modelcraft 5.0.2__py3-none-any.whl → 6.0.0__py3-none-any.whl

modelcraft/solvent.py

@@ -1,140 +1,69 @@
 import collections
 import dataclasses
-import functools
 import math
-import re
-import gemmi
-from .contents import AsuContents, Polymer, PolymerType
-from .monlib import chemcomp
-
-
-def solvent_fraction(contents: AsuContents, mtz: gemmi.Mtz) -> float:
-    volume = _contents_volume(contents)
-    asu_volume = mtz.cell.volume / len(mtz.spacegroup.operations())
-    copies = contents.copies or _guess_copies(contents, mtz)
-    return 1 - copies * volume / asu_volume
-
-
-@functools.lru_cache(maxsize=None)
-def _library_weight(code: str) -> float:
-    return sum(atom.el.weight for atom in chemcomp(code).atoms)
-
-
-@functools.lru_cache(maxsize=None)
-def _library_volume(code: str) -> float:
-    return sum(18 for atom in chemcomp(code).atoms if not atom.is_hydrogen())
-
-
-def _polymer_weight(polymer: Polymer) -> float:
-    codes = polymer.residue_codes(modified=False)
-    total = sum(_library_weight(code) for code in codes)
-    total -= _library_weight("HOH") * (len(codes) - 1)
-    return total
-
-
-def _polymer_volume(polymer: Polymer) -> float:
-    density = 1.35 if polymer.type == PolymerType.PROTEIN else 2.0
-    return _polymer_weight(polymer) / (density * 0.602214)
-
-
-def _smiles_volume(smiles: str) -> float:
-    atoms = re.findall(pattern="[A-Z][a-z]?", string=smiles)
-    return 18 * len(atoms)
 
+import gemmi
 
-def _contents_volume(contents: AsuContents) -> float:
-    return sum(
-        item.volume * item.stoichiometry for item in _volume_components(contents)
-    )
+from .contents import AsuContents
+from .monlib import MonLib
 
 
-@dataclasses.dataclass
-class _VolumeComponent:
-    description: str
-    stoichiometry: int
-    stoichiometry_assumed: bool
-    volume: float
-
-
-def _volume_components(contents: AsuContents):
-    for kind, polymers in (
-        ("Protein", contents.proteins),
-        ("RNA", contents.rnas),
-        ("DNA", contents.dnas),
-    ):
-        for polymer in polymers:
-            sequence = polymer.sequence
-            description = f"{kind} with {len(sequence)} residues: "
-            if len(sequence) > 9:
-                description += f"{sequence[:3]}...{sequence[-3:]}"
-            else:
-                description += f"{sequence:9}"
-            stoichiometry = polymer.stoichiometry or 1
-            stoichiometry_assumed = polymer.stoichiometry is None
-            volume = _polymer_volume(polymer)
-            yield _VolumeComponent(
-                description, stoichiometry, stoichiometry_assumed, volume
-            )
-    for carb in contents.carbs:
-        description = "Carb:"
-        stoichiometry = carb.stoichiometry or 1
-        stoichiometry_assumed = carb.stoichiometry is None
-        volume = 0
-        length = 0
-        for code, count in carb.codes.items():
-            description += f" {count}x{code}"
-            length += count
-            if code in contents.smiles:
-                volume += _smiles_volume(contents.smiles[code]) * count
-            else:
-                volume += _library_volume(code) * count
-        volume -= _library_volume("HOH") * length
-        yield _VolumeComponent(
-            description, stoichiometry, stoichiometry_assumed, volume
-        )
-    for ligand in contents.ligands:
-        description = "Ligand: " + ligand.code
-        stoichiometry = ligand.stoichiometry or 1
-        stoichiometry_assumed = ligand.stoichiometry is None
-        if ligand.code in contents.smiles:
-            volume = _smiles_volume(contents.smiles[ligand.code])
-        else:
-            volume = _library_volume(ligand.code)
-        yield _VolumeComponent(
-            description, stoichiometry, stoichiometry_assumed, volume
-        )
+def solvent_fraction(
+    contents: AsuContents,
+    cell: gemmi.UnitCell,
+    spacegroup: gemmi.SpaceGroup,
+    resolution: float,
+    monlib: MonLib = None,
+) -> float:
+    monlib = monlib or MonLib(contents.monomer_codes(), include_standard=True)
+    asu_volume = cell.volume / len(spacegroup.operations())
+    copies = contents.copies
+    if copies is None:
+        copies = _guess_copies(contents, cell, spacegroup, resolution, monlib)
+    return 1 - copies * contents.volume(monlib) / asu_volume
 
