pythonknot 0.1.5__tar.gz → 0.2.0__tar.gz

pythonknot-0.2.0/MANIFEST.in

@@ -0,0 +1,6 @@
+include vendor/rust_knot/Cargo.toml
+include vendor/rust_knot/Cargo.lock
+recursive-include vendor/rust_knot/src/ *.*
+recursive-include src/pythonknot/data *.txt
+prune src/cpp_module
+prune src/HOMFLY

{pythonknot-0.1.5/src/pythonknot.egg-info → pythonknot-0.2.0}/PKG-INFO

@@ -1,12 +1,17 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: pythonknot
-Version: 0.1.5
+Version: 0.2.0
 Summary: pythonknot for knot theory calculation
 Home-page: 
 Author: yjianzhu
 Author-email: yjianzhu@mail.ustc.edu.cn
-License: UNKNOWN
-Platform: UNKNOWN
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: rmsd
+Dynamic: author
+Dynamic: author-email
+Dynamic: description
+Dynamic: requires-dist
+Dynamic: summary
 
 Python Knot is a Python package for creating and manipulating knots and links, calculating knot invariants, and more.
-

pythonknot-0.2.0/README.md

@@ -0,0 +1,101 @@
+# Python Knot package: pythonknot
+
+Python Knot is a package for creating and manipulating knots and links.
+
+## 1. Installation
+
+Python 3.8+ is required.
+
+```bash
+pip install pythonknot
+```
+
+### 1.1 Alexander backend (Rust + PyO3)
+
+`pythonknot.alexander_poly` uses the Rust native backend.
+
+- packaged table: installed with wheel at `pythonknot/data/table_knot_Alexander_polynomial.txt` and auto-used on import
+- legacy fallback path: `~/.local/share/rust_knot/table_knot_Alexander_polynomial.txt`
+- override table: `PYTHONKNOT_ALEXANDER_TABLE=/path/to/table.txt`
+
+`homfly` C/C++ extension is removed from build; wheels now contain only the Rust backend.
+
+## 2. API Summary (`pythonknot.alexander_poly`)
+
+- `read_xyz(filename) -> np.ndarray[F, N, 3]`
+- `read_pdb(filename, atom_filter="all") -> np.ndarray[F, N, 3]`
+- `write_xyz(filename, input_data, append=False) -> None`
+- `knot_type(input_data, chain_type="ring", threads=None) -> List[str]`
+- `knot_size(input_data, chain_type="ring", threads=None) -> Tuple[List[str], List[List[int]]]`
+- `kmt(input_data, chain_type="ring") -> np.ndarray[N2, 3]`
+
+Notes:
+- `input_data` can be XYZ path (`str`), `(N,3)` array, or `(F,N,3)` array for `knot_type` / `knot_size`.
+- `read_pdb(..., atom_filter="all")` supports `"all"` and `"ca"`.
+- `kmt` requires a `(N,3)` array.
+- `threads=None` means single-thread path; `threads>1` enables rayon parallel processing.
+- `knot_type` and `knot_size` release Python GIL during heavy Rust computation.
+
+## 3. Usage
+
+```python
+import numpy as np
+import pythonknot.alexander_poly as alexander_poly
+
+positions = alexander_poly.read_xyz("test/traj_knot31_L300_close.txt")
+print(positions.shape)
+
+# knot type
+types_ring = alexander_poly.knot_type(positions, chain_type="ring", threads=8)
+types_open = alexander_poly.knot_type(positions, chain_type="open", threads=8)
+print(types_ring[:5])
+
+# knot size
+types, sizes = alexander_poly.knot_size(positions[:100], chain_type="ring", threads=8)
+print(types[:3], sizes[:3])
+
+# KMT simplification for one frame (N,3)
+simplified = alexander_poly.kmt(positions[0], chain_type="ring")
+print(simplified.shape)
+
+# write (overwrite by default)
+alexander_poly.write_xyz("out.xyz", positions, append=False)
+
+# append frames
+alexander_poly.write_xyz("out.xyz", positions[:10], append=True)
+
+# read PDB trajectory directly
+pdb_all = alexander_poly.read_pdb("output.pdb", atom_filter="all")
+pdb_ca = alexander_poly.read_pdb("output.pdb", atom_filter="ca")
+print(pdb_all.shape, pdb_ca.shape)
+```
+
+## 4. PDB reading
+
+Use `pythonknot.alexander_poly.read_pdb(...)` directly.
+
+## 5. Cross-platform wheel build
+
+Build is platform-native and Rust-only.
+
+Linux (manylinux, cp38-cp314):
+```bash
+./compile_chain.sh
+```
+
+macOS arm64 (run on macOS arm64 host):
+```bash
+for py in python3.8 python3.9 python3.10 python3.11 python3.12 python3.13 python3.14; do
+  "$py" -m pip install -U pip setuptools wheel
+  "$py" setup.py bdist_wheel
+done
+```
+
+Windows x64 (PowerShell, run on Windows host):
+```powershell
+$versions = @("3.8","3.9","3.10","3.11","3.12","3.13","3.14")
+foreach ($v in $versions) {
+  py -$v -m pip install -U pip setuptools wheel
+  py -$v setup.py bdist_wheel
+}
+```

