fastpdb - pypi Package Compare versions

Comparing version 1.2.0 to 1.3.0

.github/workflows/test_and_deploy.yml

@@ -18,3 +18,3 @@ ---
         os: [ubuntu-latest, windows-latest, macos-latest]
-        py-version: ["3.9", "3.10", "3.11"]
+        py-version: ["3.10", "3.11", "3.12"]
     runs-on: ${{ matrix.os }}
@@ -35,3 +35,3 @@ defaults:
       - name: Install dependencies
-        run: pip install "maturin>=0.14,<0.15" "oldest-supported-numpy" pytest
+        run: pip install "maturin==1.4" "oldest-supported-numpy" pytest
       - name: Build wheel
@@ -58,5 +58,5 @@ run: maturin build --release -i python -o dist
         with:
-          python-version: "3.11"
+          python-version: "3.12"
       - name: Install dependencies
-        run: pip install "maturin>=0.14,<0.15" pytest
+        run: pip install "maturin==1.4" pytest
       - name: Build source distribution
@@ -63,0 +63,0 @@ run: maturin sdist -o dist

Cargo.lock

@@ -19,8 +19,2 @@ # This file is automatically @generated by Cargo.
 name = "cfg-if"
-version = "0.1.10"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4785bdd1c96b2a846b2bd7cc02e86b6b3dbf14e7e53446c4f54c92a361040822"
-
-[[package]]
-name = "cfg-if"
 version = "1.0.0"
@@ -32,3 +26,3 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 name = "fastpdb"
-version = "1.2.0"
+version = "1.3.0"
 dependencies = [
@@ -41,44 +35,24 @@ "ndarray",
 [[package]]
-name = "indoc"
-version = "0.3.6"
+name = "heck"
+version = "0.4.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "47741a8bc60fb26eb8d6e0238bbb26d8575ff623fdc97b1a2c00c050b9684ed8"
-dependencies = [
- "indoc-impl",
- "proc-macro-hack",
-]
+checksum = "95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8"
 
 [[package]]
-name = "indoc-impl"
-version = "0.3.6"
+name = "indoc"
+version = "2.0.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ce046d161f000fffde5f432a0d034d0341dc152643b2598ed5bfce44c4f3a8f0"
-dependencies = [
- "proc-macro-hack",
- "proc-macro2",
- "quote",
- "syn",
- "unindent",
-]
+checksum = "1e186cfbae8084e513daff4240b4797e342f988cecda4fb6c939150f96315fd8"
 
 [[package]]
-name = "instant"
-version = "0.1.12"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7a5bbe824c507c5da5956355e86a746d82e0e1464f65d862cc5e71da70e94b2c"
-dependencies = [
- "cfg-if 1.0.0",
-]
-
-[[package]]
 name = "libc"
-version = "0.2.144"
+version = "0.2.152"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2b00cc1c228a6782d0f076e7b232802e0c5689d41bb5df366f2a6b6621cfdfe1"
+checksum = "13e3bf6590cbc649f4d1a3eefc9d5d6eb746f5200ffb04e5e142700b8faa56e7"
 