 
 @dataclasses.dataclass
-class _CopiesOption:
+class CopiesOption:
     copies: int
     solvent: float
     probability: float
 
 
-def _copies_options(contents: AsuContents, mtz: gemmi.Mtz) -> list:
+def copies_options(
+    contents: AsuContents,
+    cell: gemmi.UnitCell,
+    spacegroup: gemmi.SpaceGroup,
+    resolution: float,
+    monlib: MonLib,
+) -> list:
     options = []
     nucleic_acids = contents.rnas + contents.dnas
-    mwp = sum(_polymer_weight(p) * (p.stoichiometry or 1) for p in contents.proteins)
-    mwn = sum(_polymer_weight(n) * (n.stoichiometry or 1) for n in nucleic_acids)
-    asu_volume = mtz.cell.volume / len(mtz.spacegroup.operations())
-    contents_volume = _contents_volume(contents)
-    resolution = mtz.resolution_high()
+    mwp = sum(p.weight(monlib) * (p.stoichiometry or 1) for p in contents.proteins)
+    mwn = sum(n.weight(monlib) * (n.stoichiometry or 1) for n in nucleic_acids)
+    asu_volume = cell.volume / len(spacegroup.operations())
+    contents_volume = contents.volume(monlib)
     total_probability = 0
     for copies in range(1, 60):
         solvent = 1 - copies * contents_volume / asu_volume
-        probability = _probability(mwp, mwn, copies, asu_volume, resolution)
+        probability = _matthews_probability(mwp, mwn, copies, asu_volume, resolution)
         if solvent < 0:
             break
-        options.append(_CopiesOption(copies, solvent, probability))
+        options.append(CopiesOption(copies, solvent, probability))
         total_probability += probability
     for option in options:
         option.probability /= total_probability
     return options
 
 
-def _guess_copies(contents: AsuContents, mtz: gemmi.Mtz) -> int:
-    options = _copies_options(contents, mtz)
+def _guess_copies(
+    contents: AsuContents,
+    cell: gemmi.UnitCell,
+    spacegroup: gemmi.SpaceGroup,
+    resolution: float,
+    monlib: MonLib,
+) -> int:
+    options = copies_options(contents, cell, spacegroup, resolution, monlib)
     if len(options) == 0:
         raise ValueError("Contents are too big to fit into the asymmetric unit")
     chosen = max(options, key=lambda option: option.probability)
@@ -165,15 +94,15 @@ _MATTHEWS_PROBABILITY_SETTINGS = [
 ]
 
 
-def _probability(
+def _matthews_probability(
     protein_mw: float,
     nucleic_mw: float,
     copies: int,
     asu_volume: float,
     resolution: float,
 ) -> float:
-    total_mw = protein_mw + nucleic_mw
-    matt = asu_volume / (total_mw * copies)
+    total_mw = (protein_mw + nucleic_mw) * copies
+    matthews = asu_volume / total_mw
     if protein_mw > 0.9 * total_mw:
         for index in range(12):
             if resolution < _MATTHEWS_PROBABILITY_SETTINGS[index].rbin:
@@ -183,5 +112,5 @@ def _probability(
     else:
         index = 14
     _, p0, vmbar, w, a, s = _MATTHEWS_PROBABILITY_SETTINGS[index]
-    z = (matt - vmbar) / w
+    z = (matthews - vmbar) / w
     return p0 + a * (math.exp(-math.exp(-z) - z * s + 1))

modelcraft/structure.py

@@ -1,6 +1,8 @@
 from typing import Iterator
+
 import gemmi
-from .monlib import atom_ids, in_library, is_protein, is_nucleic
+
+from .monlib import MonLib
 
 
 def read_structure(path: str) -> gemmi.Structure:
@@ -10,25 +12,11 @@ def read_structure(path: str) -> gemmi.Structure:
     # TODO: Currently altconfs appear in CIF auth_atom_id after sheetbend
     # TODO: Keep alternative conformations after problem is fixed
     structure.remove_alternative_conformations()
+    _remove_point_mutations(structure)
     _patch_names(structure)
     return structure
 