pythonknot-0.2.0/setup.py

@@ -0,0 +1,102 @@
+import setuptools
+
+import os
+import shutil
+import subprocess
+import sys
+from pathlib import Path
+
+from setuptools import Extension
+from setuptools.command.build_ext import build_ext
+
+class RustPyo3Extension(Extension):
+    def __init__(self, name: str, manifest_path: str, crate_name: str) -> None:
+        super().__init__(name, sources=[])
+        self.manifest_path = os.fspath(Path(manifest_path).resolve())
+        self.crate_name = crate_name
+
+
+class RustBuild(build_ext):
+    def build_extension(self, ext: Extension) -> None:
+        if not isinstance(ext, RustPyo3Extension):
+            raise RuntimeError(f"Unsupported extension type: {type(ext)!r}")
+        self._build_rust_extension(ext)
+
+    def _build_rust_extension(self, ext: RustPyo3Extension) -> None:
+        ext_fullpath = Path.cwd() / self.get_ext_fullpath(ext.name)
+        ext_fullpath.parent.mkdir(parents=True, exist_ok=True)
+
+        debug = int(os.environ.get("DEBUG", 0)) if self.debug is None else self.debug
+
+        cargo_target_dir = (Path(self.build_temp) / "rust_cargo_target").resolve()
+        cargo_target_dir.mkdir(parents=True, exist_ok=True)
+        cargo_tmp_dir = cargo_target_dir / "tmp"
+        cargo_tmp_dir.mkdir(parents=True, exist_ok=True)
+
+        env = os.environ.copy()
+        env["PYO3_PYTHON"] = sys.executable
+        env["CARGO_TARGET_DIR"] = str(cargo_target_dir)
+        env["TMPDIR"] = str(cargo_tmp_dir)
+        if sys.platform.startswith("darwin"):
+            mac_link_args = "-C link-arg=-undefined -C link-arg=dynamic_lookup"
+            env["RUSTFLAGS"] = f"{env.get('RUSTFLAGS', '')} {mac_link_args}".strip()
+
+        cargo_cmd = [
+            "cargo",
+            "build",
+            "--manifest-path",
+            ext.manifest_path,
+            "--features",
+            "python",
+        ]
+        if not debug:
+            cargo_cmd.append("--release")
+
+        subprocess.run(cargo_cmd, env=env, check=True)
+
+        profile = "debug" if debug else "release"
+        if sys.platform.startswith("linux"):
+            lib_name = f"lib{ext.crate_name}.so"
+        elif sys.platform.startswith("darwin"):
+            lib_name = f"lib{ext.crate_name}.dylib"
+        elif sys.platform == "win32":
+            lib_name = f"{ext.crate_name}.dll"
+        else:
+            raise RuntimeError(f"Unsupported platform: {sys.platform}")
+
+        built_lib = cargo_target_dir / profile / lib_name
+        if not built_lib.exists():
+            raise RuntimeError(f"Rust extension build output not found: {built_lib}")
+
+        shutil.copyfile(built_lib, ext_fullpath)
+
+setuptools.setup(
+    name="pythonknot",
+    version="0.2.0",
+    author="yjianzhu",
+    author_email="yjianzhu@mail.ustc.edu.cn",
+    description="pythonknot for knot theory calculation",
+    long_description="Python Knot is a Python package for creating and manipulating knots and links, calculating knot invariants, and more.",
+    url="",
+    ext_modules=[
+        RustPyo3Extension(
+            name="pythonknot.alexander_poly",
+            manifest_path="vendor/rust_knot/Cargo.toml",
+            crate_name="rust_knot",
+        ),
+    ],
+    cmdclass={"build_ext": RustBuild},
+
+    packages=setuptools.find_packages(where='src'), 
+    package_dir={"": "src"},
+    package_data={
+        "pythonknot": ["data/table_knot_Alexander_polynomial.txt"],
+    },
+    zip_safe=False,
+    install_requires=[
+        'numpy',
+        'scipy',
+        'rmsd'
+    ],
+    include_package_data=True,
+)

