0

[mtessmer]

Hi @kylezhang1011,
Thank you for posting this. Can I please ask how you installed chilife? e.g. pip, conda or through github?

[kylezhang1011]

Hi @kylezhang1011, Thank you for posting this. Can I please ask how you installed chilife? e.g. pip, conda or through github?

I used pip to install chilife.

[mtessmer]

I am not able to reproduce this error. Is there any chance you are using a new version of chilife with an old version of the examples? Also what operating system are you using?

[kylezhang1011]

I'm using MacOS and tried updating chilife and redownloading the example codes. I still got the same error.

[mtessmer]

just tried again on Linux with a clean Python environment and still can not reproduce this error.

I would try running with a clean slate:

new python virtual environment
fresh chilife install
fresh download of example code from the github repo in a new folder without anything else in it.

make sure you use the correct environment in jupyter lab. Sometimes, it will use a different environment than the one you used to open the file and not tell you.

make sure you run all the code to create the rotlibs before trying to use them.

[mtessmer]

Hi @kylezhang1011, were you able to get the example working?

[kylezhang1011]

Hi @kylezhang1011, were you able to get the example working?

I did get the example to work on a Windows computer, but it still does not work on my MacBook for some reason.