 
-def consecutive_residues(chain: gemmi.Chain):
-    "Iterate through lists of residues with consecutive seqnums (first conformer only)"
-    consecutive = []
-    last_seqnum = None
-    for residue in chain.first_conformer():
-        if last_seqnum is None or residue.seqid.num == last_seqnum + 1:
-            consecutive.append(residue)
-        else:
-            yield consecutive
-            consecutive = [residue]
-        last_seqnum = residue.seqid.num
-    if len(consecutive) > 0:
-        yield consecutive
-
-
 def contains_residue(structure: gemmi.Structure, name: str) -> bool:
     return any(residue.name == name for residue in _residues(structure))
 
@@ -42,15 +30,6 @@ def remove_residues(structure: gemmi.Structure, names) -> None:
     structure.remove_empty_chains()
 
 
-def remove_non_library_atoms(structure: gemmi.Structure) -> None:
-    for residue in _residues(structure):
-        if in_library(residue.name):
-            for i, atom in reversed(list(enumerate(residue))):
-                if atom.name not in atom_ids(residue.name):
-                    del residue[i]
-    structure.remove_empty_chains()
-
-
 def remove_non_protein(structure: gemmi.Structure) -> None:
     for model in structure:
         for chain in model:
@@ -68,13 +47,15 @@ def write_mmcif(path: str, structure: gemmi.Structure) -> None:
 
 
 class ModelStats:
-    def __init__(self, structure: gemmi.Structure):
+    def __init__(self, structure: gemmi.Structure, monlib: MonLib = None):
         self.residues: int = 0
         self.protein: int = 0
         self.nucleic: int = 0
         self.waters: int = 0
         self.dummy_atoms: int = 0
 
+        monlib = monlib or MonLib(structure[0].get_all_residue_names())
+
         for residue in _residues(structure):
             if residue.name == "HOH":
                 self.waters += 1
@@ -82,24 +63,11 @@ class ModelStats:
                 self.dummy_atoms += 1
             else:
                 self.residues += 1
-                if is_protein(residue.name):
+                if monlib.is_protein(residue.name):
                     self.protein += 1
-                if is_nucleic(residue.name):
+                if monlib.is_nucleic(residue.name):
                     self.nucleic += 1
 
-    def __eq__(self, other):
-        if isinstance(other, ModelStats):
-            return (
-                self.residues == other.residues
-                and self.waters == other.waters
-                and self.dummy_atoms == other.dummy_atoms
-            )
-        return NotImplemented
-
-    def __ne__(self, other):
-        equal = self.__eq__(other)
-        return NotImplemented if equal is not NotImplemented else not equal
-
 
 def _residues(structure: gemmi.Structure) -> Iterator[gemmi.Residue]:
     for model in structure:
@@ -108,6 +76,19 @@ def _residues(structure: gemmi.Structure) -> Iterator[gemmi.Residue]:
                 yield residue
 
