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@mojaie
mojaie committed Nov 19, 2024
2 parents 3924d28 + 4228d7b commit 5dc8b5b
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Showing 5 changed files with 200 additions and 54 deletions.
7 changes: 3 additions & 4 deletions build/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ JULIA ?= julia
DLEXT := $(shell $(JULIA) --startup-file=no -e 'using Libdl; print(Libdl.dlext)')

TARGET="../compiled"
DEST="/usr/local"
DEST="/usr/local/moleculargraphjl"

MYLIB_INCLUDES = $(TARGET)/include/julia_init.h $(TARGET)/include/libmoleculargraph.h
MYLIB_PATH := $(TARGET)/lib/libmoleculargraph.$(DLEXT)
Expand All @@ -17,9 +17,8 @@ $(MYLIB_PATH) $(MYLIB_INCLUDES): ./build.jl ../src/MolecularGraph.jl
# For MacOS testing

link:
cp -a $(TARGET)/lib/* $(DEST)/lib
cp -a $(TARGET)/share/* $(DEST)/share
cp -a $(TARGET)/include/* $(DEST)/include
mkdir -p $(DEST)
cp -a $(TARGET)/* $(DEST)
install_name_tool -add_rpath $(DEST)/lib $(DEST)/lib/libmoleculargraph.$(DLEXT)
install_name_tool -add_rpath $(DEST)/lib/julia $(DEST)/lib/libmoleculargraph.$(DLEXT)

Expand Down
4 changes: 2 additions & 2 deletions scripts/integrate_default_queries.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@ function run()
"str_alert_221", "str_alert_222", "str_alert_247", "str_alert_1003",
"str_alert_246", "str_alert_381"
]
@info "vprops" length(vprops) - length(skip)
for (u, v) in combinations(length(vprops))
ukey = vprops[u]["key"]
vkey = vprops[v]["key"]
Expand Down Expand Up @@ -95,5 +96,4 @@ function run()
YAML.write_file(OUTPUT_FILE, vprops)
end


run()
@time run()
2 changes: 1 addition & 1 deletion scripts/python_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@

def jl_init():
dlext = "dylib" if platform.system() == "Darwin" else "so"
libdir = Path("/usr/local/lib")
libdir = Path("/usr/local/moleculargraphjl/lib")
jl = CDLL(libdir / f"libmoleculargraph.{dlext}", RTLD_GLOBAL)
jl.jl_init_with_image(bytes(libdir), f"libmoleculargraph.{dlext}".encode())
return jl
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111 changes: 80 additions & 31 deletions src/stereo.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,17 @@ export
stereocenter_from_smiles!, stereocenter_from_sdf2d!,
stereobond_from_smiles!, stereobond_from_sdf2d!


"""
Stereocenter{T} <: AbstractDict{T,Tuple{T,T,T,Bool}}
A graph-level property that describes chirality of the molecule.
The dict key represents the stereocenter vertex, and the value is a 4-tuple
in the format (l, v1, v2, is_clockwise). `is_clockwise` is a boolean value indicating
whether nodes `v1` and `v2` are arranged clockwise when viewed from node `l`
toward the stereocenter.
"""
struct Stereocenter{T} <: AbstractDict{T,Tuple{T,T,T,Bool}}
mapping::Dict{T,Tuple{T,T,T,Bool}}
end
Expand All @@ -32,6 +43,15 @@ function remap(stereo::Stereocenter{T}, vmap::Dict) where T # vmap[old] -> new
end


