SMARTS Parse Error

[BelyaevaJuly]

Dear colleagues, I am sorry for so much issues from my side, but it is quite useful and good for work, so I want to report about one new error: Calling: /home/domain/julybel/tinker/source/analyze.x /home/domain/julybel/poltype/VersionFiles/water.xyz -k /home/domain/julybel/poltype/VersionFiles/water.key e> version.out no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log [20:27:14] SMARTS Parse Error: syntax error while parsing: []~[#6@]~[#6@])~[#6] [20:27:14] SMARTS Parse Error: Failed parsing SMARTS '[]~[#6@]~[#6@])~[#6]' for input: '[*]~[#6@]~[#6@])~[#6]' Traceback (most recent call last): File "poltype.py", line 1240, in params=poltype.main() File "poltype.py", line 944, in main params= self.GenerateParameters() File "poltype.py", line 1054, in GenerateParameters bondprmstotransferinfo,angleprmstotransferinfo,torsionprmstotransferinfo,strbndprmstotransferinfo,opbendprmstotransferinfo,vdwprmstotransferinfo,torsionsmissing,classkeytotorsionparametersguess=databaseparser.GrabSmallMoleculeAMOEBAParameters(self,optmol,mol,m) File "/home/domain/julybel/poltype/PoltypeModules/databaseparser.py", line 1587, in GrabSmallMoleculeAMOEBAParameters torsionindicestotinkertypes,torsionindicestotinkerclasses,torsionindicestoparametersmartsatomorders,torsionindicestoelementtinkerdescrips,torsionindicestosmartsatomorders=GenerateAtomIndexToAtomTypeAndClassForAtomList(poltype,torsionsforprmtoparametersmarts,torsionsforprmtosmarts,smartsatomordertoelementtinkerdescrip,elementtinkerdescriptotinkertype,tinkertypetoclass,rdkitmol) File "/home/domain/julybel/poltype/PoltypeModules/databaseparser.py", line 938, in GenerateAtomIndexToAtomTypeAndClassForAtomList matches=rdkitmol.GetSubstructMatches(substructure) Boost.Python.ArgumentError: Python argument types in Mol.GetSubstructMatches(Mol, NoneType) did not match C++ signature: GetSubstructMatches(RDKit::ROMol self, RDKit::MolBundle query, RDKit::SubstructMatchParameters params) GetSubstructMatches(RDKit::ROMol self, RDKit::ROMol query, RDKit::SubstructMatchParameters params) GetSubstructMatches(RDKit::ROMol self, RDKit::MolBundle query, bool uniquify=True, bool useChirality=False, bool useQueryQueryMatches=False, unsigned int maxMatches=1000) GetSubstructMatches(RDKit::ROMol self, RDKit::ROMol query, bool uniquify=True, bool useChirality=False, bool useQueryQueryMatches=False, unsigned int maxMatches=1000)

All data are available here: https://drive.google.com/file/d/1TtKparbQfT2rNrOPAVlwV7GyRI0cT2-u/view?usp=sharing

I really appreciate your help!

[misterbrandonwalker]

Hi,

I am unable to reproduce your error, poltype works fine when I run your molecule. Is it possible that the poltype version you are using is not the latest? I have made several updates within the latter part of last week.

• Brandon

On Sun, Nov 8, 2020 at 2:50 PM BelyaevaJuly notifications@github.com wrote:

Dear colleagues, I am sorry for so much issues from my side, but it is quite useful and good for work, so I want to report about one new error: Calling: /home/domain/julybel/tinker/source/analyze.x /home/domain/julybel/poltype/VersionFiles/water.xyz -k /home/domain/julybel/poltype/VersionFiles/water.key e> version.out no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log [20:27:14] SMARTS Parse Error: syntax error while parsing: [ ][#6 https://github.com/pren/poltype/pull/6@][#6 https://github.com/pren/poltype/pull/6@])~[#6 https://github.com/pren/poltype/pull/6] [20:27:14] SMARTS Parse Error: Failed parsing SMARTS '[][#6 https://github.com/pren/poltype/pull/6@][

6 https://github.com/pren/poltype/pull/6@])[#6

https://github.com/pren/poltype/pull/6]' for input: '[*][#6 https://github.com/pren/poltype/pull/6@][#6 https://github.com/pren/poltype/pull/6@])[#6 https://github.com/pren/poltype/pull/6]' Traceback (most recent call last): File "poltype.py", line 1240, in params=poltype.main() File "poltype.py", line 944, in main params= self.GenerateParameters() File "poltype.py", line 1054, in GenerateParameters

bondprmstotransferinfo,angleprmstotransferinfo,torsionprmstotransferinfo,strbndprmstotransferinfo,opbendprmstotransferinfo,vdwprmstotransferinfo,torsionsmissing,classkeytotorsionparametersguess=databaseparser.GrabSmallMoleculeAMOEBAParameters(self,optmol,mol,m) File "/home/domain/julybel/poltype/PoltypeModules/databaseparser.py", line 1587, in GrabSmallMoleculeAMOEBAParameters

torsionindicestotinkertypes,torsionindicestotinkerclasses,torsionindicestoparametersmartsatomorders,torsionindicestoelementtinkerdescrips,torsionindicestosmartsatomorders=GenerateAtomIndexToAtomTypeAndClassForAtomList(poltype,torsionsforprmtoparametersmarts,torsionsforprmtosmarts,smartsatomordertoelementtinkerdescrip,elementtinkerdescriptotinkertype,tinkertypetoclass,rdkitmol) File "/home/domain/julybel/poltype/PoltypeModules/databaseparser.py", line 938, in GenerateAtomIndexToAtomTypeAndClassForAtomList matches=rdkitmol.GetSubstructMatches(substructure) Boost.Python.ArgumentError: Python argument types in Mol.GetSubstructMatches(Mol, NoneType) did not match C++ signature: GetSubstructMatches(RDKit::ROMol self, RDKit::MolBundle query, RDKit::SubstructMatchParameters params) GetSubstructMatches(RDKit::ROMol self, RDKit::ROMol query, RDKit::SubstructMatchParameters params) GetSubstructMatches(RDKit::ROMol self, RDKit::MolBundle query, bool uniquify=True, bool useChirality=False, bool useQueryQueryMatches=False, unsigned int maxMatches=1000) GetSubstructMatches(RDKit::ROMol self, RDKit::ROMol query, bool uniquify=True, bool useChirality=False, bool useQueryQueryMatches=False, unsigned int maxMatches=1000)

All data are available here:

https://drive.google.com/file/d/1TtKparbQfT2rNrOPAVlwV7GyRI0cT2-u/view?usp=sharing

I really appreciate your help!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/pren/poltype/issues/62, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26JPGQB6CCNAYWKD343SO4AB7ANCNFSM4TORYR7A .

[misterbrandonwalker]

I have however found a bug in zeroing out transferred torsions from database that are not of sufficiently high quality for transferring. Please delete all key files and restart with new git pull. Also, the only thing in your qm-torsion folder is files produced from ring torsion refinement (currently turned off). You can just delete that folder (since there is no quantum jobs).

• Brandon

On Mon, Nov 9, 2020 at 9:46 AM Brandon Walker notifications@github.com wrote:

Hi,

I am unable to reproduce your error, poltype works fine when I run your molecule. Is it possible that the poltype version you are using is not the latest? I have made several updates within the latter part of last week.