pythonknot-0.2.0/src/pythonknot/__init__.py

@@ -0,0 +1,18 @@
+import os
+from pathlib import Path
+
+
+_TABLE_ENV = "PYTHONKNOT_ALEXANDER_TABLE"
+_TABLE_NAME = "table_knot_Alexander_polynomial.txt"
+
+
+def _configure_default_alexander_table() -> None:
+    if os.environ.get(_TABLE_ENV):
+        return
+
+    packaged_table = Path(__file__).resolve().parent / "data" / _TABLE_NAME
+    if packaged_table.exists():
+        os.environ[_TABLE_ENV] = str(packaged_table)
+
+
+_configure_default_alexander_table()

pythonknot-0.2.0/src/pythonknot/data/__init__.py

@@ -0,0 +1 @@
+# Package data module for bundled runtime resources.

pythonknot-0.2.0/src/pythonknot/data/table_knot_Alexander_polynomial.txt

@@ -0,0 +1,251 @@
+1       1
+3_1     -1+t-t^2
+4_1     -1+3*t-t^2
+5_1     1-t+t^2-t^3+t^4
+5_2     2-3*t+2*t^2
+6_1     -2+5*t-2*t^2
+6_2     1-3*t+3*t^2-3*t^3+t^4 
+6_3     1-3*t+5*t^2-3*t^3+t^4
+7_1     1-t+t^2-t^3+t^4-t^5+t^6
+7_2     3-5*t+3*t^2
+7_3     2-3*t+3*t^2-3*t^3+2*t^4
+7_4     4-7*t+4*t^2
+7_5     2-4*t+5*t^2-4*t^3+2*t^4
+7_6     1-5*t+7*t^2-5*t^3+t^4
+7_7     1-5*t+9*t^2-5*t^3+t^4
+8_1	3-7*t+3*t^2
+8_2	1-3*t+3*t^2-3*t^3+3*t^4-3*t^5+t^6
+8_3	4-9*t+4*t^2
+8_4	2-5*t+5*t^2-5*t^3+2*t^4
+8_5	1-3*t+4*t^2-5*t^3+4*t^4-3*t^5+t^6
+8_6	2-6*t+7*t^2-6*t^3+2*t^4
+8_7	1-3*t+5*t^2-5*t^3+5*t^4-3*t^5+t^6
+8_8	2-6*t+9*t^2-6*t^3+2*t^4
+8_9	1-3*t+5*t^2-7*t^3+5*t^4-3*t^5+t^6
+8_10	1-3*t+6*t^2-7*t^3+6*t^4-3*t^5+t^6
+8_11	2-7*t+9*t^2-7*t^3+2*t^4
+8_12	1-7*t+13*t^2-7*t^3+t^4
+8_13	2-7*t+11*t^2-7*t^3+2*t^4
+8_14	2-8*t+11*t^2-8*t^3+2*t^4
+8_15	3-8*t+11*t^2-8*t^3+3*t^4
+8_16	1-4*t+8*t^2-9*t^3+8*t^4-4*t^5+t^6
+8_17	1-4*t+8*t^2-11*t^3+8*t^4-4*t^5+t^6
+8_18	1-5*t+10*t^2-13*t^3+10*t^4-5*t^5+t^6
+8_19	1-t+t^3-t^5+t^6
+8_20	1-2*t+3*t^2-2*t^3+t^4
+8_21	1-4*t+5*t^2-4*t^3+t^4
+9_1	1-t+t^2-t^3+t^4-t^5+t^6-t^7+t^8
+9_2	4-7*t+4*t^2
+9_3	2-3*t+3*t^2-3*t^3+3*t^4-3*t^5+2*t^6
+9_4	3-5*t+5*t^2-5*t^3+3*t^4
+9_5	6-11*t+6*t^2
+9_6	2-4*t+5*t^2-5*t^3+5*t^4-4*t^5+2*t^6
+9_7	3-7*t+9*t^2-7*t^3+3*t^4
+9_8	2-8*t+11*t^2-8*t^3+2*t^4
+9_9	2-4*t+6*t^2-7*t^3+6*t^4-4*t^5+2*t^6
+9_10	4-8*t+9*t^2-8*t^3+4*t^4
