Merge commit '021b0014ea1e1ca3024ffdaa7bd17492d3810d35'

build/Makefile

@@ -4,7 +4,7 @@ JULIA ?= julia
 DLEXT := $(shell $(JULIA) --startup-file=no -e 'using Libdl; print(Libdl.dlext)')
 
 TARGET="../compiled"
-DEST="/usr/local/moleculargraphjl"
+DEST="/opt/moleculargraphjl"
 
 MYLIB_INCLUDES = $(TARGET)/include/julia_init.h $(TARGET)/include/libmoleculargraph.h
 MYLIB_PATH := $(TARGET)/lib/libmoleculargraph.$(DLEXT)

build/generate_precompile.jl

@@ -47,6 +47,8 @@ function run()
     # write(f, img)
     # close(f)
     @debug "length(drawpng(io, demomol, 1000, 1000))" length(img)
+    @debug "length(molblock(demomol))" length(unsafe_string(molblock(unsafe_convert(Cstring, demomol))))
+    @debug "length(sdfmolblock(demomol))" length(unsafe_string(sdfmolblock(unsafe_convert(Cstring, demomol))))
 
     nullmol_sdf = read(open(joinpath(dirname(@__FILE__), "../assets/test/null.mol")), String)
     nullmol = unsafe_string(sdftomol(
@@ -60,8 +62,16 @@ function run()
 
     notamide = unsafe_string(smartstomol(
         unsafe_convert(Cstring, raw"[NX3;H2,H1;!$(NC=O)]")))
+    notamide2 = unsafe_string(smartstomol(
+        unsafe_convert(Cstring, raw"[NX3;H2,H1]")))
     rotatable = unsafe_string(smartstomol(
         unsafe_convert(Cstring, raw"[!$(*#*)&!D1]-!@[!$(*#*)&!D1]")))
+    @debug "notamide rotatable" has_exact_match(
+        unsafe_convert(Cstring, notamide), unsafe_convert(Cstring, rotatable),
+        unsafe_convert(Cstring, op))
+    @debug "notamide notamide2" has_substruct_match(
+        unsafe_convert(Cstring, notamide), unsafe_convert(Cstring, notamide2),
+        unsafe_convert(Cstring, op))
 
     @debug "nullsmiles nullmol" has_exact_match(
         unsafe_convert(Cstring, nullsmiles), unsafe_convert(Cstring, nullmol),

build/libmoleculargraph.h

@@ -5,6 +5,8 @@ int vertex_count(char*);
 int edge_count(char*);
 char* inchikey(char*);
 double standard_weight(char*);
+char* molblock(char*);
+char* sdfmolblock(char*);
 char* drawsvg(char*);
 char* drawpng(char*, unsigned int, unsigned int);
 int has_exact_match(char*, char*, char*);

scripts/python_test.py

@@ -1,3 +1,5 @@
+# Python >= 3.10
+
 import base64
 from ctypes import CDLL, RTLD_GLOBAL, POINTER, cast, c_char_p, c_ubyte, c_double, c_int, c_uint
 import json
@@ -7,7 +9,7 @@
 
 def jl_init():
     dlext = "dylib" if platform.system() == "Darwin" else "so"
-    libdir = Path("/usr/local/moleculargraphjl/lib")
+    libdir = Path("/opt/moleculargraphjl/lib")
     jl = CDLL(libdir / f"libmoleculargraph.{dlext}", RTLD_GLOBAL)
     jl.jl_init_with_image(bytes(libdir), f"libmoleculargraph.{dlext}".encode())
     return jl
@@ -18,7 +20,7 @@ def jl_exit(jl):
 
 
 def smiles_to_mol(jl, smiles: str) -> bytes:
-    jl.smilestomol.argtypes = [c_char_p]
+    jl.smilestomol.argtypes = [c_char_p, c_char_p]
     jl.smilestomol.restype = c_char_p
     return jl.smilestomol(smiles.encode(), r"{}".encode())
 
@@ -31,7 +33,7 @@ def smarts_to_mol(jl, smarts: str) -> bytes:
 
 def sdf_to_mol(jl, sdf: str) -> bytes:
     # sdf: SDFile string (open as f -> f.read())
-    jl.sdftomol.argtypes = [c_char_p]
+    jl.sdftomol.argtypes = [c_char_p, c_char_p]
     jl.sdftomol.restype = c_char_p
     return jl.sdftomol(sdf.encode(), r"{}".encode())
 
