| --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 |
| --keys | display smiles DB |
| --pipe | read input from standard in |
| --residue=RESIDUE | |
| use only this residue from the PDB file | |
| --chain=CHAIN | use only this chain from the PDB file |
| --all-residues | retain all residues in a 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 | |
| --newton-raphson | |
| use Newton-Raphson optimisation | |
| --gdiis | use GDIIS optimisation |
| --quicca | use QUICCA optimisation |
| --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) | |
| --opt-tol=OPT_TOL | |
| optimisation tolerance = loose, default or tight | |
| --ignore-chiral | |
| ignore the chirality in the SMILES string | |
| --user-opt | use user defined for quantum chemistry calculations |
| --user-opt-input-filename=USER_OPT_INPUT_FILENAME | |
| input filename | |
| --user-opt-xyz2input=USER_OPT_XYZ2INPUT | |
| converts xyz file to QM program input | |
| --user-opt-xyz-filename=USER_OPT_XYZ_FILENAME | |
| xyz filename | |
| --user-opt-script-filename=USER_OPT_SCRIPT_FILENAME | |
| run script filename | |
| --user-opt-program=USER_OPT_PROGRAM | |
| QM optimisation program run script or program invocation command | |
| --user-opt-output-filename=USER_OPT_OUTPUT_FILENAME | |
| output filename | |
| --user-opt-output2xyz=USER_OPT_OUTPUT2XYZ | |
| converts QM program output to xyz file | |
| --memory=QM_MEMORY | |
| maximum memory mostly for quantum method | |
| --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 |
| --silent | almost complete silence |
| --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 |
| --tripos | output is also written in TRIPOS format |
| --output=OUTPUT | |
| name for output files | |
| --pickle | use a pickle file to reload the topological information |
| --do-all | process all molecules in a SDF file |
| --add-hydrogens=ADD_HYDROGEN_BOOLEAN | |
| override the automatic hydrogen addition | |
| --write-hydrogens=WRITE_HYDROGEN_BOOLEAN | |
| override the automatic writing of hydrogens to PDB and CIF files | |
| --auto-bond-cutoff=AUTO_BOND_CUTOFF | |
| set the max bondlength for auto bond detection | |
| --pdb-assign=PDB_ASSIGN | |
| set the atom attributes in the PDB file | |
| --metal | generate metal coordination spheres |
inputs:
any_chemical_format_reader
Reads a number of chemical formats including
Returns a SimpleMoleculeClass
SMILES examples: