New style adjacency list#218

Merged

connie merged 90 commits intomasterfrom

new-style-adjacency-list

Jul 25, 2014

Commits on Jul 25, 2014

Update RMG example 1,3-hexadiene with multiplicity label

bbuesser
authored and
connie
committed
Update RMG example c3h4 with multiplicity label

bbuesser
authored and
connie
committed
Update RMG example ch3no2 with multiplicity label

bbuesser
authored and
connie
committed
Update RMG example diesel with multiplicity label

bbuesser
authored and
connie
committed
Update RMG example e85 with multiplicity label

bbuesser
authored and
connie
committed
Update RMG example liquid_phase with multiplicity label

bbuesser
authored and
connie
committed
Update RMG example methylformate with multiplicity label

bbuesser
authored and
connie
committed
Update RMG example minimal with multiplicity label

bbuesser
authored and
connie
committed
Update RMG example minimal_sensitivity with multiplicity label

bbuesser
authored and
connie
committed
Update RMG example TEOS with multiplicity label

bbuesser
authored and
connie
committed
Add multiplicity label to loadEntry for transport libraries

bbuesser
authored and
connie
committed
Add multiplicity label to loadEntry for thermo libraries and groups

bbuesser
authored and
connie
committed
Add multiplicity label to loadEntry for statmech depository

bbuesser
authored and
connie
committed
Add multiplicity label to class Entry and loadEntry for forbidden

bbuesser
authored and
connie
committed
Add multiplicity label to loadEntry for kinetics depository

bbuesser
authored and
connie
committed
Add multiplicity label to loadEntry for kinetic groups

bbuesser
authored and
connie
committed
Add multiplicity label in loadEntry for kinetic libraries

bbuesser
authored and
connie
committed
Add multiplicity label to group.py

bbuesser
authored and
connie
committed
Add printMultiplicity=True to toAdjacencyList() in

bbuesser
authored and
connie
committed
Add multiplicity label to molecule.py

bbuesser
authored and
connie
committed
Update to- and fromAdjacencyList() for multiplicity in Molecule instead

bbuesser
authored and
connie
committed
Use new molecule.multiplicity attribute in qm.molecule

bbuesser
authored and
connie
committed
Add multiplicity to read input file

bbuesser
authored and
connie
committed
Add copy() to reaction.py to make deep copies of reaction objects

bbuesser
authored and
connie
committed
Add multiplicity attribute to Species.py

bbuesser
authored and
connie
committed
Add species multiplicity model.py

bbuesser
authored and
connie
committed
Update family.py for new species multiplicity and search for spin

bbuesser
authored and
connie
committed
Change toAdjacencyList() to new adjacency list style

bbuesser
authored and
connie
committed
Add multiplicity label to saveEntry() for transport libraries.

bbuesser
authored and
connie
committed
Add multiplicity label to saveEntry() for thermo libraries.

bbuesser
authored and
connie
committed
Add multiplicity label to saveEntry() for forbiddenstructures.py

bbuesser
authored and
connie
committed
Replace strip() with split() to read adjacency lists in kinetics library

bbuesser
authored and
connie
committed
Set printMultiplicity label in toAdjacencyList() explicitely to True

bbuesser
authored and
connie
committed
Define type of maxMultiplicity in fromAdjacencyList()

bbuesser
authored and
connie
committed
Prepare molecule.py for new adjacency list style

bbuesser
authored and
connie
committed
Remove maxMultiplicity argument

bbuesser
authored and
connie
committed
Modify adjlist.py to read and write the new-style adjacency list.

bbuesser
authored and
connie
committed
Updating examples with new adjacency list style

bbuesser
authored and
connie
committed
Updating existing unit tests for new adjacency list style

bbuesser
authored and
connie
committed
Remove maxMultiplicity argument

bbuesser
authored and
connie
committed
Updating existing unit test for new adjacency list style

bbuesser
authored and
connie
committed
Update fromRDKitMol() for the new adjacency list style

bbuesser
authored and
connie
committed
Change treatment of missing lone pair card

bbuesser
authored and
connie
committed
Update existing unit test for new adjacency list style

bbuesser
authored and
connie
committed
Prevent species generation from crashing if molecule is None and add

bbuesser
authored and
connie
committed
Update existing unit tests for the new adjacency list style

bbuesser
authored and
connie
committed
Add write multiplicity label to kinetics groups

bbuesser
authored and
connie
committed
Add multiplicity and lone pairs to functions required for pickling

bbuesser
authored and
connie
committed
Add additional unit test for handling the new adjacency list styles

bbuesser
authored and
connie
committed
Prevent species creation from crashing of molecule is an empty vector

bbuesser
authored and
connie
committed
Add multiplicity to species unit test for pickling species

bbuesser
authored and
connie
committed
Update the travis config file for unit tests on the new-style-adjacency-list branch.