 
+def _remove_point_mutations(structure: gemmi.Structure) -> None:
+    for model in structure:
+        to_remove = []
+        for chain in model:
+            for group in chain.whole().residue_groups():
+                for i in range(1, len(group)):
+                    residue = group[i]
+                    key = (chain.name, str(residue.seqid), residue.name)
+                    to_remove.append(key)
+        for chain_name, residue_seqid, residue_name in to_remove:
+            del model[chain_name][residue_seqid][residue_name]
+
+
 def _patch_names(structure: gemmi.Structure) -> None:
     residue_patches = {"SUL": "SO4"}
     atom_patches = {("HOH", "O1"): "O"}
@@ -117,3 +98,45 @@ def _patch_names(structure: gemmi.Structure) -> None:
         for atom in residue:
             atom.name = atom.name.strip()
             atom.name = atom_patches.get((residue.name, atom.name), atom.name)
+
+
+def _are_connected(
+    residue1: gemmi.Residue, residue2: gemmi.Residue, monlib: MonLib
+) -> bool:
+    if (
+        monlib.is_protein(residue1.name)
+        and monlib.is_protein(residue2.name)
+        and "C" in residue1
+        and "N" in residue2
+    ):
+        for atom1 in residue1["C"]:
+            for atom2 in residue2["N"]:
+                if atom1.pos.dist(atom2.pos) < 2.5:
+                    return True
+    if (
+        monlib.is_nucleic(residue1.name)
+        and monlib.is_nucleic(residue2.name)
+        and "O3'" in residue1
+        and "P" in residue2
+    ):
+        for atom1 in residue1["O3'"]:
+            for atom2 in residue2["P"]:
+                if atom1.pos.dist(atom2.pos) < 2.5:
+                    return True
+    return False
+
+
+def remove_isolated_fragments(chain: gemmi.Chain, monlib: MonLib, max_length: int):
+    to_remove = []
+    fragment = []
+    for i, residue in enumerate(chain):
+        if i > 0 and _are_connected(chain[i - 1], residue, monlib):
+            fragment.append(i)
+        else:
+            if len(fragment) <= max_length:
+                to_remove.extend(fragment)
+            fragment = [i]
+    if len(fragment) <= max_length:
+        to_remove.extend(fragment)
+    for i in reversed(to_remove):
+        del chain[i]

modelcraft/tests/ccp4/__init__.py

@@ -1,9 +1,11 @@
 import functools
 import os
 import shutil
-import uuid
 import urllib.request
+import uuid
+
 import gemmi
+
 from modelcraft.contents import AsuContents, Ligand, Polymer, PolymerType
 from modelcraft.jobs.refmac import Refmac
 from modelcraft.reflections import DataItem
@@ -16,7 +18,7 @@ def ccp4_path(*paths: str) -> str:
 
 def in_temp_directory(func):
     def wrapper():
-        tmp_dir = "tmp%s" % uuid.uuid4()
+        tmp_dir = f"tmp{uuid.uuid4()}"
         os.mkdir(tmp_dir)
         os.chdir(tmp_dir)
         try:
@@ -66,7 +68,6 @@ def insulin_refmac():
 
 @functools.lru_cache(maxsize=None)
 def insulin_contents():
-    contents = AsuContents()
     chain_a = Polymer(
         sequence="GIVEQCCASVCSLYQLENYCN",
         polymer_type=PolymerType.PROTEIN,
@@ -75,9 +76,8 @@ def insulin_contents():
         sequence="FVNQHLCGSHLVEALYLVCGERGFFYTPKA",
         polymer_type=PolymerType.PROTEIN,
     )
-    contents.add_polymer(chain_a)
-    contents.add_polymer(chain_b)
-    return contents
+    ligand = Ligand("GOL")
+    return AsuContents(proteins=[chain_a, chain_b], ligands=[ligand])
 
 
 @functools.lru_cache(maxsize=None)
@@ -92,8 +92,4 @@ def pdb1rxf_contents():
     )
     protein = Polymer(sequence=sequence, polymer_type=PolymerType.PROTEIN)
     ligand = Ligand(code="FE")
-    contents = AsuContents()
-    contents.proteins.append(protein)
-    contents.ligands.append(ligand)
-    contents.copies = 1
-    return contents
+    return AsuContents(copies=1, proteins=[protein], ligands=[ligand])

modelcraft/tests/ccp4/test_acedrg.py

@@ -1,6 +1,8 @@
 import math
 import os
+
 import gemmi
+
 from modelcraft.jobs.acedrg import Acedrg
 
 

modelcraft/tests/ccp4/test_arguments.py

@@ -1,6 +1,9 @@
 import subprocess
+
 import pytest
+
 from modelcraft.arguments import parse
+
 from . import ccp4_path, in_temp_directory, pdbe_download
 
 

modelcraft/tests/ccp4/test_buccaneer.py

@@ -1,11 +1,12 @@
 from modelcraft.jobs.buccaneer import Buccaneer, _known_structure_ids
 from modelcraft.structure import ModelStats, read_structure
+
 from . import (
     in_temp_directory,
-    insulin_fsigf,
+    insulin_contents,
     insulin_freer,
+    insulin_fsigf,
     insulin_refmac,
-    insulin_contents,
     pdbe_download,
 )
 

modelcraft/tests/ccp4/test_cell.py

@@ -1,13 +1,16 @@
 import urllib.request
+
 import gemmi
+
 from modelcraft.cell import max_distortion, remove_scale, update_cell
 from modelcraft.structure import read_structure
+
 from . import in_temp_directory
 
