Re: [Rdkit-discuss] problem building from source - ‘CT_CHIRALITY_PROP_PREFIX’ is not a member of ‘schrodinger::mae’

2020-04-01 Thread Tim Dudgeon 

Thanks Paolo, that fixed it.

On 30/03/2020 15:05, Paolo Tosco wrote:

Hi Tim,

try rm -rf External/CoordGen/coordgen* External/CoordGen/maeparser*

you might have some outdated coordgen libs. Deleting those and 
re-running cmake will download them afresh.


Cheers,
p.

On 30/03/2020 14:51, Tim Dudgeon wrote:

I'm finding an error building from source (on master branch).

Any ideas?

cmake -DPYTHON_EXECUTABLE=/usr/bin/python3 
-DRDK_BUILD_INCHI_SUPPORT=ON  -DRDK_BUILD_AVALON_SUPPORT=ON 
-DRDK_BUILD_PYTHON_WRAPPERS=ON  -DRDK_BUILD_SWIG_WRAPPERS=ON ..

make -j 8


[ 66%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/TplFileParser.cpp.o
[ 66%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/TplFileWriter.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/PDBParser.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/PDBWriter.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/PDBSupplier.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/XYZFileWriter.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/MaeMolSupplier.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/ProximityBonds.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/SequenceParsers.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/SequenceWriters.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/SVGParser.cpp.o
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp: 
In function ‘void 
RDKit::{anonymous}::set_mol_properties(RDKit::RWMol&, const 
schrodinger::mae::Block&)’:
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:214:37: 
error: ‘CT_CHIRALITY_PROP_PREFIX’ is not a member of ‘schrodinger::mae’
  214 | } else if 
(prop.first.find(mae::CT_CHIRALITY_PROP_PREFIX) == 0 ||

  | ^~~~
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:215:37: 
error: ‘CT_PSEUDOCHIRALITY_PROP_PREFIX’ is not a member of 
‘schrodinger::mae’

  215 | prop.first.find(mae::CT_PSEUDOCHIRALITY_PROP_PREFIX) == 0) {
  | ^~
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:217:37: 
error: ‘CT_EZ_PROP_PREFIX’ is not a member of ‘schrodinger::mae’

  217 | } else if (prop.first.find(mae::CT_EZ_PROP_PREFIX) == 0) {
  | ^
make[2]: *** 
[Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/build.make:310: 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/MaeMolSupplier.cpp.o] 
Error 1

make[2]: *** Waiting for unfinished jobs
make[1]: *** [CMakeFiles/Makefile2:7238: 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/all] 
Error 2

make: *** [Makefile:163: all] Error 2




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Re: [Rdkit-discuss] problem building from source - ‘CT_CHIRALITY_PROP_PREFIX’ is not a member of ‘schrodinger::mae’

2020-03-30 Thread Tim Dudgeon 

Yes, that did the trick. Thanks.

On 30/03/2020 15:05, Paolo Tosco wrote:

Hi Tim,

try rm -rf External/CoordGen/coordgen* External/CoordGen/maeparser*

you might have some outdated coordgen libs. Deleting those and 
re-running cmake will download them afresh.


Cheers,
p.

On 30/03/2020 14:51, Tim Dudgeon wrote:

I'm finding an error building from source (on master branch).

Any ideas?

cmake -DPYTHON_EXECUTABLE=/usr/bin/python3 
-DRDK_BUILD_INCHI_SUPPORT=ON  -DRDK_BUILD_AVALON_SUPPORT=ON 
-DRDK_BUILD_PYTHON_WRAPPERS=ON  -DRDK_BUILD_SWIG_WRAPPERS=ON ..

make -j 8


[ 66%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/TplFileParser.cpp.o
[ 66%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/TplFileWriter.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/PDBParser.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/PDBWriter.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/PDBSupplier.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/XYZFileWriter.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/MaeMolSupplier.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/ProximityBonds.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/SequenceParsers.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/SequenceWriters.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/SVGParser.cpp.o
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp: 
In function ‘void 
RDKit::{anonymous}::set_mol_properties(RDKit::RWMol&, const 
schrodinger::mae::Block&)’:
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:214:37: 
error: ‘CT_CHIRALITY_PROP_PREFIX’ is not a member of ‘schrodinger::mae’
  214 | } else if 
(prop.first.find(mae::CT_CHIRALITY_PROP_PREFIX) == 0 ||

  | ^~~~
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:215:37: 
error: ‘CT_PSEUDOCHIRALITY_PROP_PREFIX’ is not a member of 
‘schrodinger::mae’

  215 | prop.first.find(mae::CT_PSEUDOCHIRALITY_PROP_PREFIX) == 0) {
  | ^~
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:217:37: 
error: ‘CT_EZ_PROP_PREFIX’ is not a member of ‘schrodinger::mae’

  217 | } else if (prop.first.find(mae::CT_EZ_PROP_PREFIX) == 0) {
  | ^
make[2]: *** 
[Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/build.make:310: 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/MaeMolSupplier.cpp.o] 
Error 1

make[2]: *** Waiting for unfinished jobs
make[1]: *** [CMakeFiles/Makefile2:7238: 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/all] 
Error 2

make: *** [Makefile:163: all] Error 2




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Re: [Rdkit-discuss] problem building from source - ‘CT_CHIRALITY_PROP_PREFIX’ is not a member of ‘schrodinger::mae’

2020-03-30 Thread Paolo Tosco 

Hi Tim,

try rm -rf External/CoordGen/coordgen* External/CoordGen/maeparser*

you might have some outdated coordgen libs. Deleting those and 
re-running cmake will download them afresh.