 [[package]]
 name = "lock_api"
-version = "0.4.9"
+version = "0.4.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "435011366fe56583b16cf956f9df0095b405b82d76425bc8981c0e22e60ec4df"
+checksum = "3c168f8615b12bc01f9c17e2eb0cc07dcae1940121185446edc3744920e8ef45"
 dependencies = [
@@ -91,5 +65,5 @@ "autocfg",
 name = "matrixmultiply"
-version = "0.3.7"
+version = "0.3.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "090126dc04f95dc0d1c1c91f61bdd474b3930ca064c1edc8a849da2c6cbe1e77"
+checksum = "7574c1cf36da4798ab73da5b215bbf444f50718207754cb522201d78d1cd0ff2"
 dependencies = [
@@ -101,2 +75,11 @@ "autocfg",
 [[package]]
+name = "memoffset"
+version = "0.9.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5a634b1c61a95585bd15607c6ab0c4e5b226e695ff2800ba0cdccddf208c406c"
+dependencies = [
+ "autocfg",
+]
+
+[[package]]
 name = "ndarray"
@@ -116,5 +99,5 @@ version = "0.15.6"
 name = "num-complex"
-version = "0.4.3"
+version = "0.4.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "02e0d21255c828d6f128a1e41534206671e8c3ea0c62f32291e808dc82cff17d"
+checksum = "1ba157ca0885411de85d6ca030ba7e2a83a28636056c7c699b07c8b6f7383214"
 dependencies = [
@@ -136,5 +119,5 @@ "num-traits",
 name = "num-traits"
-version = "0.2.15"
+version = "0.2.17"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "578ede34cf02f8924ab9447f50c28075b4d3e5b269972345e7e0372b38c6cdcd"
+checksum = "39e3200413f237f41ab11ad6d161bc7239c84dcb631773ccd7de3dfe4b5c267c"
 dependencies = [
@@ -146,12 +129,13 @@ "autocfg",
 name = "numpy"
-version = "0.14.1"
+version = "0.20.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "09c15af63aa0c74e0f7230d4e95d9a3d71a23449905f30f50b055df9a6a6a3e6"
+checksum = "bef41cbb417ea83b30525259e30ccef6af39b31c240bda578889494c5392d331"
 dependencies = [
- "cfg-if 0.1.10",
  "libc",
  "ndarray",
  "num-complex",
+ "num-integer",
  "num-traits",
  "pyo3",
+ "rustc-hash",
 ]
@@ -161,13 +145,12 @@
 name = "once_cell"
-version = "1.17.2"
+version = "1.19.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9670a07f94779e00908f3e686eab508878ebb390ba6e604d3a284c00e8d0487b"
+checksum = "3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92"
 
 [[package]]
 name = "parking_lot"
-version = "0.11.2"
+version = "0.12.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7d17b78036a60663b797adeaee46f5c9dfebb86948d1255007a1d6be0271ff99"
+checksum = "3742b2c103b9f06bc9fff0a37ff4912935851bee6d36f3c02bcc755bcfec228f"
 dependencies = [
- "instant",
  "lock_api",
@@ -179,44 +162,18 @@ "parking_lot_core",
 name = "parking_lot_core"
-version = "0.8.6"
+version = "0.9.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "60a2cfe6f0ad2bfc16aefa463b497d5c7a5ecd44a23efa72aa342d90177356dc"
+checksum = "4c42a9226546d68acdd9c0a280d17ce19bfe27a46bf68784e4066115788d008e"
 dependencies = [
- "cfg-if 1.0.0",
- "instant",
+ "cfg-if",
  "libc",
  "redox_syscall",
  "smallvec",
- "winapi",
+ "windows-targets",
 ]
 
 [[package]]
-name = "paste"
-version = "0.1.18"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "45ca20c77d80be666aef2b45486da86238fabe33e38306bd3118fe4af33fa880"
-dependencies = [
- "paste-impl",
- "proc-macro-hack",
-]
-
-[[package]]
-name = "paste-impl"
-version = "0.1.18"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d95a7db200b97ef370c8e6de0088252f7e0dfff7d047a28528e47456c0fc98b6"
-dependencies = [
- "proc-macro-hack",
-]
-
-[[package]]
-name = "proc-macro-hack"
-version = "0.5.20+deprecated"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "dc375e1527247fe1a97d8b7156678dfe7c1af2fc075c9a4db3690ecd2a148068"
-
-[[package]]
 name = "proc-macro2"
-version = "1.0.59"
+version = "1.0.76"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6aeca18b86b413c660b781aa319e4e2648a3e6f9eadc9b47e9038e6fe9f3451b"
+checksum = "95fc56cda0b5c3325f5fbbd7ff9fda9e02bb00bb3dac51252d2f1bfa1cb8cc8c"
 dependencies = [
@@ -228,12 +185,13 @@ "unicode-ident",
 name = "pyo3"
-version = "0.14.5"
+version = "0.20.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "35100f9347670a566a67aa623369293703322bb9db77d99d7df7313b575ae0c8"
+checksum = "9a89dc7a5850d0e983be1ec2a463a171d20990487c3cfcd68b5363f1ee3d6fe0"
 dependencies = [
- "cfg-if 1.0.0",
+ "cfg-if",
  "indoc",
  "libc",
+ "memoffset",
  "parking_lot",
- "paste",
  "pyo3-build-config",
+ "pyo3-ffi",
  "pyo3-macros",
@@ -245,15 +203,27 @@ "unindent",
 name = "pyo3-build-config"
-version = "0.14.5"
+version = "0.20.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d12961738cacbd7f91b7c43bc25cfeeaa2698ad07a04b3be0aa88b950865738f"
+checksum = "07426f0d8fe5a601f26293f300afd1a7b1ed5e78b2a705870c5f30893c5163be"
 dependencies = [
  "once_cell",
+ "target-lexicon",
 ]
 