 
 @in_temp_directory
 def test_1ana():
-    url = "https://files-versioned.wwpdb.org/pdb_versioned/data/entries/"
+    url = "https://ftp.ebi.ac.uk/pub/databases/pdb_versioned/data/entries/"
     url += "an/pdb_00001ana/pdb_00001ana_xyz_v1-2.cif.gz"
     urllib.request.urlretrieve(url, "1ana.cif.gz")
     structure = read_structure("1ana.cif.gz")

modelcraft/tests/ccp4/test_comit.py

@@ -1,6 +1,8 @@
 import gemmi
+
 from modelcraft.jobs.comit import Comit
 from modelcraft.reflections import DataItem
+
 from . import ccp4_path
 
 

modelcraft/tests/ccp4/test_contents.py

@@ -1,8 +1,11 @@
-from modelcraft.scripts.contents import _entry_contents, _smiles
+from pytest import approx
+
+from modelcraft.contents import AsuContents, Polymer, PolymerType
+from modelcraft.monlib import MonLib
 
 
 def _test_contents(entry: str, expected_json: list, selenomet: bool):
-    contents = _entry_contents(entry)
+    contents = AsuContents.from_pdbe(entry)
     assert contents.to_json() == expected_json
     assert contents.is_selenomet() == selenomet
     return contents
@@ -13,7 +16,10 @@ def test_1o6a():
         "copies": 2,
         "proteins": [
             {
-                "sequence": "SETRKTEVPSDKLELLLDIPLKVTVELGRTRMTLKRVLEMIHGSIIELDKLTGEPVDILVNGKLIARGEVVVIDENFGVRITEIVSPKERLELLNE",
+                "sequence": (
+                    "SETRKTEVPSDKLELLLDIPLKVTVELGRTRMTLKRVLEMIHGSIIELDKLTGEPVDILV"
+                    "NGKLIARGEVVVIDENFGVRITEIVSPKERLELLNE"
+                ),
                 "stoichiometry": 1,
                 "modifications": ["M->MSE"],
             }
@@ -23,7 +29,6 @@ def test_1o6a():
         "carbs": [],
         "ligands": [],
         "buffers": [],
-        "smiles": {},
     }
     _test_contents("1o6a", expected, selenomet=True)
 
@@ -34,7 +39,11 @@ def test_4gxy():
         "proteins": [],
         "rnas": [
             {
-                "sequence": "GGCGGCAGGUGCUCCCGACCCUGCGGUCGGGAGUUAAAAGGGAAGCCGGUGCAAGUCCGGCACGGUCCCGCCACUGUGACGGGGAGUCGCCCCUCGGGAUGUGCCACUGGCCCGAAGGCCGGGAAGGCGGAGGGGCGGCGAGGAUCCGGAGUCAGGAAACCUGCCUGCCGUC",
+                "sequence": (
+                    "GGCGGCAGGUGCUCCCGACCCUGCGGUCGGGAGUUAAAAGGGAAGCCGGUGCAAGUCCGG"
+                    "CACGGUCCCGCCACUGUGACGGGGAGUCGCCCCUCGGGAUGUGCCACUGGCCCGAAGGCC"
+                    "GGGAAGGCGGAGGGGCGGCGAGGAUCCGGAGUCAGGAAACCUGCCUGCCGUC"
+                ),
                 "stoichiometry": 1,
                 "modifications": ["1->GTP", "172->CCC"],
             }
@@ -46,7 +55,6 @@ def test_4gxy():
             {"code": "IRI", "stoichiometry": 7},
         ],
         "buffers": ["MG"],
-        "smiles": {},
     }
     _test_contents("4gxy", expected, selenomet=False)
 
