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* scripts/*: Cleanups and fixes, including for compilation

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problems with Perl. (Derives from some macro expansion for THR.)
This commit is contained in:
Geoffrey Hutchison
2006-12-02 18:56:04 +00:00
parent ebe138c944
commit aa011ebe45
16 changed files with 3847 additions and 1562 deletions
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264
scripts/python/openbabel.py
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@@ -566,31 +566,6 @@ OBResidueData_swigregister(OBResidueData)
OpenDatafile = _openbabel.OpenDatafile
FILE_SEP_CHAR = _openbabel.FILE_SEP_CHAR
class OBStopwatch(object):
thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
__repr__ = _swig_repr
def Start(*args): return _openbabel.OBStopwatch_Start(*args)
def Lap(*args): return _openbabel.OBStopwatch_Lap(*args)
def Elapsed(*args): return _openbabel.OBStopwatch_Elapsed(*args)
def __init__(self, *args):
_openbabel.OBStopwatch_swiginit(self,_openbabel.new_OBStopwatch(*args))
__swig_destroy__ = _openbabel.delete_OBStopwatch
__del__ = lambda self : None;
OBStopwatch_swigregister = _openbabel.OBStopwatch_swigregister
OBStopwatch_swigregister(OBStopwatch)
class OBSqrtTbl(object):
thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
__repr__ = _swig_repr
def __init__(self, *args):
_openbabel.OBSqrtTbl_swiginit(self,_openbabel.new_OBSqrtTbl(*args))
__swig_destroy__ = _openbabel.delete_OBSqrtTbl
__del__ = lambda self : None;
def Sqrt(*args): return _openbabel.OBSqrtTbl_Sqrt(*args)
def Init(*args): return _openbabel.OBSqrtTbl_Init(*args)
OBSqrtTbl_swigregister = _openbabel.OBSqrtTbl_swigregister
OBSqrtTbl_swigregister(OBSqrtTbl)
class DoubleType(object):
thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
__repr__ = _swig_repr
@@ -620,6 +595,31 @@ class OBRandom(object):
OBRandom_swigregister = _openbabel.OBRandom_swigregister
OBRandom_swigregister(OBRandom)
class OBStopwatch(object):
thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
__repr__ = _swig_repr
def Start(*args): return _openbabel.OBStopwatch_Start(*args)
def Lap(*args): return _openbabel.OBStopwatch_Lap(*args)
def Elapsed(*args): return _openbabel.OBStopwatch_Elapsed(*args)
def __init__(self, *args):
_openbabel.OBStopwatch_swiginit(self,_openbabel.new_OBStopwatch(*args))
__swig_destroy__ = _openbabel.delete_OBStopwatch
__del__ = lambda self : None;
OBStopwatch_swigregister = _openbabel.OBStopwatch_swigregister
OBStopwatch_swigregister(OBStopwatch)
class OBSqrtTbl(object):
thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
__repr__ = _swig_repr
def __init__(self, *args):
_openbabel.OBSqrtTbl_swiginit(self,_openbabel.new_OBSqrtTbl(*args))
__swig_destroy__ = _openbabel.delete_OBSqrtTbl
__del__ = lambda self : None;
def Sqrt(*args): return _openbabel.OBSqrtTbl_Sqrt(*args)
def Init(*args): return _openbabel.OBSqrtTbl_Init(*args)
OBSqrtTbl_swigregister = _openbabel.OBSqrtTbl_swigregister
OBSqrtTbl_swigregister(OBSqrtTbl)
class vector3(object):
thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
__repr__ = _swig_repr
@@ -1264,6 +1264,113 @@ AA_HIS = _openbabel.AA_HIS
AA_CYS = _openbabel.AA_CYS
AA_MET = _openbabel.AA_MET
AA_TRP = _openbabel.AA_TRP
class OBInternalCoord(object):
thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
__repr__ = _swig_repr
_a = _swig_property(_openbabel.OBInternalCoord__a_get, _openbabel.OBInternalCoord__a_set)
_b = _swig_property(_openbabel.OBInternalCoord__b_get, _openbabel.OBInternalCoord__b_set)
_c = _swig_property(_openbabel.OBInternalCoord__c_get, _openbabel.OBInternalCoord__c_set)
_dst = _swig_property(_openbabel.OBInternalCoord__dst_get, _openbabel.OBInternalCoord__dst_set)
_ang = _swig_property(_openbabel.OBInternalCoord__ang_get, _openbabel.OBInternalCoord__ang_set)
_tor = _swig_property(_openbabel.OBInternalCoord__tor_get, _openbabel.OBInternalCoord__tor_set)
def __init__(self, *args):
_openbabel.OBInternalCoord_swiginit(self,_openbabel.new_OBInternalCoord(*args))
__swig_destroy__ = _openbabel.delete_OBInternalCoord
__del__ = lambda self : None;
OBInternalCoord_swigregister = _openbabel.OBInternalCoord_swigregister
OBInternalCoord_swigregister(OBInternalCoord)
ACIDIC = cvar.ACIDIC
ACYCLIC = cvar.ACYCLIC
ALIPHATIC = cvar.ALIPHATIC
AROMATIC = cvar.AROMATIC
BASIC = cvar.BASIC
BURIED = cvar.BURIED
CHARGED = cvar.CHARGED
CYCLIC = cvar.CYCLIC
HYDROPHOBIC = cvar.HYDROPHOBIC
LARGE = cvar.LARGE
MEDIUM = cvar.MEDIUM
NEGATIVE = cvar.NEGATIVE
NEUTRAL = cvar.NEUTRAL
POLAR = cvar.POLAR
POSITIVE = cvar.POSITIVE
SMALL = cvar.SMALL
SURFACE = cvar.SURFACE
ALPHA_CARBON = cvar.ALPHA_CARBON
AMINO_BACKBONE = cvar.AMINO_BACKBONE
BACKBONE = cvar.BACKBONE
CYSTEINE_SULPHUR = cvar.CYSTEINE_SULPHUR
LIGAND = cvar.LIGAND
NUCLEIC_BACKBONE = cvar.NUCLEIC_BACKBONE
SHAPELY_BACKBONE = cvar.SHAPELY_BACKBONE
SHAPELY_SPECIAL = cvar.SHAPELY_SPECIAL
SIDECHAIN = cvar.SIDECHAIN
SUGAR_PHOSPHATE = cvar.SUGAR_PHOSPHATE
ALA = cvar.ALA
GLY = cvar.GLY
LEU = cvar.LEU
SER = cvar.SER
VAL = cvar.VAL
THR = cvar.THR
LYS = cvar.LYS
ASP = cvar.ASP
ILE = cvar.ILE
ASN = cvar.ASN
GLU = cvar.GLU
PRO = cvar.PRO
ARG = cvar.ARG
PHE = cvar.PHE
GLN = cvar.GLN
TYR = cvar.TYR
HIS = cvar.HIS
CYS = cvar.CYS
MET = cvar.MET
TRP = cvar.TRP
ASX = cvar.ASX
GLX = cvar.GLX
PCA = cvar.PCA
HYP = cvar.HYP
A = cvar.A
C = cvar.C
G = cvar.G
T = cvar.T
U = cvar.U
UPLUS = cvar.UPLUS
I = cvar.I
_1MA = cvar._1MA
_5MC = cvar._5MC
OMC = cvar.OMC
_1MG = cvar._1MG
_2MG = cvar._2MG
M2G = cvar.M2G
_7MG = cvar._7MG
OMG = cvar.OMG
YG = cvar.YG
H2U = cvar.H2U
_5MU = cvar._5MU
PSU = cvar.PSU
UNK = cvar.UNK
ACE = cvar.ACE
FOR = cvar.FOR
HOH = cvar.HOH
DOD = cvar.DOD
SO4 = cvar.SO4
PO4 = cvar.PO4
NAD = cvar.NAD
COA = cvar.COA
NAP = cvar.NAP
NDP = cvar.NDP
AMINO = cvar.AMINO
AMINO_NUCLEO = cvar.AMINO_NUCLEO
COENZYME = cvar.COENZYME
ION = cvar.ION
NUCLEO = cvar.NUCLEO
PROTEIN = cvar.PROTEIN
PURINE = cvar.PURINE
PYRIMIDINE = cvar.PYRIMIDINE
SOLVENT = cvar.SOLVENT
WATER = cvar.WATER
OB_4RING_ATOM = _openbabel.OB_4RING_ATOM
OB_3RING_ATOM = _openbabel.OB_3RING_ATOM
OB_AROMATIC_ATOM = _openbabel.OB_AROMATIC_ATOM