 [[package]]
+name = "pyo3-ffi"
+version = "0.20.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "dbb7dec17e17766b46bca4f1a4215a85006b4c2ecde122076c562dd058da6cf1"
+dependencies = [
+ "libc",
+ "pyo3-build-config",
+]
+
+[[package]]
 name = "pyo3-macros"
-version = "0.14.5"
+version = "0.20.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fc0bc5215d704824dfddddc03f93cb572e1155c68b6761c37005e1c288808ea8"
+checksum = "05f738b4e40d50b5711957f142878cfa0f28e054aa0ebdfc3fd137a843f74ed3"
 dependencies = [
+ "proc-macro2",
  "pyo3-macros-backend",
@@ -266,8 +236,8 @@ "quote",
 name = "pyo3-macros-backend"
-version = "0.14.5"
+version = "0.20.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "71623fc593224afaab918aa3afcaf86ed2f43d34f6afde7f3922608f253240df"
+checksum = "0fc910d4851847827daf9d6cdd4a823fbdaab5b8818325c5e97a86da79e8881f"
 dependencies = [
+ "heck",
  "proc-macro2",
- "pyo3-build-config",
  "quote",
@@ -279,5 +249,5 @@ "syn",
 name = "quote"
-version = "1.0.28"
+version = "1.0.35"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1b9ab9c7eadfd8df19006f1cf1a4aed13540ed5cbc047010ece5826e10825488"
+checksum = "291ec9ab5efd934aaf503a6466c5d5251535d108ee747472c3977cc5acc868ef"
 dependencies = [
@@ -295,5 +265,5 @@ "proc-macro2",
 name = "redox_syscall"
-version = "0.2.16"
+version = "0.4.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fb5a58c1855b4b6819d59012155603f0b22ad30cad752600aadfcb695265519a"
+checksum = "4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa"
 dependencies = [
@@ -304,18 +274,24 @@ "bitflags",
 [[package]]
-name = "scopeguard"
+name = "rustc-hash"
 version = "1.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d29ab0c6d3fc0ee92fe66e2d99f700eab17a8d57d1c1d3b748380fb20baa78cd"
+checksum = "08d43f7aa6b08d49f382cde6a7982047c3426db949b1424bc4b7ec9ae12c6ce2"
 
 [[package]]
+name = "scopeguard"
+version = "1.2.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49"
+
+[[package]]
 name = "smallvec"
-version = "1.10.0"
+version = "1.11.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a507befe795404456341dfab10cef66ead4c041f62b8b11bbb92bffe5d0953e0"
+checksum = "4dccd0940a2dcdf68d092b8cbab7dc0ad8fa938bf95787e1b916b0e3d0e8e970"
 
 [[package]]
 name = "syn"
-version = "1.0.109"
+version = "2.0.48"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237"
+checksum = "0f3531638e407dfc0814761abb7c00a5b54992b849452a0646b7f65c9f770f3f"
 dependencies = [
@@ -328,33 +304,74 @@ "proc-macro2",
 [[package]]
+name = "target-lexicon"
+version = "0.12.13"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "69758bda2e78f098e4ccb393021a0963bb3442eac05f135c30f61b7370bbafae"
+
+[[package]]
 name = "unicode-ident"
-version = "1.0.9"
+version = "1.0.12"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b15811caf2415fb889178633e7724bad2509101cde276048e013b9def5e51fa0"
+checksum = "3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b"
 
 [[package]]
 name = "unindent"
-version = "0.1.11"
+version = "0.2.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e1766d682d402817b5ac4490b3c3002d91dfa0d22812f341609f97b08757359c"
+checksum = "c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce"
 
 [[package]]
-name = "winapi"
-version = "0.3.9"
+name = "windows-targets"
+version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419"
+checksum = "9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c"
 dependencies = [
- "winapi-i686-pc-windows-gnu",
- "winapi-x86_64-pc-windows-gnu",
+ "windows_aarch64_gnullvm",
+ "windows_aarch64_msvc",
+ "windows_i686_gnu",
+ "windows_i686_msvc",
+ "windows_x86_64_gnu",
+ "windows_x86_64_gnullvm",
+ "windows_x86_64_msvc",
 ]
 