• Brandon

On Sun, Nov 8, 2020 at 2:50 PM BelyaevaJuly notifications@github.com wrote:

Dear colleagues, I am sorry for so much issues from my side, but it is quite useful and good for work, so I want to report about one new error: Calling: /home/domain/julybel/tinker/source/analyze.x /home/domain/julybel/poltype/VersionFiles/water.xyz -k /home/domain/julybel/poltype/VersionFiles/water.key e> version.out no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log [20:27:14] SMARTS Parse Error: syntax error while parsing: [ ][#6 https://github.com/pren/poltype/pull/6@][#6 https://github.com/pren/poltype/pull/6@])~[#6 https://github.com/pren/poltype/pull/6] [20:27:14] SMARTS Parse Error: Failed parsing SMARTS '[][#6 <https://github.com/pren/poltype/pull/6 @][

6 https://github.com/pren/poltype/pull/6@])[#6

https://github.com/pren/poltype/pull/6]' for input: '[*][#6 https://github.com/pren/poltype/pull/6@][#6 https://github.com/pren/poltype/pull/6@])[#6 https://github.com/pren/poltype/pull/6]' Traceback (most recent call last): File "poltype.py", line 1240, in params=poltype.main() File "poltype.py", line 944, in main params= self.GenerateParameters() File "poltype.py", line 1054, in GenerateParameters

bondprmstotransferinfo,angleprmstotransferinfo,torsionprmstotransferinfo,strbndprmstotransferinfo,opbendprmstotransferinfo,vdwprmstotransferinfo,torsionsmissing,classkeytotorsionparametersguess=databaseparser.GrabSmallMoleculeAMOEBAParameters(self,optmol,mol,m) File "/home/domain/julybel/poltype/PoltypeModules/databaseparser.py", line 1587, in GrabSmallMoleculeAMOEBAParameters

torsionindicestotinkertypes,torsionindicestotinkerclasses,torsionindicestoparametersmartsatomorders,torsionindicestoelementtinkerdescrips,torsionindicestosmartsatomorders=GenerateAtomIndexToAtomTypeAndClassForAtomList(poltype,torsionsforprmtoparametersmarts,torsionsforprmtosmarts,smartsatomordertoelementtinkerdescrip,elementtinkerdescriptotinkertype,tinkertypetoclass,rdkitmol) File "/home/domain/julybel/poltype/PoltypeModules/databaseparser.py", line 938, in GenerateAtomIndexToAtomTypeAndClassForAtomList matches=rdkitmol.GetSubstructMatches(substructure) Boost.Python.ArgumentError: Python argument types in Mol.GetSubstructMatches(Mol, NoneType) did not match C++ signature: GetSubstructMatches(RDKit::ROMol self, RDKit::MolBundle query, RDKit::SubstructMatchParameters params) GetSubstructMatches(RDKit::ROMol self, RDKit::ROMol query, RDKit::SubstructMatchParameters params) GetSubstructMatches(RDKit::ROMol self, RDKit::MolBundle query, bool uniquify=True, bool useChirality=False, bool useQueryQueryMatches=False, unsigned int maxMatches=1000) GetSubstructMatches(RDKit::ROMol self, RDKit::ROMol query, bool uniquify=True, bool useChirality=False, bool useQueryQueryMatches=False, unsigned int maxMatches=1000)

All data are available here:

https://drive.google.com/file/d/1TtKparbQfT2rNrOPAVlwV7GyRI0cT2-u/view?usp=sharing

I really appreciate your help!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/pren/poltype/issues/62, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AKNB26JPGQB6CCNAYWKD343SO4AB7ANCNFSM4TORYR7A

.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/pren/poltype/issues/62#issuecomment-724095727, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26OWWAPI7XMB4H7DPR3SPAFD7ANCNFSM4TORYR7A .

[BelyaevaJuly]

Hi, I am unable to reproduce your error, poltype works fine when I run your molecule. Is it possible that the poltype version you are using is not the latest? I have made several updates within the latter part of last week. - Brandon … On Sun, Nov 8, 2020 at 2:50 PM BelyaevaJuly @.**> wrote: Dear colleagues, I am sorry for so much issues from my side, but it is quite useful and good for work, so I want to report about one new error: Calling: /home/domain/julybel/tinker/source/analyze.x /home/domain/julybel/poltype/VersionFiles/water.xyz -k /home/domain/julybel/poltype/VersionFiles/water.key e> version.out no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log [20:27:14] SMARTS Parse Error: syntax error while parsing: [ ][#6 <#6>@][#6 <#6>@])~[#6 <#6>] [20:27:14] SMARTS Parse Error: Failed parsing SMARTS '[][#6 <#6>@][ #6 <#6>@])[#6 <#6>]' for input: '[][#6 <#6>@][#6 <#6>@])[#6 <#6>]' Traceback (most recent call last): File "poltype.py", line 1240, in params=poltype.main() File "poltype.py", line 944, in main params= self.GenerateParameters() File "poltype.py", line 1054, in GenerateParameters bondprmstotransferinfo,angleprmstotransferinfo,torsionprmstotransferinfo,strbndprmstotransferinfo,opbendprmstotransferinfo,vdwprmstotransferinfo,torsionsmissing,classkeytotorsionparametersguess=databaseparser.GrabSmallMoleculeAMOEBAParameters(self,optmol,mol,m) File "/home/domain/julybel/poltype/PoltypeModules/databaseparser.py", line 1587, in GrabSmallMoleculeAMOEBAParameters torsionindicestotinkertypes,torsionindicestotinkerclasses,torsionindicestoparametersmartsatomorders,torsionindicestoelementtinkerdescrips,torsionindicestosmartsatomorders=GenerateAtomIndexToAtomTypeAndClassForAtomList(poltype,torsionsforprmtoparametersmarts,torsionsforprmtosmarts,smartsatomordertoelementtinkerdescrip,elementtinkerdescriptotinkertype,tinkertypetoclass,rdkitmol) File "/home/domain/julybel/poltype/PoltypeModules/databaseparser.py", line 938, in GenerateAtomIndexToAtomTypeAndClassForAtomList matches=rdkitmol.GetSubstructMatches(substructure) Boost.Python.ArgumentError: Python argument types in Mol.GetSubstructMatches(Mol, NoneType) did not match C++ signature: GetSubstructMatches(RDKit::ROMol self, RDKit::MolBundle query, RDKit::SubstructMatchParameters params) GetSubstructMatches(RDKit::ROMol self, RDKit::ROMol query, RDKit::SubstructMatchParameters params) GetSubstructMatches(RDKit::ROMol self, RDKit::MolBundle query, bool uniquify=True, bool useChirality=False, bool useQueryQueryMatches=False, unsigned int maxMatches=1000) GetSubstructMatches(RDKit::ROMol self, RDKit::ROMol query, bool uniquify=True, bool useChirality=False, bool useQueryQueryMatches=False, unsigned int maxMatches=1000) All data are available here: https://drive.google.com/file/d/1TtKparbQfT2rNrOPAVlwV7GyRI0cT2-u/view?usp=sharing I really appreciate your help! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#62>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26JPGQB6CCNAYWKD343SO4AB7ANCNFSM4TORYR7A .

Is it okay to redownload by: git clone https://github.com/pren/poltype.git --branch poltype2 ?

[misterbrandonwalker]

Yes that should work too.

On Mon, Nov 9, 2020 at 11:39 AM BelyaevaJuly notifications@github.com wrote:

Hi, I am unable to reproduce your error, poltype works fine when I run your molecule. Is it possible that the poltype version you are using is not the latest? I have made several updates within the latter part of last week. - Brandon … <#m-2560852688586727143> On Sun, Nov 8, 2020 at 2:50 PM BelyaevaJuly @.**> wrote: Dear colleagues, I am sorry for so much issues from my side, but it is quite useful and good for work, so I want to report about one new error: Calling: /home/domain/julybel/tinker/source/analyze.x /home/domain/julybel/poltype/VersionFiles/water.xyz http://water.xyz -k /home/domain/julybel/poltype/VersionFiles/water.key e> version.out no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log [20:27:14] SMARTS Parse Error: syntax error while parsing: [ ][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>@][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>@])~[#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>] [20:27:14] SMARTS Parse Error: Failed parsing SMARTS '[][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>@][ #6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>@])[#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>]' for input: '[][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>@][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>@])[#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>]' Traceback (most recent call last): File "poltype.py", line 1240, in params=poltype.main() File "poltype.py", line 944, in main params= self.GenerateParameters() File "poltype.py", line 1054, in GenerateParameters bondprmstotransferinfo,angleprmstotransferinfo,torsionprmstotransferinfo,strbndprmstotransferinfo,opbendprmstotransferinfo,vdwprmstotransferinfo,torsionsmissing,classkeytotorsionparametersguess=databaseparser.GrabSmallMoleculeAMOEBAParameters(self,optmol,mol,m) File "/home/domain/julybel/poltype/PoltypeModules/databaseparser.py", line 1587, in GrabSmallMoleculeAMOEBAParameters torsionindicestotinkertypes,torsionindicestotinkerclasses,torsionindicestoparametersmartsatomorders,torsionindicestoelementtinkerdescrips,torsionindicestosmartsatomorders=GenerateAtomIndexToAtomTypeAndClassForAtomList(poltype,torsionsforprmtoparametersmarts,torsionsforprmtosmarts,smartsatomordertoelementtinkerdescrip,elementtinkerdescriptotinkertype,tinkertypetoclass,rdkitmol) File "/home/domain/julybel/poltype/PoltypeModules/databaseparser.py", line 938, in GenerateAtomIndexToAtomTypeAndClassForAtomList matches=rdkitmol.GetSubstructMatches(substructure) Boost.Python.ArgumentError: Python argument types in Mol.GetSubstructMatches(Mol, NoneType) did not match C++ signature: GetSubstructMatches(RDKit::ROMol self, RDKit::MolBundle query, RDKit::SubstructMatchParameters params) GetSubstructMatches(RDKit::ROMol self, RDKit::ROMol query, RDKit::SubstructMatchParameters params) GetSubstructMatches(RDKit::ROMol self, RDKit::MolBundle query, bool uniquify=True, bool useChirality=False, bool useQueryQueryMatches=False, unsigned int maxMatches=1000) GetSubstructMatches(RDKit::ROMol self, RDKit::ROMol query, bool uniquify=True, bool useChirality=False, bool useQueryQueryMatches=False, unsigned int maxMatches=1000) All data are available here: https://drive.google.com/file/d/1TtKparbQfT2rNrOPAVlwV7GyRI0cT2-u/view?usp=sharing I really appreciate your help! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <

62 https://github.com/pren/poltype/issues/62>, or unsubscribe

https://github.com/notifications/unsubscribe-auth/AKNB26JPGQB6CCNAYWKD343SO4AB7ANCNFSM4TORYR7A .

Is it okay to redownload by: git clone https://github.com/pren/poltype.git --branch poltype2 ?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/pren/poltype/issues/62#issuecomment-724164700, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26K2ZENE72TVQLVQOVLSPASK3ANCNFSM4TORYR7A .

[BelyaevaJuly]

Yes that should work too. On Mon, Nov 9, 2020 at 11:39 AM BelyaevaJuly notifications@github.com wrote: … Hi, I am unable to reproduce your error, poltype works fine when I run your molecule. Is it possible that the poltype version you are using is not the latest? I have made several updates within the latter part of last week. - Brandon … <#m-2560852688586727143> On Sun, Nov 8, 2020 at 2:50 PM BelyaevaJuly @.**> wrote: Dear colleagues, I am sorry for so much issues from my side, but it is quite useful and good for work, so I want to report about one new error: Calling: /home/domain/julybel/tinker/source/analyze.x /home/domain/julybel/poltype/VersionFiles/water.xyz http://water.xyz -k /home/domain/julybel/poltype/VersionFiles/water.key e> version.out no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log [20:27:14] SMARTS Parse Error: syntax error while parsing: [ ][#6 <#6> <#6 <#6>>@][#6 <#6> <#6 <#6>>@])~[#6 <#6> <#6 <#6>>] [20:27:14] SMARTS Parse Error: Failed parsing SMARTS '[][#6 <#6> <#6 <#6>>@][ #6 <#6> <#6 <#6>>@])[#6 <#6> <#6 <#6>>]' for input: '[][#6 <#6> <#6 <#6>>@][#6 <#6> <#6 <#6>>@])[#6 <#6> <#6 <#6>>]' Traceback (most recent call last): File "poltype.py", line 1240, in params=poltype.main() File "poltype.py", line 944, in main params= self.GenerateParameters() File "poltype.py", line 1054, in GenerateParameters bondprmstotransferinfo,angleprmstotransferinfo,torsionprmstotransferinfo,strbndprmstotransferinfo,opbendprmstotransferinfo,vdwprmstotransferinfo,torsionsmissing,classkeytotorsionparametersguess=databaseparser.GrabSmallMoleculeAMOEBAParameters(self,optmol,mol,m) File "/home/domain/julybel/poltype/PoltypeModules/databaseparser.py", line 1587, in GrabSmallMoleculeAMOEBAParameters torsionindicestotinkertypes,torsionindicestotinkerclasses,torsionindicestoparametersmartsatomorders,torsionindicestoelementtinkerdescrips,torsionindicestosmartsatomorders=GenerateAtomIndexToAtomTypeAndClassForAtomList(poltype,torsionsforprmtoparametersmarts,torsionsforprmtosmarts,smartsatomordertoelementtinkerdescrip,elementtinkerdescriptotinkertype,tinkertypetoclass,rdkitmol) File "/home/domain/julybel/poltype/PoltypeModules/databaseparser.py", line 938, in GenerateAtomIndexToAtomTypeAndClassForAtomList matches=rdkitmol.GetSubstructMatches(substructure) Boost.Python.ArgumentError: Python argument types in Mol.GetSubstructMatches(Mol, NoneType) did not match C++ signature: GetSubstructMatches(RDKit::ROMol self, RDKit::MolBundle query, RDKit::SubstructMatchParameters params) GetSubstructMatches(RDKit::ROMol self, RDKit::ROMol query, RDKit::SubstructMatchParameters params) GetSubstructMatches(RDKit::ROMol self, RDKit::MolBundle query, bool uniquify=True, bool useChirality=False, bool useQueryQueryMatches=False, unsigned int maxMatches=1000) GetSubstructMatches(RDKit::ROMol self, RDKit::ROMol query, bool uniquify=True, bool useChirality=False, bool useQueryQueryMatches=False, unsigned int maxMatches=1000) All data are available here: https://drive.google.com/file/d/1TtKparbQfT2rNrOPAVlwV7GyRI0cT2-u/view?usp=sharing I really appreciate your help! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < #62 <#62>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26JPGQB6CCNAYWKD343SO4AB7ANCNFSM4TORYR7A . Is it okay to redownload by: git clone https://github.com/pren/poltype.git --branch poltype2 ? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#62 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26K2ZENE72TVQLVQOVLSPASK3ANCNFSM4TORYR7A .

It still gives the same Error: [11:57:49] SMARTS Parse Error: syntax error while parsing: []~[#6@]~[#6@])~[#6] [11:57:49] SMARTS Parse Error: Failed parsing SMARTS '[]~[#6@]~[#6@])~[#6]' for input: '[*]~[#6@]~[#6@])~[#6]'

[misterbrandonwalker]

Here are the files, https://utexas.box.com/s/gtm9m3bkjf6wusnsherpw029vmglxgr9 .

You will need to finish the quantum. I am wondering if maybe we have different rdkit versions? Also is poltype being called from the same folder with all of the poltype output files or is poltype called from another directory? My rdkit version is shown below. (you can check with conda list rdkit)

(p4envtest) [bdw2292@node37 PoltypeJobs]$ conda list rdkit

packages in environment at /home/bdw2292/miniconda3/envs/p4envtest:

#

Name Version Build Channel

rdkit 2017.09.1 py36_1 rdkit

On Tue, Nov 10, 2020 at 4:12 AM BelyaevaJuly notifications@github.com wrote:

Yes that should work too. On Mon, Nov 9, 2020 at 11:39 AM BelyaevaJuly notifications@github.com wrote: … <#m6300200882296631641> Hi, I am unable to reproduce your error, poltype works fine when I run your molecule. Is it possible that the poltype version you are using is not the latest? I have made several updates within the latter part of last week. - Brandon … <#m-2560852688586727143> On Sun, Nov 8, 2020 at 2:50 PM BelyaevaJuly @.**> wrote: Dear colleagues, I am sorry for so much issues from my side, but it is quite useful and good for work, so I want to report about one new error: Calling: /home/domain/julybel/tinker/source/analyze.x /home/domain/julybel/poltype/VersionFiles/water.xyz http://water.xyz http://water.xyz http://water.xyz -k /home/domain/julybel/poltype/VersionFiles/water.key e> version.out no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log [20:27:14] SMARTS Parse Error: syntax error while parsing: [ ][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>@][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>@])~[#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>] [20:27:14] SMARTS Parse Error: Failed parsing SMARTS '[][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>@][ #6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>@])[#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>]' for input: '[][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>@][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>@])[#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>]' Traceback (most recent call last): File "poltype.py", line 1240, in params=poltype.main() File "poltype.py", line 944, in main params= self.GenerateParameters() File "poltype.py", line 1054, in GenerateParameters bondprmstotransferinfo,angleprmstotransferinfo,torsionprmstotransferinfo,strbndprmstotransferinfo,opbendprmstotransferinfo,vdwprmstotransferinfo,torsionsmissing,classkeytotorsionparametersguess=databaseparser.GrabSmallMoleculeAMOEBAParameters(self,optmol,mol,m) File "/home/domain/julybel/poltype/PoltypeModules/databaseparser.py", line 1587, in GrabSmallMoleculeAMOEBAParameters torsionindicestotinkertypes,torsionindicestotinkerclasses,torsionindicestoparametersmartsatomorders,torsionindicestoelementtinkerdescrips,torsionindicestosmartsatomorders=GenerateAtomIndexToAtomTypeAndClassForAtomList(poltype,torsionsforprmtoparametersmarts,torsionsforprmtosmarts,smartsatomordertoelementtinkerdescrip,elementtinkerdescriptotinkertype,tinkertypetoclass,rdkitmol) File "/home/domain/julybel/poltype/PoltypeModules/databaseparser.py", line 938, in GenerateAtomIndexToAtomTypeAndClassForAtomList matches=rdkitmol.GetSubstructMatches(substructure) Boost.Python.ArgumentError: Python argument types in Mol.GetSubstructMatches(Mol, NoneType) did not match C++ signature: GetSubstructMatches(RDKit::ROMol self, RDKit::MolBundle query, RDKit::SubstructMatchParameters params) GetSubstructMatches(RDKit::ROMol self, RDKit::ROMol query, RDKit::SubstructMatchParameters params) GetSubstructMatches(RDKit::ROMol self, RDKit::MolBundle query, bool uniquify=True, bool useChirality=False, bool useQueryQueryMatches=False, unsigned int maxMatches=1000) GetSubstructMatches(RDKit::ROMol self, RDKit::ROMol query, bool uniquify=True, bool useChirality=False, bool useQueryQueryMatches=False, unsigned int maxMatches=1000) All data are available here: https://drive.google.com/file/d/1TtKparbQfT2rNrOPAVlwV7GyRI0cT2-u/view?usp=sharing I really appreciate your help! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < #62 https://github.com/pren/poltype/issues/62 <#62 https://github.com/pren/poltype/issues/62>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26JPGQB6CCNAYWKD343SO4AB7ANCNFSM4TORYR7A . Is it okay to redownload by: git clone https://github.com/pren/poltype.git --branch poltype2 ? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#62 (comment) https://github.com/pren/poltype/issues/62#issuecomment-724164700>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26K2ZENE72TVQLVQOVLSPASK3ANCNFSM4TORYR7A .

It still gives the same Error: [11:57:49] SMARTS Parse Error: syntax error while parsing: [ ][#6 https://github.com/pren/poltype/pull/6@][#6 https://github.com/pren/poltype/pull/6@])~[#6 https://github.com/pren/poltype/pull/6] [11:57:49] SMARTS Parse Error: Failed parsing SMARTS '[][#6 https://github.com/pren/poltype/pull/6@][

6 https://github.com/pren/poltype/pull/6@])[#6

https://github.com/pren/poltype/pull/6]' for input: '[*][#6 https://github.com/pren/poltype/pull/6@][#6 https://github.com/pren/poltype/pull/6@])[#6 https://github.com/pren/poltype/pull/6]'

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/pren/poltype/issues/62#issuecomment-724604153, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26MS7ZLPXQDZLHQX7I3SPEGY7ANCNFSM4TORYR7A .