rwest
authored and
connie
committed
Update lone pairs and multiplicity for qm calculation before HBI

pierrelb
authored and
connie
committed
Update lone pairs and multiplicity for solvation corrections

pierrelb
authored and
connie
committed
Only write multiplicity in adjacency lists, and store on Molecules.

rwest
authored and
connie
committed
Correct "special cases" for carbon monoxide SMILES strings.

rwest
authored and
connie
committed
Remove multiplicities from Species declarations in all examples files.
connie
committed
Don't bother printing default multiplicity values in toAdjacencyList

rwest
authored and
connie
committed
fromAdjacencyList returns multiplicity even when reading groups.

rwest
authored and
connie
committed
Added fromOldAdjacencyList method.

rwest
authored and
connie
committed
Group.toAdjacencyList needs to pass multiplicity.

rwest
authored and
connie
committed
New adjlistTest.py to just test adjacency list functions.

rwest
authored and
connie
committed
Splitting adjacency list tests into separate tests.

rwest
authored and
connie
committed
Restore a test for reading old adjacency lists, with implicit H's

rwest
authored and
connie
committed
Detect old style adjacency lists via regular expressions

rwest
authored and
connie
committed
Add unit tests for reading old style adjacency lists

rwest
authored and
connie
committed
Migrate back to master RMG-database in travis build.
connie
committed
Print multiplicity in adjacency lists of anything with a radical electron.

rwest
authored and
connie
committed
fromOldAdjacencyList: reduce nesting of if statements

rwest
authored and
connie
committed
fromOldAdjacencyList: reduce code duplication

rwest
authored and
connie
committed
Tweak some comments, docstrings, and debug logging.

rwest
authored and
connie
committed
fromAdjacencyList: make last-line sniffing safer

rwest
authored and
connie
committed
fromOldAdjacencyList: stricter syntax checking of multiplicity line

rwest
authored and
connie
committed
to/fromAdjacencyList: SYNTAX CHANGE: wildcard 'x' now includes 0.

rwest
authored and
connie
committed
Tidy indentation in fromAdjacancyList

rwest
authored and
connie
committed
toAdjacencyList: rename internal variable to atomUnpairedElectrons

rwest
authored and
connie
committed
Molecule __init__ and __repr__ respect multiplicity.

rwest
authored and
connie
committed
fromOldAdjacencyList: condense radical list [2,2] into 2

rwest
authored and
connie
committed
toAdjacencyList: multiplicity list printed without spaces.

rwest
authored and
connie
committed
fromOldAdjacencyList: rename variable to lonePairsOfElectrons

rwest
authored and
connie
committed
fromOldAdjacencyList: blank lone pairs on group interpreted as undefined (wildcard).

rwest
authored and
connie
committed
Small tweak in Atom.isSpecificCaseOf; use list iterator instead of index, range, len, lookup etc.

rwest
authored and
connie
committed
TODO: lone pairs and charges are not compared when comparing Atoms or GroupAtoms

rwest
authored and
connie
committed
Adjacency list I/O for groups better for Lone Pairs

rwest
authored and
connie
committed
Changing the style of new adjacency list to use lowercase letters.
connie
committed
Change adjlists in example files to new lowercase style.
connie
committed
Update unit tests with lower case labels in adjacency lists

rwest
authored and
connie
committed
Switch from using {Cs,Cd} to [Cs,Cd] and u{0,1} to u[0,1] in Adjacency List syntax.

rwest
authored and
connie
committed
A first attempt to document the new adjacency list syntax.

rwest
authored and
connie
committed
Add note about update to top of adjacency list documentation, and the FAQ.

rwest
authored and
connie
committed