+9_11	1-5*t+7*t^2-7*t^3+7*t^4-5*t^5+t^6
+9_12	2-9*t+13*t^2-9*t^3+2*t^4
+9_13	4-9*t+11*t^2-9*t^3+4*t^4
+9_14	2-9*t+15*t^2-9*t^3+2*t^4
+9_15	2-10*t+15*t^2-10*t^3+2*t^4
+9_16	2-5*t+8*t^2-9*t^3+8*t^4-5*t^5+2*t^6
+9_17	1-5*t+9*t^2-9*t^3+9*t^4-5*t^5+t^6
+9_18	4-10*t+13*t^2-10*t^3+4*t^4
+9_19	2-10*t+17*t^2-10*t^3+2*t^4
+9_20	1-5*t+9*t^2-11*t^3+9*t^4-5*t^5+t^6
+9_21	2-11*t+17*t^2-11*t^3+2*t^4
+9_22	1-5*t+10*t^2-11*t^3+10*t^4-5*t^5+t^6
+9_23	4-11*t+15*t^2-11*t^3+4*t^4
+9_24	1-5*t+10*t^2-13*t^3+10*t^4-5*t^5+t^6
+9_25	3-12*t+17*t^2-12*t^3+3*t^4
+9_26	1-5*t+11*t^2-13*t^3+11*t^4-5*t^5+t^6
+9_27	1-5*t+11*t^2-15*t^3+11*t^4-5*t^5+t^6
+9_28	1-5*t+12*t^2-15*t^3+12*t^4-5*t^5+t^6
+9_29	1-5*t+12*t^2-15*t^3+12*t^4-5*t^5+t^6
+9_30	1-5*t+12*t^2-17*t^3+12*t^4-5*t^5+t^6
+9_31	1-5*t+13*t^2-17*t^3+13*t^4-5*t^5+t^6
+9_32	1-6*t+14*t^2-17*t^3+14*t^4-6*t^5+t^6
+9_33	1-6*t+14*t^2-19*t^3+14*t^4-6*t^5+t^6
+9_34	1-6*t+16*t^2-23*t^3+16*t^4-6*t^5+t^6
+9_35	7-13*t+7*t^2
+9_36	1-5*t+8*t^2-9*t^3+8*t^4-5*t^5+t^6
+9_37	2-11*t+19*t^2-11*t^3+2*t^4
+9_38	5-14*t+19*t^2-14*t^3+5*t^4
+9_39	3-14*t+21*t^2-14*t^3+3*t^4
+9_40	1-7*t+18*t^2-23*t^3+18*t^4-7*t^5+t^6
+9_41	3-12*t+19*t^2-12*t^3+3*t^4
+9_42	1-2*t+t^2-2*t^3+t^4
+9_43	1-3*t+2*t^2-t^3+2*t^4-3*t^5+t^6
+9_44	1-4*t+7*t^2-4*t^3+t^4
+9_45	1-6*t+9*t^2-6*t^3+t^4
+9_46	2-5*t+2*t^2
+9_47	1-4*t+6*t^2-5*t^3+6*t^4-4*t^5+t^6
+9_48	1-7*t+11*t^2-7*t^3+t^4
+9_49	3-6*t+7*t^2-6*t^3+3*t^4
+10_1	4-9*t+4*t^2
+10_2	1-3*t+3*t^2-3*t^3+3*t^4-3*t^5+3*t^6-3*t^7+t^8
+10_3	6-13*t+6*t^2
+10_4	3-7*t+7*t^2-7*t^3+3*t^4
+10_5	1-3*t+5*t^2-5*t^3+5*t^4-5*t^5+5*t^6-3*t^7+t^8
+10_6	2-6*t+7*t^2-7*t^3+7*t^4-6*t^5+2*t^6
+10_7	3-11*t+15*t^2-11*t^3+3*t^4
+10_8	2-5*t+5*t^2-5*t^3+5*t^4-5*t^5+2*t^6
+10_9	1-3*t+5*t^2-7*t^3+7*t^4-7*t^5+5*t^6-3*t^7+t^8
+10_10	3-11*t+17*t^2-11*t^3+3*t^4
+10_11	4-11*t+13*t^2-11*t^3+4*t^4
+10_12	2-6*t+10*t^2-11*t^3+10*t^4-6*t^5+2*t^6
+10_13	2-13*t+23*t^2-13*t^3+2*t^4
+10_14	2-8*t+12*t^2-13*t^3+12*t^4-8*t^5+2*t^6
+10_15	2-6*t+9*t^2-9*t^3+9*t^4-6*t^5+2*t^6
+10_16	4-12*t+15*t^2-12*t^3+4*t^4
+10_17	1-3*t+5*t^2-7*t^3+9*t^4-7*t^5+5*t^6-3*t^7+t^8
+10_18	4-14*t+19*t^2-14*t^3+4*t^4