[BelyaevaJuly]

Here are the files, https://utexas.box.com/s/gtm9m3bkjf6wusnsherpw029vmglxgr9 . You will need to finish the quantum. I am wondering if maybe we have different rdkit versions? Also is poltype being called from the same folder with all of the poltype output files or is poltype called from another directory? My rdkit version is shown below. (you can check with conda list rdkit) (p4envtest) [bdw2292@node37 PoltypeJobs]$ conda list rdkit # packages in environment at /home/bdw2292/miniconda3/envs/p4envtest: # # Name Version Build Channel rdkit 2017.09.1 py36_1 rdkit On Tue, Nov 10, 2020 at 4:12 AM BelyaevaJuly notifications@github.com wrote: … Yes that should work too. On Mon, Nov 9, 2020 at 11:39 AM BelyaevaJuly @. wrote: … <#m6300200882296631641> Hi, I am unable to reproduce your error, poltype works fine when I run your molecule. Is it possible that the poltype version you are using is not the latest? I have made several updates within the latter part of last week. - Brandon … <#m-2560852688586727143> On Sun, Nov 8, 2020 at 2:50 PM BelyaevaJuly @.> wrote: Dear colleagues, I am sorry for so much issues from my side, but it is quite useful and good for work, so I want to report about one new error: Calling: /home/domain/julybel/tinker/source/analyze.x /home/domain/julybel/poltype/VersionFiles/water.xyz http://water.xyz http://water.xyz http://water.xyz -k /home/domain/julybel/poltype/VersionFiles/water.key e> version.out no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log [20:27:14] SMARTS Parse Error: syntax error while parsing: [ ][#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>>@][#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>>@])~[#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>>] [20:27:14] SMARTS Parse Error: Failed parsing SMARTS '[][#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>>@][ #6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>>@])[#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>>]' for input: '[][#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>>@][#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>>@])[#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>>]' Traceback (most recent call last): File "poltype.py", line 1240, in params=poltype.main() File "poltype.py", line 944, in main params= self.GenerateParameters() File "poltype.py", line 1054, in GenerateParameters bondprmstotransferinfo,angleprmstotransferinfo,torsionprmstotransferinfo,strbndprmstotransferinfo,opbendprmstotransferinfo,vdwprmstotransferinfo,torsionsmissing,classkeytotorsionparametersguess=databaseparser.GrabSmallMoleculeAMOEBAParameters(self,optmol,mol,m) File "/home/domain/julybel/poltype/PoltypeModules/databaseparser.py", line 1587, in GrabSmallMoleculeAMOEBAParameters torsionindicestotinkertypes,torsionindicestotinkerclasses,torsionindicestoparametersmartsatomorders,torsionindicestoelementtinkerdescrips,torsionindicestosmartsatomorders=GenerateAtomIndexToAtomTypeAndClassForAtomList(poltype,torsionsforprmtoparametersmarts,torsionsforprmtosmarts,smartsatomordertoelementtinkerdescrip,elementtinkerdescriptotinkertype,tinkertypetoclass,rdkitmol) File "/home/domain/julybel/poltype/PoltypeModules/databaseparser.py", line 938, in GenerateAtomIndexToAtomTypeAndClassForAtomList matches=rdkitmol.GetSubstructMatches(substructure) Boost.Python.ArgumentError: Python argument types in Mol.GetSubstructMatches(Mol, NoneType) did not match C++ signature: GetSubstructMatches(RDKit::ROMol self, RDKit::MolBundle query, RDKit::SubstructMatchParameters params) GetSubstructMatches(RDKit::ROMol self, RDKit::ROMol query, RDKit::SubstructMatchParameters params) GetSubstructMatches(RDKit::ROMol self, RDKit::MolBundle query, bool uniquify=True, bool useChirality=False, bool useQueryQueryMatches=False, unsigned int maxMatches=1000) GetSubstructMatches(RDKit::ROMol self, RDKit::ROMol query, bool uniquify=True, bool useChirality=False, bool useQueryQueryMatches=False, unsigned int maxMatches=1000) All data are available here: https://drive.google.com/file/d/1TtKparbQfT2rNrOPAVlwV7GyRI0cT2-u/view?usp=sharing I really appreciate your help! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < #62 <#62> <#62 <#62>>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26JPGQB6CCNAYWKD343SO4AB7ANCNFSM4TORYR7A . Is it okay to redownload by: git clone https://github.com/pren/poltype.git --branch poltype2 ? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#62 (comment) <#62 (comment)>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26K2ZENE72TVQLVQOVLSPASK3ANCNFSM4TORYR7A . It still gives the same Error: [11:57:49] SMARTS Parse Error: syntax error while parsing: [ ][#6 <#6>@][#6 <#6>@])~[#6 <#6>] [11:57:49] SMARTS Parse Error: Failed parsing SMARTS '[][#6 <#6>@][ #6 <#6>@])[#6 <#6>]' for input: '[][#6 <#6>@][#6 <#6>@])[#6 <#6>]' — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#62 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26MS7ZLPXQDZLHQX7I3SPEGY7ANCNFSM4TORYR7A .

Yup, I have: # packages in environment at /home/domain/data/prog/miniconda3/envs/poltype: # # Name Version Build Channel rdkit 2020.09.1 py36hce6e9d5_0 conda-forge

[misterbrandonwalker]

I am not really sure what to tell you, I uninstalled and resinstalled to the 2020 version. I notice my build number is different, but the version on left is same. Which OS and OS version are you running poltype on?

packages in environment at /home/bdw2292/miniconda3/envs/p4envtest:

#

Name Version Build Channel

rdkit 2020.09.1 py36hf6a1616_0 conda-forge (p4envtest) [bdw2292@g2-node38 ami_2020_BW]$

On Tue, Nov 10, 2020 at 10:42 AM BelyaevaJuly notifications@github.com wrote:

Here are the files, https://utexas.box.com/s/gtm9m3bkjf6wusnsherpw029vmglxgr9 . You will need to finish the quantum. I am wondering if maybe we have different rdkit versions? Also is poltype being called from the same folder with all of the poltype output files or is poltype called from another directory? My rdkit version is shown below. (you can check with conda list rdkit) (p4envtest) [bdw2292@node37 PoltypeJobs]$ conda list rdkit # packages in environment at /home/bdw2292/miniconda3/envs/p4envtest: # # Name Version Build Channel rdkit 2017.09.1 py36_1 rdkit On Tue, Nov 10, 2020 at 4:12 AM BelyaevaJuly notifications@github.com wrote: … <#m8960401689549010815> Yes that should work too. On Mon, Nov 9, 2020 at 11:39 AM BelyaevaJuly @.* wrote: … <#m6300200882296631641> Hi, I am unable to reproduce your error, poltype works fine when I run your molecule. Is it possible that the poltype version you are using is not the latest? I have made several updates within the latter part of last week. - Brandon … <#m-2560852688586727143> On Sun, Nov 8, 2020 at 2:50 PM BelyaevaJuly @ .> wrote: Dear colleagues, I am sorry for so much issues from my side, but it is quite useful and good for work, so I want to report about one new error: Calling: /home/domain/julybel/tinker/source/analyze.x /home/domain/julybel/poltype/VersionFiles/water.xyz http://water.xyz http://water.xyz http://water.xyz http://water.xyz http://water.xyz http://water.xyz http://water.xyz -k /home/domain/julybel/poltype/VersionFiles/water.key e> version.out no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log [20:27:14] SMARTS Parse Error: syntax error while parsing: [ ][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>>@][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>>@])~[#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>>] [20:27:14] SMARTS Parse Error: Failed parsing SMARTS '[][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>>@][ #6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>>@])[#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>>]' for input: '[][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>>@][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>>@])[#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>>]' Traceback (most recent call last): File "poltype.py", line 1240, in params=poltype.main() File "poltype.py", line 944, in main params= self.GenerateParameters() File "poltype.py", line 1054, in GenerateParameters bondprmstotransferinfo,angleprmstotransferinfo,torsionprmstotransferinfo,strbndprmstotransferinfo,opbendprmstotransferinfo,vdwprmstotransferinfo,torsionsmissing,classkeytotorsionparametersguess=databaseparser.GrabSmallMoleculeAMOEBAParameters(self,optmol,mol,m) File "/home/domain/julybel/poltype/PoltypeModules/databaseparser.py", line 1587, in GrabSmallMoleculeAMOEBAParameters torsionindicestotinkertypes,torsionindicestotinkerclasses,torsionindicestoparametersmartsatomorders,torsionindicestoelementtinkerdescrips,torsionindicestosmartsatomorders=GenerateAtomIndexToAtomTypeAndClassForAtomList(poltype,torsionsforprmtoparametersmarts,torsionsforprmtosmarts,smartsatomordertoelementtinkerdescrip,elementtinkerdescriptotinkertype,tinkertypetoclass,rdkitmol) File "/home/domain/julybel/poltype/PoltypeModules/databaseparser.py", line 938, in GenerateAtomIndexToAtomTypeAndClassForAtomList matches=rdkitmol.GetSubstructMatches(substructure) Boost.Python.ArgumentError: Python argument types in Mol.GetSubstructMatches(Mol, NoneType) did not match C++ signature: GetSubstructMatches(RDKit::ROMol self, RDKit::MolBundle query, RDKit::SubstructMatchParameters params) GetSubstructMatches(RDKit::ROMol self, RDKit::ROMol query, RDKit::SubstructMatchParameters params) GetSubstructMatches(RDKit::ROMol self, RDKit::MolBundle query, bool uniquify=True, bool useChirality=False, bool useQueryQueryMatches=False, unsigned int maxMatches=1000) GetSubstructMatches(RDKit::ROMol self, RDKit::ROMol query, bool uniquify=True, bool useChirality=False, bool useQueryQueryMatches=False, unsigned int maxMatches=1000) All data are available here: https://drive.google.com/file/d/1TtKparbQfT2rNrOPAVlwV7GyRI0cT2-u/view?usp=sharing https://drive.google.com/file/d/1TtKparbQfT2rNrOPAVlwV7GyRI0cT2-u/view?usp=sharing I really appreciate your help! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < #62 https://github.com/pren/poltype/issues/62 <#62 https://github.com/pren/poltype/issues/62> <#62 https://github.com/pren/poltype/issues/62 <#62 https://github.com/pren/poltype/issues/62>>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26JPGQB6CCNAYWKD343SO4AB7ANCNFSM4TORYR7A https://github.com/notifications/unsubscribe-auth/AKNB26JPGQB6CCNAYWKD343SO4AB7ANCNFSM4TORYR7A . Is it okay to redownload by: git clone https://github.com/pren/poltype.git https://github.com/pren/poltype.git --branch poltype2 ? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#62 https://github.com/pren/poltype/issues/62 (comment) <#62 (comment) https://github.com/pren/poltype/issues/62#issuecomment-724164700>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26K2ZENE72TVQLVQOVLSPASK3ANCNFSM4TORYR7A https://github.com/notifications/unsubscribe-auth/AKNB26K2ZENE72TVQLVQOVLSPASK3ANCNFSM4TORYR7A . It still gives the same Error: [11:57:49] SMARTS Parse Error: syntax error while parsing: [ ][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>@][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>@])~[#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>] [11:57:49] SMARTS Parse Error: Failed parsing SMARTS '[][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>@][ #6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>@])[#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>]' for input: '[*][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>@][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>@])[#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>]' — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#62 (comment) https://github.com/pren/poltype/issues/62#issuecomment-724604153>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26MS7ZLPXQDZLHQX7I3SPEGY7ANCNFSM4TORYR7A .

Yup, I have: packages in environment at /home/domain/data/prog/miniconda3/envs/poltype: Name Version Build Channel

rdkit 2020.09.1 py36hce6e9d5_0 conda-forge

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/pren/poltype/issues/62#issuecomment-724822836, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26NKASVYEMFDJDXKENTSPFUPHANCNFSM4TORYR7A .

[BelyaevaJuly]

