Index

_

__init__() (acpype.logger.LogFormatter method) (acpype.mol.Angle method) (acpype.mol.Atom method) (acpype.mol.AtomType method) (acpype.mol.Bond method) (acpype.mol.Dihedral method) (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) (acpype.topol.Topology_14 method)

A

AbstractTopol (class in acpype.topol) acpype module acpype.acs_api module acpype.cli module acpype.logger module acpype.mol module acpype.params module

acpype.parser_args module acpype.topol module acpype.utils module acpype_api() (in module acpype.acs_api) ACTopol (class in acpype.topol) Angle (class in acpype.mol) Atom (acpype.mol.acpype.mol attribute) (class in acpype.mol) AtomType (acpype.mol.acpype.mol attribute) (class in acpype.mol)

B

balanceCharges() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method)

Bond (class in acpype.mol)

C

checkFrcmod() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) checkLeapLog() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) checkOpenBabelVersion() (in module acpype.utils) checkSmiles() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) checkXyzAndTopFiles() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) clearFileInMemory() (in module acpype.acs_api)

converter() (acpype.logger.LogFormatter method) convertPdbToMol2() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) convertSmilesToMol2() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) copy_log() (in module acpype.logger) createACTopol() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) createMolTopol() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) cross_product() (in module acpype.utils)

D

delOutputFiles() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method)

Dihedral (class in acpype.mol) distanceAA() (in module acpype.utils) dotproduct() (in module acpype.utils)

E

elapsedTime() (in module acpype.utils) execAntechamber() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) execObabel() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method)

execParmchk() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) execTleap() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method)

F

find_bin() (in module acpype.utils) format() (acpype.logger.LogFormatter method)

formatException() (acpype.logger.LogFormatter method) formatStack() (acpype.logger.LogFormatter method) formatTime() (acpype.logger.LogFormatter method)

G

get_option_parser() (in module acpype.parser_args) getABCOEFs() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) getAngles() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) getAtoms() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) getBonds() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) getChirals() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method)

getCoords() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) getDihedrals() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) getFlagData() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) getResidueLabel() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) guessCharge() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method)

H

hasNondefault14() (acpype.topol.Topology_14 method)

I

imprDihAngle() (in module acpype.utils)

init_main() (in module acpype.cli)

J

job_pids_family() (in module acpype.utils)

L

length() (in module acpype.utils) locateDat() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method)

LogFormatter (class in acpype.logger)

M

makeDir() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) module acpype acpype.acs_api acpype.cli acpype.logger acpype.mol acpype.params acpype.parser_args acpype.topol acpype.utils

MolTopol (class in acpype.topol)

P

p7_array_read() (acpype.topol.Topology_14 method) parmMerge() (in module acpype.utils) parseFrcmod() (in module acpype.utils) patch_gmx_topol14() (acpype.topol.Topology_14 method) pickleSave() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) print_gmx_pairs() (acpype.topol.Topology_14 method) printDebug() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) printDebugQuoted() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method)

printError() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) printErrorQuoted() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) printMess() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) printWarn() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method)

R

read_amber_topology() (acpype.topol.Topology_14 method) readFiles() (in module acpype.acs_api)

readMol2TotalCharge() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method)

S

search() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) set_for_pip() (in module acpype.utils) set_logging_conf() (in module acpype.logger) setAtomType4Gromacs() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) setProperDihedralsCoef() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method)

setResNameCheckCoords() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) signal_handler() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) skipline() (acpype.topol.Topology_14 static method) sortAtomsForGromacs() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) splitBlock() (in module acpype.utils)

T

Topology_14 (class in acpype.topol)

U

usesTime() (acpype.logger.LogFormatter method)

V

vec_sub() (in module acpype.utils)

W

while_replace() (in module acpype.utils) writeCharmmTopolFiles() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) writeCnsTopolFiles() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) writeGroFile() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) writeGromacsTop() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method)

writeGromacsTopolFiles() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) writeMdpFiles() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) writePdb() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method) writePosreFile() (acpype.topol.AbstractTopol method) (acpype.topol.ACTopol method) (acpype.topol.MolTopol method)