Greg Landrum
e08e0d16d8
first pass, using google style
2015-11-14 14:58:11 +01:00
Greg Landrum
5992c6fd23
- made the ResonanceMolSupplier really lazy, i.e. resonance structure enumeration is only carried out when the user asks for a structure or when the user explicitly request that calling the enumerate() member function. This makes object creation fast and enables calling getNumConjGrps(), getBondConjGrpIdx() and getAtomConjGrpIdx() member function without incurring in the cost of necessarily enumerating resonance structures
...
- now bonds and atoms with do not belong to conjugated groups get a -1 index
- added a few Python wrappers
- added a few tests
2015-11-04 05:39:46 +01:00
Paolo Tosco
3d48ba72e1
- added threading support to ResonanceMolSupplier and relevant tests
...
- added threading support to the ResonanceMolSupplier-enabled
SubstructMatch() and relevant tests
- modified/removed some code in O3AAlignMolecules.cpp which doesn't
seem necessary anymore
- modified Code/GraphMol/CMakeLists.txt to allow building
on Windows
2015-11-01 23:01:34 +00:00
Paolo Tosco
f43677b978
- fixed a problem with thiocarboxylates/thiolates not being perceived
...
as conjugated like their oxygen analogs
- fixed an issue with large numbers of resonance structures exceeding
the unsigned int allowance
- implemented the uniquify feature properly
- uniquify now defaults to false when using the ResonanceMolSupplier-
enabled SubstructMatch() version
- the concept of 'laziness' is now clearer
- TODO:
* remove some debugging info
* move classes from .h to .cpp
* SWIG wrappers
* improve resonance structure sorting for degenerate resonance
structures
I will do all of the above ASAP
2015-10-21 20:06:53 +01:00
Paolo Tosco
eaa187b03d
- added ResonanceMolSupplier
...
- added overloaded SubstructMatch() version supporting ResonanceMolSupplier
- added relevant Python wrappers
- added C++/Python tests
2015-10-04 23:21:28 +01:00
Greg Landrum
4b8caf2ceb
Fixes #409
2015-01-10 07:21:55 +01:00
Greg Landrum
34ab68ca2a
introduce QueryBond::QueryMatch, as with QueryAtoms;
...
all tests passing;
performance tests still needed
2014-05-07 05:29:25 +02:00
Greg Landrum
4a14a52674
Fixes #153
2013-11-15 06:47:18 +01:00
Greg Landrum
f3fbef45c5
update copyright statements
2010-09-26 17:04:37 +00:00
Greg Landrum
4db8233db6
sync with trunk
2010-09-10 05:12:41 +00:00
Greg Landrum
052ec66542
cleanups:
...
remove x bit from headers and sources;
remove a couple empty files from Code/GraphMol
2010-09-08 04:25:57 +00:00
Greg Landrum
0ce95829a5
cleanup deprecated args
2010-08-21 00:16:55 +00:00
Greg Landrum
f42f479d28
enabling infrastructure for making repeated recursive
...
smarts queries run faster (like vector bindings). Though there is an addition to the smarts parser
exposed here, I do not recommend using it in client code.
2010-06-03 10:02:15 +00:00
Greg Landrum
ec2c2042e8
remove the vflib usage code from Substruct area
2010-04-19 07:45:22 +00:00
Greg Landrum
30fe77b609
initial commit: passes all tests and seems to be faster than the original code
2009-02-09 16:19:31 +00:00
Greg Landrum
e450f5beeb
doc updates and some minor formatting changes
2007-10-24 16:37:37 +00:00
Greg Landrum
7cfa8cde0b
another substruct caching try
2007-09-23 06:56:13 +00:00
Greg Landrum
d5ffea669d
add support for chirality in substructure searches;
...
this only is going to work in cases where CIP codes have been (i.e. can be)
assigned to atoms.
2006-11-03 06:35:14 +00:00
Greg Landrum
88d596abca
get the AR_MOLGRAPH caching write with substructs; the current implementation introduces a core leak, so it is disabled by default
2006-10-19 05:24:05 +00:00
Greg Landrum
a5d7fc550a
try to get ChemTransforms checked in
2006-07-18 05:35:12 +00:00
Greg Landrum
75a79b6327
initial import
2006-05-06 22:20:08 +00:00