@@ -1411,91 +1518,6 @@ class OBAtom(OBBase):
def MatchesSMARTS(*args): return _openbabel.OBAtom_MatchesSMARTS(*args)
OBAtom_swigregister = _openbabel.OBAtom_swigregister
OBAtom_swigregister(OBAtom)
ACIDIC = cvar.ACIDIC
ACYCLIC = cvar.ACYCLIC
ALIPHATIC = cvar.ALIPHATIC
AROMATIC = cvar.AROMATIC
BASIC = cvar.BASIC
BURIED = cvar.BURIED
CHARGED = cvar.CHARGED
CYCLIC = cvar.CYCLIC
HYDROPHOBIC = cvar.HYDROPHOBIC
LARGE = cvar.LARGE
MEDIUM = cvar.MEDIUM
NEGATIVE = cvar.NEGATIVE
NEUTRAL = cvar.NEUTRAL
POLAR = cvar.POLAR
POSITIVE = cvar.POSITIVE
SMALL = cvar.SMALL
SURFACE = cvar.SURFACE
ALPHA_CARBON = cvar.ALPHA_CARBON
AMINO_BACKBONE = cvar.AMINO_BACKBONE
BACKBONE = cvar.BACKBONE
CYSTEINE_SULPHUR = cvar.CYSTEINE_SULPHUR
LIGAND = cvar.LIGAND
NUCLEIC_BACKBONE = cvar.NUCLEIC_BACKBONE
SHAPELY_BACKBONE = cvar.SHAPELY_BACKBONE
SHAPELY_SPECIAL = cvar.SHAPELY_SPECIAL
SIDECHAIN = cvar.SIDECHAIN
SUGAR_PHOSPHATE = cvar.SUGAR_PHOSPHATE
ALA = cvar.ALA
GLY = cvar.GLY
LEU = cvar.LEU
SER = cvar.SER
VAL = cvar.VAL
THR = cvar.THR
LYS = cvar.LYS
ASP = cvar.ASP
ILE = cvar.ILE
ASN = cvar.ASN
GLU = cvar.GLU
PRO = cvar.PRO
ARG = cvar.ARG
PHE = cvar.PHE
GLN = cvar.GLN
TYR = cvar.TYR
HIS = cvar.HIS
CYS = cvar.CYS
MET = cvar.MET
TRP = cvar.TRP
ASX = cvar.ASX
GLX = cvar.GLX
PCA = cvar.PCA
HYP = cvar.HYP
A = cvar.A
C = cvar.C
G = cvar.G
T = cvar.T
U = cvar.U
UPLUS = cvar.UPLUS
I = cvar.I
OMC = cvar.OMC
M2G = cvar.M2G
OMG = cvar.OMG
YG = cvar.YG
H2U = cvar.H2U
PSU = cvar.PSU
UNK = cvar.UNK
ACE = cvar.ACE
FOR = cvar.FOR
HOH = cvar.HOH
DOD = cvar.DOD
SO4 = cvar.SO4
PO4 = cvar.PO4
NAD = cvar.NAD
COA = cvar.COA
NAP = cvar.NAP
NDP = cvar.NDP
AMINO = cvar.AMINO
AMINO_NUCLEO = cvar.AMINO_NUCLEO
COENZYME = cvar.COENZYME
ION = cvar.ION
NUCLEO = cvar.NUCLEO
PROTEIN = cvar.PROTEIN
PURINE = cvar.PURINE
PYRIMIDINE = cvar.PYRIMIDINE
SOLVENT = cvar.SOLVENT
WATER = cvar.WATER
OB_AROMATIC_BOND = _openbabel.OB_AROMATIC_BOND
OB_WEDGE_BOND = _openbabel.OB_WEDGE_BOND
@@ -2814,5 +2836,27 @@ class OBResidueAtomIter(object):
OBResidueAtomIter_swigregister = _openbabel.OBResidueAtomIter_swigregister
OBResidueAtomIter_swigregister(OBResidueAtomIter)
class doubleArray(object):
thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
__repr__ = _swig_repr
def __init__(self, *args):
_openbabel.doubleArray_swiginit(self,_openbabel.new_doubleArray(*args))
__swig_destroy__ = _openbabel.delete_doubleArray
__del__ = lambda self : None;
def __getitem__(*args): return _openbabel.doubleArray___getitem__(*args)
def __setitem__(*args): return _openbabel.doubleArray___setitem__(*args)
def cast(*args): return _openbabel.doubleArray_cast(*args)
frompointer = staticmethod(_openbabel.doubleArray_frompointer)
doubleArray_swigregister = _openbabel.doubleArray_swigregister
doubleArray_swigregister(doubleArray)
doubleArray_frompointer = _openbabel.doubleArray_frompointer
def double_array(mylist):
"""Create a C array of doubles from a list."""
c = doubleArray(len(mylist))
for i,v in enumerate(mylist):
c[i] = v
return c

1657
scripts/python/openbabel_python.cpp
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