libmoleculargraph instruction

build/README.md

@@ -4,20 +4,37 @@ libmoleculargraph
 
 A library builder for calling some functions of MolecularGraph.jl from external applications. See [PackageCompiler.jl](https://github.com/JuliaLang/PackageCompiler.jl) for details.
 
-### tested environment
-
-```
-julia> versioninfo()
-Julia Version 1.8.2
-Commit 36034abf260 (2022-09-29 15:21 UTC)
-Platform Info:
-  OS: macOS (x86_64-apple-darwin21.4.0)
-  CPU: 4 × Intel(R) Core(TM) i5-8210Y CPU @ 1.60GHz
-  WORD_SIZE: 64
-  LIBM: libopenlibm
-  LLVM: libLLVM-13.0.1 (ORCJIT, skylake)
-  Threads: 1 on 4 virtual cores
-```
-
-- ./scripts/test_lib.py worked with Python 3.10.0
-- did not work with Julia version 1.7.3 due to a link error.
+
+### Dockerfile (recommended)
+
+- See `./docker-example`
+- A test script `../scripts/python_test.py` worked with Python 3.10.0
+
+
+### Other platforms
+
+Building in environments shown below and other platforms are not supported.
+
+
+#### For Intel Mac
+
+- Building MacOS binary has some potential issues.
+- Run `make` to build binary and then `sudo make link` to copy them to `/usr/local`
+- Testing environment:
+
+  ```
+  julia> versioninfo()
+  Julia Version 1.10.0
+  Commit 3120989f39b (2023-12-25 18:01 UTC)
+  Build Info:
+    Official https://julialang.org/ release
+  Platform Info:
+    OS: macOS (x86_64-apple-darwin22.4.0)
+    CPU: 4 × Intel(R) Core(TM) i5-8210Y CPU @ 1.60GHz
+    WORD_SIZE: 64
+    LIBM: libopenlibm
+    LLVM: libLLVM-15.0.7 (ORCJIT, skylake)
+    Threads: 1 on 4 virtual cores
+  ```
+
+  - did not work with Julia version 1.7.3 (and below) due to a link error.