@@ -56,7 +64,24 @@ def test_6as7():
         "copies": 1,
         "proteins": [
             {
-                "sequence": "DEEQVFHFYWLDAYEDQYNQPGVVFLFGKVWIESAETHVSCCVMVKNIERTLYFLPREMKIDLNTGKETGTPISMKDVYEEFDEKIATKYKIMKFKSKPVEKNYAFEIPDVPEKSEYLEVKYSAEMPQLPQDLKGETFSHVFGTNTSSLELFLMNRKIKGPCWLEVKSPQLLNQPVSWCKAEAMALKPDLVNVIKDVSPPPLVVMAFSMKTMQNAKNHQNEIIAMAALVHHSFALDKAAPKPPFQSHFCVVSKPKDCIFPYAFKEVIEKKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPHWSKIGRLKRSNMPKLGGRSGFGERNATCGRMICDVEISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESSQLLYLLEHTWKDAKFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKPQQKLGDEDEEIDGDTNKYKKGRKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQKVTEDGEQEQIPELPDPSLEMGILPREIRKLVERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDGVFKSLLLLKKKKYAALVVEPTSDGNYVTKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDTVSYVICQDGSNLTASQRAYAPEQLQKQDNLTIDTQYYLAQQIHPVVARICEPIDGIDAVLIATWLGLDPTQFRVHHYHKDEEN",
+                "sequence": (
+                    "DEEQVFHFYWLDAYEDQYNQPGVVFLFGKVWIESAETHVSCCVMVKNIERTLYFLPREMK"
+                    "IDLNTGKETGTPISMKDVYEEFDEKIATKYKIMKFKSKPVEKNYAFEIPDVPEKSEYLEV"
+                    "KYSAEMPQLPQDLKGETFSHVFGTNTSSLELFLMNRKIKGPCWLEVKSPQLLNQPVSWCK"
+                    "AEAMALKPDLVNVIKDVSPPPLVVMAFSMKTMQNAKNHQNEIIAMAALVHHSFALDKAAPK"
+                    "PPFQSHFCVVSKPKDCIFPYAFKEVIEKKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGH"
+                    "NIYGFELEVLLQRINVCKAPHWSKIGRLKRSNMPKLGGRSGFGERNATCGRMICDVEISAK"
+                    "ELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESSQLLYLLEHTWKDAKFILQIMCEL"
+                    "NVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKPQQKLGDED"
+                    "EEIDGDTNKYKKGRKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQR"
+                    "VASEAQKVTEDGEQEQIPELPDPSLEMGILPREIRKLVERRKQVKQLMKQQDLNPDLILQY"
+                    "DIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEVIYGDT"
+                    "DSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDGVFKSLLLLKKKKYAALVVEPTS"
+                    "DGNYVTKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLN"
+                    "GSVPVSQFEINKALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDTVSYVICQDGSNL"
+                    "TASQRAYAPEQLQKQDNLTIDTQYYLAQQIHPVVARICEPIDGIDAVLIATWLGLDPTQFR"
+                    "VHHYHKDEEN"
+                ),
                 "stoichiometry": 1,
                 "modifications": [],
             }
@@ -77,7 +102,6 @@ def test_6as7():
         "carbs": [],
         "ligands": [{"code": "DCP", "stoichiometry": 1}],
         "buffers": ["MG", "CO"],
-        "smiles": {},
     }
     _test_contents("6as7", expected, selenomet=False)
 
@@ -87,7 +111,17 @@ def test_4aqd():
         "copies": 1,
         "proteins": [
             {
-                "sequence": "RSEDDIIIATKNGKVRGMNLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDNYTKAEEILSRSIVKRWANFAKYGNPNETQNNSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV",
+                "sequence": (
+                    "RSEDDIIIATKNGKVRGMNLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNA"
+                    "TKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGF"
+                    "QTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWV"
+                    "QKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYE"
+                    "ARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDF"
+                    "LTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFF"
+                    "PGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFF"
+                    "YYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDNYTKAEEILSRSIVKRWANFAKYG"
+                    "NPNETQNNSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV"
+                ),
                 "stoichiometry": 2,
                 "modifications": [],
             }
@@ -105,8 +139,7 @@ def test_4aqd():
             {"code": "PG4", "stoichiometry": 2},
             {"code": "PEG", "stoichiometry": 2},
         ],
-        "buffers": ["EDO", "CL", "GLY"],
-        "smiles": {},
+        "buffers": ["EDO", "UNX", "CL", "GLY"],
     }
     _test_contents("4aqd", expected, selenomet=False)
 