"""
Stereobond{T} <: AbstractDict{Edge{T},Tuple{T,T,Bool}}
A graph-level property that describes cis-trans isomerism of the molecule.
The dict key represents the stereogenic double bond edge, and the value is a 3-tuple
in the format (e1, e2, is_cis). `is_cis` is a boolean value indicating
whether edges `e1` and `e2` are placed in the same side of the stereogenic bond.
"""
struct Stereobond{T} <: AbstractDict{Edge{T},Tuple{T,T,Bool}}
mapping::Dict{Edge{T},Tuple{T,T,Bool}}
end
Expand Down Expand Up @@ -151,7 +171,7 @@ Return stereocenter information obtained from 2D SDFile.
function stereocenter_from_sdf2d(g::SimpleGraph{T}, e_order, e_notation, e_isordered, v_coords2d) where T
centers = Stereocenter{T}()
edgerank = Dict(e => i for (i, e) in enumerate(edges(g)))
comments = Dict{Int,String}()
comments = String[]
for i in vertices(g)
degree(g, i) in (3, 4) || continue
nbrs = ordered_neighbors(g, i)
Expand All @@ -169,37 +189,56 @@ function stereocenter_from_sdf2d(g::SimpleGraph{T}, e_order, e_notation, e_isord
end
push!(drs, :unspecified)
end
length(drs) == degree(g, i) || (@debug "multiple bond"; continue)
length(drs) == degree(g, i) || (@debug "$(i): multiple bond"; continue)
upcnt = count(x -> x === :up, drs)
dwcnt = count(x -> x === :down, drs)
(upcnt == 0 && dwcnt == 0) && (@debug "unspecified"; continue)
(upcnt == 0 && dwcnt == 0) && (@debug "$(i): unspecified"; continue)
sortorder = [1, map(x -> x + 1, anglesort(v_coords2d, i, nbrs[1], nbrs[2:end]))...]
ons = nbrs[sortorder]
ods = drs[sortorder]
ons = nbrs[sortorder] # node indices of neighbors in angular order
ods = drs[sortorder] # direction symbols of neighbors in angular order
if length(nbrs) == 3
if upcnt + dwcnt == 1
# if there is implicit hydrogen, an up-wedge -> clockwise, a down-edge -> ccw
centers[i] = (ons[1], ons[2], ons[3], dwcnt == 0)
if upcnt == 1 && dwcnt == 1 || upcnt + dwcnt == 3
@debug "$(i): a reference plane cannot be defined $(ons) $(ods)"
push!(comments, "$(i): a reference plane cannot be defined")
elseif upcnt == 2 || dwcnt == 2
centers[i] = (ons[1], ons[2], ons[3], upcnt == 0)
else
@debug "Ambiguous stereochemistry (maybe need explicit hydrogen)"
comments[i] = "$(ons) $(ods) Ambiguous stereochemistry (maybe need explicit hydrogen)"
continue
centers[i] = (ons[1], ons[2], ons[3], dwcnt == 0)
end
elseif (ods[1] !== :unspecified && ods[3] !== :unspecified && ods[1] !== ods[3] ||
ods[2] !== :unspecified && ods[4] !== :unspecified && ods[2] !== ods[4])
@debug "Ambiguous stereochemistry (opposite direction wedges at opposite side)"
comments[i] = "$(ons) $(ods) Ambiguous stereochemistry (opposite direction wedges at opposite side)"
continue
elseif (ods[1] !== :unspecified && ods[1] === ods[2] ||
ods[2] !== :unspecified && ods[2] === ods[3] ||
ods[3] !== :unspecified && ods[3] === ods[4] ||
ods[4] !== :unspecified && ods[4] === ods[1])
@debug "Ambiguous stereochemistry (same direction wedges at same side)"
comments[i] = "$(ons) $(ods) Ambiguous stereochemistry (same direction wedges at same side)"
continue
elseif upcnt != 0
end
if upcnt == 4 || dwcnt == 4
@debug "$(i): a reference plane cannot be defined $(ons) $(ods)"
push!(comments, "$(i): a reference plane cannot be defined")
elseif upcnt == 3
centers[i] = (ons[1], ons[2], ons[3], ods[1] === :up && ods[3] === :up)
elseif dwcnt == 3
centers[i] = (ons[1], ons[2], ons[3], ods[2] === :down && ods[4] === :down)
elseif upcnt == 2
if (ods[1] === :up && ods[3] === :up) || (ods[2] === :up && ods[4] === :up)
centers[i] = (ons[1], ons[2], ons[3], ods[1] === :up)
else
@debug "$(i): adjacent wedges lie on the same side of the reference plane $(ons) $(ods)"
push!(comments, "$(i): adjacent wedges lie on the same side of the reference plane")
end
elseif dwcnt == 2
if (ods[1] === :down && ods[3] === :down) || (ods[2] === :down && ods[4] === :down)
centers[i] = (ons[1], ons[2], ons[3], ods[1] !== :down)
else
@debug "$(i): adjacent wedges lie on the same side of the reference plane $(ons) $(ods)"
push!(comments, "$(i): adjacent wedges lie on the same side of the reference plane")
end
elseif upcnt == 1 && dwcnt == 1
if ((ods[1] === :unspecified && ods[3] === :unspecified)
|| (ods[2] === :unspecified && ods[4] === :unspecified))
@debug "$(i): non-adjacent wedges lie on the opposite side of the reference plane $(ons) $(ods)"
push!(comments, "$(i): non-adjacent wedges lie on the opposite side of the reference plane")
else
centers[i] = (ons[1], ons[2], ons[3], ods[1] === :up || ods[3] === :up)
end
elseif upcnt == 1
centers[i] = (ons[1], ons[2], ons[3], ods[1] === :up || ods[3] === :up)
else # down wedges only
else # dwcnt == 1
centers[i] = (ons[1], ons[2], ons[3], ods[2] === :down || ods[4] === :down)
end
end
Expand All @@ -222,8 +261,8 @@ Set stereocenter information obtained from 2D SDFile.
function stereocenter_from_sdf2d!(mol::MolGraph)
centers, comments = stereocenter_from_sdf2d(mol)
mol.gprops[:stereocenter] = centers
if length(comments) > 0
mol.gprops[:stereocenter_ignored] = comments
if length(comments) > 0
mol.gprops[:stereocenter_ignored] = join(comments, "; ")
end
end