scripts/python_test.py

@@ -0,0 +1,139 @@
+from ctypes import CDLL, RTLD_GLOBAL, POINTER, cast, c_char_p, c_ubyte, c_double, c_int, c_uint
+import json
+from pathlib import Path
+import platform
+
+
+def jl_init():
+    dlext = "dylib" if platform.system() == "Darwin" else "so"
+    libdir = Path("/usr/local/lib")
+    jl = CDLL(libdir / f"libmoleculargraph.{dlext}", RTLD_GLOBAL)
+    jl.jl_init_with_image(bytes(libdir), f"libmoleculargraph.{dlext}".encode())
+    return jl
+
+
+def jl_exit(jl):
+    jl.jl_atexit_hook(0)
+
+
+def smiles_to_mol(jl, smiles: str) -> bytes:
+    jl.smilestomol.argtypes = [c_char_p]
+    jl.smilestomol.restype = c_char_p
+    return jl.smilestomol(smiles.encode(), r"{}".encode())
+
+
+def smarts_to_mol(jl, smarts: str) -> bytes:
+    jl.smartstomol.argtypes = [c_char_p]
+    jl.smartstomol.restype = c_char_p
+    return jl.smartstomol(smarts.encode())
+
+
+def sdf_to_mol(jl, sdf: str) -> bytes:
+    # sdf: SDFile string (open as f -> f.read())
+    jl.sdftomol.argtypes = [c_char_p]
+    jl.sdftomol.restype = c_char_p
+    return jl.sdftomol(sdf.encode(), r"{}".encode())
+
+
+def vertex_count(jl, mol: bytes) -> int:
+    # mol: json.dumps(mol_dict).encode()
+    jl.vertex_count.argtypes = [c_char_p]
+    jl.vertex_count.restype = c_int
+    return jl.vertex_count(mol)
+
+
+def edge_count(jl, mol: bytes) -> int:
+    # mol: json.dumps(mol_dict).encode()
+    jl.edge_count.argtypes = [c_char_p]
+    jl.edge_count.restype = c_int
+    return jl.edge_count(mol)
+
+
+def inchikey(jl, mol: bytes) -> str:
+    # mol: json.dumps(mol_dict).encode()
+    jl.inchikey.argtypes = [c_char_p]
+    jl.inchikey.restype = c_char_p
+    return jl.inchikey(mol).decode("utf-8")
+
+
+def standard_weight(jl, mol: bytes) -> float:
+    # mol: json.dumps(mol_dict).encode()
+    jl.standard_weight.argtypes = [c_char_p]
+    jl.standard_weight.restype = c_double
+    return jl.standard_weight(mol)
+
+
+def mol_to_svg(jl, mol: bytes) -> str:
+    # mol: json.dumps(mol_dict).encode()
+    jl.drawsvg.argtypes = [c_char_p]
+    jl.drawsvg.restype = c_char_p
+    return jl.drawsvg(mol).decode("utf-8")
+
+
+def sdf_to_svg(jl, sdf: str) -> str:
+    mol = sdf_to_mol(jl, sdf)
+    return mol_to_svg(jl, mol)
+
+
+def smiles_to_svg(jl, smiles: str) -> str:
+    mol = smiles_to_mol(jl, smiles)
+    return mol_to_svg(jl, mol)
+
+
+def mol_to_png(jl, mol: bytes, width: int, height: int) -> bytes:
+    # mol: json.dumps(mol_dict).encode()
+    buf = (c_ubyte * 200_000).from_buffer(bytearray(200_000))  # 200 kB buffer, tentative
+    jl.drawpng.argtypes = [c_ubyte * 200_000, c_char_p, c_uint, c_uint]
+    jl.drawpng.restype = c_int
+    size = jl.drawpng(buf, mol, c_uint(width), c_uint(height))
+    return bytes(buf[:size])
+
+
+def sdf_to_png(jl, sdf: str, width: int, height: int) -> bytes:
+    mol = sdf_to_mol(jl, sdf)
+    return mol_to_png(jl, mol, width, height)
+
+
+def smiles_to_png(jl, smiles: str, width: int, height: int) -> bytes:
+    mol = smiles_to_mol(jl, smiles)
+    return mol_to_png(jl, mol, width, height)
+
+
+def has_exact_match(jl, mol1: bytes, mol2: bytes, options: bytes) -> bool:
+    # mol1, mol2, options: json.dumps(dict).encode()
+    jl.has_exact_match.argtypes = [c_char_p, c_char_p, c_char_p]
+    jl.has_exact_match.restype = c_int
+    return jl.has_exact_match(mol1, mol2, options)
+
+
+def has_substruct_match(jl, mol1: bytes, mol2: bytes, options: bytes) -> bool:
+    # mol1, mol2, options: json.dumps(dict).encode()
+    jl.has_substruct_match.argtypes = [c_char_p, c_char_p, c_char_p]
+    jl.has_substruct_match.restype = c_int
+    return jl.has_substruct_match(mol1, mol2, options)
+
+
+def tdmcis_size(jl, mol1: bytes, mol2: bytes, options: bytes) -> int:
+    # mol1, mol2, options: json.dumps(dict).encode()
+    jl.tdmcis_size.argtypes = [c_char_p, c_char_p, c_char_p]
+    jl.tdmcis_size.restype = c_int
+    return jl.tdmcis_size(mol1, mol2, options)
+
+
+def tdmces_size(jl, mol1: bytes, mol2: bytes, options: bytes) -> int:
+    # mol1, mol2, options: json.dumps(dict).encode()
+    jl.tdmces_size.argtypes = [c_char_p, c_char_p, c_char_p]
+    jl.tdmces_size.restype = c_int
+    return jl.tdmces_size(mol1, mol2, options)
+
+
+if __name__ == "__main__":
+    jl = jl_init()
+    mol1 = smiles_to_mol(jl, "CC(=O)OC1=CC=CC=C1C(=O)O")
+    mol2 = smiles_to_mol(jl, "OC1=CC=CC=C1C(=O)O")
+    print(standard_weight(jl, mol1))
+    print(inchikey(jl, mol1))
+    print(has_substruct_match(jl, mol1, mol2, json.dumps({}).encode()))
+    print(tdmces_size(jl, mol1, mol2, json.dumps({}).encode()))
+    print(mol_to_svg(jl, mol1))
+    jl_exit(jl)