+10_19	2-7*t+11*t^2-11*t^3+11*t^4-7*t^5+2*t^6
+10_20	3-9*t+11*t^2-9*t^3+3*t^4
+10_21	2-7*t+9*t^2-9*t^3+9*t^4-7*t^5+2*t^6
+10_22	2-6*t+10*t^2-13*t^3+10*t^4-6*t^5+2*t^6
+10_23	2-7*t+13*t^2-15*t^3+13*t^4-7*t^5+2*t^6
+10_24	4-14*t+19*t^2-14*t^3+4*t^4
+10_25	2-8*t+14*t^2-17*t^3+14*t^4-8*t^5+2*t^6
+10_26	2-7*t+13*t^2-17*t^3+13*t^4-7*t^5+2*t^6
+10_27	2-8*t+16*t^2-19*t^3+16*t^4-8*t^5+2*t^6
+10_28	4-13*t+19*t^2-13*t^3+4*t^4
+10_29	1-7*t+15*t^2-17*t^3+15*t^4-7*t^5+t^6
+10_30	4-17*t+25*t^2-17*t^3+4*t^4
+10_31	4-14*t+21*t^2-14*t^3+4*t^4
+10_32	2-8*t+15*t^2-19*t^3+15*t^4-8*t^5+2*t^6
+10_33	4-16*t+25*t^2-16*t^3+4*t^4
+10_34	3-9*t+13*t^2-9*t^3+3*t^4
+10_35	2-12*t+21*t^2-12*t^3+2*t^4
+10_36	3-13*t+19*t^2-13*t^3+3*t^4
+10_37	4-13*t+19*t^2-13*t^3+4*t^4
+10_38	4-15*t+21*t^2-15*t^3+4*t^4
+10_39	2-8*t+13*t^2-15*t^3+13*t^4-8*t^5+2*t^6
+10_40	2-8*t+17*t^2-21*t^3+17*t^4-8*t^5+2*t^6
+10_41	1-7*t+17*t^2-21*t^3+17*t^4-7*t^5+t^6
+10_42	1-7*t+19*t^2-27*t^3+19*t^4-7*t^5+t^6
+10_43	1-7*t+17*t^2-23*t^3+17*t^4-7*t^5+t^6
+10_44	1-7*t+19*t^2-25*t^3+19*t^4-7*t^5+t^6
+10_45	1-7*t+21*t^2-31*t^3+21*t^4-7*t^5+t^6
+10_46	1-3*t+4*t^2-5*t^3+5*t^4-5*t^5+4*t^6-3*t^7+t^8
+10_47	1-3*t+6*t^2-7*t^3+7*t^4-7*t^5+6*t^6-3*t^7+t^8
+10_48	1-3*t+6*t^2-9*t^3+11*t^4-9*t^5+6*t^6-3*t^7+t^8
+10_49	3-8*t+12*t^2-13*t^3+12*t^4-8*t^5+3*t^6
+10_50	2-7*t+11*t^2-13*t^3+11*t^4-7*t^5+2*t^6
+10_51	2-7*t+15*t^2-19*t^3+15*t^4-7*t^5+2*t^6
+10_52	2-7*t+13*t^2-15*t^3+13*t^4-7*t^5+2*t^6
+10_53	6-18*t+25*t^2-18*t^3+6*t^4
+10_54	2-6*t+10*t^2-11*t^3+10*t^4-6*t^5+2*t^6
+10_55	5-15*t+21*t^2-15*t^3+5*t^4
+10_56	2-8*t+14*t^2-17*t^3+14*t^4-8*t^5+2*t^6
+10_57	2-8*t+18*t^2-23*t^3+18*t^4-8*t^5+2*t^6
+10_58	3-16*t+27*t^2-16*t^3+3*t^4
+10_59	1-7*t+18*t^2-23*t^3+18*t^4-7*t^5+t^6
+10_60	1-7*t+20*t^2-29*t^3+20*t^4-7*t^5+t^6
+10_61	2-5*t+6*t^2-7*t^3+6*t^4-5*t^5+2*t^6
+10_62	1-3*t+6*t^2-8*t^3+9*t^4-8*t^5+6*t^6-3*t^7+t^8
+10_63	5-14*t+19*t^2-14*t^3+5*t^4
+10_64	1-3*t+6*t^2-10*t^3+11*t^4-10*t^5+6*t^6-3*t^7+t^8
+10_65	2-7*t+14*t^2-17*t^3+14*t^4-7*t^5+2*t^6
+10_66	3-9*t+16*t^2-19*t^3+16*t^4-9*t^5+3*t^6
+10_67	4-16*t+23*t^2-16*t^3+4*t^4
+10_68	4-14*t+21*t^2-14*t^3+4*t^4