 [[package]]
-name = "winapi-i686-pc-windows-gnu"
-version = "0.4.0"
+name = "windows_aarch64_gnullvm"
+version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6"
+checksum = "2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8"
 
 [[package]]
-name = "winapi-x86_64-pc-windows-gnu"
-version = "0.4.0"
+name = "windows_aarch64_msvc"
+version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f"
+checksum = "dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc"
+
+[[package]]
+name = "windows_i686_gnu"
+version = "0.48.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e"
+
+[[package]]
+name = "windows_i686_msvc"
+version = "0.48.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406"
+
+[[package]]
+name = "windows_x86_64_gnu"
+version = "0.48.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e"
+
+[[package]]
+name = "windows_x86_64_gnullvm"
+version = "0.48.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc"
+
+[[package]]
+name = "windows_x86_64_msvc"
+version = "0.48.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538"

Cargo.toml

 [package]
 name = "fastpdb"
-version = "1.2.0"
+version = "1.3.0"
 edition = "2018"
 
 [dependencies]
-numpy = "0.14"
+numpy = "0.20"
 ndarray = "0.15"
 
 [dependencies.pyo3]
-version = "0.14"
+version = "0.20"
 features = ["extension-module"]
@@ -16,2 +16,2 @@
 name = "fastpdb"
-crate-type = ["cdylib"]
+crate-type = ["cdylib"]

PKG-INFO

 Metadata-Version: 2.1
 Name: fastpdb
-Version: 1.2.0
+Version: 1.3.0
 Classifier: Development Status :: 5 - Production/Stable
@@ -13,3 +13,3 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Requires-Dist: biotite >= 0.37
+Requires-Dist: biotite >=0.39
 License-File: LICENSE
@@ -16,0 +16,0 @@ Summary: A high performance drop-in replacement for Biotite's PDBFile.

pyproject.toml

 [project]
 name = "fastpdb"
-version = "1.2.0"
+version = "1.3.0"
 description = "A high performance drop-in replacement for Biotite's PDBFile."
@@ -28,3 +28,3 @@ readme = "README.rst"
 dependencies = [
-  "biotite >= 0.37"
+  "biotite >= 0.39"
 ]
@@ -42,5 +42,5 @@
 requires = [
-    "maturin>=0.14,<0.15",
+    "maturin==1.4",
     "oldest-supported-numpy"
 ]
 build-backend = "maturin"

python-src/fastpdb/__init__.py

 __name__ = "fastpdb"
 __author__ = "Patrick Kunzmann"
 __all__ = ["PDBFile"]
-__version__ = "1.2.0"
+__version__ = "1.3.0"
 
 import os
+import warnings
 import numpy as np
@@ -19,3 +20,3 @@ from biotite.file import is_text
         self._pdb_file = RustPDBFile([])
-    
+
     @staticmethod
@@ -34,11 +35,11 @@ def read(file):
             pdb_file._pdb_file = RustPDBFile(file.read().splitlines())
-    
-        # Synchronize with PDB file representation in Rust            
+
+        # Synchronize with PDB file representation in Rust
         pdb_file.lines = pdb_file._pdb_file.lines
         pdb_file._index_models_and_atoms()
         return pdb_file
-    
+
     def get_model_count(self):
         return self._pdb_file.get_model_count()
-    
+
     def get_remark(self, number):
@@ -53,7 +54,7 @@ return self._pdb_file.parse_remark(int(number))
         return coord
-    
+
     def get_structure(self, model=None, altloc="first", extra_fields=None, include_bonds=False):
         """
         Get an :class:`AtomArray` or :class:`AtomArrayStack` from the PDB file.
-        
+
         Parameters
@@ -92,3 +93,3 @@ ----------
             does not support bond orders.
-        
+
         Returns
@@ -115,3 +116,3 @@ -------
 