Cheers,
p.

On 30/03/2020 14:51, Tim Dudgeon wrote:

I'm finding an error building from source (on master branch).

Any ideas?

cmake -DPYTHON_EXECUTABLE=/usr/bin/python3 
-DRDK_BUILD_INCHI_SUPPORT=ON  -DRDK_BUILD_AVALON_SUPPORT=ON 
-DRDK_BUILD_PYTHON_WRAPPERS=ON  -DRDK_BUILD_SWIG_WRAPPERS=ON  ..

make -j 8


[ 66%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/TplFileParser.cpp.o
[ 66%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/TplFileWriter.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/PDBParser.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/PDBWriter.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/PDBSupplier.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/XYZFileWriter.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/MaeMolSupplier.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/ProximityBonds.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/SequenceParsers.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/SequenceWriters.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/SVGParser.cpp.o
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp: 
In function ‘void 
RDKit::{anonymous}::set_mol_properties(RDKit::RWMol&, const 
schrodinger::mae::Block&)’:
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:214:37: 
error: ‘CT_CHIRALITY_PROP_PREFIX’ is not a member of ‘schrodinger::mae’
  214 | } else if (prop.first.find(mae::CT_CHIRALITY_PROP_PREFIX) 
== 0 ||

  | ^~~~
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:215:37: 
error: ‘CT_PSEUDOCHIRALITY_PROP_PREFIX’ is not a member of 
‘schrodinger::mae’

  215 | prop.first.find(mae::CT_PSEUDOCHIRALITY_PROP_PREFIX) == 0) {
  | ^~
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:217:37: 
error: ‘CT_EZ_PROP_PREFIX’ is not a member of ‘schrodinger::mae’

  217 | } else if (prop.first.find(mae::CT_EZ_PROP_PREFIX) == 0) {
  | ^
make[2]: *** 
[Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/build.make:310: 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/MaeMolSupplier.cpp.o] 
Error 1

make[2]: *** Waiting for unfinished jobs
make[1]: *** [CMakeFiles/Makefile2:7238: 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/all] Error 2

make: *** [Makefile:163: all] Error 2




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[Rdkit-discuss] problem building from source - ‘CT_CHIRALITY_PROP_PREFIX’ is not a member of ‘schrodinger::mae’

2020-03-30 Thread Tim Dudgeon 

I'm finding an error building from source (on master branch).

Any ideas?

cmake -DPYTHON_EXECUTABLE=/usr/bin/python3 
-DRDK_BUILD_INCHI_SUPPORT=ON  -DRDK_BUILD_AVALON_SUPPORT=ON 
-DRDK_BUILD_PYTHON_WRAPPERS=ON  -DRDK_BUILD_SWIG_WRAPPERS=ON  ..

make -j 8


[ 66%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/TplFileParser.cpp.o
[ 66%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/TplFileWriter.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/PDBParser.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/PDBWriter.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/PDBSupplier.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/XYZFileWriter.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/MaeMolSupplier.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/ProximityBonds.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/SequenceParsers.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/SequenceWriters.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/SVGParser.cpp.o
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp: 
In function ‘void 
RDKit::{anonymous}::set_mol_properties(RDKit::RWMol&, const 
schrodinger::mae::Block&)’:
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:214:37: 
error: ‘CT_CHIRALITY_PROP_PREFIX’ is not a member of ‘schrodinger::mae’
  214 | } else if (prop.first.find(mae::CT_CHIRALITY_PROP_PREFIX) 
== 0 ||

  | ^~~~
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:215:37: 
error: ‘CT_PSEUDOCHIRALITY_PROP_PREFIX’ is not a member of 
‘schrodinger::mae’

  215 | prop.first.find(mae::CT_PSEUDOCHIRALITY_PROP_PREFIX) == 0) {
  | ^~
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:217:37: 
error: ‘CT_EZ_PROP_PREFIX’ is not a member of ‘schrodinger::mae’

  217 | } else if (prop.first.find(mae::CT_EZ_PROP_PREFIX) == 0) {
  | ^
make[2]: *** 
[Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/build.make:310: 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/MaeMolSupplier.cpp.o] 
Error 1

make[2]: *** Waiting for unfinished jobs
make[1]: *** [CMakeFiles/Makefile2:7238: 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/all] Error 2

make: *** [Makefile:163: all] Error 2




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