+10_69	1-7*t+21*t^2-29*t^3+21*t^4-7*t^5+t^6
+10_70	1-7*t+16*t^2-19*t^3+16*t^4-7*t^5+t^6
+10_71	1-7*t+18*t^2-25*t^3+18*t^4-7*t^5+t^6
+10_72	2-9*t+16*t^2-19*t^3+16*t^4-9*t^5+2*t^6
+10_73	1-7*t+20*t^2-27*t^3+20*t^4-7*t^5+t^6
+10_74	4-16*t+23*t^2-16*t^3+4*t^4
+10_75	1-7*t+19*t^2-27*t^3+19*t^4-7*t^5+t^6
+10_76	2-7*t+12*t^2-15*t^3+12*t^4-7*t^5+2*t^6
+10_77	2-7*t+14*t^2-17*t^3+14*t^4-7*t^5+2*t^6
+10_78	1-7*t+16*t^2-21*t^3+16*t^4-7*t^5+t^6
+10_79	1-3*t+7*t^2-12*t^3+15*t^4-12*t^5+7*t^6-3*t^7+t^8
+10_80	3-9*t+15*t^2-17*t^3+15*t^4-9*t^5+3*t^6
+10_81	1-8*t+20*t^2-27*t^3+20*t^4-8*t^5+t^6
+10_82	1-4*t+8*t^2-12*t^3+13*t^4-12*t^5+8*t^6-4*t^7+t^8
+10_83	2-9*t+19*t^2-23*t^3+19*t^4-9*t^5+2*t^6
+10_84	2-9*t+20*t^2-25*t^3+20*t^4-9*t^5+2*t^6
+10_85	1-4*t+8*t^2-10*t^3+11*t^4-10*t^5+8*t^6-4*t^7+t^8
+10_86	2-9*t+19*t^2-25*t^3+19*t^4-9*t^5+2*t^6
+10_87	2-9*t+18*t^2-23*t^3+18*t^4-9*t^5+2*t^6
+10_88	1-8*t+24*t^2-35*t^3+24*t^4-8*t^5+t^6
+10_89	1-8*t+24*t^2-33*t^3+24*t^4-8*t^5+t^6
+10_90	2-8*t+17*t^2-23*t^3+17*t^4-8*t^5+2*t^6
+10_91	1-4*t+9*t^2-14*t^3+17*t^4-14*t^5+9*t^6-4*t^7+t^8
+10_92	2-10*t+20*t^2-25*t^3+20*t^4-10*t^5+2*t^6
+10_93	2-8*t+15*t^2-17*t^3+15*t^4-8*t^5+2*t^6
+10_94	1-4*t+9*t^2-14*t^3+15*t^4-14*t^5+9*t^6-4*t^7+t^8
+10_95	2-9*t+21*t^2-27*t^3+21*t^4-9*t^5+2*t^6
+10_96	1-7*t+22*t^2-33*t^3+22*t^4-7*t^5+t^6
+10_97	5-22*t+33*t^2-22*t^3+5*t^4
+10_98	2-9*t+18*t^2-23*t^3+18*t^4-9*t^5+2*t^6
+10_99	1-4*t+10*t^2-16*t^3+19*t^4-16*t^5+10*t^6-4*t^7+t^8
+10_100	1-4*t+9*t^2-12*t^3+13*t^4-12*t^5+9*t^6-4*t^7+t^8
+10_101	7-21*t+29*t^2-21*t^3+7*t^4
+10_102	2-8*t+16*t^2-21*t^3+16*t^4-8*t^5+2*t^6
+10_103	2-8*t+17*t^2-21*t^3+17*t^4-8*t^5+2*t^6
+10_104	1-4*t+9*t^2-15*t^3+19*t^4-15*t^5+9*t^6-4*t^7+t^8
+10_105	1-8*t+22*t^2-29*t^3+22*t^4-8*t^5+t^6
+10_106	1-4*t+9*t^2-15*t^3+17*t^4-15*t^5+9*t^6-4*t^7+t^8
+10_107	1-8*t+22*t^2-31*t^3+22*t^4-8*t^5+t^6
+10_108	2-8*t+14*t^2-15*t^3+14*t^4-8*t^5+2*t^6
+10_109	1-4*t+10*t^2-17*t^3+21*t^4-17*t^5+10*t^6-4*t^7+t^8
+10_110	1-8*t+20*t^2-25*t^3+20*t^4-8*t^5+t^6
+10_111	2-9*t+17*t^2-21*t^3+17*t^4-9*t^5+2*t^6
+10_112	1-5*t+11*t^2-17*t^3+19*t^4-17*t^5+11*t^6-5*t^7+t^8