I am not really sure what to tell you, I uninstalled and resinstalled to the 2020 version. I notice my build number is different, but the version on left is same. Which OS and OS version are you running poltype on? # packages in environment at /home/bdw2292/miniconda3/envs/p4envtest: # # Name Version Build Channel rdkit 2020.09.1 py36hf6a1616_0 conda-forge (p4envtest) [bdw2292@g2-node38 ami_2020_BW]$ On Tue, Nov 10, 2020 at 10:42 AM BelyaevaJuly notifications@github.com wrote: … Here are the files, https://utexas.box.com/s/gtm9m3bkjf6wusnsherpw029vmglxgr9 . You will need to finish the quantum. I am wondering if maybe we have different rdkit versions? Also is poltype being called from the same folder with all of the poltype output files or is poltype called from another directory? My rdkit version is shown below. (you can check with conda list rdkit) (p4envtest) @. PoltypeJobs]$ conda list rdkit # packages in environment at /home/bdw2292/miniconda3/envs/p4envtest: # # Name Version Build Channel rdkit 2017.09.1 py36_1 rdkit On Tue, Nov 10, 2020 at 4:12 AM BelyaevaJuly @. wrote: … <#m8960401689549010815> Yes that should work too. On Mon, Nov 9, 2020 at 11:39 AM BelyaevaJuly @.* wrote: … <#m6300200882296631641> Hi, I am unable to reproduce your error, poltype works fine when I run your molecule. Is it possible that the poltype version you are using is not the latest? I have made several updates within the latter part of last week. - Brandon … <#m-2560852688586727143> On Sun, Nov 8, 2020 at 2:50 PM BelyaevaJuly @ .> wrote: Dear colleagues, I am sorry for so much issues from my side, but it is quite useful and good for work, so I want to report about one new error: Calling: /home/domain/julybel/tinker/source/analyze.x /home/domain/julybel/poltype/VersionFiles/water.xyz http://water.xyz http://water.xyz http://water.xyz http://water.xyz http://water.xyz http://water.xyz http://water.xyz -k /home/domain/julybel/poltype/VersionFiles/water.key e> version.out no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log [20:27:14] SMARTS Parse Error: syntax error while parsing: [ ][#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>> <#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>>>@][#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>> <#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>>>@])~[#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>> <#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>>>] [20:27:14] SMARTS Parse Error: Failed parsing SMARTS '[][#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>> <#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>>>@][ #6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>> <#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>>>@])[#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>> <#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>>>]' for input: '[][#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>> <#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>>>@][#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>> <#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>>>@])[#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>> <#6 <#6> <#6 <#6>> <#6 <#6> <#6 <#6>>>>]' Traceback (most recent call last): File "poltype.py", line 1240, in params=poltype.main() File "poltype.py", line 944, in main params= self.GenerateParameters() File "poltype.py", line 1054, in GenerateParameters bondprmstotransferinfo,angleprmstotransferinfo,torsionprmstotransferinfo,strbndprmstotransferinfo,opbendprmstotransferinfo,vdwprmstotransferinfo,torsionsmissing,classkeytotorsionparametersguess=databaseparser.GrabSmallMoleculeAMOEBAParameters(self,optmol,mol,m) File "/home/domain/julybel/poltype/PoltypeModules/databaseparser.py", line 1587, in GrabSmallMoleculeAMOEBAParameters torsionindicestotinkertypes,torsionindicestotinkerclasses,torsionindicestoparametersmartsatomorders,torsionindicestoelementtinkerdescrips,torsionindicestosmartsatomorders=GenerateAtomIndexToAtomTypeAndClassForAtomList(poltype,torsionsforprmtoparametersmarts,torsionsforprmtosmarts,smartsatomordertoelementtinkerdescrip,elementtinkerdescriptotinkertype,tinkertypetoclass,rdkitmol) File "/home/domain/julybel/poltype/PoltypeModules/databaseparser.py", line 938, in GenerateAtomIndexToAtomTypeAndClassForAtomList matches=rdkitmol.GetSubstructMatches(substructure) Boost.Python.ArgumentError: Python argument types in Mol.GetSubstructMatches(Mol, NoneType) did not match C++ signature: GetSubstructMatches(RDKit::ROMol self, RDKit::MolBundle query, RDKit::SubstructMatchParameters params) GetSubstructMatches(RDKit::ROMol self, RDKit::ROMol query, RDKit::SubstructMatchParameters params) GetSubstructMatches(RDKit::ROMol self, RDKit::MolBundle query, bool uniquify=True, bool useChirality=False, bool useQueryQueryMatches=False, unsigned int maxMatches=1000) GetSubstructMatches(RDKit::ROMol self, RDKit::ROMol query, bool uniquify=True, bool useChirality=False, bool useQueryQueryMatches=False, unsigned int maxMatches=1000) All data are available here: https://drive.google.com/file/d/1TtKparbQfT2rNrOPAVlwV7GyRI0cT2-u/view?usp=sharing https://drive.google.com/file/d/1TtKparbQfT2rNrOPAVlwV7GyRI0cT2-u/view?usp=sharing I really appreciate your help! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < #62 <#62> <#62 <#62>> <#62 <#62> <#62 <#62>>>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26JPGQB6CCNAYWKD343SO4AB7ANCNFSM4TORYR7A https://github.com/notifications/unsubscribe-auth/AKNB26JPGQB6CCNAYWKD343SO4AB7ANCNFSM4TORYR7A . Is it okay to redownload by: git clone https://github.com/pren/poltype.git https://github.com/pren/poltype.git --branch poltype2 ? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#62 <#62> (comment) <#62 (comment) <#62 (comment)>>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26K2ZENE72TVQLVQOVLSPASK3ANCNFSM4TORYR7A https://github.com/notifications/unsubscribe-auth/AKNB26K2ZENE72TVQLVQOVLSPASK3ANCNFSM4TORYR7A . It still gives the same Error: [11:57:49] SMARTS Parse Error: syntax error while parsing: [ ][#6 <#6> <#6 <#6>>@][#6 <#6> <#6 <#6>>@])~[#6 <#6> <#6 <#6>>] [11:57:49] SMARTS Parse Error: Failed parsing SMARTS '[][#6 <#6> <#6 <#6>>@][ #6 <#6> <#6 <#6>>@])[#6 <#6> <#6 <#6>>]' for input: '[*][#6 <#6> <#6 <#6>>@][#6 <#6> <#6 <#6>>@])[#6 <#6> <#6 <#6>>]' — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#62 (comment) <#62 (comment)>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26MS7ZLPXQDZLHQX7I3SPEGY7ANCNFSM4TORYR7A . Yup, I have: packages in environment at /home/domain/data/prog/miniconda3/envs/poltype: Name Version Build Channel rdkit 2020.09.1 py36hce6e9d5_0 conda-forge — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#62 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26NKASVYEMFDJDXKENTSPFUPHANCNFSM4TORYR7A .

Linux 4.15.0-54-generic x86_64

[misterbrandonwalker]

okay sorry to bother, I found another issue. I was accidently zeroing out torsions transferred from database that are in ring bond. This was unintentional, I only meant to zero out torsions (for torsion spinning and fitting procedure) for rotatable bonds (non-ring). So you can just delete key_4 and all keys in qm-torsion, or just delete all key files and restart that is fine too.

On Tue, Nov 10, 2020 at 11:42 AM BelyaevaJuly notifications@github.com wrote:

I am not really sure what to tell you, I uninstalled and resinstalled to the 2020 version. I notice my build number is different, but the version on left is same. Which OS and OS version are you running poltype on? # packages in environment at /home/bdw2292/miniconda3/envs/p4envtest: # # Name Version Build Channel rdkit 2020.09.1 py36hf6a1616_0 conda-forge (p4envtest) [bdw2292@g2-node38 ami_2020BW]$ On Tue, Nov 10, 2020 at 10:42 AM BelyaevaJuly notifications@github.com wrote: … <#m-8822906756127487900_> Here are the files, https://utexas.box.com/s/gtm9m3bkjf6wusnsherpw029vmglxgr9 . You will need to finish the quantum. I am wondering if maybe we have different rdkit versions? Also is poltype being called from the same folder with all of the poltype output files or is poltype called from another directory? My rdkit version is shown below. (you can check with conda list rdkit) (p4envtest) @. PoltypeJobs]$ conda list rdkit # packages in environment at /home/bdw2292/miniconda3/envs/p4envtest: # # Name Version Build Channel rdkit 2017.09.1 py36_1 rdkit On Tue, Nov 10, 2020 at 4:12 AM BelyaevaJuly @. wrote: … <#m8960401689549010815> Yes that should work too. On Mon, Nov 9, 2020 at 11:39 AM BelyaevaJuly @.* wrote: … <#m6300200882296631641> Hi, I am unable to reproduce your error, poltype works fine when I run your molecule. Is it possible that the poltype version you are using is not the latest? I have made several updates within the latter part of last week. - Brandon … <#m-2560852688586727143> On Sun, Nov 8, 2020 at 2:50 PM BelyaevaJuly @ .> wrote: Dear colleagues, I am sorry for so much issues from my side, but it is quite useful and good for work, so I want to report about one new error: Calling: /home/domain/julybel/tinker/source/analyze.x /home/domain/julybel/poltype/VersionFiles/water.xyz http://water.xyz http://water.xyz http://water.xyz http://water.xyz http://water.xyz http://water.xyz http://water.xyz -k /home/domain/julybel/poltype/VersionFiles/water.key e> version.out no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error /home/domain/julybel/poltype/PoltypeModules/ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log no longer error ami_2020-opt.log [20:27:14] SMARTS Parse Error: syntax error while parsing: [ ][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>>>@][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>>>@])[#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>>>] [20:27:14] SMARTS Parse Error: Failed parsing SMARTS '[][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>>>@][ #6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>>>@])[#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>>>]' for input: '[][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>>>@][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>>>@])[#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>>>]' Traceback (most recent call last): File "poltype.py", line 1240, in params=poltype.main() File "poltype.py", line 944, in main params= self.GenerateParameters() File "poltype.py", line 1054, in GenerateParameters bondprmstotransferinfo,angleprmstotransferinfo,torsionprmstotransferinfo,strbndprmstotransferinfo,opbendprmstotransferinfo,vdwprmstotransferinfo,torsionsmissing,classkeytotorsionparametersguess=databaseparser.GrabSmallMoleculeAMOEBAParameters(self,optmol,mol,m) File "/home/domain/julybel/poltype/PoltypeModules/databaseparser.py", line 1587, in GrabSmallMoleculeAMOEBAParameters torsionindicestotinkertypes,torsionindicestotinkerclasses,torsionindicestoparametersmartsatomorders,torsionindicestoelementtinkerdescrips,torsionindicestosmartsatomorders=GenerateAtomIndexToAtomTypeAndClassForAtomList(poltype,torsionsforprmtoparametersmarts,torsionsforprmtosmarts,smartsatomordertoelementtinkerdescrip,elementtinkerdescriptotinkertype,tinkertypetoclass,rdkitmol) File "/home/domain/julybel/poltype/PoltypeModules/databaseparser.py", line 938, in GenerateAtomIndexToAtomTypeAndClassForAtomList matches=rdkitmol.GetSubstructMatches(substructure) Boost.Python.ArgumentError: Python argument types in Mol.GetSubstructMatches(Mol, NoneType) did not match C++ signature: GetSubstructMatches(RDKit::ROMol self, RDKit::MolBundle query, RDKit::SubstructMatchParameters params) GetSubstructMatches(RDKit::ROMol self, RDKit::ROMol query, RDKit::SubstructMatchParameters params) GetSubstructMatches(RDKit::ROMol self, RDKit::MolBundle query, bool uniquify=True, bool useChirality=False, bool useQueryQueryMatches=False, unsigned int maxMatches=1000) GetSubstructMatches(RDKit::ROMol self, RDKit::ROMol query, bool uniquify=True, bool useChirality=False, bool useQueryQueryMatches=False, unsigned int maxMatches=1000) All data are available here: https://drive.google.com/file/d/1TtKparbQfT2rNrOPAVlwV7GyRI0cT2-u/view?usp=sharing https://drive.google.com/file/d/1TtKparbQfT2rNrOPAVlwV7GyRI0cT2-u/view?usp=sharing I really appreciate your help! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < #62 https://github.com/pren/poltype/issues/62 <#62 https://github.com/pren/poltype/issues/62> <#62 https://github.com/pren/poltype/issues/62 <#62 https://github.com/pren/poltype/issues/62>> <#62 https://github.com/pren/poltype/issues/62 <#62 https://github.com/pren/poltype/issues/62> <#62 https://github.com/pren/poltype/issues/62 <#62 https://github.com/pren/poltype/issues/62>>>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26JPGQB6CCNAYWKD343SO4AB7ANCNFSM4TORYR7A https://github.com/notifications/unsubscribe-auth/AKNB26JPGQB6CCNAYWKD343SO4AB7ANCNFSM4TORYR7A . Is it okay to redownload by: git clone https://github.com/pren/poltype.git https://github.com/pren/poltype.git --branch poltype2 ? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#62 https://github.com/pren/poltype/issues/62 <#62 https://github.com/pren/poltype/issues/62> (comment) <#62 https://github.com/pren/poltype/issues/62 (comment) <#62 (comment) https://github.com/pren/poltype/issues/62#issuecomment-724164700>>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26K2ZENE72TVQLVQOVLSPASK3ANCNFSM4TORYR7A https://github.com/notifications/unsubscribe-auth/AKNB26K2ZENE72TVQLVQOVLSPASK3ANCNFSM4TORYR7A . It still gives the same Error: [11:57:49] SMARTS Parse Error: syntax error while parsing: [ ][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>@][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>@])[#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>] [11:57:49] SMARTS Parse Error: Failed parsing SMARTS '[][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>@][ #6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>@])[#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>]' for input: '[*][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>@][#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>@])[#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6> <#6 https://github.com/pren/poltype/pull/6 <#6 https://github.com/pren/poltype/pull/6>>]' — You are receiving this because you commented. Reply to this email directly, view it on GitHub <

62 https://github.com/pren/poltype/issues/62 (comment) <#62 (comment)

https://github.com/pren/poltype/issues/62#issuecomment-724604153>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26MS7ZLPXQDZLHQX7I3SPEGY7ANCNFSM4TORYR7A . Yup, I have: packages in environment at /home/domain/data/prog/miniconda3/envs/poltype: Name Version Build Channel rdkit 2020.09.1 py36hce6e9d5_0 conda-forge — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#62 (comment) https://github.com/pren/poltype/issues/62#issuecomment-724822836>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26NKASVYEMFDJDXKENTSPFUPHANCNFSM4TORYR7A .

Linux 4.15.0-54-generic x86_64

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/pren/poltype/issues/62#issuecomment-724858569, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKNB26OSYFXBR4MQFEKHV6TSPF3NPANCNFSM4TORYR7A .

[BelyaevaJuly]

Oh, God, I still have [09:06:28] SMARTS Parse Error: syntax error while parsing: []~[#6@]~[#6@])~[#6] [09:06:28] SMARTS Parse Error: Failed parsing SMARTS '[]~[#6@]~[#6@])~[#6]' for input: '[*]~[#6@]~[#6@])~[#6]' when I restarted your system. Maybe, it is connected with RDKit?

[misterbrandonwalker]

I will provide you with key_4. I can't think of any other possible difference. Which OS and OS version are you running poltype on?

---

From: BelyaevaJuly notifications@github.com Sent: Wednesday, November 11, 2020 12:54:55 AM To: pren/poltype poltype@noreply.github.com Cc: Brandon Walker bdw2292@utexas.edu; Comment comment@noreply.github.com Subject: Re: [pren/poltype] SMARTS Parse Error (#62)

Oh, God, I still have [09:06:28] SMARTS Parse Error: syntax error while parsing: [][#6https://github.com/pren/poltype/pull/6@][#6https://github.com/pren/poltype/pull/6@])~[#6https://github.com/pren/poltype/pull/6] [09:06:28] SMARTS Parse Error: Failed parsing SMARTS '[][#6https://github.com/pren/poltype/pull/6@][#6https://github.com/pren/poltype/pull/6@])[#6https://github.com/pren/poltype/pull/6]' for input: '[*][#6https://github.com/pren/poltype/pull/6@][#6https://github.com/pren/poltype/pull/6@])[#6https://github.com/pren/poltype/pull/6]' when I restarted your system. Maybe, it is connected with RDKit?

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/pren/poltype/issues/62#issuecomment-725239972, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AKNB26JBNXIC7XOJLCWBH5TSPIYL7ANCNFSM4TORYR7A.

[misterbrandonwalker]

ami_2020.key_4.txt Okay I have uploaded the key_4 file. You can replace with the key_4 you are using and it should skip to running quantum. Just rename file to get rid of the .txt extension, GitHub only allows me to upload file types it recognizes.

[BelyaevaJuly]

ami_2020.key_4.txt Okay I have uploaded the key_4 file. You can replace with the key_4 you are using and it should skip to running quantum. Just rename file to get rid of the .txt extension, GitHub only allows me to upload file types it recognizes.

Thanks you a lot, I will try it