New style adjacency list and multiplicity label - #217

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bbuesser:new-style-adjacency-list

Commits on May 19, 2014

Update RMG example 1,3-hexadiene with multiplicity label
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d7f7fcb
Update RMG example c3h4 with multiplicity label
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302f9ef
Update RMG example ch3no2 with multiplicity label
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9f67f08
Update RMG example diesel with multiplicity label
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7406845
Update RMG example e85 with multiplicity label
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141803d
Update RMG example liquid_phase with multiplicity label
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a536e37
Update RMG example methylformate with multiplicity label
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Update RMG example minimal with multiplicity label
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44b86f6
Update RMG example minimal_sensitivity with multiplicity label
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bab0769
Update RMG example TEOS with multiplicity label
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b7b4725
Add multiplicity label to loadEntry for transport libraries
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795b41b
Add multiplicity label to loadEntry for thermo libraries and groups
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2239906
Add multiplicity label to loadEntry for statmech depository
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ab77c8a
Add multiplicity label to class Entry and loadEntry for forbidden
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f67bab4
Add multiplicity label to loadEntry for kinetics depository
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9e6ac85
Add multiplicity label to loadEntry for kinetic groups
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09fc652
Add multiplicity label in loadEntry for kinetic libraries
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00db033
Add multiplicity label to group.py
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f1572c0
Add printMultiplicity=True to toAdjacencyList() in
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a58ba69
Add multiplicity label to molecule.py
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b260eb5
Update to- and fromAdjacencyList() for multiplicity in Molecule instead
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d723666
Use new molecule.multiplicity attribute in qm.molecule
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13a5393
Add multiplicity to read input file
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b84567d
Add copy() to reaction.py to make deep copies of reaction objects
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ed1b8c7
Add multiplicity attribute to Species.py
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4b7d957
Add species multiplicity model.py
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871c712
Update family.py for new species multiplicity and search for spin
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2f4d651
Change toAdjacencyList() to new adjacency list style
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712fecb
Add multiplicity label to saveEntry() for transport libraries.
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d4e0ce4
Add multiplicity label to saveEntry() for thermo libraries.
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c36551b
Add multiplicity label to saveEntry() for forbiddenstructures.py
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a73f602
Replace strip() with split() to read adjacency lists in kinetics library
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2faa10c
Set printMultiplicity label in toAdjacencyList() explicitely to True
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8aedab8
Define type of maxMultiplicity in fromAdjacencyList()
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d714d75
Prepare molecule.py for new adjacency list style
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154eb1c
Remove maxMultiplicity argument
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af961ac
Modify adjlist.py to read and write the new-style adjacency list.
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49bd3dd
Updating examples with new adjacency list style
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8db74f9
Updating existing unit tests for new adjacency list style
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5b2145c
Remove maxMultiplicity argument
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16a0cea
Updating existing unit test for new adjacency list style
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31322a5
Update fromRDKitMol() for the new adjacency list style
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ca65b4d
Change treatment of missing lone pair card
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d4dd500
Update existing unit test for new adjacency list style
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5be8ba1
Prevent species generation from crashing if molecule is None and add
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a37b47d
Update existing unit tests for the new adjacency list style
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472b828
Remove merge conflicts
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6ac5b9c
Add write multiplicity label to kinetics groups
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c2199b9