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Link any residues#29

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js1710 wants to merge 13 commits intodevjag1g13/pycgtool:devfrom link_any_residuesjag1g13/pycgtool:link_any_residuesCopy head branch name to clipboard

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Commits on Dec 19, 2018

• first commit. The linking of residues is not fully implemented.

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• first commit. The linking of residues is not fully implemented.

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Commits on Dec 22, 2018

• Now can connect residues using the [ global ] section. Will only work for one molecule in water at the moment

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• Updated documentation

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Commits on Jan 18, 2019

• Fixed multiple bugs in the output of multi-residue information. At the moment only one multi-residue molecule is supported.

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• updated tests

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Commits on Jan 21, 2019

• Global section removed. Now can enter inter residue connections under a molecule section [< mol >] and the name used for mol will apper in the itp file.

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• updated inter residue test files

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Commits on Feb 22, 2019

• updated all bonset workflow to go via Molecule objects. Added test for multi residue molecule itp output

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• fixed bug in previous commit

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• refactored output to make more streamlined for molecules with any number of residues

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Commits on Feb 23, 2019

• removed any overlap between Molecule instances and Bead instances

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Commits on Feb 25, 2019

• updated documentation

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