@@ -99,6 +101,20 @@ def smiles_to_png(jl, smiles: str, width: int, height: int) -> bytes:
     return mol_to_png(jl, mol, width, height)
 
 
+def mol_to_molblock(jl, mol: bytes) -> str:
+    # mol: json.dumps(mol_dict).encode()
+    jl.molblock.argtypes = [c_char_p]
+    jl.molblock.restype = c_char_p
+    return jl.molblock(mol).decode("utf-8")
+
+
+def mol_to_sdfblock(jl, mol: bytes) -> str:
+    # mol: json.dumps(mol_dict).encode()
+    jl.sdfmolblock.argtypes = [c_char_p]
+    jl.sdfmolblock.restype = c_char_p
+    return jl.sdfmolblock(mol).decode("utf-8")
+
+
 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]
@@ -137,4 +153,6 @@ def tdmces_size(jl, mol1: bytes, mol2: bytes, options: bytes) -> int:
     print(tdmces_size(jl, mol1, mol2, json.dumps({}).encode()))
     print(len(mol_to_svg(jl, mol1)))
     print(len(mol_to_png(jl, mol1, 100, 100)))
+    print(len(mol_to_molblock(jl, mol1)))
+    print(len(mol_to_sdfblock(jl, mol1)))
     jl_exit(jl)

src/draw/svg.jl

@@ -72,9 +72,12 @@ svgtransform(tf::Array{Float64,2}
     ) = @sprintf "%.2f %.2f %.2f %.2f %.2f %.2f" tf[1] tf[2] tf[4] tf[5] tf[7] tf[8]
 
 
-function tosvg(canvas::SvgCanvas; width="100%", height="100%", kwargs...)
+function tosvg(canvas::SvgCanvas; width="100%", height="100%", viewbox=true, kwargs...)
     vbWf = @sprintf "%.2f" canvas.viewboxW
     vbHf = @sprintf "%.2f" canvas.viewboxH
+    vb = viewbox ? " viewBox=\"0 0 $(vbWf) $(vbHf)\"" : ""
+    w = viewbox ? width : vbWf
+    h = viewbox ? height : vbHf
     bgc = svgcolor(canvas.bgcolor)
     header = """<svg xmlns="http://www.w3.org/2000/svg"
      xmlns:xlink="http://www.w3.org/1999/xlink"
@@ -83,8 +86,7 @@ function tosvg(canvas::SvgCanvas; width="100%", height="100%", kwargs...)
      preserveAspectRatio="xMidYMid meet"
      font-weight="$(canvas.fontweight)"
      font-family="$(canvas.fontfamily)"
-     width="$(width)" height="$(height)"
-     viewBox="0 0 $(vbWf) $(vbHf)">
+     width="$(w)" height="$(h)"$(vb)>
     """
     bg = """<rect x="0" y="0" width="$(vbWf)" height="$(vbHf)"
      fill="$(bgc)" opacity="$(canvas.bgopacity)"/>

src/libmoleculargraph.jl

@@ -8,6 +8,7 @@ using Base64
 
 export
     vertex_count, edge_count,
+    molblock, sdfmolblock,
     tdmcis_size, tdmces_size, tdmcis_gls, tdmces_gls
 
 
@@ -97,6 +98,30 @@ Base.@ccallable function standard_weight(mol::Cstring)::Cdouble
 end
 
 
+Base.@ccallable function molblock(mol::Cstring)::Cstring
+    return try
+        molobj = MolGraph(JSON.parse(unsafe_string(mol)))
+        return unsafe_convert(Cstring, printv2mol(molobj))
+    catch
+        Base.invokelatest(Base.display_error, Base.catch_stack())
+    end
+end
+
+
+Base.@ccallable function sdfmolblock(mol::Cstring)::Cstring
+    return try
+        molobj = MolGraph(JSON.parse(unsafe_string(mol)))
+        buf = IOBuffer(write=true)
+        printv2sdf(buf, molobj)
+        res = String(take!(buf))
+        close(buf)
+        return unsafe_convert(Cstring, res)
+    catch
+        Base.invokelatest(Base.display_error, Base.catch_stack())
+    end
+end
+
+
 Base.@ccallable function drawsvg(mol::Cstring)::Cstring
     return try
         molobj = MolGraph(JSON.parse(unsafe_string(mol)))