-        
+
         if model is None:
@@ -139,7 +140,7 @@ coord = self._pdb_file.parse_coord_multi_model()
         ins_code  = np.frombuffer(ins_code,  dtype="U1")
-        res_name  = np.frombuffer(res_name,  dtype="U3")
+        res_name  = np.frombuffer(res_name,  dtype="U5")
         atom_name = np.frombuffer(atom_name, dtype="U6")
         element   = np.frombuffer(element,   dtype="U2")
         altloc_id = np.frombuffer(altloc_id, dtype="U1")
-        
+
         if coord.ndim == 3:
@@ -159,6 +160,6 @@ atoms = struc.AtomArrayStack(coord.shape[0], coord.shape[1])
         atoms.element   = element
-        
+
         for field in (extra_fields if extra_fields is not None else []):
             if field == "atom_id":
-                # Copy is necessary to avoid double masking in 
+                # Copy is necessary to avoid double masking in
                 # later altloc ID filtering
@@ -175,7 +176,10 @@ atoms.set_annotation("atom_id", atom_id.copy())
 
-        
-        box = self._pdb_file.parse_box()
-        if box is None:
-            atoms.box = None
-        else:
+
+        try:
+            box = self._pdb_file.parse_box()
+        except:
+            warnings.warn(
+                "File contains invalid 'CRYST1' record, box is ignored"
+            )
+        if box is not None:
             len_a, len_b, len_c, alpha, beta, gamma = box
@@ -192,4 +196,4 @@ box = struc.vectors_from_unitcell(
                 )
-        
 
+
         # Filter altloc IDs
@@ -210,4 +214,4 @@ if altloc == "occupancy":
             raise ValueError(f"'{altloc}' is not a valid 'altloc' option")
-        
 
+
         if include_bonds:
@@ -222,4 +226,4 @@ bond_list = struc.BondList(
         return atoms
-    
 
+
     def set_structure(self, atoms):
@@ -229,3 +233,3 @@ """
         file.
-        
+
         This makes also use of the optional annotation arrays
@@ -236,3 +240,3 @@ ``'atom_id'``, ``'b_factor'``, ``'occupancy'`` and ``'charge'``.
         continuous numbering.
-        
+
         Parameters
@@ -244,3 +248,3 @@ ----------
             model.
-        
+
         Notes
@@ -267,12 +271,12 @@ -----
             )
-        
-        
+
+
         # Write 'ATOM' and 'MODEL' records
         # Convert Unicode arrays into uint32 arrays for usage in Rust
-        chain_id  = np.frombuffer(atoms.chain_id,  dtype=np.uint32).reshape(-1, 4)
-        ins_code  = np.frombuffer(atoms.ins_code,  dtype=np.uint32).reshape(-1, 1)
-        res_name  = np.frombuffer(atoms.res_name,  dtype=np.uint32).reshape(-1, 3)
-        atom_name = np.frombuffer(atoms.atom_name, dtype=np.uint32).reshape(-1, 6)
-        element   = np.frombuffer(atoms.element,   dtype=np.uint32).reshape(-1, 2)
-        
+        chain_id  = _convert_unicode_to_uint32(atoms.chain_id)
+        ins_code  = _convert_unicode_to_uint32(atoms.ins_code)
+        res_name  = _convert_unicode_to_uint32(atoms.res_name)
+        atom_name = _convert_unicode_to_uint32(atoms.atom_name)
+        element   = _convert_unicode_to_uint32(atoms.element)
+
         categories = atoms.get_annotation_categories()
@@ -296,7 +300,7 @@ atom_id   = atoms.atom_id   if "atom_id"   in categories else None
             charge = charge.astype(np.int64, copy=False)
-        
+
         # Treat a single model as multi-model structure
         if coord.ndim == 2:
             coord = coord[np.newaxis, :, :]
-        
+
         self._pdb_file.write_models(
@@ -307,3 +311,3 @@ coord, chain_id, res_id, ins_code,
         )
-       
+
         # Write 'CONECT' records
@@ -331,7 +335,7 @@ if atoms.bonds is not None:
 
-        # Synchronize with PDB file representation in Rust            
+        # Synchronize with PDB file representation in Rust
         self.lines = self._pdb_file.lines
         self._index_models_and_atoms()
-    
 
+
     def _index_models_and_atoms(self):
@@ -341,1 +345,16 @@ self._pdb_file.index_models_and_atoms()
         self._atom_line_i = self._pdb_file.atom_line_i
+
+
+def _convert_unicode_to_uint32(array):
+    """
+    Convert a unicode string array into a 2D uint32 array.
+
+    The second dimension corresponds to the character position within a
+    string.
+    """
+    dtype = array.dtype
+    if not np.issubdtype(dtype, np.str_):
+        raise TypeError("Expected unicode string array")
+    length = array.shape[0]
+    n_char = dtype.itemsize // 4
+    return np.frombuffer(array, dtype=np.uint32).reshape(length, n_char)

src/lib.rs

@@ -46,3 +46,3 @@ //! Low-level PDB file parsing and writing.
 impl PDBFile {
-    
+
     /// Create an new [`PDBFile`].
@@ -103,3 +103,3 @@ /// The lines of text are given to `lines`.
 