Expand Down Expand Up @@ -308,6 +347,7 @@ Return cis-trans diastereomerism information obtained from SMILES.
"""
function stereobond_from_smiles(g::SimpleGraph{T}, e_order, e_direction) where T
stereobonds = Stereobond{T}()
comments = String[]
edgerank = Dict(e => i for (i, e) in enumerate(edges(g)))
for (i, e) in enumerate(edges(g))
e_order[i] == 2 || continue
Expand Down Expand Up @@ -335,11 +375,15 @@ function stereobond_from_smiles(g::SimpleGraph{T}, e_order, e_direction) where T
end
(isempty(sds) || isempty(dds)) && continue # no :up or :down bonds
# Conflicting cis/trans will be ignored (adopts OpenSMILES specs)
length(sds) == 2 && sds[1][2] == sds[2][2] && continue
length(dds) == 2 && dds[1][2] == dds[2][2] && continue
if (length(sds) == 2 && sds[1][2] == sds[2][2]) || (
length(dds) == 2 && dds[1][2] == dds[2][2])
@debug "$(e): conflicting up and down bonds $(sds) $(dds)"
push!(comments, "$(e): conflicting up and down bonds")
continue
end
stereobonds[e] = (sds[1][1], dds[1][1], sds[1][2] !== dds[1][2])
end
return stereobonds
return stereobonds, comments
end

stereobond_from_smiles(mol::SimpleMolGraph) = stereobond_from_smiles(
Expand All @@ -353,8 +397,13 @@ stereobond_from_smiles(mol::SimpleMolGraph) = stereobond_from_smiles(
Set cis-trans diastereomerism information obtained from SMILES.
"""
stereobond_from_smiles!(mol::MolGraph
) = begin mol.gprops[:stereobond] = stereobond_from_smiles(mol) end
function stereobond_from_smiles!(mol::MolGraph)
bonds, comments = stereobond_from_smiles(mol)
mol.gprops[:stereobond] = bonds
if length(comments) > 0
mol.gprops[:stereobond_ignored] = join(comments, "; ")
end
end

# TODO: axial chirality
# TODO: hypervalent chirality
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