@@ -116,7 +149,13 @@ def test_1vjr():
         "copies": 1,
         "proteins": [
             {
-                "sequence": "MGSDKIHHHHHHVLDKIELFILDMDGTFYLDDSLLPGSLEFLETLKEKNKRFVFFTNNSSLGAQDYVRKLRNMGVDVPDDAVVTSGEITAEHMLKRFGRCRIFLLGTPQLKKVFEAYGHVIDEENPDFVVLGFDKTLTYERLKKACILLRKGKFYIATHPDINCPSKEGPVPDAGSIMAAIEASTGRKPDLIAGKPNPLVVDVISEKFGVPKERMAMVGDRLYTDVKLGKNAGIVSILVLTGETTPEDLERAETKPDFVFKNLGELAKAVQ",
+                "sequence": (
+                    "MGSDKIHHHHHHVLDKIELFILDMDGTFYLDDSLLPGSLEFLETLKEKNKRFVFFTNNSS"
+                    "LGAQDYVRKLRNMGVDVPDDAVVTSGEITAEHMLKRFGRCRIFLLGTPQLKKVFEAYGHV"
+                    "IDEENPDFVVLGFDKTLTYERLKKACILLRKGKFYIATHPDINCPSKEGPVPDAGSIMAA"
+                    "IEASTGRKPDLIAGKPNPLVVDVISEKFGVPKERMAMVGDRLYTDVKLGKNAGIVSILVL"
+                    "TGETTPEDLERAETKPDFVFKNLGELAKAVQ"
+                ),
                 "stoichiometry": 1,
                 "modifications": ["M->MSE"],
             }
@@ -126,7 +165,6 @@ def test_1vjr():
         "carbs": [],
         "ligands": [],
         "buffers": ["NI", "CL"],
-        "smiles": {},
     }
     _test_contents("1vjr", expected, selenomet=True)
 
@@ -157,7 +195,6 @@ def test_1cag():
         "carbs": [],
         "ligands": [],
         "buffers": ["ACY"],
-        "smiles": {},
     }
     contents = _test_contents("1cag", expected, selenomet=False)
     polymer = contents.proteins[0]
@@ -182,10 +219,55 @@ def test_1iha():
         "carbs": [],
         "ligands": [{"code": "RHD", "stoichiometry": 1}],
         "buffers": ["CL"],
-        "smiles": {},
     }
     _test_contents("1iha", expected, selenomet=False)
 
 
-def test_0pr_smiles():
-    assert _smiles("0PR") == "Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](Cc2ccc(cc2)O)C(=O)O)O"
+def test_3ue7():
+    expected = {
+        "copies": 1,
+        "proteins": [
+            {
+                "sequence": "TTCCPSIVARSNFNACRLPGTPEALCATYTGCIIIPGATCPGDYAN",
+                "stoichiometry": 1,
+                "modifications": [
+                    "T->DTH",
+                    "C->DCY",
+                    "P->DPR",
+                    "S->DSN",
+                    "I->DIL",
+                    "V->DVA",
+                    "A->DAL",
+                    "R->DAR",
+                    "N->DSG",
+                    "F->DPN",
+                    "L->DLE",
+                    "E->DGL",
+                    "Y->DTY",
+                    "D->DAS",
+                ],
+            },
+            {
+                "sequence": "TTCCPSIVAKSNFNACRLPGTPEALCATYTGCIIIPGATCPGDYAN",
+                "stoichiometry": 1,
+                "modifications": [],
+            },
+        ],
+        "rnas": [],
+        "dnas": [],
+        "carbs": [],
+        "ligands": [],
+        "buffers": [],
+    }
+    _test_contents("3ue7", expected, selenomet=False)
+
+
+def test_5vz8():
+    contents = AsuContents.from_pdbe("5vz8")
+    contents.monomer_codes()
+
+
+def test_polymer_weight():
+    polymer = Polymer("GG", polymer_type=PolymerType.PROTEIN)
+    monlib = MonLib(["GLY"], include_standard=True)
+    assert polymer.weight(monlib) == approx(132.12, abs=0.01)