-    
+
     /// Get the number of models contained in the file.
@@ -185,3 +185,3 @@ fn get_model_count(&self) -> usize {
     /// The returned tuple contains the following annotations in the given order:
-    /// 
+    ///
     /// - `chain_id`
@@ -217,7 +217,7 @@ /// - `res_id`
         let atom_line_i: Vec<usize> = self.get_atom_indices(model)?;
-        
+
         let mut chain_id:  Array<u32,  Ix2> = Array::zeros((atom_line_i.len(), 4));
         let mut res_id:    Array<i64,  Ix1> = Array::zeros(atom_line_i.len());
         let mut ins_code:  Array<u32,  Ix2> = Array::zeros((atom_line_i.len(), 1));
-        let mut res_name:  Array<u32,  Ix2> = Array::zeros((atom_line_i.len(), 3));
+        let mut res_name:  Array<u32,  Ix2> = Array::zeros((atom_line_i.len(), 5));
         let mut hetero:    Array<bool, Ix1> = Array::default(atom_line_i.len());
@@ -227,3 +227,3 @@ let mut atom_name: Array<u32,  Ix2> = Array::zeros((atom_line_i.len(), 6));
         let mut altloc_id: Array<u32,  Ix2> = Array::zeros((atom_line_i.len(), 1));
-        
+
         let mut atom_id: Array<i64, Ix1>;
@@ -258,3 +258,3 @@ if include_atom_id {
         }
-        
+
         // Iterate over ATOM and HETATM records to write annotation arrays
@@ -302,3 +302,3 @@ for (atom_i, line_i) in atom_line_i.iter().enumerate() {
         }
-        
+
         Python::with_gil(|py| {
@@ -336,3 +336,3 @@ Ok((
         });
-        
+
         // Cannot preemptively determine number of bonds
@@ -420,7 +420,7 @@ // -> Memory allocation for all bonds is not possible
             let mut suffix: Vec<String> = Vec::new();
-            
+
             for i in 0..coord.shape()[1] {
                 let element_i = parse_string_from_array(&element, i)?;
                 let atom_name_i = parse_string_from_array(&atom_name, i)?;
-                
+
                 prefix.push(format!(
@@ -461,3 +461,3 @@ "{:6}{:>5} {:4} {:>3} {:1}{:>4}{:1}   ",
                 }
-                for atom_i in 0..coord.shape()[1] { 
+                for atom_i in 0..coord.shape()[1] {
                     let coord_string = format!(
@@ -484,3 +484,3 @@ "{:>8.3}{:>8.3}{:>8.3}",
     /// to atom indices.
-    fn write_bonds(&mut self, 
+    fn write_bonds(&mut self,
                    bonds: Py<PyArray<i32, Ix2>>,
@@ -491,3 +491,3 @@ atom_id: Py<PyArray<i64, Ix1>>) -> PyResult<()> {
             let atom_id = atom_id.as_ref(py).to_owned_array();
-        
+
             for (center_i, bonded_indices) in bonds.outer_iter().enumerate() {
@@ -567,3 +567,3 @@ let mut n_added: usize = 0;
             },
-            
+
             None => {
@@ -607,3 +607,3 @@ let length = self.get_model_length()?;
         }
-        
+
         // Get the start and stop line index for this model index
@@ -617,3 +617,3 @@ let (model_start, model_stop) = match model_i.cmp(&(self.model_start_i.len() as isize - 1)){
             Ordering::Equal => (
-                self.model_start_i[model_i as usize], 
+                self.model_start_i[model_i as usize],
                 self.lines.len()
@@ -624,3 +624,3 @@ ),
         };
-        
+
         // Get the atom records within these line boundaries
@@ -633,4 +633,4 @@ Ok(
     }
-    
 
+
     /// Get the number of atoms in each model of the PDB file.
@@ -655,3 +655,3 @@ /// A `PyErr` is returned if the number of atoms per model differ from each other.
         }
-    
+
         match length {
@@ -658,0 +658,0 @@ None => panic!("Length cannot be 'None'"),

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