+10_113	2-11*t+26*t^2-33*t^3+26*t^4-11*t^5+2*t^6
+10_114	2-10*t+21*t^2-27*t^3+21*t^4-10*t^5+2*t^6
+10_115	1-9*t+26*t^2-37*t^3+26*t^4-9*t^5+t^6
+10_116	1-5*t+12*t^2-19*t^3+21*t^4-19*t^5+12*t^6-5*t^7+t^8
+10_117	2-10*t+24*t^2-31*t^3+24*t^4-10*t^5+2*t^6
+10_118	1-5*t+12*t^2-19*t^3+23*t^4-19*t^5+12*t^6-5*t^7+t^8
+10_119	2-10*t+23*t^2-31*t^3+23*t^4-10*t^5+2*t^6
+10_120	8-26*t+37*t^2-26*t^3+8*t^4
+10_121	2-11*t+27*t^2-35*t^3+27*t^4-11*t^5+2*t^6
+10_122	2-11*t+24*t^2-31*t^3+24*t^4-11*t^5+2*t^6
+10_123	1-6*t+15*t^2-24*t^3+29*t^4-24*t^5+15*t^6-6*t^7+t^8
+10_124	1-t+t^3-t^4+t^5-t^7+t^8
+10_125	1-2*t+2*t^2-t^3+2*t^4-2*t^5+t^6
+10_126	1-2*t+4*t^2-5*t^3+4*t^4-2*t^5+t^6
+10_127	1-4*t+6*t^2-7*t^3+6*t^4-4*t^5+t^6
+10_128	2-3*t+t^2+t^3+t^4-3*t^5+2*t^6
+10_129	2-6*t+9*t^2-6*t^3+2*t^4
+10_130	2-4*t+5*t^2-4*t^3+2*t^4
+10_131	2-8*t+11*t^2-8*t^3+2*t^4
+10_132	1-t+t^2-t^3+t^4
+10_133	1-5*t+7*t^2-5*t^3+t^4
+10_134	2-4*t+4*t^2-3*t^3+4*t^4-4*t^5+2*t^6
+10_135	3-9*t+13*t^2-9*t^3+3*t^4
+10_136	1-4*t+5*t^2-4*t^3+t^4
+10_137	1-6*t+11*t^2-6*t^3+t^4
+10_138	1-5*t+8*t^2-7*t^3+8*t^4-5*t^5+t^6
+10_139	1-t+2*t^3-3*t^4+2*t^5-t^7+t^8
+10_140	1-2*t+3*t^2-2*t^3+t^4
+10_141	1-3*t+4*t^2-5*t^3+4*t^4-3*t^5+t^6
+10_142	2-3*t+2*t^2-t^3+2*t^4-3*t^5+2*t^6
+10_143	1-3*t+6*t^2-7*t^3+6*t^4-3*t^5+t^6
+10_144	3-10*t+13*t^2-10*t^3+3*t^4
+10_145	1+t-3*t^2+t^3+t^4
+10_146	2-8*t+13*t^2-8*t^3+2*t^4
+10_147	2-7*t+9*t^2-7*t^3+2*t^4
+10_148	1-3*t+7*t^2-9*t^3+7*t^4-3*t^5+t^6
+10_149	1-5*t+9*t^2-11*t^3+9*t^4-5*t^5+t^6
+10_150	1-4*t+6*t^2-7*t^3+6*t^4-4*t^5+t^6
+10_151	1-4*t+10*t^2-13*t^3+10*t^4-4*t^5+t^6
+10_152	1-t-t^2+4*t^3-5*t^4+4*t^5-t^6-t^7+t^8
+10_153	1-t-t^2+3*t^3-t^4-t^5+t^6
+10_154	1-4*t^2+7*t^3-4*t^4+t^6
+10_155	1-3*t+5*t^2-7*t^3+5*t^4-3*t^5+t^6
+10_156	1-4*t+8*t^2-9*t^3+8*t^4-4*t^5+t^6
+10_157	1-6*t+11*t^2-13*t^3+11*t^4-6*t^5+t^6
+10_158	1-4*t+10*t^2-15*t^3+10*t^4-4*t^5+t^6
+10_159	1-4*t+9*t^2-11*t^3+9*t^4-4*t^5+t^6
+10_160	1-4*t+4*t^2-3*t^3+4*t^4-4*t^5+t^6
+10_161	1-2*t^2+3*t^3-2*t^4+t^6
+10_162	3-9*t+11*t^2-9*t^3+3*t^4
+10_163	1-5*t+12*t^2-15*t^3+12*t^4-5*t^5+t^6
+10_164	3-11*t+17*t^2-11*t^3+3*t^4
+10_165	2-10*t+15*t^2-10*t^3+2*t^4
+

