e-LBOW builder help

Options:

--version	show program's version number and exit
-h, --help	show this help message and exit
--long-help	show even more help and exit
--smiles=SMILES
	use the passed SMILES
--file=FILE	use file for chemical input
--key=KEY	use SMILES from smilesDB for chemical input
--pipe	read input from standard in
--residue=RESIDUE
	use only this residue from the PDB file
--name=LIGAND_NAME
	name of ligand to be used in various output files
--sequence=SEQUENCE
	use sequence (limited to 20 residues and no semi- empirical optimisation)
--read-only	read the input but don't do any processing
--opt	use the best optimisation method available
--template=TEMPLATE
	use file for naming of atoms e.g. PDB file
--mopac	use MOPAC for quantum chemistry calculations (requires MOPAC be installed)
--gamess	use GAMESS for quantum chemistry calculations (requires GAMESS be installed)
--gaussian	use Gaussian for quantum chemistry calculations (requires Gaussian be installed)
--final-geometry
	use this file to obtain final geometry
--initial-geometry
	use this file to obtain the intital geometry for QM
--restart	restart the optimisation with lowest previous geometry
--opt-steps=OPT_STEPS
	optimisation steps (currently for ELBOW opt only)
--ignore-chiral
	ignore the chirality in the SMILES string
--method=QM_METHOD
	run QM with this method, if possible
--basis=QM_BASIS
	run QM with this basis, if possible
--random-seed=RANDOM_SEED
	random number seed
--quiet	less print out
--view=VIEW	viewing software command
--pymol	use PyMOL from the PHENIX install to view geometries
--overwrite	clobber any existing output files
--bonding=BONDING
	file that specifies the bond of the input molecule
--id=ID	three letter code used in the CIF output
--xyz	output is also written in XYZ format

inputs:

any_chemical_format_reader

Reads a number of chemical formats including

• SMILES: string or file
• PDB: string or file
• XYZ: string or file
• Molfile (V2000, V3000 and SDFile): string or file
• TRIPOS MOL2: string or file
• GAMESS input: string or file
• GAMESS output: string or file
• Gaussian input: string or file
• Gaussian output: string or file
• PyQuante input: list or tuple

Returns a SimpleMoleculeClass

SMILES examples:

Water:

elbow.builder --smiles O

Ethanol:

elbow.builder --smiles CCO

Benzene:

elbow.builder --smiles c1ccccc1

Isobutane:

elbow.builder --smiles "CC(C)C"

ATP:

elbow.builder --smiles "Nc1ncnc2[n](cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)OP(O)(O)=O)[C@@H](O)[C@H]3O"

Other examples:

elbow.builder --file file.pdb

User defined database of SMILES:

To set SMILES key

elbow.builder --key ethanol --smiles CCO

To recall SMILES string

elbow.builder --key ethanol

To remove SMILES string

elbow.builder --key ethanol --smiles ""