pythonknot-0.2.0/src/pythonknot/knot_generator.py

@@ -0,0 +1,22 @@
+import numpy as np
+
+# design for generating knot configurations for diffrent simulation software
+# lammps read_data, gromacs gmx editconf, openmm pdb
+# get the coordinates of the knot, then write to the corresponding file
+class KnotGenerator:
+    def __init__(self, knot):
+        """ knot should be a numpy array with shape (N_atoms, 3)"""
+        self.knot = knot
+
+    def write_lammps_data(self, filename):
+        pass
+
+    def write_gromacs_gro(self, filename):
+        pass
+
+    def write_openmm_pdb(self, filename):
+        pass
+
+    def write_xyz(self, filename):
+        pass
+

{pythonknot-0.1.5 → pythonknot-0.2.0}/src/pythonknot/xyz.py

@@ -17,4 +17,15 @@ def read_xyz(file):
                 coords[i,j,2] = float(line[3])
             lines = lines[N_atoms:]
 
-    return coords
+    return coords
+
+def write_xyz(file, coords):
+    """Write xyz file with coords, coords is a N_frames*N_atoms*3 np array, all the frames have same number of atoms"""
+    N_atoms = coords.shape[1]
+    N_frames = coords.shape[0]
+    with open(file, 'w') as f:
+        for i in range(N_frames):
+            f.write(str(N_atoms)+'\n')
+            f.write('frame '+str(i)+'\n')
+            for j in range(N_atoms):
+                f.write('1 '+str(coords[i,j,0])+' '+str(coords[i,j,1])+' '+str(coords[i,j,2])+'\n')

{pythonknot-0.1.5 → pythonknot-0.2.0/src/pythonknot.egg-info}/PKG-INFO

@@ -1,12 +1,17 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: pythonknot
-Version: 0.1.5
+Version: 0.2.0
 Summary: pythonknot for knot theory calculation
 Home-page: 
 Author: yjianzhu
 Author-email: yjianzhu@mail.ustc.edu.cn
-License: UNKNOWN
-Platform: UNKNOWN
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: rmsd
+Dynamic: author
+Dynamic: author-email
+Dynamic: description
+Dynamic: requires-dist
+Dynamic: summary
 
 Python Knot is a Python package for creating and manipulating knots and links, calculating knot invariants, and more.
-

pythonknot-0.2.0/src/pythonknot.egg-info/SOURCES.txt

@@ -0,0 +1,33 @@
+MANIFEST.in
+README.md
+setup.py
+src/pythonknot/__init__.py
+src/pythonknot/knot_generator.py
+src/pythonknot/polymer.py
+src/pythonknot/rmsd.py
+src/pythonknot/xyz.py
+src/pythonknot.egg-info/PKG-INFO
+src/pythonknot.egg-info/SOURCES.txt
+src/pythonknot.egg-info/dependency_links.txt
+src/pythonknot.egg-info/not-zip-safe
+src/pythonknot.egg-info/requires.txt
+src/pythonknot.egg-info/top_level.txt
+src/pythonknot/data/__init__.py
+src/pythonknot/data/table_knot_Alexander_polynomial.txt
+vendor/rust_knot/Cargo.lock
+vendor/rust_knot/Cargo.toml
+vendor/rust_knot/src/alexander_table.rs
+vendor/rust_knot/src/batch.rs
+vendor/rust_knot/src/config.rs
+vendor/rust_knot/src/error.rs
+vendor/rust_knot/src/geometry.rs
+vendor/rust_knot/src/hull.rs
+vendor/rust_knot/src/io.rs
+vendor/rust_knot/src/kmt.rs
+vendor/rust_knot/src/knotsize.rs
+vendor/rust_knot/src/knottype.rs
+vendor/rust_knot/src/lib.rs
+vendor/rust_knot/src/main.rs
+vendor/rust_knot/src/point.rs
+vendor/rust_knot/src/polynomial.rs
+vendor/rust_knot/src/python_module.rs

pythonknot-0.2.0/src/pythonknot.egg-info/requires.txt

@@ -0,0 +1,3 @@
+numpy
+scipy
+rmsd